Compositions and methods for detecting group B streptococcal nucleic acids
阅读说明：本技术 用于检测b群链球菌核酸的组合物和方法 (Compositions and methods for detecting group B streptococcal nucleic acids ) 是由 B·L·伊顿 B·格罗巴奇克 Y·奥宗 R·克洛斯 L·弗兰齐 于 2019-08-09 设计创作，主要内容包括：公开了用于检测B群链球菌(GBS；无乳链球菌)核酸的核酸寡聚物,包括扩增寡聚物和检测探针。还公开了使用所述公开的寡聚物进行特异性核酸扩增和检测的方法以及相应的反应混合物和试剂盒。(Nucleic acid oligomers, including amplification oligomers and detection probes, for detecting group B Streptococcus (GBS; Streptococcus agalactiae) nucleic acids are disclosed. Also disclosed are methods for specific nucleic acid amplification and detection using the disclosed oligomers, as well as corresponding reaction mixtures and kits.)
1. A composition for determining the presence or absence of Group B Streptococcus (GBS) in a sample, the composition comprising:
(I) at least one of a first amplification oligomer combination and a second amplification oligomer combination, wherein the first amplification oligomer combination comprises first and second SIP-specific amplification oligomers capable of amplifying a target region of a GBS SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (A) and second (B) SIP-specific target-hybridizing sequences, respectively, selected from the group consisting of:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof;
and is
(II) the second amplification oligomer combination comprises first and second CFB-specific amplification oligomers capable of amplifying a target region of a GBS CFB target nucleic acid, wherein the first and second CFB-specific amplification oligomers comprise first (a ') and second (B') CFB-specific target-hybridizing sequences, respectively, selected from:
(a) (A') as a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence of SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13 or SEQ ID NO 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A') SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A') SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:21, or an RNA equivalent or DNA/RNA chimera thereof.
2. The composition of claim 1, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (a).
3. The composition of claim 1, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (b).
4. The composition of any one of claims 1-3, wherein if the composition comprises the first amplification oligomer combination, the composition further comprises a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by the first and second SIP-specific amplification oligomers.
5. The composition of claim 4, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (a), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO 9, or an RNA equivalent or DNA/RNA chimera thereof.
6. The composition of claim 4, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (b), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO 11, or an RNA equivalent or DNA/RNA chimera thereof.
7. The composition of any one of claims 4-6, wherein the SIP-specific detection probe oligomer further comprises a detectable label.
8. The composition of claim 7, wherein the detectable label is a fluorescent or chemiluminescent label.
9. The composition of claim 7, wherein the detectable label is a fluorescent label and the SIP-specific detection probe oligomer further comprises a non-fluorescent quencher.
10. The composition of any one of claims 1-9, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (b).
11. The composition of any one of claims 1-9, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (d).
12. The composition of any one of claims 1-9, wherein the CFB-specific target-hybridizing sequence is the target-hybridizing sequence of (II) (a).
13. The composition of claim 12, wherein the first CFB-specific target-hybridizing sequence of (II) (a) comprises at least the sequence of SEQ ID NO:28, or an RNA equivalent or DNA/RNA chimera thereof.
14. The composition of claim 13, wherein the first CFB-specific target-hybridizing sequence of (II) (a) is comprised in the sequence of SEQ ID NO:27, or an RNA equivalent or DNA/RNA chimera thereof.
15. The composition of claim 14, wherein the first CFB-specific target-hybridizing sequence of (II) (a) is SEQ ID No. 12 or SEQ ID No. 14, or an RNA equivalent or DNA/RNA chimera thereof.
16. The composition of claim 12, wherein the first CFB-specific target-hybridizing sequence of (II) (a) is SEQ ID NO:18, or an RNA equivalent or DNA/RNA chimera thereof.
17. The composition of claim 12, wherein the first (a ') and second (B') CFB-specific target-hybridizing sequences of (II) (a) are selected from
(i) (A') SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13, or an RNA equivalent or DNA/RNA chimera thereof;
(ii) (A') SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof;
(iii) (A') SEQ ID NO:14, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(iv) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof.
18. The composition of any one of claims 1-9, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (c).
19. The composition of any one of claims 1-18, wherein if the composition comprises the second amplification oligomer combination, the composition further comprises a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a CFB amplicon amplifiable by the first and second CFB-specific amplification oligomers.
20. The composition of claim 19, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (b), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO 24, or an RNA equivalent or DNA/RNA chimera thereof.
21. The composition of claim 19, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (d) and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:25, or an RNA equivalent or DNA/RNA chimera thereof.
22. The composition of claim 19, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (a) and the CFB-specific detection probe target-hybridizing sequence is SEQ ID No. 22 or SEQ ID No. 23, or an RNA equivalent or DNA/RNA chimera thereof.
23. The composition of claim 19, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (c), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO 23, or an RNA equivalent or DNA/RNA chimera thereof.
24. The composition of any one of claims 19-23, wherein the CFB-specific detection probe oligomer further comprises a detectable label.
25. The composition of claim 24, wherein the detectable label is a fluorescent or chemiluminescent label.
26. The composition of claim 24, wherein the detectable label is a fluorescent label and the detection probe oligomer further comprises a non-fluorescent quencher.
27. The composition of any one of claims 1-26, wherein the composition comprises both the first and second amplification oligomer combinations.
28. A composition for determining the presence or absence of Group B Streptococcus (GBS) in a sample, the composition comprising:
an amplification oligomer combination comprising first and second SIP-specific amplification oligomers capable of amplifying a target region of a GBS SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (A) and second (B) SIP-specific target-hybridizing sequences, respectively, selected from the group consisting of:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof.
29. The composition of claim 28, wherein said first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (a).
30. The composition of claim 28, wherein said first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (b).
31. The composition of any one of claims 28-30, wherein the composition further comprises a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a SIP amplicon amplifiable by the first and second SIP-specific amplification oligomers.
32. The composition of claim 31, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (a) and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO 9, or an RNA equivalent or DNA/RNA chimera thereof.
33. The composition of claim 32, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (b), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:11, or an RNA equivalent or DNA/RNA chimera thereof.
34. The composition of any one of claims 31-33, wherein the detection probe oligomer further comprises a detectable label.
35. The composition of claim 34, wherein the detectable label is a fluorescent or chemiluminescent label.
36. The composition of claim 34, wherein the detectable label is a fluorescent label and the detection probe oligomer further comprises a non-fluorescent quencher.
37. The composition of any one of claims 28-36, further comprising a second amplification oligomer combination capable of amplifying a target region of a GBSCFB target nucleic acid.
38. A composition for determining the presence or absence of Group B Streptococcus (GBS) in a sample, the composition comprising:
an amplification oligomer combination comprising first and second CFB-specific amplification oligomers capable of amplifying a target region of a GBS CFB target nucleic acid, wherein the first and second CFB-specific amplification oligomers comprise first (a) and second (B) CFB-specific target-hybridizing sequences, respectively, selected from:
(a) (A) a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence as SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 13 or 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A) SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A) SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A) SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 21, or an RNA equivalent or DNA/RNA chimera thereof.
39. The composition of claim 38, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (b).
40. The composition of claim 38, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (d).
41. The composition of claim 38, wherein the CFB-specific target-hybridizing sequence is the target-hybridizing sequence of (a).
42. The composition of claim 41, wherein the first CFB-specific target-hybridizing sequence of (a) comprises at least the sequence of SEQ ID NO 28, or an RNA equivalent or DNA/RNA chimera thereof.
43. The composition of claim 42, wherein the first CFB-specific target-hybridizing sequence of (a) is comprised in the sequence of SEQ ID NO:27, or an RNA equivalent or DNA/RNA chimera thereof.
44. The composition of claim 43, wherein the first CFB-specific target-hybridizing sequence of (a) is SEQ ID NO 12 or SEQ ID NO 14, or an RNA equivalent or DNA/RNA chimera thereof.
45. The composition of claim 41, wherein the first CFB-specific target-hybridizing sequence of (a) is SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof.
46. The composition of claim 41, wherein said first (A) and second (B) CFB-specific target-hybridizing sequences of (a) are selected from
(i) (A) SEQ ID NO 12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 13, or an RNA equivalent or DNA/RNA chimera thereof;
(ii) (A) SEQ ID NO 12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof;
(iii) (A) SEQ ID NO 14, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof; and
(iv) (A) SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof.
47. The composition of claim 38, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (c).
48. The composition of any one of claims 38-47, wherein the composition further comprises a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a CFB amplicon amplifiable by the first and second CFB-specific amplification oligomers.
49. The composition of claim 48, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (b), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO 24, or an RNA equivalent or DNA/RNA chimera thereof.
50. The composition of claim 48, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (d), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO 25, or an RNA equivalent or DNA/RNA chimera thereof.
51. The composition of claim 48, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (a), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:22 or SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimera thereof.
52. The composition of claim 48, wherein said first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (c), and said CFB-specific detection probe target-hybridizing sequence is SEQ ID NO 23, or an RNA equivalent or DNA/RNA chimera thereof.
53. The composition of any one of claims 48-52, wherein the detection probe oligomer further comprises a detectable label.
54. The composition of claim 53, wherein the detectable label is a fluorescent or chemiluminescent label.
55. The composition of claim 53, wherein the detectable label is a fluorescent label and the detection probe oligomer further comprises a non-fluorescent quencher.
56. The composition of any one of claims 38-55, further comprising a second amplification oligomer combination capable of amplifying a target region of a GBS SIP target nucleic acid.
57. A kit for determining the presence or absence of Group B Streptococcus (GBS) in a sample, the kit comprising:
(I) at least one of a first amplification oligomer combination and a second amplification oligomer combination, wherein the first amplification oligomer combination comprises first and second SIP-specific amplification oligomers capable of amplifying a target region of a GBS SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (A) and second (B) SIP-specific target-hybridizing sequences, respectively, selected from the group consisting of:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof;
and is
(II) the second amplification oligomer combination comprises first and second CFB-specific amplification oligomers capable of amplifying a target region of a GBS CFB target nucleic acid, wherein the first and second CFB-specific amplification oligomers comprise first (a ') and second (B') CFB-specific target-hybridizing sequences, respectively, selected from:
(a) (A') as a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence of SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13 or SEQ ID NO 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A') SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A') SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:21, or an RNA equivalent or DNA/RNA chimera thereof.
58. The kit of claim 57, wherein said first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (a).
59. The kit of claim 57, wherein said first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (b).
60. The kit of any one of claims 57-59, wherein if the kit comprises the first amplification oligomer combination, the kit further comprises a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by the first and second SIP-specific amplification oligomers.
61. The kit of claim 60, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (a) and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO 9, or an RNA equivalent or DNA/RNA chimera thereof.
62. The kit of claim 60, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (b), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO 11, or an RNA equivalent or DNA/RNA chimera thereof.
63. The kit of any one of claims 60-62, wherein the SIP-specific detection probe oligomer further comprises a detectable label.
64. The kit of claim 63, wherein the detectable label is a fluorescent or chemiluminescent label.
65. The kit of claim 63, wherein the detectable label is a fluorescent label and the SIP-specific detection probe oligomer further comprises a non-fluorescent quencher.
66. The kit of any one of claims 57-65, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (b).
67. The kit of any one of claims 57-65, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (d).
68. The kit of any one of claims 57-65, wherein the CFB-specific target-hybridizing sequence is the target-hybridizing sequence of (II) (a).
69. The kit of claim 68, wherein the first CFB-specific target-hybridizing sequence of (II) (a) comprises at least the sequence of SEQ ID NO 28, or an RNA equivalent or DNA/RNA chimera thereof.
70. The kit of claim 69, wherein the first CFB-specific target-hybridizing sequence of (II) (a) is comprised in the sequence of SEQ ID NO:27, or an RNA equivalent or DNA/RNA chimera thereof.
71. The kit of claim 70, wherein the first CFB-specific target-hybridizing sequence of (II) (a) is SEQ ID NO 12 or SEQ ID NO 14, or an RNA equivalent or DNA/RNA chimera thereof.
72. The kit of claim 68, wherein the first CFB-specific target-hybridizing sequence of (II) (a) is SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof.
73. The kit of claim 68, wherein the first (A ') and second (B') CFB-specific target-hybridizing sequences of (II) (a) are selected from
(i) (A') SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13, or an RNA equivalent or DNA/RNA chimera thereof;
(ii) (A') SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof;
(iii) (A') SEQ ID NO:14, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(iv) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof.
74. The kit of any one of claims 57-65, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (c).
75. The kit of any one of claims 57-74, wherein if the kit comprises the second amplification oligomer combination, the kit further comprises a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a CFB amplicon amplifiable by the first and second CFB-specific amplification oligomers.
76. The kit of claim 75, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (b), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO 24, or an RNA equivalent or DNA/RNA chimera thereof.
77. The kit of claim 75, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (d), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO 25, or an RNA equivalent or DNA/RNA chimera thereof.
78. The kit of claim 75, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (a), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:22 or SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimera thereof.
79. The kit of claim 75, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (c), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimera thereof.
80. The kit of any one of claims 75-79, wherein the CFB-specific detection probe oligomer further comprises a detectable label.
81. The kit of claim 80, wherein the detectable label is a fluorescent or chemiluminescent label.
82. The kit of claim 80, wherein the detectable label is a fluorescent label and the detection probe oligomer further comprises a non-fluorescent quencher.
83. The kit of any one of claims 57-82, wherein the kit comprises both the first and second amplification oligomer combinations.
84. A kit for determining the presence or absence of Group B Streptococcus (GBS) in a sample, the kit comprising:
an amplification oligomer combination comprising first and second SIP-specific amplification oligomers capable of amplifying a target region of a GBS SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (A) and second (B) SIP-specific target-hybridizing sequences, respectively, selected from the group consisting of:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof.
85. The kit of claim 84, wherein said first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (a).
86. The kit of claim 84, wherein said first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (b).
87. The kit of any one of claims 84-86, wherein the kit further comprises a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a SIP amplicon amplifiable by the first and second SIP-specific amplification oligomers.
88. The kit of claim 87, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (a) and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO 9, or an RNA equivalent or DNA/RNA chimera thereof.
89. The kit of claim 88, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (b), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO 11, or an RNA equivalent or DNA/RNA chimera thereof.
90. The kit of any one of claims 87-89, wherein the detection probe oligomer further comprises a detectable label.
91. The kit of claim 90, wherein the detectable label is a fluorescent or chemiluminescent label.
92. The kit of claim 90, wherein the detectable label is a fluorescent label and the detection probe oligomer further comprises a non-fluorescent quencher.
93. The kit of any one of claims 84-92, further comprising a second amplification oligomer combination capable of amplifying a target region of a GBS CFB target nucleic acid.
94. A kit for determining the presence or absence of Group B Streptococcus (GBS) in a sample, the kit comprising:
an amplification oligomer combination comprising first and second CFB-specific amplification oligomers capable of amplifying a target region of a GBS CFB target nucleic acid, wherein the first and second CFB-specific amplification oligomers comprise first (a) and second (B) CFB-specific target-hybridizing sequences, respectively, selected from:
(a) (A) a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence as SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 13 or 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A) SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A) SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A) SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 21, or an RNA equivalent or DNA/RNA chimera thereof.
95. The kit of claim 94, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (b).
96. The kit of claim 94, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (d).
97. The kit of claim 94, wherein the CFB-specific target-hybridizing sequence is the target-hybridizing sequence of (a).
98. The kit of claim 97, wherein the first CFB-specific target-hybridizing sequence of (a) comprises at least the sequence of SEQ ID NO:28, or an RNA equivalent or DNA/RNA chimera thereof.
99. The kit of claim 98, wherein said first CFB-specific target-hybridizing sequence of (a) is comprised in the sequence of SEQ ID No. 27, or an RNA equivalent or DNA/RNA chimera thereof.
100. The kit of claim 99, wherein the first CFB-specific target-hybridizing sequence of (a) is SEQ ID No. 12 or SEQ ID No. 14, or an RNA equivalent or DNA/RNA chimera thereof.
101. The kit of claim 97, wherein the first CFB-specific target-hybridizing sequence of (a) is SEQ ID NO:18, or an RNA equivalent or DNA/RNA chimera thereof.
102. The kit of claim 97, wherein the first (a) and second (B) CFB-specific target-hybridizing sequences of (a) are selected from the group consisting of
(i) (A) SEQ ID NO 12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 13, or an RNA equivalent or DNA/RNA chimera thereof;
(ii) (A) SEQ ID NO 12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof;
(iii) (A) SEQ ID NO 14, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof; and
(iv) (A) SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof.
103. The kit of claim 94, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (c).
104. The kit of any one of claims 94-103, wherein the kit further comprises a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a CFB amplicon amplifiable by the first and second CFB-specific amplification oligomers.
105. The kit of claim 104, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (b), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimera thereof.
106. The kit of claim 104, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (d), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:25, or an RNA equivalent or DNA/RNA chimera thereof.
107. The kit of claim 104, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (a) and the CFB-specific detection probe target-hybridizing sequence is SEQ ID No. 22 or SEQ ID No. 23, or an RNA equivalent or DNA/RNA chimera thereof.
108. The kit of claim 104, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (c), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO 23, or an RNA equivalent or DNA/RNA chimera thereof.
109. The kit of any one of claims 104-108, wherein the detection probe oligomer further comprises a detectable label.
110. The kit of claim 109, wherein the detectable label is a fluorescent or chemiluminescent label.
111. The kit of claim 109, wherein the detectable label is a fluorescent label and the detection probe oligomer further comprises a non-fluorescent quencher.
112. The kit of any one of claims 94-111, further comprising a second amplification oligomer combination capable of amplifying a target region of a GBS SIP target nucleic acid.
113. A method for determining the presence or absence of Group B Streptococcus (GBS) in a sample, the method comprising:
(1) contacting a sample suspected of containing GBS with at least one of a first amplification oligomer combination and a second amplification oligomer combination, wherein
(I) The first amplification oligomer combination comprises first and second SIP-specific amplification oligomers for amplifying a target region of a GBS SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (a) and second (B) SIP-specific target-hybridizing sequences, respectively, selected from:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof;
and is
(II) the second amplification oligomer combination comprises first and second CFB-specific amplification oligomers for amplifying a target region of a GBS CFB target nucleic acid, wherein the first and second CFB-specific amplification oligomers comprise first (a ') and second (B') CFB-specific target-hybridizing sequences, respectively, selected from:
(a) (A') as a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence of SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13 or SEQ ID NO 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A') SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A') SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 21, or an RNA equivalent or DNA/RNA chimera thereof;
(2) performing an in vitro nucleic acid amplification reaction, wherein any GBS SIP and/or CFB target nucleic acid, when present in the sample, is used as a template to produce one or more amplicons corresponding to at least one of the SIP and CFB target regions; and
(3) detecting the presence or absence of the one or more amplicons, thereby determining the presence or absence of GBS in the sample.
114. The method of claim 113, wherein the method comprises contacting the sample with both the first and second amplification oligomer combinations.
115. The method of claim 114, wherein the method is a multiplexing method comprising contacting the sample with both the first and second amplification oligomer combinations within the same reaction mixture.
116. The method of any one of claims 113-115, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (a).
117. The method of claim 113-115 wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (b).
118. The method of any one of claims 113-117 wherein if the method comprises contacting the sample with the first amplification oligomer combination, the detecting step comprises contacting the in vitro nucleic acid amplification reaction with a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by the first and second SIP-specific amplification oligomers.
119. The method of claim 118, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequence of (I) (a) and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:9, or an RNA equivalent or DNA/RNA chimera thereof.
120. The method of claim 118, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (b), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:11, or an RNA equivalent or DNA/RNA chimera thereof.
121. The method of any one of claims 118-120, wherein the SIP-specific detection probe oligomer further comprises a detectable label.
122. The method of claim 121, wherein the detectable label is a fluorescent or chemiluminescent label.
123. The method of claim 121, wherein the detectable label is a fluorescent label and the SIP-specific detection probe oligomer further comprises a non-fluorescent quencher.
