阅读说明：本技术 检测军团菌属的方法 (Method for detecting legionella ) 是由 E·P·约翰逊 于 2020-01-30 设计创作，主要内容包括：本公开文本提供了用于确定表现出肺炎样症状的患者是否将受益于用抑制军团菌属物种(Legionella sp.)的治疗剂进行的治疗的方法。这些方法是基于检测生物样品中的军团菌属物种和/或嗜肺军团菌(Legionella pneumophila)。还提供了用于实践所述方法的试剂盒。(The present disclosure provides methods for determining whether a patient exhibiting pneumonic symptoms will benefit from treatment with a therapeutic agent that inhibits Legionella species (Legionella sp.). These methods are based on the detection of Legionella species and/or Legionella pneumophila (Legionella pneumophila) in a biological sample. Kits for practicing the methods are also provided.)

1. A method for detecting the presence of at least one Legionella (Legionella) species in a biological sample, the method comprising:

(a) providing a first primer pair suitable for amplifying a ssrA target nucleic acid;

(b) providing a second primer pair suitable for amplifying the 16S rRNA target nucleic acid;

(c) amplifying the ssrA target nucleic acid and the 16S rRNA target nucleic acid, if present; and

(d) detecting one or more amplification products produced in step (c);

wherein the presence of the ssrA target nucleic acid identifies the presence of at least one Legionella species, and the presence of the 16S rRNA target nucleic acid identifies the presence of Legionella pneumophila (Legionella).

2. The method of claim 1, wherein the first primer pair comprises at least one degenerate primer.

3. The method of claim 1 or 2, wherein the first primer pair comprises a first forward primer comprising 5 'TCGACGTGGGTTGCRAAACG 3' (SEQ ID NO:1) or a complement thereof.

4. The method of any one of the preceding claims, wherein the first primer pair comprises a first reverse primer comprising 5 'TATGACCGTTGATTCGATACC 3' (SEQ ID NO:2) or a complement thereof.

5. The method of any one of the preceding claims, wherein the second primer pair comprises at least one degenerate primer.

6. The method of any one of the preceding claims, wherein the second primer pair comprises a second forward primer comprising 5 'TACCTACCCTTGACATACAGTG 3' (SEQ ID NO:4) or a complement thereof.

7. The method of any one of the preceding claims, wherein the second primer pair comprises a second reverse primer comprising 5 'CTTCCTCCGGTTTGTCAC 3' (SEQ ID NO:5) or a complement thereof.

8. The method of any one of the preceding claims, further comprising contacting the biological sample with one or more oligonucleotide probes capable of specifically hybridizing to an amplification product or its complement.

9. The method of claim 8, wherein the oligonucleotide probe is detectably labeled.

10. The method of claim 9, wherein the detectable label is a fluorescent label.

11. The method of claim 10, wherein the fluorescent label is selected from the group consisting of fluorescein, Cy3, Cy5, cy5.5, tetrachloro-6-carboxyfluorescein, 2, 7-dimethoxy-4, 5-dichloro-6-carboxy-fluorescein, jagewasabi, texas red, TYE 563, ROX, TEX 615, TYE 665, TYE 705, and hexachloro-6-carboxyfluorescein.

12. The method of claim 10, wherein the oligonucleotide probe further comprises at least one quencher.

13. The method of claim 12, wherein the quencher is selected from the group consisting of TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa Black FQ, Iowa Black RQ, and DABCYL.

14. The method of any of claims 8-13, wherein said oligonucleotide probe specifically hybridizes to an ssrA amplification product, and wherein said oligonucleotide probe comprises 5 'TAAATATAAATGCAAACGATGAAAACTTTGC 3' (SEQ ID NO:3) or a complement thereof.

15. The method of any one of claims 8-14, wherein the oligonucleotide probe specifically hybridizes to a 16s rrna amplification product, and wherein the oligonucleotide probe comprises 5 'CCAGCATGTGATGGTGGGGACTCTA 3' (SEQ ID NO:6) or a complement thereof.

16. The method of any one of claims 1-15, further comprising mixing an exogenous control DNA with the biological sample.

17. The method of claim 16, further comprising contacting the biological sample with a third primer pair suitable for amplifying an exogenous control target nucleic acid, and amplifying the exogenous control target nucleic acid.