124. The method of any one of claims 113-123, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (b).
125. The method of any one of claims 113-123, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (d).
126. The method of any one of claims 113-123, wherein the CFB-specific target-hybridizing sequence is the target-hybridizing sequence of (II) (a).
127. The method of claim 126, wherein the first CFB-specific target-hybridizing sequence of (II) (a) comprises at least the sequence of SEQ ID NO:28, or an RNA equivalent or DNA/RNA chimera thereof.
128. The method of claim 127, wherein the first CFB-specific target-hybridizing sequence of (II) (a) is comprised in the sequence of SEQ ID NO:27, or an RNA equivalent or DNA/RNA chimera thereof.
129. The method of claim 128, wherein the first CFB-specific target-hybridizing sequence of (II) (a) is SEQ ID No. 12 or SEQ ID No. 14, or an RNA equivalent or DNA/RNA chimera thereof.
130. The method of claim 126, wherein the first CFB-specific target-hybridizing sequence of (II) (a) is SEQ ID NO:18, or an RNA equivalent or DNA/RNA chimera thereof.
131. The method of claim 126, wherein the first (a ') and second (B') CFB-specific target-hybridizing sequences of (II) (a) are selected from
(i) (A') SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13, or an RNA equivalent or DNA/RNA chimera thereof;
(ii) (A') SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof;
(iii) (A') SEQ ID NO:14, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(iv) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof.
132. The method of any one of claims 113-123, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (c).
133. The method of any one of claims 113-132 wherein if the method comprises contacting the sample with the second amplification oligomer combination, the detecting step comprises contacting the in vitro nucleic acid amplification reaction with a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a CFB amplicon that is amplifiable by the first and second CFB-specific amplification oligomers.
134. The method of claim 133, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (b), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO 24, or an RNA equivalent or DNA/RNA chimera thereof.
135. The method of claim 133, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (d) and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:25, or an RNA equivalent or DNA/RNA chimera thereof.
136. The method of claim 133, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (a) and the CFB-specific detection probe target-hybridizing sequence is SEQ ID No. 22 or SEQ ID No. 23, or an RNA equivalent or DNA/RNA chimera thereof.
137. The method of claim 133, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (c), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO 23, or an RNA equivalent or DNA/RNA chimera thereof.
138. The method of any one of claims 133-137, wherein the CFB-specific detection probe oligomer further comprises a detectable label.
139. The method of claim 138, wherein the detectable label is a fluorescent or chemiluminescent label.
140. The method of claim 138, wherein the detectable label is a fluorescent label and the CFB-specific detection probe oligomer further comprises a non-fluorescent quencher.
141. The method of any one of claims 188-137, 133-137, wherein the detecting step is performed in real-time.
142. The method of any one of claims 113-141, wherein the in vitro nucleic acid amplification reaction is a PCR amplification reaction.
143. The method of claim 114 or 115, wherein the detecting step comprises contacting an in vitro nucleic acid amplification reaction with:
(i) a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by the first and second SIP-specific amplification oligomers, and
(ii) a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a CFB amplicon that is amplifiable by the first and second CFB-specific amplification oligomers,
wherein each of the SIP-specific detection probe oligomer and the CFB-specific detection probe oligomer comprises a fluorescent label and a non-fluorescent quencher.
144. The method of claim 143, wherein the in vitro nucleic acid amplification reaction is a real-time PCR amplification reaction.
145. A method for determining the presence or absence of Group B Streptococcus (GBS) in a sample, the method comprising:
(1) contacting a sample suspected of containing GBS with an amplification oligomer combination comprising first and second SIP-specific amplification oligomers for amplifying a target region of a GBS SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (a) and second (B) SIP-specific target-hybridizing sequences, respectively, selected from the group consisting of:
(a) (A) SEQ ID NO 3, or an RNA equivalent or a DNA/RNA chimera thereof, and (B) SEQ ID NO 4, or an RNA equivalent or a DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or a DNA/RNA chimera thereof, and (B) SEQ ID NO 8, or an RNA equivalent or a DNA/RNA chimera thereof;
(2) performing an in vitro nucleic acid amplification reaction, wherein any GBS SIP target nucleic acid, when present in the sample, is used as a template to generate an amplicon corresponding to the SIP target region; and
(3) detecting the presence or absence of the amplicon, thereby determining the presence or absence of GBS in the sample.
146. The method of claim 145, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (a).
147. The method of claim 145, wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (b).
148. The method of any one of claims 145-147 wherein the detecting step comprises contacting the in vitro nucleic acid amplification reaction with a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by the first and second SIP-specific amplification oligomers.
149. The method of claim 148 wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequence of (a) and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO 9, or an RNA equivalent or DNA/RNA chimera thereof.
150. The method of claim 148 wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (b) and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:11, or an RNA equivalent or DNA/RNA chimera thereof.
151. The method of any one of claims 145-150, wherein the detection probe oligomer further comprises a detectable label.
152. The method of claim 151, wherein the detectable label is a fluorescent or chemiluminescent label.
153. The method of claim 151, wherein the detectable label is a fluorescent label and the detection probe oligomer further comprises a non-fluorescent quencher.
154. The method of any one of claims 145-150, wherein the detecting step is performed in real-time.
155. The method of any one of claims 145-154, wherein the in vitro nucleic acid amplification reaction is a PCR amplification reaction.
156. The method of claim 153, wherein the in vitro nucleic acid amplification reaction is a real-time PCR amplification reaction.
157. The method of any one of claims 145-156 further comprising contacting the sample with a second combination of amplification oligomers comprising first and second CFB specific amplification oligomers for amplifying a target region of a GBS CFB target nucleic acid, wherein in the amplifying step any GBS CFB target nucleic acid when present in the sample is used as a template to produce an amplicon corresponding to the CFB target region, and wherein the detecting step comprises detecting the presence or absence of the amplicon corresponding to the CFB target region.
158. A method for determining the presence or absence of Group B Streptococcus (GBS) in a sample, the method comprising:
(1) contacting a sample suspected of containing GBS with an amplification oligomer combination comprising first and second CFB-specific amplification oligomers for amplifying a target region of a GBS CFB target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (a) and second (B) SIP-specific target-hybridizing sequences, respectively, selected from:
(a) (A) a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence as SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 13 or 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A) SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A) SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A) SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 21, or an RNA equivalent or DNA/RNA chimera thereof;
(2) performing an in vitro nucleic acid amplification reaction, wherein any GBS CFB target nucleic acid, when present in the sample, is used as a template to produce an amplicon corresponding to the CFB target region; and
(3) detecting the presence or absence of the amplicon, thereby determining the presence or absence of GBS in the sample.
159. The method of claim 158, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (b).
160. The method of claim 158, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (d).
161. The method of claim 158, wherein the CFB-specific target-hybridizing sequence is the target-hybridizing sequence of (a).
162. The method of claim 161, wherein the first CFB-specific target-hybridizing sequence of (a) comprises at least the sequence of SEQ ID NO:28, or an RNA equivalent or DNA/RNA chimera thereof.
163. The method of claim 162, wherein the first CFB-specific target-hybridizing sequence of (a) is comprised in the sequence of SEQ ID No. 27, or an RNA equivalent or DNA/RNA chimera thereof.
164. The method of claim 163, wherein the first CFB-specific target-hybridizing sequence of (a) is SEQ ID No. 12 or SEQ ID No. 14, or an RNA equivalent or DNA/RNA chimera thereof.
165. The method of claim 161, wherein the first CFB-specific target-hybridizing sequence of (a) is SEQ ID NO:18, or an RNA equivalent or DNA/RNA chimera thereof.
166. The method of claim 161, wherein the first (a) and second (B) CFB-specific target-hybridizing sequences of (a) are selected from
(i) (A) SEQ ID NO 12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 13, or an RNA equivalent or DNA/RNA chimera thereof;
(ii) (A) SEQ ID NO 12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof;
(iii) (A) SEQ ID NO 14, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof; and
(iv) (A) SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof.
167. The method of claim 158, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (c).
168. The method of any one of claims 158-167 wherein the detecting step comprises contacting the in vitro nucleic acid amplification reaction with a CFB specific detection probe target hybridization sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a CFB amplicon amplifiable by the first and second CFB specific amplification oligomers.
169. The method of claim 168, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (b), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimera thereof.
170. The method of claim 168, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (d), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:25, or an RNA equivalent or DNA/RNA chimera thereof.
171. The method of claim 168, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (a) and the CFB-specific detection probe target-hybridizing sequence is SEQ ID No. 22 or SEQ ID No. 23, or an RNA equivalent or DNA/RNA chimera thereof.
172. The method of claim 168, wherein the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (c), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO 23, or an RNA equivalent or DNA/RNA chimera thereof.
173. The method of any one of claims 168-172, wherein the detection probe oligomer further comprises a detectable label.
174. The method of claim 173, wherein the detectable label is a fluorescent or chemiluminescent label.
175. The method of claim 173, wherein the detectable label is a fluorescent label and the detection probe oligomer further comprises a non-fluorescent quencher.
176. The method as recited in any one of claims 168-172, wherein the detecting step is performed in real-time.
177. The method of any one of claims 168-176, wherein the in vitro nucleic acid amplification reaction is a PCR amplification reaction.
178. The method of claim 175, wherein the in vitro nucleic acid amplification reaction is a real-time PCR amplification reaction.
179. The method of any one of claims 168-178 further comprising contacting the sample with a second amplification oligomer combination comprising first and second SIP-specific amplification oligomers for amplifying a target region of a GBS SIP target nucleic acid, wherein in the amplifying step any GBS SIP target nucleic acid when present in the sample is used as a template to produce an amplicon corresponding to the SIP target region, and wherein the detecting step comprises detecting the presence or absence of the amplicon corresponding to the SIP target region.
180. The method according to any one of claims 113-179, wherein the method determines the presence or absence of any of GBS serotypes Ia, Ib, Ic, II, III, IV, V, VI, VII, VIII and IX.
181. The method of claim 181, wherein the method further determines the presence or absence of a non-hemolytic strain of GBS.
182. A detection probe oligomer, comprising:
a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by a first amplification oligomer combination comprising first and second SIP-specific amplification oligomers capable of amplifying a target region of a Group B Streptococcus (GBS) SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (a) and second (B) SIP-specific target-hybridizing sequences selected from the group consisting of:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof.
183. A detection probe oligomer, comprising:
a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a CFB amplicon that is amplifiable by a second amplification oligomer combination comprising first and second CFB-specific amplification oligomers capable of amplifying a target region of a Group B Streptococcus (GBS) CFB target nucleic acid, wherein the first and second CFB-specific amplification oligomers comprise first (a ') and second (B') CFB-specific target-hybridizing sequences, respectively, selected from the group consisting of:
(a) (A') as a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence of SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13 or SEQ ID NO 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A') SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A') SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:21, or an RNA equivalent or DNA/RNA chimera thereof.
184. The detection probe oligomer of claim 182 or 183, wherein the detection probe oligomer further comprises a detectable label.
185. The detection probe oligomer of claim 184, wherein the detectable label is a fluorescent or chemiluminescent label.
186. A composition, comprising:
(1) a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by a first amplification oligomer combination comprising first and second SIP-specific amplification oligomers that are capable of amplifying a target region of a Group B Streptococcus (GBS) SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (a) and second (B) SIP-specific target-hybridizing sequences, respectively, selected from the group consisting of:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof;
and is
(2) A CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a CFB amplicon that is amplifiable by a second amplification oligomer combination comprising first and second CFB-specific amplification oligomers capable of amplifying a target region of a Group B Streptococcus (GBS) CFB target nucleic acid, wherein the first and second CFB-specific amplification oligomers comprise first (a ') and second (B') CFB-specific target-hybridizing sequences, respectively, selected from the group consisting of:
(a) (A') as a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence of SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13 or SEQ ID NO 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A') SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A') SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:21, or an RNA equivalent or DNA/RNA chimera thereof.
187. The composition of claim 186, wherein the SIP-specific detection probe oligomer further comprises a detectable label.
188. The composition of claim 186 or 187, wherein the CFB-specific detection probe oligomer further comprises a detectable label.
189. The composition of claim 187 or 188, wherein the detectable label is a fluorescent or chemiluminescent label.
190. An aqueous formulation for amplifying Group B Streptococcus (GBS) nucleic acids, wherein the aqueous formulation comprises:
the composition of any one of claims 1-56, and
an organic buffer.
191. The aqueous formulation of claim 190, further comprising a DNA polymerase.
192. The aqueous formulation of claim 190 or 191, further comprising a reverse transcriptase.
193. The aqueous formulation of any of claims 190-192 further comprising a detection probe oligomer.
194. The aqueous formulation of any one of claims 190-193 further comprising an extender selected from the group consisting of trehalose, raffinose, and combinations thereof.
195. The aqueous formulation of any one of claims 190 to 194, wherein said formulation contains an inorganic salt at a concentration of 4mM or less.
196. A dry formulation for amplifying Group B Streptococcus (GBS) nucleic acids, wherein the aqueous formulation comprises:
the composition of any one of claims 1-56, and
an extender.
197. The dry formulation of claim 196, wherein the bulking agent is selected from the group consisting of trehalose, raffinose, and combinations thereof.
198. The dry formulation of claim 196 or 197, further comprising an inorganic salt, wherein the percentage of the mass of the inorganic salt relative to the mass of the dry formulation is 0.249% or less.
199. The dry formulation of any one of claims 196-198, further comprising a DNA polymerase.
200. The dry formulation of any one of claims 196 and 199, further comprising a reverse transcriptase.
201. The dry formulation of any one of claims 196 and 200, further comprising a detection probe oligomer.
202. The dry formulation of any one of claims 196-201, wherein the formulation is a lyophilized formulation.
203. An aqueous formulation for detecting Group B Streptococcus (GBS) nucleic acids, wherein the aqueous formulation comprises:
the detection probe oligomer as defined in any one of claims 182-185 or the composition as defined in any one of claims 186-189, and
an organic buffer.
204. The aqueous formulation of claim 203, further comprising a surfactant.
205. The aqueous formulation of claim 204, wherein the surfactant is a non-linear surfactant.
206. The aqueous formulation of claim 204, wherein the surfactant is selected from
Polyethylene glycol mono [4- (1,1,3, 3-tetramethyl butyl) phenyl ] ether,
Polysorbate 20, and
combinations thereof.
207. The aqueous formulation of any one of claims 204 and 206, further comprising a DNA polymerase.
208. The aqueous formulation of any of claims 204 and 207 further comprising a reverse transcriptase.
209. The aqueous formulation of any one of claims 204 and 208, further comprising at least one amplification oligomer.
210. The aqueous formulation of any one of claims 204 and 209 further comprising an extender selected from the group consisting of trehalose, raffinose, and combinations thereof.
211. The aqueous formulation of any one of claims 204 and 210 wherein the formulation contains an inorganic salt at a concentration of 4mM or less.
212. A dry formulation for detecting Group B Streptococcus (GBS) nucleic acids, wherein the dry formulation comprises:
the detection probe oligomer as defined in any one of claims 182-185 or the composition as defined in any one of claims 186-189, and
an extender.
213. The dry formulation of claim 212, wherein said bulking agent is selected from the group consisting of trehalose, raffinose, and combinations thereof.
214. The dry formulation of claim 212 or 213, further comprising an inorganic salt, wherein the percentage of the mass of the inorganic salt relative to the mass of the dry formulation is 0.249% or less.
215. The dry formulation of any one of claims 212-214, further comprising a DNA polymerase.
216. The dry formulation of any one of claims 212-215, further comprising a reverse transcriptase.
217. The dry formulation of any one of claims 212-216, further comprising at least one amplification oligomer.
218. The dry formulation of any one of claims 212-217, further comprising a surfactant.
219. The dry formulation of claim 218, wherein the surfactant is a non-linear surfactant.
220. The dry formulation of claim 218, wherein the surfactant is selected from
Polyethylene glycol mono [4- (1,1,3, 3-tetramethyl butyl) phenyl ] ether,
Polysorbate 20, and
combinations thereof.
221. The dry formulation of any one of claims 212-220, wherein the formulation is a lyophilized formulation.
222. A reaction mixture for amplifying a Group B Streptococcus (GBS) nucleic acid, wherein the reaction mixture comprises the aqueous formulation according to any one of claims 190 and 195.
223. A reaction mixture for amplifying Group B Streptococcus (GBS) nucleic acids, wherein the reaction mixture is reconstituted with water or an organic buffer from a dried formulation according to any one of claims 196-202.
224. The reaction mixture of claim 223, wherein the reaction mixture comprises an inorganic salt.
225. The reaction mixture of claim 224, wherein said inorganic salt is selected from the group consisting of magnesium, potassium, and sodium.
226. The reaction mixture of claim 224 or 225, wherein the concentration of said inorganic salt is 4mM or less.
227. A reaction mixture for detecting Group B Streptococcus (GBS) nucleic acids, wherein the reaction mixture comprises an aqueous formulation according to any one of claims 203-211.
228. A reaction mixture for detecting Group B Streptococcus (GBS) nucleic acids, wherein the reaction mixture is reconstituted with water or an organic buffer from a dried formulation according to any one of claims 212-221.
229. The reaction mixture of claim 228, wherein the reaction mixture contains an inorganic salt.
230. The reaction mixture of claim 229, wherein said inorganic salt is selected from the group consisting of magnesium, potassium, and sodium.
231. The reaction mixture of claim 229 or 230, wherein the concentration of said inorganic salt is 4mM or less.
Background
Group B Streptococcus (GBS) or Streptococcus agalactiae (Streptococcus agalactiae) is a gram-positive bacterium that is associated with transient colonization of the mucosa of the whole body, including the vagina, gastrointestinal tract and urethra. GBS rarely causes disease in healthy individuals, but can cause severe disease in immunocompromised patients, elderly individuals, and neonates. Of particular concern are neonatal infections caused by vertical transmission during labor and delivery. Transmission from asymptomatic colonised mothers to newborns can lead to early onset invasive GBS disease, a major cause of sepsis and meningitis in us newborns. Early onset GBS disease in newborns can lead to death or long-term disability, such as mental retardation and hearing or vision loss. Buchan et al, J.Clin.Microbiol.53: 443. sub.448 (2015).
Identification of GBS during routine screening results in administration of labor phase prophylaxis to mitigate bacterial transmission and reduce the likelihood of invasive disease. Implementation of this screening and prevention strategy has reduced the incidence of early-onset G BS by 60% to 86%. Lin et al, am.J.Obstet.Gynecol.184:1204-1210, 2001. Since 2010, CDC guidelines have included molecular diagnostic tests as an option in parallel or in addition to culture. Current tests include Cephei d GBS LB and BD max GBS tests targeting the CFB gene.
There is a need in the art for GBS assays with improved sensitivity and/or potential to protect against isolated variation of a single gene, including for example assays that can detect GBS serotypes Ia, Ib, Ic, II, III, IV, V, VI, VII, VIII and IX (including non-hemolytic isolates).
Disclosure of Invention
In one aspect, the invention provides a composition for determining the presence or absence of Group B Streptococcus (GBS) in a sample. In some embodiments, the composition comprises at least one of a first amplification oligomer combination and a second amplification oligomer combination, wherein
(I) The first amplification oligomer combination comprises first and second SIP-specific amplification oligomers capable of amplifying a target region of a GBS SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (a) and second (B) SIP-specific target-hybridizing sequences, respectively, selected from:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof;
and is
(II) the second amplification oligomer combination comprises first and second CFB-specific amplification oligomers capable of amplifying a target region of a GBS CFB target nucleic acid, wherein the first and second CFB-specific amplification oligomers comprise first (a ') and second (B') CFB-specific target-hybridizing sequences, respectively, selected from:
(a) (A ') as a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence of SEQ ID NO:26, or an RNA equivalent or a DNA/RNA chimera thereof, and (B') SEQ ID NO:13 or SEQ ID NO:15, or an RNA equivalent or a DNA/RNA chimera thereof;
(b) (A') SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A') SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:21, or an RNA equivalent or DNA/RNA chimera thereof.
In some embodiments of the compositions described above, wherein the composition comprises the first amplification oligomer combination, the composition further comprises a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by the first and second SIP-specific amplification oligomers. In some such embodiments, the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (a), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:9, or an RNA equivalent or DNA/RNA chimera thereof. In other embodiments, the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (b), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:11, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the SIP-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the SIP-specific detection probe oligomer further comprises a non-fluorescent quencher.
In some embodiments of the compositions described above, wherein the CFB-specific target-hybridizing sequence is the target-hybridizing sequence of (II) (a), the first CFB-specific target-hybridizing sequence of (II) (a) comprises at least the sequence of SEQ ID NO:28, or an RNA equivalent or DNA/RNA chimera thereof. In some such embodiments, the first CFB-specific target-hybridizing sequence of (II) (a) is comprised in the sequence of SEQ ID No. 27, or an RNA equivalent or DNA/RNA chimera thereof; in some such variations, the first CFB-specific target-hybridizing sequence of (II) (a) is SEQ ID No. 12 or SEQ ID No. 14, or an RNA equivalent or DNA/RNA chimera thereof. In other embodiments wherein the CFB-specific target-hybridizing sequence is the target-hybridizing sequence of (II) (a), the first CFB-specific target-hybridizing sequence of (II) (a) is SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof. Particularly suitable first (A ') and second (B') CFB-specific target-hybridizing sequences of (II) (a) include
(i) (A') SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13, or an RNA equivalent or DNA/RNA chimera thereof;
(ii) (A') SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof;
(iii) (A') SEQ ID NO:14, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(iv) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof.
In some embodiments of the compositions described above, wherein the composition comprises a first amplification oligomer combination, the composition further comprises a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a CFB amplicon that is amplifiable by the first and second CFB-specific amplification oligomers. In some such embodiments, the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (b), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimera thereof; (II) the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (d) and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:25, or an RNA equivalent or DNA/RNA chimera thereof; (II) the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (a) and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:22 or SEQ ID NO:23, or an RNA equivalent or a DNA/RNA chimera thereof; or the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (c), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the CFB-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the CFB-specific detection probe oligomer further comprises a non-fluorescent quencher.
In certain embodiments of the composition for determining the presence or absence of GBS in a sample as described above, the composition comprises both the first and second amplification oligomer combinations.
In another aspect, the invention provides a composition for determining the presence or absence of GBS in a sample, wherein the composition comprises an amplification oligomer combination comprising first and second SIP-specific amplification oligomers capable of amplifying a target region of a GBS SIP target nucleic acid. Particularly suitable first and second SIP-specific amplification oligomers comprise a first (a) and a second (B) SIP-specific target-hybridizing sequence, respectively, selected from the group consisting of:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the composition further comprises a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by the first and second SIP-specific amplification oligomers. In some such embodiments, the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (a), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:9, or an RNA equivalent or DNA/RNA chimera thereof. In other embodiments, the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (b), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:11, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the SIP-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the SIP-specific detection probe oligomer further comprises a non-fluorescent quencher. In some variations of the compositions described above, the composition further comprises a second amplification oligomer combination capable of amplifying a target region of a GBS CFB target nucleic acid.
In another aspect, the invention provides a composition for determining the presence or absence of GBS in a sample, wherein the composition comprises an amplification oligomer combination comprising first and second CFB-specific amplification oligomers capable of amplifying a target region of a GBS CFB target nucleic acid. Particularly suitable first and second CFB-specific amplification oligomers comprise a first (a) and a second (B) CFB-specific target-hybridizing sequence, respectively, selected from:
(a) (A) a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence as SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 13 or 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A) SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A) SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A) SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 21, or an RNA equivalent or DNA/RNA chimera thereof. In certain embodiments, the first CFB-specific target-hybridizing sequence of (a) comprises at least the sequence of SEQ ID No. 28, or an RNA equivalent or DNA/RNA chimera thereof. In some such embodiments, the first CFB-specific target-hybridizing sequence of (a) is comprised in the sequence of SEQ ID No. 27, or an RNA equivalent or DNA/RNA chimera thereof; in some such variations, the first CFB-specific target-hybridizing sequence of (a) is SEQ ID No. 12 or SEQ ID No. 14, or an RNA equivalent or DNA/RNA chimera thereof. In other embodiments, the first CFB-specific target-hybridizing sequence of (a) is SEQ ID NO:18, or an RNA equivalent or DNA/RNA chimera thereof. (a) Particularly suitable first (A) and second (B) CFB-specific target-hybridizing sequences include
(i) (A) SEQ ID NO 12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 13, or an RNA equivalent or DNA/RNA chimera thereof;
(ii) (A) SEQ ID NO 12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof;
(iii) (A) SEQ ID NO 14, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof; and
(iv) (A) SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the composition further comprises a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a CFB amplicon that is amplifiable by the first and second CFB-specific amplification oligomers. In some such embodiments, the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (b), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimera thereof; the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (d), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:25, or an RNA equivalent or DNA/RNA chimera thereof; the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (a), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:22 or SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimera thereof; or said first and second CFB-specific target-hybridizing sequences are said target-hybridizing sequences of (c), and said CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the CFB-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the CFB-specific detection probe oligomer further comprises a non-fluorescent quencher. In some variations of the compositions described above, the composition further comprises a second amplification oligomer combination capable of amplifying a target region of a GBS SIP target nucleic acid.
In another aspect, the present invention provides an aqueous formulation for amplifying GBS nucleic acids comprising a composition as described above and an organic buffer. In some embodiments, the aqueous formulation further comprises one or more components selected from the group consisting of: DNA polymerase, reverse transcriptase, detection probe oligomers, and bulking agents (e.g., trehalose, raffinose, or combinations thereof). In some embodiments, the aqueous formulation contains an inorganic salt at a concentration of 4mM or less.
In another aspect, the present invention provides a reaction mixture for amplifying GBS nucleic acids comprising an aqueous formulation as described above.
In another aspect, the present invention provides a dry formulation for amplifying GBS nucleic acids comprising a composition as described above and an extender. In some embodiments, the bulking agent is trehalose, raffinose, or a combination thereof. In some embodiments, the dry formulation further comprises one or more components selected from the group consisting of: inorganic salts, DNA polymerase, reverse transcriptase, and detection probe oligomers. In some embodiments further comprising an inorganic salt, the percentage of the mass of the inorganic salt relative to the mass of the dry formulation is 0.249% or less. In certain variations, the dry formulation is a lyophilized formulation.
In another aspect, the present invention provides a reaction mixture for amplifying GBS nucleic acids, wherein the reaction mixture is reconstituted with water or an organic buffer from a dried formulation as described above. In some embodiments, the reaction mixture contains an inorganic salt, such as, for example, magnesium, potassium, or sodium; in some such variations, the concentration of the inorganic salt is 4mM or less.
In another aspect, the invention provides a kit for determining the presence or absence of GBS in a sample. In some embodiments, the kit comprises at least one of a first amplification oligomer combination and a second amplification oligomer combination, wherein
(I) The first amplification oligomer combination comprises first and second SIP-specific amplification oligomers capable of amplifying a target region of a GBS SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (A) and second (B), respectively, selected from
SIP-specific target-hybridizing sequence:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof;
and is
(II) the second amplification oligomer combination comprises first and second CFB-specific amplification oligomers capable of amplifying a target region of a GBS CFB target nucleic acid, wherein the first and second CFB-specific amplification oligomers comprise first (a ') and second (B') CFB-specific target-hybridizing sequences, respectively, selected from:
(a) (A') as a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence of SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13 or SEQ ID NO 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A') SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A') SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:21, or an RNA equivalent or DNA/RNA chimera thereof.
In some embodiments of the kits described above, wherein the kit comprises a first amplification oligomer combination, the kit further comprises a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by the first and second SIP-specific amplification oligomers. In some such embodiments, the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (a), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:9, or an RNA equivalent or DNA/RNA chimera thereof. In other embodiments, the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (b), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:11, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the SIP-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the SIP-specific detection probe oligomer further comprises a non-fluorescent quencher.
In some embodiments of the kits as described above, wherein the CFB-specific target-hybridizing sequence is the target-hybridizing sequence of (II) (a), the first CFB-specific target-hybridizing sequence of (II) (a) comprises at least the sequence of SEQ ID NO:28, or an RNA equivalent or DNA/RNA chimera thereof. In some such embodiments, the first CFB-specific target-hybridizing sequence of (II) (a) is comprised in the sequence of SEQ ID No. 27, or an RNA equivalent or DNA/RNA chimera thereof; in some such variations, the first CFB-specific target-hybridizing sequence of (II) (a) is SEQ ID No. 12 or SEQ ID No. 14, or an RNA equivalent or DNA/RNA chimera thereof. In other embodiments wherein the CFB-specific target-hybridizing sequence is the target-hybridizing sequence of (II) (a), the first CFB-specific target-hybridizing sequence of (II) (a) is SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof. Particularly suitable first (A ') and second (B') CFB-specific target-hybridizing sequences of (II) (a) include
(i) (A') SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13, or an RNA equivalent or DNA/RNA chimera thereof;
(ii) (A') SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof;
(iii) (A') SEQ ID NO:14, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(iv) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof.
In some embodiments of the kits described above, wherein the kit comprises a first amplification oligomer combination, the kit further comprises a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target hybridization sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a CFB amplicon that is amplifiable by the first and second CFB-specific amplification oligomers. In some such embodiments, the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (b), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimera thereof; (II) the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (d) and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:25, or an RNA equivalent or DNA/RNA chimera thereof; (II) the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (a) and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:22 or SEQ ID NO:23, or an RNA equivalent or a DNA/RNA chimera thereof; or the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (c), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the CFB-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the CFB-specific detection probe oligomer further comprises a non-fluorescent quencher.
In certain embodiments of the kit for determining the presence or absence of GBS in a sample as described above, the kit comprises both the first and second amplification oligomer combinations.
In another aspect, the invention provides a kit for determining the presence or absence of GBS in a sample, wherein the kit comprises an amplification oligomer combination comprising first and second SIP-specific amplification oligomers capable of amplifying a target region of a GBS SIP target nucleic acid. Particularly suitable first and second SIP-specific amplification oligomers comprise a first (a) and a second (B) SIP-specific target-hybridizing sequence, respectively, selected from the group consisting of:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the kit further comprises a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by the first and second SIP-specific amplification oligomers. In some such embodiments, the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (a), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:9, or an RNA equivalent or DNA/RNA chimera thereof. In other embodiments, the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (b), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:11, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the SIP-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the SIP-specific detection probe oligomer further comprises a non-fluorescent quencher. In some variations of the kits described above, the kit further comprises a second amplification oligomer combination capable of amplifying a target region of a GBS CFB target nucleic acid.
In another aspect, the invention provides a kit for determining the presence or absence of GBS in a sample, wherein the kit comprises an amplification oligomer combination comprising first and second CFB-specific amplification oligomers capable of amplifying a target region of a GBS CFB target nucleic acid. Particularly suitable first and second CFB-specific amplification oligomers comprise a first (a) and a second (B) CFB-specific target-hybridizing sequence, respectively, selected from:
(a) (A) a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence as SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 13 or 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A) SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A) SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A) SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 21, or an RNA equivalent or DNA/RNA chimera thereof. In certain embodiments, the first CFB-specific target-hybridizing sequence of (a) comprises at least the sequence of SEQ ID No. 28, or an RNA equivalent or DNA/RNA chimera thereof. In some such embodiments, the first CFB-specific target-hybridizing sequence of (a) is comprised in the sequence of SEQ ID No. 27, or an RNA equivalent or DNA/RNA chimera thereof; in some such variations, the first CFB-specific target-hybridizing sequence of (a) is SEQ ID No. 12 or SEQ ID No. 14, or an RNA equivalent or DNA/RNA chimera thereof. In other embodiments, the first CFB-specific target-hybridizing sequence of (a) is SEQ ID NO:18, or an RNA equivalent or DNA/RNA chimera thereof. (a) Particularly suitable first (A) and second (B) CFB-specific target-hybridizing sequences include
(i) (A) SEQ ID NO 12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 13, or an RNA equivalent or DNA/RNA chimera thereof;
(ii) (A) SEQ ID NO 12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof;
(iii) (A) SEQ ID NO 14, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof; and
(iv) (A) SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the kit further comprises a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a CFB amplicon that is amplifiable by the first and second CFB-specific amplification oligomers. In some such embodiments, the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (b), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimera thereof; the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (d), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:25, or an RNA equivalent or DNA/RNA chimera thereof; the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (a), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:22 or SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimera thereof; or said first and second CFB-specific target-hybridizing sequences are said target-hybridizing sequences of (c), and said CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the CFB-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the CFB-specific detection probe oligomer further comprises a non-fluorescent quencher. In some variations of the kits above, the kit further comprises a second amplification oligomer combination capable of amplifying the target region of the GBS SIP target nucleic acid.
In another aspect, the invention provides a method for determining the presence or absence of GBS in a sample. In some embodiments, the method comprises
(1) Contacting a sample suspected of containing GBS with at least one of a first amplification oligomer combination and a second amplification oligomer combination, wherein
(I) The first amplification oligomer combination comprises first and second SIP-specific amplification oligomers for amplifying a GBS SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (a) and second (B) target region SIP-specific target-hybridizing sequences selected from:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof; and is
(II) the second amplification oligomer combination comprises first and second CFB-specific amplification oligomers for amplifying a target region of a GBS CFB target nucleic acid, wherein the first and second CFB-specific amplification oligomers comprise first (a ') and second (B') CFB-specific target-hybridizing sequences, respectively, selected from:
(a) (A') as a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence of SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13 or SEQ ID NO 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A') SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A') SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 21, or an RNA equivalent or DNA/RNA chimera thereof;
(2) performing an in vitro nucleic acid amplification reaction, wherein any GBS SIP and/or CFB target nucleic acid, when present in the sample, is used as a template to produce one or more amplicons corresponding to at least one of the SIP and CFB target regions; and
(3) detecting the presence or absence of the one or more amplicons, thereby determining the presence or absence of GBS in the sample.
In some embodiments of the methods described above, the method comprises contacting the sample with both the first and second amplification oligomer combinations. In some such embodiments, the method is a multiplexing method comprising contacting the sample with both the first and second amplification oligomer combinations within the same reaction mixture.
In some embodiments of the methods described above, wherein the methods comprise contacting the sample with the first amplification oligomer combination, the detecting step comprises contacting the in vitro nucleic acid amplification reaction with a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by the first and second SIP-specific amplification oligomers. In some such embodiments, the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (a), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:9, or an RNA equivalent or DNA/RNA chimera thereof. In other embodiments, the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (I) (b), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:11, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the SIP-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the SIP-specific detection probe oligomer further comprises a non-fluorescent quencher.
In some embodiments of the methods described above, wherein the CFB-specific target-hybridizing sequence is the target-hybridizing sequence of (II) (a), the first CFB-specific target-hybridizing sequence of (II) (a) comprises at least the sequence of SEQ ID NO:28, or an RNA equivalent or DNA/RNA chimera thereof. In some such embodiments, the first CFB-specific target-hybridizing sequence of (II) (a) is comprised in the sequence of SEQ ID No. 27, or an RNA equivalent or DNA/RNA chimera thereof; in some such variations, the first CFB-specific target-hybridizing sequence of (II) (a) is SEQ ID No. 12 or SEQ ID No. 14, or an RNA equivalent or DNA/RNA chimera thereof. In other embodiments wherein the CFB-specific target-hybridizing sequence is the target-hybridizing sequence of (II) (a), the first CFB-specific target-hybridizing sequence of (II) (a) is SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof. Particularly suitable first (A ') and second (B') CFB-specific target-hybridizing sequences of (II) (a) include
(i) (A') SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13, or an RNA equivalent or DNA/RNA chimera thereof;
(ii) (A') SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof;
(iii) (A') SEQ ID NO:14, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(iv) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof.
In some embodiments of the methods described above, wherein the method comprises contacting the sample with the second amplification oligomer combination, the detecting step comprises contacting the in vitro nucleic acid amplification reaction with a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a CFB amplicon that is amplifiable by the first and second CFB-specific amplification oligomers. In some such embodiments, the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (b), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimera thereof; (II) the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (d) and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:25, or an RNA equivalent or DNA/RNA chimera thereof; (II) the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (a) and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:22 or SEQ ID NO:23, or an RNA equivalent or a DNA/RNA chimera thereof; or the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (II) (c), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the CFB-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the CFB-specific detection probe oligomer further comprises a non-fluorescent quencher.
In certain variations of the method for determining the presence or absence of GBS in a sample, as described above, the detecting step is performed in real-time.
In certain variations of the methods for determining the presence or absence of GBS in a sample as described above, the in vitro nucleic acid amplification reaction is a PCR amplification reaction (e.g., a real-time PCR amplification reaction).
In some embodiments of the methods described above, wherein the method comprises contacting the sample with both the first and second amplification oligomer combinations (e.g., a multiplexing method), the detecting step comprises contacting the in vitro nucleic acid amplification reaction with (i) a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a SIP amplicon amplifiable by the first and second SIP-specific amplification oligomers, and (ii) a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a CFB amplicon amplifiable by the first and second CFB-specific amplification oligomers, wherein each of the SIP-specific detection probe oligomer and the CFB-specific detection probe oligomer comprises a fluorescent label and a non-fluorescent quencher. In some such embodiments, the in vitro nucleic acid amplification reaction is a real-time PCR amplification reaction.
In another aspect, the present invention provides a method for determining the presence or absence of GBS in a sample, wherein the method comprises
(1) Contacting a sample suspected of containing GBS with an amplification oligomer combination comprising first and second SIP-specific amplification oligomers for amplifying a target region of a GBS SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (a) and second (B) SIP-specific target-hybridizing sequences, respectively, selected from the group consisting of:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof;
(2) performing an in vitro nucleic acid amplification reaction, wherein any GBS SIP target nucleic acid, when present in the sample, is used as a template to generate an amplicon corresponding to the SIP target region; and
(3) detecting the presence or absence of the amplicon, thereby determining the presence or absence of GBS in the sample.
In some variations, the detecting step comprises contacting the in vitro nucleic acid amplification reaction with a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by the first and second SIP-specific amplification oligomers. In some such embodiments, the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (a), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:9, or an RNA equivalent or DNA/RNA chimera thereof. In other embodiments, the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (b), and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:11, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the SIP-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the SIP-specific detection probe oligomer further comprises a non-fluorescent quencher. In certain variations, the detecting step is performed in real-time. In certain variations, the in vitro nucleic acid amplification reaction is a PCR amplification reaction (e.g., a real-time PCR amplification reaction). In some embodiments, the method further comprises contacting the sample with a second amplification oligomer combination comprising first and second CFB-specific amplification oligomers for amplifying a target region of a GBS CFB target nucleic acid, wherein in the amplifying step, any GBS CFB target nucleic acid, when present in the sample, is used as a template to produce an amplicon corresponding to the CFB target region, and wherein the detecting step comprises detecting the presence or absence of the amplicon corresponding to the CFB target region.
In another aspect, the present invention provides a method for determining the presence or absence of GBS in a sample, wherein the method comprises
(1) Contacting a sample suspected of containing GBS with an amplification oligomer combination comprising first and second CFB-specific amplification oligomers for amplifying a target region of a GBS CFB target nucleic acid, wherein the first and second CFB-specific amplification oligomers comprise first (a) and second (B) CFB-specific target-hybridizing sequences, respectively, selected from:
(a) (A) a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence as SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 13 or 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A) SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A) SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A) SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 21, or an RNA equivalent or DNA/RNA chimera thereof;
(2) performing an in vitro nucleic acid amplification reaction, wherein any GBS CFB target nucleic acid, when present in the sample, is used as a template to produce an amplicon corresponding to the CFB target region; and
(3) detecting the presence or absence of the amplicon, thereby determining the presence or absence of GBS in the sample.