18. The method of claim 17, wherein the exogenous control target nucleic acid comprises SEQ ID No. 20.

19. The method of claim 18, wherein the third primer pair consists of a third forward primer comprising 5 'GCTTCAGTACCTTCGGCTTG 3' (SEQ ID NO:17) and a third reverse primer comprising 5 'TTGCAGGCATCTCTGACAAC 3' (SEQ ID NO: 18).

20. The method of claim 17 or 18, further comprising contacting the biological sample with a third oligonucleotide probe, wherein the third oligonucleotide probe is detectably labeled and comprises 5 'TGGCTCTTGGCGGTCCAGATG 3' (SEQ ID NO: 19).

21. The method of any one of claims 1-20, wherein real-time PCR amplification is performed in a direct amplification dish in cooperation with an integrated thermal cycler.

22. The method of any one of claims 1-21, wherein the biological sample is a bronchoalveolar lavage fluid sample, a bronchial wash sample, a sputum sample, a Nasopharyngeal (NP) aspirate or wash sample, a nasal swab, or a bacterial isolate.

23. A kit for detecting the presence of at least one legionella species in a biological sample, the kit comprising:

(a) a first primer pair for amplifying the ssrA target nucleic acid;

(b) a second primer pair for amplifying the 16S rRNA target nucleic acid;

(c) a first oligonucleotide probe capable of specifically hybridizing to a segment of the ssrA target nucleic acid; and

(d) a second oligonucleotide probe capable of specifically hybridizing to a segment of the 16S rRNA target nucleic acid;

wherein the first oligonucleotide probe and the second oligonucleotide probe are detectably labeled.

24. The kit of claim 23, further comprising a third primer pair that amplifies a control target nucleic acid.

25. The kit of claim 23 or 24, wherein the first primer pair is capable of specifically hybridizing to an ssrA target nucleic acid comprising at least 85% -95% identical nucleotides to SEQ ID NO 1 or a complement thereof.

26. The kit of any one of claims 23-25, wherein the second primer pair is capable of specifically hybridizing to a 16S rRNA target nucleic acid comprising at least 85% -95% identical nucleotides to SEQ ID No. 2 or its complement.

27. The kit of any one of claims 23-26, wherein the first primer pair comprises at least one degenerate primer.

28. The kit of any one of claims 23-27, wherein the first primer pair comprises a first forward primer comprising 5 'TCGACGTGGGTTGCRAAACG 3' (SEQ ID NO:1) or a complement thereof.

29. The kit of any one of claims 23-28, wherein the first primer pair comprises a first reverse primer comprising 5 'TATGACCGTTGATTCGATACC 3' (SEQ ID NO:2) or a complement thereof.

30. The kit of any one of claims 23-29, wherein the second primer pair comprises at least one degenerate primer.

31. The kit of any one of claims 23-30, wherein the second primer pair comprises a second forward primer comprising 5 'TACCTACCCTTGACATACAGTG 3' (SEQ ID NO:4) or a complement thereof.

32. The kit of any one of claims 23-31, wherein the second primer pair comprises a second reverse primer comprising 5 'CTTCCTCCGGTTTGTCAC 3' (SEQ ID NO:5) or a complement thereof.

33. The kit of any one of claims 23-32, wherein the first nucleic acid probe comprises 5 'TAAATATAAATGCAAACGATGAAAACTTTGC 3' (SEQ ID NO:3) or a complement thereof.

34. The kit of any one of claims 23-33, wherein the second nucleic acid probe comprises 5 'CAACCAGCCGCTGCTGACGGTC 3' (SEQ ID NO:9) or a complement thereof.

35. The kit of any one of claims 23-34, wherein the detectable label is a fluorescent label.

36. The kit of claim 35, wherein the fluorescent label is selected from the group consisting of fluorescein, Cy3, Cy5, cy5.5, tetrachloro-6-carboxyfluorescein, 2, 7-dimethoxy-4, 5-dichloro-6-carboxy-fluorescein, jagewasabi, texas red, TYE 563, ROX, TEX 615, TYE 665, TYE 705, and hexachloro-6-carboxyfluorescein.