In certain embodiments, the first CFB-specific target-hybridizing sequence of (a) comprises at least the sequence of SEQ ID No. 28, or an RNA equivalent or DNA/RNA chimera thereof. In some such embodiments, the first CFB-specific target-hybridizing sequence of (a) is comprised in the sequence of SEQ ID No. 27, or an RNA equivalent or DNA/RNA chimera thereof; in some such variations, the first CFB-specific target-hybridizing sequence of (a) is SEQ ID No. 12 or SEQ ID No. 14, or an RNA equivalent or DNA/RNA chimera thereof. In other embodiments, the first CFB-specific target-hybridizing sequence of (a) is SEQ ID NO:18, or an RNA equivalent or DNA/RNA chimera thereof. (a) Particularly suitable first (A) and second (B) CFB-specific target-hybridizing sequences include
(i) (A) SEQ ID NO 12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 13, or an RNA equivalent or DNA/RNA chimera thereof;
(ii) (A) SEQ ID NO 12, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof;
(iii) (A) SEQ ID NO 14, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof; and
(iv) (A) SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 15, or an RNA equivalent or DNA/RNA chimera thereof.
In some variations, the detecting step comprises contacting the in vitro nucleic acid amplification reaction with a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a CFB amplicon that is amplifiable by the first and second CFB-specific amplification oligomers. In some such embodiments, the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (b), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimera thereof; the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (d), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:25, or an RNA equivalent or DNA/RNA chimera thereof; the first and second CFB-specific target-hybridizing sequences are the target-hybridizing sequences of (a), and the CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:22 or SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimera thereof; or said first and second CFB-specific target-hybridizing sequences are said target-hybridizing sequences of (c), and said CFB-specific detection probe target-hybridizing sequence is SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the CFB-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the CFB-specific detection probe oligomer further comprises a non-fluorescent quencher. In certain variations, the detecting step is performed in real-time. In certain variations, the in vitro nucleic acid amplification reaction is a PCR amplification reaction (e.g., a real-time PCR amplification reaction). In some embodiments, the method further comprises contacting the sample with a second amplification oligomer combination comprising first and second SIP-specific amplification oligomers for amplifying a target region of a GBS SIP target nucleic acid, wherein in the amplifying step, any GBS SIP target nucleic acid, when present in the sample, is used as a template to produce an amplicon corresponding to the SIP target region, and wherein the detecting step comprises detecting the presence or absence of the amplicon corresponding to the SIP target region.
In some embodiments of the methods for determining the presence or absence of GBS in a sample as described above, the method determines the presence or absence of any of GBS serotypes Ia, Ib, Ic, II, III, IV, V, VI, VII, VIII, and IX. In some such embodiments, the method further determines the presence or absence of a non-hemolytic strain of GBS.
In another aspect, the invention provides a detection probe oligomer. In some embodiments, the detection probe oligomer is a SIP-specific detection probe oligomer comprising a SIP-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and that is configured to hybridize to a target sequence contained within a SIP amplicon that is amplifiable by a first amplification oligomer combination comprising first and second SIP-specific amplification oligomers capable of amplifying a target region of a GBS SIP target nucleic acid, wherein the first and second SIP-specific amplification oligomers comprise first (a) and second (B) SIP-specific target-hybridizing sequences, respectively, selected from the group consisting of:
(a) (A) SEQ ID NO 3, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 4, or an RNA equivalent or DNA/RNA chimera thereof; and
(b) (A) SEQ ID NO 7, or an RNA equivalent or DNA/RNA chimera thereof, and
(B) 8, or an RNA equivalent or DNA/RNA chimera thereof.
In some embodiments of the SIP-specific detection probe oligomer described above, the SIP-specific detection probe target-hybridizing sequence is selected from (a) SEQ ID NO 9, or an RNA equivalent or DNA/RNA chimera thereof; and (b) SEQ ID NO 11, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the SIP-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the SIP-specific detection probe oligomer further comprises a non-fluorescent quencher.
In other embodiments, the detection probe oligomer is a CFB-specific detection probe oligomer comprising a CFB-specific detection probe target-hybridizing sequence that is about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a CFB amplicon that is amplifiable by a second amplification oligomer combination comprising first and second CFB-specific amplification oligomers capable of amplifying a target region of a GBS CFB target nucleic acid, wherein the first and second CFB-specific amplification oligomers comprise first (a ') and second (B') CFB-specific target-hybridizing sequences, respectively, selected from the group consisting of:
(a) (A') as a sequence of about 17 to about 24 consecutive nucleotides contained in the sequence of SEQ ID NO:26, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 13 or SEQ ID NO 15, or an RNA equivalent or DNA/RNA chimera thereof;
(b) (A') SEQ ID NO 16, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO 17, or an RNA equivalent or DNA/RNA chimera thereof;
(c) (A') SEQ ID NO 18, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:15, or an RNA equivalent or DNA/RNA chimera thereof; and
(d) (A') SEQ ID NO 20, or an RNA equivalent or DNA/RNA chimera thereof, and
(B') SEQ ID NO:21, or an RNA equivalent or DNA/RNA chimera thereof. In some embodiments of the CFB-specific detection probe oligomer described above, the CFB-specific detection probe target-hybridizing sequence is selected from (a) SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimera thereof; (b) 25, or an RNA equivalent or DNA/RNA chimera thereof; (c) 22, or an RNA equivalent or DNA/RNA chimera thereof; and (d) SEQ ID NO 23, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the CFB-specific detection probe oligomer further comprises a detectable label, such as, for example, a fluorescent or chemiluminescent label. In some embodiments of probe oligomers comprising a detectable label, the detectable label is a fluorescent label and the CFB-specific detection probe oligomer further comprises a non-fluorescent quencher.
In another aspect, the invention provides a composition comprising a SIP-specific detection probe oligomer and a CFB-specific detection probe oligomer as described above.
In another aspect, the present invention provides an aqueous formulation for detecting GBS nucleic acids comprising (1) an SIP-specific detection probe oligomer and/or a CFB-specific detection probe oligomer as described above and (2) an organic buffer. In some embodiments, the aqueous formulation further comprises one or more components selected from the group consisting of: a surfactant (e.g., polyethylene glycol mono [4- (1,1,3, 3-tetramethylbutyl) phenyl ] ether, polysorbate 20, or a combination thereof), a DNA polymerase, a reverse transcriptase, at least one amplification oligomer, and an extender (e.g., trehalose, raffinose, or a combination thereof). In certain variations comprising a surfactant, the surfactant is a non-linear surfactant, such as polysorbate 20, for example. In some embodiments, the aqueous formulation contains an inorganic salt at a concentration of 4mM or less. In a related aspect, the invention provides a reaction mixture for the detection of GBS comprising an aqueous formulation as described above.
In another aspect, the invention provides a dry formulation for detecting GBS nucleic acids comprising (1) an SIP-specific detection probe oligomer and/or a CFB-specific detection probe oligomer as described above and (2) a bulking agent. In some embodiments, the bulking agent is trehalose, raffinose, or a combination thereof. In some embodiments, the dry formulation further comprises one or more components selected from the group consisting of: inorganic salts, DNA polymerase, reverse transcriptase, at least one amplification oligomer, and a surfactant (e.g., polyethylene glycol mono [4- (1,1,3, 3-tetramethylbutyl) phenyl ] ether, polysorbate 20, or a combination thereof). In some embodiments further comprising an inorganic salt, the percentage of the mass of the inorganic salt relative to the mass of the dry formulation is 0.249% or less. In certain variations comprising a surfactant, the surfactant is a non-linear surfactant, such as polysorbate 20, for example. In certain variations, the dry formulation is a lyophilized formulation. In a related aspect, the invention provides a reaction mixture for detecting GBS, wherein the reaction mixture is reconstituted with water and an organic buffer from a dried formulation as described above. In some embodiments, the reaction mixture contains an inorganic salt, such as, for example, magnesium, potassium, or sodium; in some such variations, the concentration of the inorganic salt is 4mM or less.
These and other aspects of the invention will become apparent upon reference to the following detailed description of the invention and the accompanying drawings.
Definition of
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the methods and compositions belong. General definitions can be found in technical books related to The field of Molecular Biology, such as The Dictionary of Microbiology and Molecular Biology, 2 nd edition (Singleton et al, 1994, John Wiley & Sons, New York, N.Y.) or The Harper Collins Dictionary of Biology (Hale and Marham,1991, Harper Perennial, N.Y.). As used herein, the following terms and phrases have the meanings assigned to them, unless otherwise indicated.
The terms "a", "an" and "the" ("the") include a plurality of the indicators unless the context clearly dictates otherwise. For example, as used herein, "nucleic acid" is understood to mean one or more nucleic acids. Thus, the terms "a" (or "an"), "one or more" and "at least one" are used interchangeably herein.
It is understood that there is an implicit "about" preceding the temperature, concentration, time, etc. discussed in this disclosure, such that slight and insubstantial deviations are within the scope of the present teachings herein. Generally, the term "about" indicates an insubstantial change in the amount of a component of a composition that does not have any significant effect on the activity or stability of the composition. To the extent that such exclusion is not explicitly recited (e.g., "excluding endpoints"), all ranges are to be interpreted as encompassing the endpoints; thus, for example, "within 10-15" includes the values 10 and 15. Furthermore, the use of "comprising", "containing" and "including" is not limiting. It is to be understood that both the foregoing general description and the detailed description are exemplary and explanatory only and are not restrictive of the present teachings. In the event that any material incorporated by reference is inconsistent with the express content of this disclosure, the express content controls.
Unless specifically stated otherwise, embodiments in which "comprising" various components are recited in the specification are also contemplated as "consisting of" or "consisting essentially of the recited components"; embodiments in the specification reciting "consisting of various components" are also contemplated as "comprising" or "consisting essentially of the recited components"; and embodiments in which the specification recites "consisting essentially of" a variety of components are also contemplated as "consisting of" or "including the recited components" (such interchangeability does not apply to the use of these terms in the claims). "consisting essentially of … …" means that one or more additional components, one or more compositions, or one or more method steps that do not materially alter the basic and novel characteristics of the compositions and methods described herein can be included in those compositions or methods. Such features include specificity to distinguish GBS nucleic acids from other known pathogens, optionally sensitivity to detect bacteria present in the sample at a concentration of about 100CFU/ml, optionally the ability to detect Group B Streptococcus (GBS) nucleic acid sequences present in the sample within about 60 minutes and/or within about 40 cycles from the start of the amplification reaction when a cyclic amplification reaction is used.
A "sample" includes any sample that may contain GBS or a component thereof (e.g., a nucleic acid or nucleic acid fragment). Samples include "biological samples" including any tissue or material from a living or dead human that may contain GBS or a target nucleic acid derived therefrom, including, for example, vaginal swab samples, cervical brush samples, respiratory tissue or exudates such as bronchoscopy, bronchoalveolar lavage (BAL) or lung biopsy, sputum, saliva, peripheral blood, plasma, serum, lymph nodes, gastrointestinal tissue, stool, urine, semen, or other bodily fluids or substances. The biological sample may be treated to physically or mechanically disrupt tissue or cellular structures, thereby releasing intracellular components into a solution that may further contain enzymes, buffers, salts, detergents, etc. used to prepare the biological sample for analysis using standard methods. In addition, the sample may comprise a processed sample, for example a sample obtained by passing the sample through or through a filtration device, or subsequent centrifugation, or by adherence to a culture medium, matrix or support.
"nucleic acid" and "polynucleotide" refer to a multimeric compound comprising nucleosides or nucleoside analogs having nitrogen-containing nucleobases or base analogs linked together to form a polynucleotide, including conventional RNA, DNA, mixed RNA-DNA, and polymers as analogs thereof. A nucleic acid "backbone" can be composed of a variety of linkages including one or more of sugar-phosphodiester linkages, peptide-nucleic acid linkages ("peptide nucleic acids" or PNAs; PCT publication No. WO 95/32305), phosphorothioate linkages, methylphosphonate linkages, or combinations thereof. The sugar moiety of the nucleic acid may be ribose, deoxyribose, or similar compounds with substitutions (e.g., 2 'methoxy or 2' halide substitutions). The nitrogenous base may be a conventional base (A, G, C, T, U), an analogue thereof (e.g.inosine or otherwise; see The Biochemistry of The Nucleic Acids 5-36, edited by Adams et al, 11 th edition, 1992), a derivative of a purine or pyrimidine (e.g.N)4-methyldeoxyguanosine, deaza or aza purine, deaza or aza pyrimidine, pyrimidine base with substituent in position 5 or 6, purine base with substituent in position 2, 6 or 8, 2-amino-6-methylaminopurine, O6-methylguanine, 4-thio-pyrimidine, 4-amino-pyrimidine, 4-dimethylhydrazine-pyrimidine and O4-alkyl-pyrimidines; U.S. patent No. 5,378,825 and PCT publication No. WO 93/13121). Nucleic acids can comprise one or more "abasic" residues, wherein the backbone does not comprise nitrogenous bases for one or more positions of the polymer (U.S. Pat. No. 5,585,481). The nucleic acid may comprise only conventional RNA or DNA sugars, bases, and linkages, or may comprise both conventional components and substituents (e.g., a conventional base with a 2' methoxy linkage, or a polymer containing a conventional base and one or more base analogs). Nucleic acids include "locked nucleic acids" (LNAs), which are LNA nucleotide monomers containing one or more bicyclic furanose units with a locked conformation of RNA mimicking sugars to enhance mutual interactionsAnalogs that complement the hybridization affinity of RNA and DNA sequences (Vester and Wengel,2004, Biochemistry 43(42): 13233-41). Embodiments of oligomers that may affect the stability of the hybridization complex include PNA oligomers, oligomers that include 2 '-methoxy or 2' -fluoro substituted RNAs, or oligomers that affect the overall charge, charge density, or spatial association of the hybridization complex, including oligomers containing charged linkages (e.g., phosphorothioates) or neutral groups (e.g., methylphosphonates). Unless otherwise specified, 5-methylcytosine can be used in conjunction with any of the aforementioned backbones/sugar/linkages (including RNA or DNA backbones) (or mixtures thereof). It will be understood that when referring to ranges of lengths of oligonucleotides, amplicons, or other nucleic acids, the ranges include all integers (e.g., 19 to 25 consecutive nucleotides in length include 19, 20, 21, 22, 23, 24, and 25).
As used herein, a "nucleotide" is a subunit of a nucleic acid that consists of a phosphate group, a 5-carbon sugar, and a nitrogenous base (also referred to herein as a "nucleobase"). The 5-carbon sugar present in RNA is ribose. In DNA the 5-carbon sugar is 2' -deoxyribose. The term also includes analogs of such subunits, such as a methoxy group at the 2' position of the ribose sugar (also referred to herein as "2 ' -O-Me" or "2 ' -methoxy").
By "RNA and DNA equivalents" is meant RNA and DNA molecules having substantially the same complementary base pair hybridization characteristics. RNA and DNA equivalents have different sugar moieties (i.e., ribose and deoxyribose), and may differ by the presence of uracil in RNA and thymine in DNA. Differences between RNA and DNA equivalents do not result in homology differences because these equivalents have the same degree of complementarity to a particular sequence. By "DNA/RNA chimera" is meant a nucleic acid comprising both DNA and RNA nucleotides. Unless the context clearly indicates otherwise, reference to GBS nucleic acids includes GBS RNA and DNA equivalents and DNA/RNA chimeras thereof.
As used herein, a "target nucleic acid" is a nucleic acid that comprises a target sequence to be amplified. The target nucleic acid may be DNA or RNA, and may be single-stranded or double-stranded. In addition to the target sequence, the target nucleic acid may also comprise other sequences that may not be amplified.
As used herein, the term "target sequence" refers to a specific nucleotide sequence of a target nucleic acid to be amplified and/or detected. "target sequence" includes a composite sequence with which an oligonucleotide (e.g., a primer oligonucleotide and/or a promoter oligonucleotide) is complexed during an amplification process (e.g., PCR, TMA). In the case where the target nucleic acid is initially single-stranded, the term "target sequence" will also refer to a sequence that is complementary to the "target sequence" as present in the target nucleic acid. In the case of a target nucleic acid that is initially double-stranded, the term "target sequence" refers to both the sense (+) strand and the antisense (-) strand.
"target-hybridizing sequence" or "target-specific sequence" is used herein to refer to the portion of an oligomer that is configured to hybridize to a target nucleic acid sequence. Preferably, the target-hybridizing sequence is configured to specifically hybridize to a target nucleic acid sequence. Target-hybridizing sequences may be 100% complementary to the portion of the target sequence they are configured to hybridize to, but need not be. The target-hybridizing sequence may also comprise insertions, deletions and/or substitutions of nucleotide residues relative to the target sequence. For example, it may occur that the target-hybridizing sequence is less than 100% complementary to the target sequence, e.g., when the target nucleic acid is a plurality of strains within a species, as is the case for oligomers configured to hybridize to multiple GBS serotypes. It is understood that there are other reasons for configuring a target-hybridizing sequence to have less than 100% complementarity with a target nucleic acid.
The term "targeting sequence" as used herein with respect to a region of a GBS nucleic acid refers to a process in which an oligonucleotide hybridizes to a target sequence in a manner that allows for amplification and detection as described herein. In a preferred embodiment, the oligonucleotide is complementary to the targeted GBS nucleic acid sequence and contains no mismatches. In another preferred embodiment, the oligonucleotide is complementary to the targeted GBS nucleic acid sequence, but contains 1,2, 3, 4 or 5 mismatches. Preferably, the oligomer specifically hybridizes to a target sequence.
The term "configured" refers to the actual arrangement of the polynucleotide sequence configuration of a reference oligonucleotide target-hybridizing sequence. For example, an amplification oligomer configured to produce a specified amplicon from a target sequence has a polynucleotide sequence that hybridizes to the target sequence and can be used in an amplification reaction to produce the amplicon. Also for example, an oligonucleotide configured to specifically hybridize to a target sequence has a polynucleotide sequence that specifically hybridizes to a reference sequence under stringent hybridization conditions.
As used herein, the term "configured to specifically hybridize to … …" means that the target-hybridizing region of an amplification oligonucleotide, detection probe, or other oligonucleotide is designed to have a polynucleotide sequence that can target a sequence of a reference GBS target region. Such oligonucleotides are not limited to targeting only this sequence, but may be used as compositions for targeting a GBS target nucleic acid, in kits for targeting a GBS target nucleic acid, or in methods of targeting a GBS target nucleic acid. The oligonucleotides are designed to be used as components of an assay for amplifying and detecting GBS from a sample, and are therefore designed to target GBS in the presence of other nucleic acids typically found in a test sample. As understood in the art, "specifically hybridizes to … …" does not mean hybridizing exclusively to … …, as some low level of hybridization to non-target nucleic acids may occur. Specifically, "specifically hybridizes to … …" means that the oligonucleotide is configured for hybridization primarily to a target in an assay such that accurate detection of the target nucleic acid in a sample can be determined.
The term "region" as used herein refers to a portion of a nucleic acid, wherein the portion is less than the entire nucleic acid. For example, when reference is made to a nucleic acid being an oligonucleotide promoter primer, the term "region" may be used to refer to a smaller promoter portion. Similarly, and also by way of example only, when the nucleic acid is a GBS target nucleic acid, the term "region" may be used to refer to a smaller region of the nucleic acid, wherein the smaller region is targeted by one or more oligonucleotides of the disclosure. As another non-limiting example, when referring to a nucleic acid that is an amplicon, the term region can be used to refer to the identification of a smaller nucleotide sequence for hybridization by the target-hybridizing sequence of the probe.
"oligomer", "oligonucleotide" or "oligonucleotide" refers to a nucleic acid of typically less than 1,000 nucleotides (nt), including those in a size range having a lower limit of about 2 to 5nt and an upper limit of about 500 to 900 nt. Some particular embodiments are oligomers in a size range having a lower limit of about 5 to 15, 16, 17, 18, 19, or 20nt and an upper limit of about 50 to 600nt, and other particular embodiments are in a size range having a lower limit of about 10 to 20nt and an upper limit of about 22 to 100 nt. Oligomers can be purified from naturally occurring sources, but can be synthesized by using any well-known enzymatic or chemical method. The term oligonucleotide does not denote any particular function of the agent; rather, it is used generically to encompass all such agents described herein. Oligonucleotides may serve a variety of different functions. For example, it can be used as a primer if it is specific for and capable of hybridizing to a complementary strand and can be further extended in the presence of a nucleic acid polymerase; if it contains a sequence recognized by RNA polymerase and allows transcription, it can be used as a primer and provide a promoter (e.g., T7 primer); and it can be used to detect a target nucleic acid if it is capable of hybridizing to the target nucleic acid or an amplicon thereof and further provides a detectable moiety (e.g., an acridinium ester compound). Oligomers may be referred to by functional name (e.g., capture probe, primer, or promoter primer), but those skilled in the art will understand that such terms refer to oligomers.
As used herein, an oligonucleotide "substantially corresponding" to a given reference nucleic acid sequence means that the oligonucleotide is sufficiently similar to the reference nucleic acid sequence such that the oligonucleotide has similar hybridization properties to the reference nucleic acid sequence, i.e., it will hybridize to the same target nucleic acid sequence under stringent hybridization conditions. One skilled in the art will appreciate that a "substantially corresponding oligonucleotide" can be different from a reference sequence and still hybridize to the same target nucleic acid sequence. It is also understood that, unless the context clearly indicates otherwise, a first nucleic acid corresponding to a second nucleic acid includes its RNA or DNA equivalent and its DNA/RNA chimera, and includes its complement. Such variations in nucleic acid can be stated in terms of the percentage of identical bases within the sequence or the percentage of perfectly complementary bases between the probe or primer and its target sequence; thus, in certain embodiments, an oligonucleotide "substantially corresponds" to a reference nucleic acid sequence if these percentages of base identity or complementarity are from 100% to about 80%, preferably from 100% to about 85%, or more preferably from 100% to about 90% or from 100% to about 95%. Such variations in nucleic acid can also be expressed in terms of the number of nucleobase substitutions in the nucleic acid sequence relative to a reference sequence or the number of mismatches within the sequence relative to a target sequence; thus, in certain embodiments, an oligonucleotide "substantially corresponds" to a reference nucleic acid sequence if the number of nucleobase substitutions or mismatches is at most four, preferably at most three, or more preferably at most two or at most one substitution or mismatch (i.e., zero to four, preferably zero to three, or more preferably zero to two or zero to one, inclusive). Similarly, a region of a nucleic acid or amplified nucleic acid may be referred to herein as corresponding to a reference nucleic acid sequence. One skilled in the art will appreciate that various modifications to the hybridization conditions may be required at various percentages of complementarity to allow hybridization to a particular target sequence without causing unacceptable levels of non-specific hybridization.
As used herein, the phrase "or the complement thereof, or an RNA equivalent or a DNA/RNA chimera thereof (in addition to a reference DNA sequence) with respect to a DNA sequence includes the complement of the DNA sequence, the RNA equivalent of the reference DNA sequence, the RNA equivalent of the complement of the reference DNA sequence, the DNA/RNA chimera of the reference DNA sequence and the DNA/RNA chimera of the complement of the reference DNA sequence. Similarly, the phrase "or its complement, or a DNA equivalent or a DNA/RNA chimera thereof (in addition to a reference RNA sequence) with respect to an RNA sequence includes the complement of an RNA sequence, a DNA equivalent of a reference RNA sequence, a DNA equivalent of the complement of a reference RNA sequence, a DNA/RNA chimera of a reference RNA sequence and a DNA/RNA chimera of the complement of a reference RNA sequence.
An "amplification oligonucleotide" or "amplification oligomer" is an oligonucleotide that hybridizes to a target nucleic acid or its complement and participates in a nucleic acid amplification reaction (e.g., acts as a primer or promoter primer). Particular amplification oligomers contain at least about 10 contiguous bases, and optionally at least 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 contiguous bases that are complementary to a region of the target nucleic acid sequence or its complementary strand. The contiguous bases may be at least about 80%, at least about 90%, or fully complementary to the target sequence to which the amplification oligomer binds. Those skilled in the art will appreciate that the recited ranges include all integers and rational numbers within the recited range (e.g., 92% or 98.377%). Particular amplification oligomers are about 10 to about 60 bases in length and may optionally comprise modified nucleotides.
A "primer" is an oligomer that hybridizes to a template nucleic acid and has a 3' end extended by polymerization. The primer may optionally be modified, for example by comprising a 5' region that is not complementary to the target sequence. Such modifications may include functional additions such as tags, promoters, or other non-target specific sequences for or useful in manipulating or amplifying primers or target oligonucleotides.
In the context of transcription-mediated amplification, primers modified with a 5' promoter sequence are referred to herein as "promoter primers". One of ordinary skill in the art of molecular biology or biochemistry will appreciate that an oligomer that can be used as a primer can be modified to include a 5 'promoter sequence and then used as a promoter-primer, and similarly, any promoter-primer can function as a primer with or without its 5' promoter sequence. Promoter-primers modified to incorporate a blocked 3' end are referred to herein as "promoter providers" that are capable of hybridizing to a target nucleic acid and providing an upstream promoter sequence for initiating transcription, but do not provide a primer for oligonucleotide extension.
As used herein, "non-target-specific sequence" or "non-target-hybridizing sequence" refers to a region of an oligomer sequence, wherein the region does not stably hybridize to a target sequence under standard hybridization conditions. Oligomers with non-target specificity include, but are not limited to, promoter primers and molecular beacons.
"nucleic acid amplification" refers to any in vitro procedure that produces multiple copies of a target nucleic acid sequence or its complement, or a fragment thereof (i.e., an amplified sequence containing less than the entire target nucleic acid). Examples of nucleic acid amplification procedures include transcription-related methods such as transcription-mediated amplification (TMA), nucleic acid sequence-based amplification (NASBA), and other methods (e.g., U.S. Pat. nos. 5,399,491, 5,554,516, 5,437,990, 5,130,238, 4,868,105, and 5,124,246), replicase-mediated amplification (e.g., U.S. Pat. No. 4,786,600), Polymerase Chain Reaction (PCR) (e.g., U.S. Pat. nos. 4,683,195, 4,683,202, and 4,800,159), Ligase Chain Reaction (LCR) (e.g., european patent No. 0320308), helicase-dependent amplification (e.g., U.S. Pat. No. 7,282,328), and Strand Displacement Amplification (SDA) (e.g., U.S. Pat. No. 5,422,252). Amplification may be linear or exponential. Replicase-mediated amplification uses self-replicating RNA molecules, and replicases, such as QB replicase. PCR amplification uses DNA polymerase, primers, and a thermal cycling step to synthesize multiple copies of two complementary strands of DNA or cDNA. LCR amplification uses at least four individual oligonucleotides to amplify the target and its complementary strand by using multiple cycles of hybridization, ligation, and denaturation. Helicase-dependent amplification separates the two strands of a DNA duplex using helicase to produce a single-stranded template, after which a sequence-specific primer is hybridized to the template and extended by a DNA polymerase to amplify the target sequence. SDA uses primers that contain recognition sites for restriction enzymes that nick one strand of a hemimodified DNA duplex containing a target sequence, followed by amplification in a series of primer extension and strand displacement steps. Particular embodiments use PCR or TMA, but it will be clear to one of ordinary skill in the art that the oligomers disclosed herein can be readily used as primers in other amplification methods.
Transcription-related amplification uses DNA polymerase, RNA polymerase, deoxyribonucleoside triphosphates, ribonucleoside triphosphates, promoter-containing oligonucleotides (and optionally may include other oligonucleotides) to ultimately produce multiple RNA transcripts from a nucleic acid template (described in detail in, for example, U.S. Pat. Nos. 5,399,491 and 5,554,516 to Kacian et al, U.S. Pat. No. 5,437,990 to Burg et al, PCT publication Nos. WO 88/01302 and WO 88/10315 (SanggeGinger et al), U.S. Pat. No. 5,130,238 to Malek et al, U.S. Pat. Nos. 4,868,105 and 5,124,246 to Urdea et al, PCT publication No. WO 94/03472(McDonough et al), and PCT publication No. WO 95/03430(Ryder et al), methods of using TMA have been previously described in detail (e.g., U.S. Pat. Nos. 5,399,491 and 5,554,516).
In a cyclic amplification method for detecting amplicons in real time, the term "threshold cycle" (Ct) is a measure of the time of occurrence of the signal associated with amplification of the target, and is typically 10 times the standard deviation of the normalized report signal. Once amplification reaches a "threshold cycle," positive amplification products of the sequence to which the probe binds are generally considered to be present. The identity of the amplification product can then be determined by methods known to those skilled in the art, such as gel electrophoresis, nucleic acid sequencing, and other such analytical procedures.
"amplicon" or "amplification product" means a nucleic acid molecule produced in a nucleic acid amplification reaction and derived from a target nucleic acid. The amplicon or amplification product contains a target nucleic acid sequence that may have the same or opposite meaning as the target nucleic acid.
As used herein, the term "relative fluorescence unit" ("RFU") is a unit of measurement of fluorescence intensity. The RFU varies with the characteristics of the detection means used for the measurement and can be used as a measure to compare the relative intensity between the sample and the control.
"detection probe oligomer," "detection probe," or "probe" refers to an oligomer that specifically hybridizes to a target sequence (including amplified sequences) under conditions that promote nucleic acid hybridization to detect a target nucleic acid. Detection can be direct (i.e., the probe hybridizes directly to the target) or indirect (i.e., the probe hybridizes to an intermediate structure that links the probe to the target). The detection probes can be DNA, RNA, analogs thereof, or combinations thereof (e.g., DNA/RNA chimeras), and they can be labeled or unlabeled. The detection probe may further comprise alternating backbone linkages, such as, for example, 2' -O-methyl linkages. The target sequence of a probe generally refers to a specific sequence within a larger sequence to which the probe specifically hybridizes. The detection probes may comprise one or more target-specific sequences and one or more non-target-specific sequences. Such non-target specific sequences may include sequences that give rise to desired secondary or tertiary structures (e.g., hairpin structures) that can be used to facilitate detection and/or amplification (see, e.g., U.S. Pat. nos. 5,118,801, 5,312,728, 6,835,542, and 6,849,412). Probes of defined sequences can be generated by techniques known to those of ordinary skill in the art, such as by chemical synthesis, and by expression from recombinant nucleic acid molecules in vitro or in vivo.
"hybridization" or "hybridization" means the ability of two fully or partially complementary nucleic acid strands to come together in a parallel or antiparallel orientation under specified hybridization assay conditions to form a stable structure with a duplex region. The two component strands of such a double-stranded structure (sometimes referred to as a hybrid) are held together by hydrogen bonds. Although these hydrogen bonds are most commonly formed between nucleotides containing the bases adenine and thymine or uracil (a and T or U) or cytosine and guanine (C and G) on a single nucleic acid strand, base pairing can also be formed between bases that are not members of these "canonical" pairs. Non-canonical base pairing is well known in the art. See, e.g., R.L.P.Adams et al, The Biochemistry of The Nucleic Acids (11 th edition 1992).
By "preferentially hybridize" is meant that under stringent hybridization conditions, an amplification or detection probe oligomer can hybridize to its target nucleic acid to form a stable oligo to target hybrid, but not a sufficient number of stable oligo to non-target hybrids. Amplification and detection oligomers that preferentially hybridize to a target nucleic acid can be used to amplify and detect the target nucleic acid without amplifying and detecting non-targeted organisms, particularly organisms that are phylogenetically closely related. Thus, the extent of hybridization of the oligomer to the target nucleic acid is sufficiently large, as compared to the non-target nucleic acid, to enable one of ordinary skill in the art to appropriately and accurately amplify and/or detect the presence (or absence) of nucleic acid derived from the designated target. Generally, reducing the degree of complementarity between an oligonucleotide sequence and its target sequence will reduce the degree or rate of hybridization of the oligonucleotide to its target region. However, the inclusion of one or more non-complementary nucleosides or nucleobases may facilitate the ability of the oligonucleotide to distinguish non-target organisms.
Preferential hybridization can be measured using techniques known in the art and described herein (as in the examples provided below). In some embodiments, there is at least a 10-fold difference, at least a 100-fold difference, or at least a1,000-fold difference between the target-hybridization signal and the non-target-hybridization signal in the test sample. In some embodiments, the non-target hybridization signal in the test sample does not exceed the background signal level.
"stringent hybridization conditions" or "stringent conditions" means conditions that allow an oligomer to preferentially hybridize to a target nucleic acid but not to nucleic acids derived from closely related non-target nucleic acids. Although the definition of stringent hybridization conditions does not vary, the actual reaction environment that can be used for stringent hybridization may vary depending on factors including the GC content and length of the oligomer, the degree of similarity between the sequence of the oligomer and non-target nucleic acid sequences that may be present in the test sample, and the target sequence. Hybridization conditions include temperature and hybridization reagents or solutions and compositions. Exemplary hybridization assay conditions for amplification and/or detection of target nucleic acids derived from one or more GBS serotypes with the oligomers of the present disclosure correspond to a temperature of about 60 ℃ when the salt concentration (e.g., monovalent salt such as KCl) is in the range of about 0.6-0.9M. Other acceptable stringent hybridization conditions are readily determined by one of ordinary skill in the art.
"assay conditions" means conditions that allow stable hybridization of an oligonucleotide to a target nucleic acid. The assay conditions do not require preferential hybridization of the oligonucleotide to the target nucleic acid.
"Label" or "detectable label" refers to a moiety or compound that is directly or indirectly conjugated to a probe that is detected or results in a detectable signal. Direct conjugation may use covalent or non-covalent interactions (e.g., hydrogen bonding, hydrophobic or ionic interactions, and chelate or coordination complex formation), while indirect conjugation may use a bridging moiety or linker that amplifies the detectable signal (e.g., via an antibody or another oligonucleotide or oligonucleotides). Any detectable moiety can be used, for example, radionuclides, ligands (such as biotin or avidin), enzymes, enzyme substrates, reactive groups, chromophores that impart a detectable color (such as dyes or particles (e.g., latex or metal beads)), luminescent compounds (e.g., bioluminescent, phosphorescent, or chemiluminescent compounds), and fluorescent compounds (i.e., fluorophores). Embodiments of fluorophores include those that absorb light in the range of about 495nm to 650nm and emit light in the range of about 520nm to 670nm, including what is known as FAMTM、TETTM、CAL FLUORTM(orange or red) and QUASARTMThose of the compounds. The fluorophore may be used in conjunction with a quencher molecule that absorbs light in close proximity to the fluorophore to reduce background fluorescence. Such QUENCHERs are well known in the art and include, for example, BLACK HOLE QUENCHERTM(or BHQ)TM) Or TAMRATMA compound is provided. Particular embodiments include a "homogeneous detectable label" that is detectable in a homogeneous system, wherein bound labeled probe in the mixture exhibits a detectable change as compared to unbound labeled probe, which allows the label to be detected without physically removing hybridized labeled probe from unhybridized labeled probe (e.g., U.S. patent nos. 5,283,174, 5,656,207, and 5,658,737). Specific homogeneous detectable labels include chemiluminescent compounds, including acridinium ester ("AE") compounds, such as the well-known standard AE or AE derivatives (U.S. patent nos. 5,656,207, 5,658,737, and 5,639,604). Methods of synthesizing labels, attaching labels to nucleic acids, and detecting signals from labels are well known (e.g., Sambrook et al, Molecular Cloning, A Laboratory Manual, 2 nd edition (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989) in Chapter 10, and U.S. Pat. Nos. 5,658,737, 5,656,207, 5,547,842, 5,283,174 and 4,581,333, as well as European patent application 0747706). Specific methods of attaching AE compounds to nucleic acids are known (e.g., U.S. Pat. No. 5,585,481 and U.S. Pat. No. 5,639,604, see column 10, line 6 to column 11, line 3, and example 8). The particular AE marker location is in the central region of the probe and near the region of near a/T base pairs, at the 3 'or 5' end of the probe, or at or near the site of mismatch with known sequences that the probe should not detect compared to the desired target sequence. Other detectably labeled probes include TaqManTMProbes, molecular torches, and molecular beacons. TaqManTMThe probe includes donor and acceptor labels, wherein fluorescence is detected after enzymatic degradation of the probe to release the fluorophore from the presence of the quencher during amplification. The molecular torch and the molecular beacon are present in an open and closed configuration, wherein the closed configuration quenches the fluorophore and the open position quenches the fluorophoreSeparate from the quencher to allow fluorescence to occur. Hybridization to the target opens the otherwise blocked probe.
Sequences are "sufficiently complementary" if they allow stable hybridization of two nucleic acid sequences (e.g., a stable hybrid of a probe and a target sequence), but the sequences need not be completely complementary. That is, a "sufficiently complementary" sequence hybridizes to another sequence through hydrogen bonding between a subset series of complementary nucleotides using standard base pairing (e.g., G: C, A: T or A: U), but the two sequences may contain one or more non-complementary residues (including no base positions) so long as the entire sequence forms a stable hybridization complex under appropriate hybridization conditions. Sequences that are sufficiently complementary may be at least about 80%, at least about 90%, or completely complementary of the sequences that hybridize together. Suitable hybridization conditions are well known to those of skill in the art, can be predicted based on sequence composition, or can be determined empirically by using conventional tests (e.g., Sambrook et al, Molecular Cloning, A Laboratory Manual, 2 nd edition at § 1.90-1.91, 7.37-7.57, 9.47-9.51 and 11.47-11.57, particularly § 9.50-9.51, 11.12-11.13, 11.45-11.47 and 11.55-11.57).
An "inextensible" oligomer comprises a blocking moiety at or near its 3' terminus to prevent extension. In some embodiments, the blocking group near the 3' end is within five residues of the 3' end and is large enough to limit binding of the polymerase to the oligomer, and other embodiments contain a blocking group covalently attached to the 3' end. The 3' end can be capped using a number of different chemical groups, such as alkyl groups, non-nucleotide linkers, alkane-diol dideoxynucleotide residues, and cordycepin. Additional examples of capping moieties include 3' -deoxynucleotides (e.g., 2',3' -dideoxynucleotides); 3' -phosphorylated nucleotides; a fluorophore, quencher or other label that interferes with extension; inverted nucleotides (e.g., linked to the previous nucleotide by a 3' to 3' phosphodiester, optionally with an exposed 5' -OH or phosphate); or a protein or peptide that binds to the oligonucleotide to prevent further extension of the nascent nucleic acid strand by the polymerase. The non-extendable oligonucleotides of the present disclosure may be at least 10 bases in length, and may be as many as 15, 20, 25, 30, 35, 40, 50 or more nucleotides in length. Non-extendible oligonucleotides comprising a detectable label may be used as probes.
In particular in the claims, reference to "a sequence of SEQ ID NO: X" refers to a base sequence of a corresponding sequence listing item and does not require the identity of the backbone (e.g., RNA, 2' -O-Me RNA or DNA) or base modification (e.g., methylation of cytosine residues), unless the context clearly indicates otherwise.
"sample preparation" refers to any step or method of processing a sample for subsequent amplification and/or detection of GBS nucleic acid present in the sample. The sample can be a complex mixture of components, where the target nucleic acid is a minority component. Sample preparation may include any known method of concentrating components (such as microorganisms or nucleic acids) from a larger sample volume, for example by filtering airborne or waterborne particles from a larger volume sample or by isolating microorganisms from a sample using standard microbiology. Sample preparation may include physical disruption and/or chemical lysis of cellular components to release intracellular components into a substantially aqueous or organic phase, and removal of debris, such as by using filtration, centrifugation, or adsorption. Sample preparation can include the use of nucleic acid oligonucleotides that selectively or non-specifically capture and separate target nucleic acids from other sample components (e.g., as described in U.S. patent No. 6,110,678 and international patent application publication No. WO 2008/016988, each of which is incorporated herein by reference).
"isolating" or "purifying" means removing or separating one or more components of a sample from other sample components. Sample components include target nucleic acids, typically in an overall aqueous solution phase, which may also include cell fragments, proteins, carbohydrates, lipids, and other nucleic acids. "isolated" or "purified" does not imply any degree of purification. Typically, isolation or purification removes at least 70%, or at least 80%, or at least 95% of the target nucleic acid from other sample components.
As used herein, the term "nonlinear surfactant" means a surfactant having a branched structure. The nonlinear surfactant may comprise one or more ring structures, which may be, for example, in the backbone and/or one or more branches. Exemplary non-linear surfactants include polysorbate 20, polysorbate 40, polysorbate 60, and digitonin. In certain variations, the non-linear surfactant is non-ionic.
In the context of an amplification and/or detection system, the term "specificity" is used herein to refer to a characteristic of the system that describes its ability to distinguish between target and non-target sequences according to sequence and assay conditions. In the context of nucleic acid amplification, specificity generally refers to the ratio of the number of specific amplicons produced to the number of byproducts (e.g., signal-to-noise ratio). For detection, specificity generally refers to the ratio of signal generated from a target nucleic acid to signal generated from a non-target nucleic acid.
The term "sensitivity" is used herein to refer to the accuracy with which a nucleic acid amplification reaction can be detected or quantified. The sensitivity of an amplification reaction is generally a measure of the minimum copy number of a target nucleic acid that can be reliably detected in an amplification system and will depend, for example, on the detection assay employed and the specificity of the amplification reaction, e.g., the ratio of specific amplicons to byproducts.
Detailed Description
The present invention provides compositions, kits and methods for amplifying and detecting group B Streptococcus (GBS; Streptococcus agalactiae) nucleic acids from a sample. Preferably, the sample is a biological sample. The compositions, kits, and methods provide oligonucleotide sequences that recognize target sequences of the GBS genome, including target sequences of GBS serotypes Ia, Ib, Ic, II, III, IV, V, VI, VII, VIII, and IX, or complements thereof. Such oligonucleotides may be used as amplification oligonucleotides, which may include primers, promoter primers, capped oligonucleotides, and promoter provider oligonucleotides, the functions of which have been previously described (see, e.g., U.S. Pat. Nos. 4,683,195; 4,683,202; 4,800,159; 5,399,491; 5,554,516; 5,824,518; and 7,374,885; each of which is incorporated herein by reference). Other oligonucleotides may be used as amplified sequences for detecting GBS, or as probes for capturing GBS target nucleic acids.
The methods provide sensitive and specific detection of GBS nucleic acids. The method comprises performing nucleic acid amplification of the GBS target region and detecting the amplified product, for example, by: the amplified product is specifically hybridized to a nucleic acid detection probe that provides a signal indicative of the presence of GBS in the sample. The amplifying step comprises contacting the sample with one or more amplification oligomers specific for a target sequence in the GBS target nucleic acid to produce an amplified product in the presence of the GBS nucleic acid in the sample. Amplification synthesizes additional copies of the target sequence or its complement by: copies are generated from the template strand using at least one nucleic acid polymerase and an amplification oligomer (e.g., by extending a sequence from a primer using the template strand). One embodiment for detecting the amplified products uses a hybridization step that includes contacting the amplified products with at least one detection probe oligomer specific for a sequence amplified by the selected amplification oligomer (e.g., a sequence flanked by a pair of the selected amplification oligomers contained in the target sequence).
Preferred compositions of the invention are configured to specifically hybridize to all GBS serotypes Ia, Ib, Ic, II, III, IV, V, VI, VII, VIII and IX with minimal cross-reactivity to other non-GBS nucleic acids (e.g., other bacterial pathogens) suspected of being in the sample. In certain variants, the compositions of the invention further allow for the detection of sequences on non-hemolytic strains of GBS. In some aspects, the compositions of the invention are configured to specifically hybridize to a GBS nucleic acid with minimal cross-reactivity to one or more non-GBS pathogens listed in any one of tables 9-11, 15, 16, 20, and 22 (see examples below). In one aspect, the compositions of the invention are part of a multiplexing system that further includes components and methods for detecting one or more of these non-GBS pathogens.
In certain aspects of the invention, compositions comprising at least two amplification oligomers are provided for determining the presence or absence of GBS in a sample. Typically, the composition comprises at least two amplification oligomers for amplifying a target region of a GBS target nucleic acid corresponding to the sequence of SEQ ID NO:1(SIP gene) or SEQ ID NO:2(CFB gene). In such embodiments, the at least one amplification oligomer comprises a target-hybridizing sequence in a sense orientation ("sense THS"), and the at least one amplification oligomer comprises a target-hybridizing sequence in an antisense orientation ("antisense THS"), wherein the sense THS and the antisense THS are each configured to specifically hybridize to a GBS target sequence corresponding to a sequence contained within SEQ ID NO:1 or SEQ ID NO:2, and wherein the target-hybridizing sequence is selected such that the GBS sequence targeted by the antisense THS is located downstream of the GBS sequence targeted by the sense THS (i.e., the at least two amplification oligomers are positioned such that they flank the target region to be amplified).
In some variations, a composition comprises (i) a SIP-specific amplification oligomer comprising a SIP-specific target-hybridizing sequence substantially corresponding to or identical to: 3, 4,7, or 8, or a complement thereof, or an RNA equivalent or DNA/RNA chimera thereof. In some variations, the composition comprises (ii) a CFB-specific amplification oligomer comprising a CFB-specific target-hybridizing sequence having from about 17 to about 24 contiguous nucleotides and substantially corresponding to or identical to a sequence contained in the sequence of SEQ ID No. 26, or a complement thereof, or an RNA equivalent thereof, or a DNA/RNA chimera thereof; in some such embodiments, the CFB-specific target-hybridizing sequence comprises a sequence substantially corresponding to or identical to the sequence of SEQ ID No. 28 or SEQ ID No. 27, or a complement thereof, or an RNA equivalent thereof or a DNA/RNA chimera (e.g., a sequence substantially corresponding to or identical to the sequence set forth in SEQ ID No. 12 or SEQ ID No. 14, or a complement thereof, or an RNA equivalent thereof or a DNA/RNA chimera), or a sequence substantially corresponding to or identical to the sequence set forth in SEQ ID No. 18, or a complement thereof, or an RNA equivalent thereof or a DNA/RNA chimera. In some variations, the composition comprises (iii) a CFB-specific amplification oligomer comprising a CFB-specific target-hybridizing sequence substantially corresponding to or identical to: 13, 15, 16, 17, 20 or 21, or the complement thereof, or an RNA equivalent or DNA/RNA chimera thereof. In variations comprising SIP-specific or CFB-specific amplification oligomers of (i), (ii), or (iii) as described above, the oligomer combination comprises at least one amplification oligomer comprising a SIP-specific or CFB-specific target-hybridizing sequence having a polarity (sense versus antisense, or vice versa) opposite to that of the target-hybridizing sequence of the oligomer of (i), (ii), or (iii), such that at least two amplification oligomers flank the target region to be amplified. In certain embodiments, the compositions are provided in the form of an aqueous or dry formulation for amplifying GBS nucleic acids or a reaction mixture comprising or reconstituted from such a formulation.
In a more specific embodiment of the invention, a composition for determining the presence or absence of GBS in a sample comprises (1) at least one amplification oligomer comprising a SIP-specific or CFB-specific target-hybridization region substantially corresponding to at least one sense oligomer sequence depicted in table 1 below; and (2) at least one amplification oligomer comprising a SIP-specific or CFB-specific target-hybridizing region substantially corresponding to at least one antisense oligomer sequence depicted in table 1. In some such embodiments, the composition comprises a first SIP-specific amplification oligomer and a first CFB-specific amplification oligomer of (1) above, and a second SIP-specific and a second CFB-specific amplification oligomer of (2) above. In particular variations, the one or more sense and/or antisense target-hybridizing sequences of the amplification oligomer combination comprise or consist of one or more sense and/or antisense sequences selected from table 1.
Table 1: exemplary sense and antisense amplification oligomer target-hybridizing sequences for amplification of GBS SIP or CFB target regions
1Sense/antisense designations of these sequences are for exemplary purposes only. Such names do not necessarily limit the sequence to the accompanying names.
In certain variations, the composition for determining the presence or absence of GBS in a sample as described herein further comprises at least one detection probe oligomer configured to specifically hybridize to a GBS SIP or CFB target sequence that can be amplified using the first and second amplification oligomers (e.g., a SIP or CFB target sequence contained within SEQ ID NO:1 or SEQ ID NO:2 or a complement thereof flanked by target-hybridizing sequences of the first and second amplification oligomers). Particularly suitable SIP-specific detection probe oligomers include, for example, oligomers comprising a SIP-specific target-hybridizing sequence substantially corresponding to or identical to the sequence set forth in SEQ ID NO 9 or SEQ ID NO 11, or the complement thereof, or an RNA equivalent or DNA/RNA chimera thereof. Particularly suitable CFB-specific detection probe oligomers include, for example, oligomers comprising a CFB-specific target-hybridizing sequence substantially corresponding to or identical to the sequence set forth in SEQ ID NO 22, SEQ ID NO 23, SEQ ID NO 24 or SEQ ID NO 25, or the complement thereof, or an RNA equivalent or DNA/RNA chimera thereof. The detection probe oligomer can contain a 2' -methoxy backbone at one or more junctions in the nucleic acid backbone. In some variations, the composition comprises at least two detection probe oligomers. In certain embodiments, the detection probe oligomer is provided in the form of an aqueous or dry formulation for detecting GBS nucleic acid or a reaction mixture comprising or reconstituted from such a formulation.
Typically, the detection probe oligomer according to the invention further comprises a label. Particularly suitable labels include compounds that emit a detectable optical signal, such as a fluorophore or a luminescent (e.g., chemiluminescent) compound that can be detected in a homogeneous mixture. More than one label and more than one type of label may be present on a particular probe, or detection may rely on the use of a mixture of probes, each labeled with a compound that produces a detectable signal (see, e.g., U.S. Pat. Nos. 6,180,340 and 6,350,579, each of which is incorporated herein by reference). The label may be attached to the probe by various means, including covalent attachment, chelation, and ionic interaction, but it is preferred that the label is covalently attached. For example, in some embodiments, the detection probes have attached chemiluminescent labels, such as, for example, Acridinium Ester (AE) compounds (see, e.g., U.S. Pat. Nos. 5,185,439; 5,639,604; 5,585,481, and 5,656,744; each of which is incorporated herein by reference). Labels, such as, for example, fluorescent or chemiluminescent labels, are typically attached to the probes via non-nucleotide linkers (see, for example, U.S. Pat. Nos. 5,585,481; 5,656,744; and 5,639,604, particularly at column 10, line 6 to column 11, line 3, and example 8; each of which is incorporated herein by reference).
In some embodiments, the probe (e.g., comprising a fluorescent label) further comprises a second label that interacts with the first label. For example, the second label can be a quencher. Detection probes comprising both a fluorescent label and a quencher are particularly useful in Fluorescence Resonance Energy Transfer (FRET) assays. Specific variations of such detection probes include, for example, TaqManTMDetection probes (Roche Molecular Diagnostics) and "Molecular beacons" (see, e.g., Tyagi et al, Nature Biotechnol.16:49-53,1998; U.S. Pat. Nos. 5,118,801 and 5,312,728; each of which is incorporated herein by reference). TaqManTMProbes (or similar dual-labeled linear probes comprising both a fluorescent label and a quencher) can be used in assays where hybridization of the probe to a target or amplicon followed by nucleic acid degradation by a polymerase enzyme comprising 5'-3' exonuclease activity results in release of the fluorescent label and thereby increased fluorescence, or detachment of fluorescence from interaction with a second label.
In some applications, detection of a probe, target duplex, in a test sample is facilitated using a detection probe that exhibits at least some degree of self-complementarity without first removing unhybridized probe prior to detection. Specific embodiments of such detection probes include, for example, probes that form a conformation that is maintained by intramolecular hybridization (e.g., a conformation commonly referred to as a hairpin). Suitable hairpin probes include "molecular torches" (see, e.g., U.S. Pat. No. 6,849412; 6,835,542, respectively; 6,534,274, respectively; and 6,361,945) and "molecular beacons" (see, e.g., U.S. Pat. No. 5,118,801 and U.S. Pat. No. 5,312,728). Molecular torches comprise complementary distinct regions (termed "target-binding domains" and "target-closing domains") that pass through a junction region (e.g., - (CH)2CH2O)3-linkers) and hybridize to each other under predetermined hybridization assay conditions. When exposed to the appropriate target or denaturing conditions, the two complementary regions of the molecular torch (which may be fully or partially complementary) melt, thereby making the target binding domain available for hybridization to the target sequence when the predetermined hybridization assay conditions are restored. The molecular torch is designed such that the target binding domain facilitates hybridization to the target sequence compared to the target closing domain. The target binding domain and the target closure domain of the molecular torch include interactive labels (e.g., fluorescent/quencher) positioned such that a different signal is produced when the molecular torch is self-hybridizing relative to when the molecular torch is hybridized to the target nucleic acid, thereby allowing detection of the probe: target duplex in the test sample in the presence of an unhybridized probe having a viable label associated therewith.
In other embodiments, the detection probe is a linear oligomer that does not substantially form a conformation maintained by intramolecular bonds. In a specific variation, the linear detection probe oligomer comprises a chemiluminescent compound as the label (e.g., an Acridinium Ester (AE) compound). In other embodiments, the linear detection probe oligomer comprises a fluorophore as a label. In some embodiments of a linear detection probe oligomer comprising a fluorophore, the oligomer further comprises a quenching moiety (e.g., a TaqMan probe).
Examples of interactive donor/acceptor label pairs that may be used in conjunction with the present disclosure without attempting to distinguish FRET from non-FRET pairs include fluorescein/tetramethylrhodamine, IAEDANS/fluorescein (fluoroscein), EDANS/DABCYL, coumarin/DABCYL, fluorescein/fluorescein, BODIPY FL/BODIPY FL, fluorescein/DABCYL, luciferin/DABCYL, BODIPY/DABCYL, eosin/DABCYL, erythrosine/DABCYL, tetramethylrhodamine/DABCYL, texas red/DABCYL, CY5/BH1, CY5/BH2, CY3/BH1, CY3/BH2, and fluorescein/qsqsqsy 7 dyes. One of ordinary skill in the art will appreciate that when the donor and acceptor dyes are different, the energy transfer can be detected by the appearance of sensitized fluorescence of the acceptor or by quenching the donor fluorescence. Non-fluorescent acceptors (such as DABCYL and QSY7 dyes) advantageously eliminate the potential problem of background fluorescence caused by direct (i.e., non-sensitizing) acceptor excitation. Exemplary fluorophore moieties that can be used as one member of a donor-acceptor pair include fluorescein, ROX, and CY dyes (e.g., CY 5). Exemplary QUENCHER moieties that can be used as the other member of the donor-acceptor pair include DABCYL and BLACK HOLE QUENCHER moieties, available from Biosearch Technologies, Inc. (Novartor, Calif.).
In some embodiments, the labeled oligomer (e.g., detection probe) is not extendable. For example, the labeled oligomer may be rendered non-extendable by: 3' -phosphorylated, 3' -deoxynucleotides with a 3' terminus (e.g., terminal 2',3' -dideoxynucleotides), nucleotides with a 3' terminal inversion (e.g., where the last nucleotide is inverted such that it is joined to the penultimate nucleotide by a 3' to 3' phosphodiester linkage or analog thereof (such as a phosphorothioate)), or with an attached fluorophore, quencher, or other extension-interfering label (which may, but need not, be attached via the 3' position of the terminal nucleotide). In some embodiments, the 3' -terminal nucleotide is unmethylated.
The invention also provides compositions comprising one or more detection probe oligomers as described herein.
In some aspects, the invention provides methods of using an oligomer or a combination of oligomers as described herein. Any process disclosed herein is also to be understood as a disclosure of the corresponding use of the materials involved in the process for the purpose of the process. Any oligomer comprising a GBS SIP or CFB target-hybridizing sequence, as well as any combination (e.g., kits and compositions) comprising such oligomers, should be understood to also be disclosed for use in detecting or quantifying GBS, as well as for use in preparing a composition for detecting or quantifying GBS.
Broadly, the method may include one or more of the following components: target capture, wherein GBS nucleic acids (e.g., from a sample, such as a clinical sample) are annealed to a capture oligomer; separating, e.g., washing, to remove material not associated with the capture oligomer; amplification; and amplicon detection (e.g., amplicon quantification), which can be performed in real time with amplification. Certain embodiments involve each of the foregoing steps. Certain embodiments relate to exponential amplification, optionally with a preceding linear amplification step. Certain embodiments relate to exponential amplification and amplicon detection. Certain embodiments relate to any two components listed above. Certain embodiments relate to any two components listed adjacently above, e.g., washing and amplification, or amplification and detection.
In some embodiments, the invention provides methods for determining the presence or absence of Group B Streptococcus (GBS) in a sample using a combination of oligomers as described herein. Such methods generally comprise (1) contacting the sample with at least two amplification oligomers for amplifying a GBS SIP or CFB nucleic acid target region corresponding to a SIP or CFB target nucleic acid, wherein the at least two amplification oligomers are as described above; (2) performing an in vitro nucleic acid amplification reaction, wherein any GBS SIP or CFB target nucleic acid present in the sample is used as a template to produce an amplification product; and (3) detecting the presence or absence of the amplification product, thereby determining the presence or absence of GBS in the sample. The detection method according to the invention generally further comprises the following steps: obtaining a sample to be contacted with the at least two amplification oligomers. In certain embodiments, "obtaining" a sample to be used in steps (1) - (3) comprises, for example, receiving the sample at a testing facility or other location at which one or more steps of the method are performed, and/or retrieving the sample from a location within the facility at which one or more steps of the method are performed (e.g., from a storage or other storage location).
Amplifying the GBS target sequence utilizes an in vitro amplification reaction using at least two amplification oligomers flanking the target region to be amplified. In particular embodiments, the target region to be amplified is a GBS SIP target region that substantially corresponds to SEQ ID No. 1 from about nucleotide position 56 to about nucleotide position 189 or from about nucleotide position 349 to about nucleotide position 489. Particularly suitable oligomer combinations for amplifying these GBS SIP target regions are described herein. For example, in some embodiments, an amplification oligomer combination for amplifying a SIP target region comprises first and second SIP-specific amplification oligomers comprising (a) a first SIP-specific target-hybridizing sequence that is SEQ ID NO:3 or a sequence substantially corresponding to SEQ ID NO:3, or an RNA equivalent or a DNA/RNA chimera thereof, and (B) a second SIP-specific target-hybridizing sequence that is SEQ ID NO:4 or a sequence substantially corresponding to SEQ ID NO:4, or an RNA equivalent or a DNA/RNA chimera thereof, respectively. In other embodiments, the amplification oligomer combination for amplifying a SIP target region comprises first and second SIP-specific amplification oligomers comprising (a) a first SIP-specific target-hybridizing sequence that is SEQ ID NO:7 or a sequence substantially corresponding to SEQ ID NO:7, or an RNA equivalent or a DNA/RNA chimera thereof, and (B) a second SIP-specific target-hybridizing sequence that is SEQ ID NO:8 or a sequence substantially corresponding to SEQ ID NO:8, or an RNA equivalent or a DNA/RNA chimera thereof, respectively.
In other embodiments, the target region to be amplified is a GBS CFB target region that substantially corresponds to from about nucleotide position 38 to about nucleotide position 151, from about nucleotide position 22 to about nucleotide position 151, from about nucleotide position 192 to about nucleotide position 329, or from about nucleotide position 585 to about nucleotide position 716 of SEQ ID No. 2. Particularly suitable oligomer combinations for amplifying these GBS CFB target regions are described herein. For example, in some embodiments, an amplification oligomer combination for amplifying a CFB target region comprises first and second CFB-specific amplification oligomers comprising (a) a first CFB-specific target-hybridizing sequence that is about 17 to about 24 contiguous nucleotides and substantially corresponds to or is identical to a sequence contained in the sequence of SEQ ID No. 26, or an RNA equivalent thereof or a DNA/RNA chimera, and (B) a second CFB-specific target-hybridizing sequence that is SEQ ID No. 13 or SEQ ID No. 15, or a sequence substantially corresponding to SEQ ID No. 13 or SEQ ID No. 15, or an RNA equivalent thereof or a DNA/RNA chimera, respectively; in a more specific variant of this first CFB-specific target-hybridizing sequence of (a), the CFB-specific target-hybridizing sequence is selected from (i) a sequence substantially corresponding or identical to the sequence of SEQ ID NO:28 or SEQ ID NO:27, or an RNA equivalent or DNA/RNA chimera thereof (e.g., a sequence as SEQ ID NO:12 or SEQ ID NO:14 or a sequence substantially corresponding to SEQ ID NO:12 or SEQ ID NO:14, or an RNA equivalent or DNA/RNA chimera thereof), and (ii) a sequence as SEQ ID NO:18 or a sequence substantially corresponding to SEQ ID NO:18, an RNA equivalent or a DNA/RNA chimera thereof. In other embodiments, the amplification oligomer combination for amplifying a CFB target region comprises first and second CFB-specific amplification oligomers comprising (a) a first CFB-specific target-hybridizing sequence as SEQ ID NO:16 or a sequence substantially corresponding to SEQ ID NO:16, or an RNA equivalent or a DNA/RNA chimera thereof, and (B) a second CFB-specific target-hybridizing sequence as SEQ ID NO:17 or a sequence substantially corresponding to SEQ ID NO:17, or an RNA equivalent or a DNA/RNA chimera thereof, respectively. In other embodiments, the amplification oligomer combination for amplifying a CFB target region includes first and second CFB-specific amplification oligomers comprising (A) a first CFB-specific target-hybridizing sequence as SEQ ID NO:18 or a sequence substantially corresponding to SEQ ID NO:18, or an RNA equivalent or a DNA/RNA chimera thereof, and (B) a second CFB-specific target-hybridizing sequence as SEQ ID NO:15 or a sequence substantially corresponding to SEQ ID NO:15, or an RNA equivalent or a DNA/RNA chimera thereof, respectively. In other embodiments, the amplification oligomer combination for amplifying a CFB target region includes first and second CFB-specific amplification oligomers comprising (A) a first CFB-specific target-hybridizing sequence as SEQ ID NO:20 or a sequence substantially corresponding to SEQ ID NO:20, or an RNA equivalent or a DNA/RNA chimera thereof, and (B) a second CFB-specific target-hybridizing sequence as SEQ ID NO:21 or a sequence substantially corresponding to SEQ ID NO:21, or an RNA equivalent or a DNA/RNA chimera thereof, respectively.
The detection method according to the present disclosure may further include the steps of: obtaining a sample to be subjected to a subsequent step of the method. In certain embodiments, "obtaining" a sample to be used comprises, for example, receiving the sample at a testing facility or other location where one or more steps of the method are performed, and/or retrieving the sample from a location within the facility where one or more steps of the method are performed (e.g., from a storage or other storage).
In certain embodiments, the methods further comprise purifying the GBS target nucleic acid from other components in the sample, e.g., prior to amplification (e.g., prior to the capturing step). Such purification may include the following methods: separating and/or concentrating the organisms contained in the sample from other sample components, or removing or degrading non-nucleic acid sample components, such as proteins, carbohydrates, salts, lipids, and the like. In some embodiments, the DNA in the sample is degraded, e.g., with dnase, and optionally the dnase is removed or inactivated or the degraded DNA is removed.
In particular embodiments, purifying the target nucleic acid comprises capturing the target nucleic acid to specifically or non-specifically separate the target nucleic acid from other sample components. Non-specific target capture methods may involve selective precipitation of nucleic acids from a substantially aqueous mixture; adhering the nucleic acid to a support, washing the support to remove other sample components; or other means of physically separating nucleic acids from a mixture containing GBS nucleic acids and other sample components.
Target capture typically occurs in a solution phase mixture containing one or more capture probe oligomers that hybridize under hybridization conditions to a GBS SIP or CFB target sequence. For embodiments comprising a capture probe tail, the GBS target is captured by adjusting hybridization conditions such that the capture probe tail hybridizes to the immobilized probe. Certain embodiments use a particulate solid support, such as paramagnetic beads.
Separation may be performed after capture, where, for example, the complexes on the solid support are separated from other sample components. Separation can be accomplished by any suitable technique, e.g., washing the support associated with the GBS SIP or CFB target sequence one or more times (e.g., two or three times) to remove other sample components and/or unbound oligomers. In some embodiments using a particulate solid support (e.g., paramagnetic beads), the particles associated with the GBS target can be suspended in a wash solution and in some embodiments retrieved from the wash solution by using magnetic attraction. To limit the number of manipulation steps, the GBS SIP or CFB target nucleic acid can be amplified by: the GBS target sequence in the complex on the support is simply mixed with the amplification oligomer and the amplification step is continued.
Exponentially amplifying GBS target sequences utilizes an in vitro amplification reaction using at least two amplification oligomers flanking a target region to be amplified. In some embodiments, at least first and second oligomers as described herein are provided. In some embodiments, a plurality of oligomer pairs is provided; in some such variations, the plurality of oligomer pairs includes oligomer pairs configured to hybridize to at least two GBS target nucleic acids (e.g., at least one oligomer pair is configured to hybridize to an SIP target nucleic acid and at least one oligomer pair is configured to hybridize to a CFB target nucleic acid). The amplification reaction may be cyclic or isothermal. Suitable amplification methods include, for example, replicase-mediated amplification, Polymerase Chain Reaction (PCR), Ligase Chain Reaction (LCR), Strand Displacement Amplification (SDA), and transcription-mediated or transcription-associated amplification (TMA).
The detection step can be performed using any of a variety of known techniques to detect a signal specifically associated with the amplified target sequence, such as, for example, by hybridizing the amplification product to a labeled detection probe and detecting the signal generated by the labeled probe (including, in some embodiments, by the label released from the probe after hybridization). In some embodiments, the labeled probe comprises a second moiety, such as a quencher or other moiety that interacts with the first label, as described above. The detection step may also provide additional information about the amplified sequence (e.g., as all or a portion of its nucleobase sequence). Detection may be performed after the amplification reaction is complete, or may be performed simultaneously with the amplification of the target region, e.g., in real time. In one embodiment, the detection step allows homogeneous detection, e.g., detection of hybridized probes without removing unhybridized probes from the mixture (see, e.g., U.S. Pat. nos. 5,639,604 and 5,283,174). In some embodiments, the nucleic acid is associated with a surface that causes a physical change (e.g., a detectable electrical change). The amplified nucleic acid can be detected by: concentrating the amplified nucleic acid in or on a matrix and detecting the nucleic acid or a dye associated therewith (e.g., an intercalator such as ethidium bromide or cyber green), or detecting an increase in the dye associated with the nucleic acid in a solution phase. Other detection methods may use nucleic acid detection probes configured to specifically hybridize to sequences in the amplified product and detect the presence of a probe-product complex, or by using probe complexes that can amplify a detectable signal associated with the amplified product (e.g., U.S. Pat. Nos. 5,424,413, 5,451,503 and 5,849,481; each of which is incorporated herein by reference). Directly or indirectly labeled probes specifically associated with the amplified product provide a detectable signal indicative of the presence of the target nucleic acid in the sample. In particular, the amplified product will contain a target sequence in the GBS SIP or CFB gene or a target sequence complementary to a sequence in the GBS SIP or CFB gene, and the probe will bind, directly or indirectly, to the sequence contained in the amplified product to indicate the presence of GBS nucleic acid in the test sample.
In embodiments where the amplified products are detected near or at the end of the amplification step, a linear detection probe may be used to provide a signal indicative of hybridization of the probe to the amplified products. An example of such detection is the use of a luminescently labeled probe that hybridizes to the target nucleic acid. The luminescent label is then hydrolyzed from the unhybridized probe. Detection was performed by chemiluminescence using a luminometer. (see, e.g., International patent application publication No. U.S. Pat. No. WO 89/002476, which is incorporated herein by reference). In other embodiments using real-time detection, the detection probe can be a hairpin probe labeled with a reporter moiety that is detected upon binding of the probe to the amplified product, such as, for example, a molecular beacon, a molecular torch, or a hybridization switch probe (e.g., a dual-labeled hairpin probe comprising both a fluorescent label and a quenching moiety). In other embodiments for real-time detection, the detection probe is a linear oligomer, such as, for example, an oligomer labeled with both a fluorophore and a quenching moiety (e.g., a TaqMan probe). Such probes may comprise target-hybridizing sequences and non-target-hybridizing sequences. Various forms of such probes have been previously described (see, e.g., U.S. Pat. Nos. 5,210,015, 5,487,972, 5,118,801, 5,312,728, 5,925,517, 6,150,097, 6,849,412, 6,835,542, 6,534,274, and 6,361,945; and U.S. patent application publication Nos. 20060068417A1 and 20060194240A 1; each of which is incorporated herein by reference).
The assay for detecting GBS nucleic acids can optionally include a non-GBS Internal Control (IC) nucleic acid that is amplified and detected in the same assay reaction mixture by using amplification and detection oligomers specific for IC sequences. The IC nucleic acid sequence may be, for example, a DNA plasmid, an RNA template sequence (e.g., an in vitro transcript), or a synthetic nucleic acid that is spiked into the sample. Alternatively, the IC nucleic acid sequence may be a cellular component, which may be from an exogenous cellular source or an endogenous cellular source relative to the sample. In these cases, the internal control nucleic acid is co-amplified with the GBS nucleic acid in the amplification reaction mixture. The internal control amplification product and the GBS target sequence amplification product can be detected independently.
In certain embodiments, amplification and detection of signals from amplified IC sequences demonstrates that use of assay reagents, conditions, and assay steps in the assay is appropriate if a signal is not obtained for the intended target GBS nucleic acid (e.g., a sample that is negative for a GBS test). When quantitative results are required, IC may also be used as an internal standard for the assay, i.e. the signal obtained from IC amplification and detection is used to set the parameters used in the algorithm for quantifying the amount of GBS nucleic acid in a sample based on the signal obtained for the amplified GBS target sequence. The IC may also be used to monitor the integrity of one or more steps in the assay. The primers and probes for the IC target sequence are configured and synthesized by using any well-known method, provided that the primers and probes function to amplify the IC target sequence and detect the amplified IC sequence using essentially the same assay conditions used to amplify and detect the GBS target sequence. In preferred embodiments comprising a target capture-based purification step, it is preferred to include target capture probes specific for IC targets in the target capture step of the assay, such that the IC is treated in the assay in a manner similar to that for the intended GBS analyte in all assay steps.
The invention also provides formulations for determining the presence or absence of GBS in a sample. In some embodiments, the formulation is an aqueous formulation comprising (1) at least two SIP-specific or CFB-specific amplification oligomers as described herein for amplifying SIP or CFB target regions and (2) an organic buffer. The aqueous formulation for amplifying GBS nucleic acids may comprise one or more additional components, such as, for example, a DNA polymerase, a reverse transcriptase, or a detection probe oligomer. In some embodiments, the formulation is an aqueous formulation comprising (1) an SIP-specific and/or CFB-specific detection probe oligomer as described herein and (2) an organic buffer. The aqueous formulation comprising one or more detection probe oligomers may comprise one or more additional components, such as, for example, a surfactant, a DNA polymerase, a reverse transcriptase, or at least one amplification oligomer. Particularly suitable surfactants include, for example, polyethylene glycol mono [4- (1,1,3, 3-tetramethylbutyl) phenyl ] ether and polyoxyethylene sorbitan fatty acid esters (e.g., polysorbate 20, polysorbate 40 or polysorbate 60). In some embodiments, the surfactant in the aqueous detection probe formulation is a non-linear surfactant, such as, for example, a polyoxyethylene sorbitan fatty acid ester (e.g., polysorbate 20, polysorbate 40, or polysorbate 60) or digitonin. The aqueous formulation for amplifying or detecting GBS nucleic acids as described above may further comprise an extender, such as for example trehalose, raffinose or combinations thereof. In some embodiments, the aqueous formulation as described above contains inorganic salts, such as, for example, magnesium, potassium, or sodium; in some such variations, the concentration of the inorganic salt is 4mM or less. A particularly suitable organic buffer for use in the aqueous formulation described above is Tris (2-amino-2- (hydroxymethyl) -1, 3-propanediol).
In a related aspect, for long term storage, an aqueous formulation as described herein is aliquoted into, for example, vials, ampoules, or other containers, and may be dried (e.g., lyophilized) according to procedures known in the art. The dried product is usually presented in the form of a powder or cake. The container is then sealed. Methods of preparing such dry formulations from aqueous formulations and dry formulations prepared by such methods are further aspects of the invention. In yet another aspect, the present invention provides a dry formulation capable of being reconstituted into an aqueous formulation as described herein. In addition to one or more amplification oligomers and/or detection probes as described herein, the dried formulations for amplifying or detecting GBS nucleic acids typically contain an extender, such as, for example, trehalose, raffinose, or combinations thereof. In some embodiments further comprising an inorganic salt, the percentage of the mass of the inorganic salt relative to the mass of the dry formulation is 0.249% or less, 0.222% or less, or 0.195% or less. Methods of preparing dry formulations from lyophilized formulations as described herein are also encompassed by the present invention; such methods typically include dissolving the dried formulation in a suitable diluent (e.g., an organic buffer or water) to provide a reconstituted formulation.
The invention also provides a reaction mixture for determining the presence or absence of a GBS target nucleic acid in a sample. The reaction mixture according to the present disclosure comprises one or both of the following: (1) oligomer combinations for amplifying GBS SIP and/or CFB target nucleic acids as described herein and (2) one or more detection probe oligomers for determining the presence or absence of GBS SIP and/or CFB amplification products as described herein. The reaction mixture may further comprise a variety of optional components, such as for example a capture probe, e.g. a poly- (k) capture probe as described in US 2013/0209992, which is incorporated herein by reference. For amplification reaction mixtures, the reaction mixture will typically comprise other reagents suitable for performing in vitro amplification, such as, for example, buffers, salt solutions, appropriate nucleotide triphosphates (e.g., dATP, dCTP, dGTP, and dTTP; and/or ATP, CTP, GTP, and UTP) and/or enzymes (e.g., thermostable DNA polymerases or reverse transcriptases and/or RNA polymerases), and will typically comprise the test sample components, in which the GBS target nucleic acid may or may not be present. The reaction mixture may comprise amplification oligomers for only one target region of the GBS genome, or it may comprise amplification oligomers for multiple GBS target regions (e.g., both SIP target regions and CFB target regions). In addition, for reaction mixtures comprising a combination of detection probes and amplification oligomers, the selection of amplification oligomers and detection probe oligomers for the reaction mixture are linked by a common target region (i.e., the reaction mixture will comprise probes that bind to sequences that can be amplified by the amplification oligomer combination of the reaction mixture). In some embodiments, the reaction mixture comprises an aqueous formulation as described above. In some embodiments, the reaction mixture is reconstituted with water or an organic buffer from a dried formulation as described above.
The invention also provides kits for carrying out the methods as described herein. The kit according to the present disclosure comprises one or both of: (1) oligomer combinations for amplifying GBS SIP and/or CFB target nucleic acids as described herein and (2) one or more detection probe oligomers for determining the presence or absence of GBS SIP and/or CFB amplification products as described herein. In some embodiments, any of the oligomer combinations described herein are present in the kit. The kit may further comprise a variety of optional components, such as for example a capture probe, e.g. a poly- (k) capture probe as described in US 2013/0209992. Other reagents that may be present in the kit comprise reagents suitable for performing in vitro amplification, such as, for example, buffers, salt solutions, appropriate nucleotide triphosphates (e.g., dATP, dCTP, dGTP, dTTP; and/or ATP, CTP, GTP, and UTP) and/or enzymes (e.g., thermostable DNA polymerase or reverse transcriptase and/or RNA polymerase). Oligomers as described herein can be packaged in a variety of different embodiments, and one of skill in the art will appreciate that the disclosure encompasses many different kit configurations. For example, the kit may comprise amplification oligomers for only one target region of the GBS genome, or it may comprise amplification oligomers for multiple GBS target regions (e.g., both SIP target regions and CFB target regions). In addition, for kits comprising a detection probe and a combination of amplification oligomers, the selection of amplification oligomers and detection probe oligomers for use in the kit are linked by a common target region (i.e., the kit will comprise probes that bind to sequences that can be amplified by the amplification oligomer combination of the kit). In certain embodiments, the kit further comprises a set of instructions for performing a method according to the present disclosure, wherein the instructions may be associated with a package insert and/or a package of the kit or components thereof.
The invention is further illustrated by the following non-limiting examples.
Example 1
17 primer and probe combinations as shown in Table 2 were evaluated for the in vitro Streptococcus agalactiae (GBS) assay.
Table 2: primer and probe combination
As input material, undefined GBS serotypes from clinical cultures are used. It was extracted in multiple replicate experiments using the MagNA Pure 96 system (Roche). After extraction, the concentration of DNA was determined by OD 260/280 measurement. PCR was performed in rapid real-time on Applied Biosystems (ABI)7500And (4) performing on the system. The PCR profile used was as follows:
table 3: overview of PCR
All samples were tested without adding an internal control to the sample. One concentration of GBS target nucleic acid (1000 copies/. mu.l in PCR) was used and tested in four replicate experiments. The concentration of the primers was fixed at 600nM and the probe concentration was 200 nM.
Ct and number of positive reactions for different primer/probe combinations are shown in Table 4. The reported Ct is the cycle at which the Relative Fluorescence Unit (RFU) signal exceeds a set RFU threshold.
TABLE 4
Combination of
Ct (average)
Number of positives
1
24.81
4/4
2
/
0/4
3
25.66
4/4
4
25.69
4/4
5
27.51
4/4
6
24.72
4/4
7
26.79
3/4
8
24.96
4/4
9
27.62
4/4
10
25.25
4/4
11
27.60
3/4
12
25.50
4/4
13
19.92
3/4
14
27.65
4/4
15
26.03
3/4
16
25.62
4/4
17
24.95
4/4
For each target gene, two combinations of primers and probes were selected based on this data for further evaluation. For CFB, combinations 12 and 17 show the combination of lowest Ct with highest RFU. For SIP, combinations 1 and 3 are selected. These combinations are tested with respect to lower concentrations of GBS target nucleic acid, allowing for better discrimination. The results shown in Table 5 were obtained at 1, 10 and 100 copies/. mu.l in the test PCR.
TABLE 5
Combinations 1,3, 12 and 17 were also tested for 1 and 10 copies/. mu.l at different primer/probe concentrations (600/200nM, 400/150nM and 300/100 nM). Table 6 shows the results obtained with these different concentrations.
TABLE 6
Based on the results summarized above, primer/probe combinations 3 and 17 (for SIP and CFB target genes, respectively) were selected to further evaluate sensitivity and specificity. These primer combinations were able to detect five (5) theoretical copies at Ct of 36-37 in each PCR reaction.
Example 2
For the detection of the internal control, two primer and probe combinations were evaluated: SD-PLP/GIC combinations and novel GIC combinations having primer and probe sequences as shown in Table 7. The first step is to examine which oligonucleotide set and at which concentration gives the best results when using Cy5 as fluorophore. The second step being focused on705 dye selection concentration. In the automated PANTERFUSION lineTraditionally, the Cy5 dye produced a low signal and should be detected using QUASAR705 dye. Since the signal of Cy5 was different from that produced by QUASAR705, the concentration of primers and probes was re-evaluated.
Table 7: internal control primers and probes
KINGFISHERTMAfter extraction, initial testing of primers and probes was performed on the ABI 7500fast real-time PCR system. Three different primer/probe concentrations were used: 600/200nM, 400/150nM and 300/100 nM. Furthermore, IC oligonucleotides were tested in combination with SIP oligonucleotides when GBS targets (serotypes II and IV: strains obtained from CHU de Li ge) were present. The second step of the IC test was performed on a BioRad CFX-96qPCR apparatus capable of detecting both Cy5 and QUASAR 705. Initially, QUASAR705 combinations were tested in comparison to Cy5 combinationsTo determine the final concentration of primers and probes.
The data from the initial tests show that the new GIC combination provides a higher signal than the SD-PLP/GIC combination. The new GIC combinations (300/100nM) were further tested in the presence of SIP primers (600/200nM) and different GBS types (10^6, 10^5, 10^4 dilutions of serotypes II and IV). The data from this test show that the presence of IC primers and probes has no significant effect on GBS detection. Likewise, the IC signal is not affected by the presence of higher concentrations of GBS. Based on the data, a combination of SIP combination (FAM) at 600/200nM and IC new GIC combination (Cy5) at 300/100nM was selected.
The comparison between Cy5 and QUSAR705 dyes was performed on a BioRad CFX-96. The data shows good agreement between the two conditions. The neo-GIC QUASAR705 combination at 400/150nM was used for further testing of the GBS strain.
In the following experiments, SIP (600/200nM) and New GIC (400/150nM) oligonucleotides (clinical cultures collected on the Roy day at the university of Rie Hospital center, Saltt-Tellmann university district, building B35, B-4000 Belgian) were tested in serial dilutions against different GBS serotypes. Table 8 below reports ct values for both the SIP target and the new GIC target and shows overall low standard deviations between different serotypes and different dilutions.
TABLE 8
Example 3
This example describes the evaluation of the specificity and sensitivity of primer/probe combination 3 targeting the GBS SIP gene.
At KINGFISHERTMAfter extraction in the system, different samples were tested on ABI 7500fast real-time PCR system using SIP + new GIC (Cy5) mix. Using the PCR profile shown in Table 3 aboveThe method is described.
For specificity, the strains shown in table 9 were evaluated for cross-reactivity.
TABLE 9
For inclusion, GBS serotypes shown in table 10 were tested.
Watch 10
All GBS serotypes to be detected are initially tested at a given stock concentration. Thereafter, the strains were also tested at lower concentrations (as low as 100 CFU/mL).
Table 11 below shows the specificity data obtained on the ABI 7500FAST system. All tested bacteria showed no interaction with SIP primers and probes. The effectiveness of the PCR was assessed by a positive control providing a positive signal.
TABLE 11
The initial group tested at high concentration on ABI 7500FAST system gave the results shown in table 12.
TABLE 12
Bacterial strains
Ct mean value
Standard deviation of
Streptococcus agalactiae serotype Ia
16.705
0.007
Streptococcus agalactiae serotype Ib
17.655
0.120
Streptococcus agalactiae serotype Ic
17.715
0.332
Streptococcus agalactiae serotype III
18.240
0.141
Streptococcus agalactiae serotype IV
15.740
0.014
Streptococcus agalactiae type strains
15.550
0.057
Table 13 below shows data obtained when GBS strains were tested at lower concentrations (100 CFU/ml in the sample).
Watch 13
Serotype
Concentration of
Mean Ct +/-standard deviation
Serotype Ia
100CFU/ml in the sample
38.6+/-1.9
Serotype Ib
100CFU/ml in the sample
38.1+/-1.4
Serotype Ic
100CFU/ml in the sample
37.7+/-0.4
Serotype III
100CFU/ml in the sample
37.9+/-0.6
Serotype IV
100CFU/ml in the sample
38.1+/-1.6
These serotypes (Ia, Ib, Ic, III, IV) were further used to test PCR efficiency. To this end, serial dilutions of these serotypes (ranging from 10^6CFU/ml to 10^1CFU/ml) were prepared and extracted on the MagNA Pure 96 System (Roche) and PCR was performed on the ABI 7500 Rapid System. The data show that the expected slope is about-3.3 between different serotypes, and the efficiency is between 92% and 98%. Further, the data confirmed that all serotypes were detected at 100CFU/ml in the sample.
Example 4
This example describes the use of the enzyme in the Automation of PANTHERSystematic evaluation of the specificity of primer/probe combination 3 targeting the GBS SIP gene.
To evaluate specificity, GBS strains shown in table 15 below were tested directly on the panarter FUSION system without the addition of additional STM or Lim broth. The cartridge used contained SIP oligonucleotides and Cy5 oligonucleotides for IC detection.
Watch 15
All GBS serotypes (53 to 58) were detected in FAM channels, while other strains (59-66) were negative and provided only IC signals in RED647 channels. This confirms the specificity of the SIP oligonucleotides for the test strains.
In addition, other potential cross-reactive bacteria and the remaining GBS serotypes as shown in table 16 were also tested using the same cassette (SIP + IC (Cy5)) and testing on the panarter FUSION system.
TABLE 16
Strains 38 to 43 returned positive signals in the FAM channel, while other strains returned IC signals only in the RED channel.
Example 5
The performance of primer/probe combination 3 targeting only the GBS SIP gene was compared to the performance of both primer/probe combinations 3 and 17 targeting the SIP and CFB genes, respectively, as a multiplexing reaction. At KINGFISHERTMFollowing systematic extraction, GBS primers/probes at different concentrations were tested on GBS strains spiked in Sample Transport Medium (STM) using an ABI 7500 rapid real-time PCR system at 3000 CFU/PCR. Nucleic acid isolation, amplification and detection reactions are generally performed as described above. No significant difference in Ct values was observed between the SIP/CFB primer/probe set alone and the SIP/CFB primer/probe set, whereas higher endpoint fluorescence levels were found using the multiplexed SIP/CFB primer/probe set relative to the SIP primer/probe set alone.
Example 6
A preliminary study was conducted to use a probabilistic unit analysis (17 software) determine multiplexed SIP/CFB primer/probe combinations 3 and 17 pairs of GBS bloodLimit of detection (LoD) for serotype III (from ATCC).
Starting from a previous GBS culture (stock in Sample Transport Medium (STM)), GBS strain serotype III was serially diluted in Lis broth (plating basis) at the following eight concentrations: 20,000.0, 10,000.0, 5,000.0, 2,500.0, 1,250.0, 625.0, 312.5, and 156.3 CFU/mL.
These eight dilutions were added to the respective sample tubes as follows: 250.0 μ L of sample was added to 750.0 μ L of transfer solution (transfer solution is a mixture of STM + Target Capture Oligonucleotide (TCO) (at 1667pmol/750 μ L STM)). Since the final 1:4 dilution occurred in the sample tubes, the final concentrations were 5,000.0, 2,500.0, 1,250.0, 625.0, 312.5, 156.3, 78.1, and 39.1 CFU/mL.
Each dilution was tested in 20 extraction replicates and one PCR replicate in PANTERERThe system was run twice. Positive controls (mixture of GBS SIP and CFB plasmids at 141 and 781c/μ L in STM) and negative controls (Lim broth) were also tested in one or two extraction replicates and one PCR replicate, respectively.
Use ofSoftware for performing probabilistic unit analysis based on the tested concentrations, the number of positive calls obtained per concentration and the number of trials.
Three distribution patterns (lognormal, Weibull (Weibull) and log-logic) were compared and one was selected that gave the best P-value, i.e. the regression table was close to 0.000 and the goodness-of-fit test was closest to 1.000, as summarized in table 17 below. Based on this table, LoD was determined using a weibull distribution pattern.
TABLE 17
The results obtained on the PANTHER FUSION system are summarized in Table 18 below. The last dilution was removed from the statistical analysis.
Watch 18
Finding LoD of GBS serotype III95％1,294CFU/mL in LB, i.e., 324CFU/mL in the test sample.
Example 7
The sensitivity and inclusion of the assay using SIP primer/probe combination 3 multiplexed with CFB primer/probe combination 17 was evaluated by testing serial dilutions of cell lysates in Lim broth negative clinical matrix for GBS serotypes Ia, Ib, Ic, II, III, IV, V, VI, VII, VIII and IX. In addition, a Nonhemolytic (NH) strain was evaluated. Determination of PANTHER Using probabilistic Unit regression analysisGBS measures the 95% detection limit for each serotype, and the predicted detection limit is confirmed for 12 GBS serotypes. Cross-reactivity and interference of microorganisms were evaluated using 45 bacterial or fungal species in the presence and absence of GBS serotype III at 3-fold LoD. A method comparison study was performed testing Lim broth enriched samples (n 255) collected from prenatal women receiving standard care GBS culture screening from two different hospitals. For the PANTHER FUSION GBS assay, sensitivity and specificity relative to the culture was determined. Samples with inconsistent results were tested using the BDMax GBS assay. All tests were performed on the PANTHER FUSION system.
Sensitivity and inclusion of the assay. The detection suite (panel) was created by spiking a lysate stock of known CFU/mL concentration into Lim broth enrichment medium. Each test panel was tested in 30 replicate experiments using three PANTHER FUSION systems, with each of three assay reagent lots. The 50% and 95% predicted LoD for each strain and reagent lot was estimated by probabilistic unit analysis (shown in table 19 below). LoD is reported in table 19 as CFU/mL in Lim broth samples (back calculated to CFU/mL in the PANTHER FUSION test sample, which is a 1:4 dilution in Specimen Transport Medium (STM)). Confirmation tests to predict detection limits were performed and > 95% positivity was observed for all serotypes.
Watch 19
Microbial cross-reactivity and interference. The bacterial and fungal species shown in table 20 below were introduced into the negative Lim broth matrix at a concentration of 1e 6CFU/mL in the test samples. Test panels were tested with and without 3-fold estimation of GBS serotype III at LoD. Each test set was tested in triplicate with one assay reagent lot. No cross-reactivity was observed in the detection set without GBS target. No interference was observed in the detection set containing the GBS target.
Table 20: test organisms
Method comparison according to the CDC recommended guidelines, a total of 255 vaginal-rectal swabs were collected from prenatal women. Each sample was enriched in Lim broth for 18 to 24 hours at 35 ℃ -37 ℃. Each sample was evaluated using a reference culture and tested in the PANTHER FUSION GBS assay. Clinical sensitivity and specificity were determined from reference culture results. The results are summarized in table 21 below. The sensitivity and specificity of the PANTHER FUSION GBS assay were 100% and 98.6%, respectively. There were three culture negative PANTERHER FUSION GBS assay positive samples, and duplicate PANTERHER FUSION GBS assay tests of all the samples yielded positive results. Inconsistent samples were analyzed using the second molecular test method, the BDMax GBS assay, and GBS was detected in all three samples.
TABLE 21
Preliminary analytical studies demonstrated that the assay has a consistent assay for GBS in the serotype evaluated, and comparison with culture methods shows that the assay has high sensitivity and specificity.
Example 8
This example describes the automation of PANTEREREvaluation of specificity of the assay on the system for SIP primer/probe combination 3 multiplexed with CFB primer/probe combination 17.
A set of 124 organism tests representative of microorganisms commonly found in the vaginal/anal flora or belonging to the same family/genus as the GBS selected for the assay specific test, consisting of: 104 bacteria, 12 viruses, 4 yeasts/fungi and 4 protozoa/parasites strains. The assay specific detection set is detailed in table 22. Of the 124 organisms selected, 14 were not available for testing at the time of the study. Potential cross-reactivity with GBS assay primers and probes against these 14 unusable organisms was assessed by BLAST analysis, where no alignment was identified.
The assay specificity was evaluated using two methods:
(1) cross-reactivity (exclusivity): testing whether these organisms cross-react with GBS assay primers and probes and induce false positive results in a validated GBS negative sample;
(2) microbial interference: testing whether these organisms would interfere with normal GBS detection in GBS positive samples at concentrations near LoD.
Pools consisting of five (5) microorganisms were used at high concentrations (minimum 10 for bacteria and yeast)6CFU/mL, and a minimum of 10 for a virus or equivalent5PFU/mL) was diluted in Sample Transport Medium (STM). Pool compositions are detailed in table 22. For cross-reactivity (exclusive) assessment, these microbial pools were added to a clinically negative Lim broth matrix sample (GBS negative sample). For microbiological interference assessment, these microbial pools were added to a clinically negative Lim broth matrix sample (GBS positive sample) spiked with GBS serotype III at 3-fold LoD.
For each pool of microorganisms to be evaluated, the PANTTHER FUSION GBS assay was tested in three replicates of GBS positive and GBS negative samples and the data reported.
And (4) acceptance standard:
(1) for one or more microorganisms (pools) to be considered non-cross-reactive, three replicates of a clinically negative Lim broth matrix sample (GBS negative sample) must be reported as negative;
(2) for one or more microorganisms (pools) to be considered non-interfering, three replicates of GBS serotype III positive samples (GBS positive samples) must be reported as positive.
Table 22: analytical specificity panel
And (5) research results. The runs were valid and an Internal Control (IC) was detected in each reaction, resulting in 0% inefficient run and 0% IC inefficiency, respectively. All GBS negative samples tested for cross-reactivity assessment with GBS primers and probes on the PANTHER FUSION system gave negative, valid results, while all GBS positive samples tested for microbiological interference assessment with the PANTHER FUSION GBS assay gave GBS positive results. The results are reported in table 23 below.
Table 23: analytical specificity results
Sequence of
Table 24: exemplary oligomer sequences, reference sequences and regions
From the foregoing it will be appreciated that, although specific embodiments of the invention have been described herein for purposes of illustration, various modifications may be made without deviating from the spirit and scope of the invention. Accordingly, the invention is not limited except as by the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.
Sequence listing
<110> brief Probe Ltd
B, L, Eton
B, Gerobackie
Y-ao zong
R-clos
L-frangula
<120> compositions and methods for detecting group B streptococcal nucleic acids
<130> DIA.0078.01
<160> 28
<170> PatentIn 3.5 edition
<210> 1
<211> 1305
<212> DNA
<213> Artificial sequence
<220>
<223> reference sequence
<400> 1
atgaaaatga ataaaaaggt actattgaca tcgacaatgg cagcttcgct attatcagtc 60
gcaagtgttc aagcacaaga aacagatacg acgtggacag cacgtactgt ttcagaggta 120
aaggctgatt tggtaaagca agacaataaa tcatcatata ctgtgaaata tggtgataca 180
ctaagcgtta tttcagaagc aatgtcaatt gatatgaatg tcttagcaaa aattaataac 240
attgcagata tcaatcttat ttatcctgag acaacactga cagtaactta cgatcagaag 300
agtcacactg ccacttcaat gaaaatagaa acaccagcaa caaatgctgc tggtcaaaca 360
acagctactg tggatttgaa aaccaatcaa gtttctgttg cagaccaaaa agtttctctc 420
aatacaattt cggaaggtat gacaccagaa gcagcaccaa cgattgtttc gccaatgaag 480
acatattctt ctgcgccagc tttgaaatca aaagaagtat tagcacaaga gcaagctgtt 540
agtcaagccg cagctaatga acaggtatca ccagctcctg tgaagtcgat tacttcagaa 600
gttccagcag ctaaagagga agttaaacca actcagacgt cagtcagtca gtcaacaaca 660
gtatcaccag cttctgttgc cactgaaaca ccagctctag tagctaaagt agcaccggta 720
agaactgtag cagcccctag agtgacaagt gctaaagtag tcactcctaa agtagaaact 780
ggtgcatcac cagagcatgt atcagctcca gcagttcctg tgactacgac ttcaacagct 840
acagacaata agttacaagc gactgaagtt aagagcgttc cggtagcaca aaaagctcca 900
acagcaacac cggtagcaca accagcttca acaacaaatg cagtagctgc acatcctgaa 960
aatgcagggc tccaacctca tgttgcagct tataaagaaa aagtagcgtc aacttatgga 1020
gttaatgaat tcagtacata ccgtgcggga gatccaggtg atcatggtaa aggtttagca 1080
gttgacttta ttgtaggtac caatcaagca cttggtaatg aagttgcaca gtactctaca 1140
caaaatatgg cagcaaataa catttcatat gttatctggc aacaaaagtt ttactcaaat 1200
acaaatagta tttatggacc tgctaatact tggaatgcaa tgccagatcg tggtggcgtt 1260
actgccaacc actatgacca cgttcacgta tcatttaaca aataa 1305
<210> 2
<211> 768
<212> DNA
<213> Artificial sequence
<220>
<223> reference sequence
<400> 2
atgaacgtta aacatatgat gtatctatct ggaactcgag tggctggtgc attgttattt 60
tcaccagctg tattagaagt acatgctgat caagtgacaa ctccacaagt ggtaaatcaa 120
gtaaatagta ataatcaagc ccagcaaatg gctcaaaagc ttgatcaaga tagcattcag 180
ttgagaaata tcaaagataa tgttcaggga acagattatg aaaaaccggt taatgaggct 240
attactagcg ttgaaaaatt aaagacttca ttgcgtgcca accctgagac agtttatgat 300
ttgaattcta ttggtagtcg tgtagaagcc ttaacagatg tgattgaagc aatcactttt 360
tcaactcaac atttaacaaa taaggttagt caagcaaata ttgatatggg atttgggata 420
actaagctag ttattcgcat tttagatcca tttgcttcag ttgattcaat taaagctcaa 480
gttaacgatg taaaggcatt agaacaaaag gttttaactt atcctgattt aaaaccaact 540
gatagagcta ccatctacac aaaatcaaaa cttgataagg aaatttggaa tacacgtttt 600
actagagata aaaaagtact taacgtcaaa gaatttaaag tttacaatac tttaaataaa 660
gcaatcacac atgctgttgg agttcagttg aatccaaatg ttacggtaca acaagttgat 720
caagagattg taacattaca agcagcactt caaacagcat taaaataa 768
<210> 3
<211> 19
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 3
cagtcgcaag tgttcaagc 19
<210> 4
<211> 22
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 4
aacgcttagt gtatcaccat at 22
<210> 5
<211> 20
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 5
cggtaagaac tgtagcagcc 20
<210> 6
<211> 21
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 6
gctcttaact tcagtcgctt g 21
<210> 7
<211> 20
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 7
aacaaatgct gctggtcaaa 20
<210> 8
<211> 22
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 8
agaatatgtc ttcattggcg aa 22
<210> 9
<211> 34
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 9
actgtttcag aggtaaaggc tgatttggta aagc 34
<210> 10
<211> 29
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 10
gctccagcag ttcctgtgac tacgacttc 29
<210> 11
<211> 26
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 11
cggaaggtat gacaccagaa gcagca 26
<210> 12
<211> 21
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 12
gtggctggtg cattgttatt t 21
<210> 13
<211> 22
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 13
ccatttgctg ggcttgatta tt 22
<210> 14
<211> 19
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 14
tagtggctgg tgcattgtt 19
<210> 15
<211> 24
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 15
catttgctgg gcttgattat tact 24
<210> 16
<211> 26
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 16
ctggaataca cgctttacta gagata 26
<210> 17
<211> 23
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 17
acttgttgta ccgtaacatt tgg 23
<210> 18
<211> 24
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 18
tatctatctg gaactctagt ggct 24
<210> 19
<400> 19
000
<210> 20
<211> 24
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 20
caaagataat gttcagggaa caga 24
<210> 21
<211> 23
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 21
gcttctacac gactaccaat aga 23
<210> 22
<211> 29
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 22
accacttgtg gagttgtcac ttgatcagc 29
<210> 23
<211> 32
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 23
caagtgacaa ctccacaagt ggtaaatcat gt 32
<210> 24
<211> 29
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 24
agcaatcaca catgctgttg gagttcagt 29
<210> 25
<211> 26
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 25
ttgcgtgcca accctgagac agttta 26
<210> 26
<211> 39
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 26
tatctatctg gaactctagt ggctggtgca ttgttattt 39
<210> 27
<211> 23
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 27
tagtggctgg tgcattgtta ttt 23
<210> 28
<211> 17
<212> DNA
<213> Artificial sequence
<220>
<223> Synthesis of oligonucleotide
<400> 28
gtggctggtg cattgtt 17
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