37. The kit of any one of claims 23-36, wherein at least one oligonucleotide probe further comprises at least one quencher.

38. The kit of claim 37, wherein the quencher is selected from the group consisting of TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa Black FQ, Iowa Black RQ, and DABCYL.

39. A composition comprising a detectably labeled oligonucleotide probe comprising 5 'TAAATATAAATGCAAACGATGAAAACTTTGC 3' (SEQ ID NO: 3).

40. The composition of claim 39, wherein the detectable label is a fluorescent label.

41. The composition of claim 40, wherein the fluorescent label is selected from the group consisting of fluorescein, Cy3, Cy5, Cy5.5, tetrachloro-6-carboxyfluorescein, 2, 7-dimethoxy-4, 5-dichloro-6-carboxy-fluorescein, Jacobian yellow, Texas Red, TYE 563, ROX, TEX 615, TYE 665, TYE 705, and hexachloro-6-carboxyfluorescein.

42. The composition of any one of claims 39-41, wherein the oligonucleotide probe further comprises at least one quencher.

43. The kit of claim 42, wherein the quencher is selected from TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa Black FQ, Iowa Black RQ, and DABCYL.

44. A method for selecting a subject exhibiting pneumonic symptoms for treatment with a therapeutic agent that inhibits legionella pneumophila, the method comprising:

(a) contacting a sample isolated from the subject with a first primer pair suitable for amplifying an ssrA target nucleic acid;

(b) contacting the sample with a second primer pair suitable for amplifying the 16S rRNA target nucleic acid;

(c) amplifying the ssrA target nucleic acid and the 16S rRNA target nucleic acid, if present; and

(d) detecting one or more amplification products produced in step (c); and

(e) selecting the subject for treatment with a therapeutic agent that inhibits legionella pneumophila if an amplification product of the 16S rRNA target nucleic acid is detected.

45. A method of treating a subject having a Legionella pneumophila infection, the method comprising administering to a subject selected by the method of claim 44 a therapeutic agent that inhibits Legionella pneumophila.

46. The method of claim 44 or 45, wherein the first primer pair comprises at least one degenerate primer.

47. The method of any one of claims 44-46, wherein the first primer pair comprises a first forward primer comprising 5 'TCGACGTGGGTTGCRAAACG 3' (SEQ ID NO:10) or a complement thereof.

48. The method of any one of claims 44-47, wherein the first primer pair comprises a first reverse primer comprising 5 'TATGACCGTTGATTCGATACC 3' (SEQ ID NO:2) or a complement thereof.

49. The method of any one of claims 44-48, wherein the second primer pair comprises at least one degenerate primer.

50. The method of any one of claims 44-49, wherein the second primer pair comprises a second forward primer comprising 5 'TACCTACCCTTGACATACAGTG 3' (SEQ ID NO:4) or a complement thereof.

51. The method of any one of claims 44-50, wherein the second primer pair comprises a second reverse primer comprising 5' CTTCCTCCGGTTTGTCAC 3 (SEQ ID NO:5) or a complement thereof.

52. The method of any one of claims 44-51, further comprising contacting the biological sample with one or more oligonucleotide probes capable of specifically hybridizing to an amplification product or its complement.

53. The method of claim 52, wherein the oligonucleotide probe is detectably labeled.

54. The method of claim 53, wherein the detectable label is a fluorescent label.

55. The method of claim 54, wherein the fluorescent label is selected from the group consisting of fluorescein, Cy3, Cy5, Cy5.5, tetrachloro-6-carboxyfluorescein, 2, 7-dimethoxy-4, 5-dichloro-6-carboxyfluorescein, Yagewaflavum, Texas Red, TYE 563, ROX, TEX 615, TYE 665, TYE 705, and hexachloro-6-carboxyfluorescein.

56. The method of any one of claims 52-55, wherein the oligonucleotide probe further comprises at least one quencher.

57. The method of claim 56, wherein the quencher is selected from the group consisting of TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa Black FQ, Iowa Black RQ, and DABCYL.

58. The method of any of claims 52-57, wherein the oligonucleotide probe specifically hybridizes to an ssrA amplification product, and wherein the oligonucleotide probe comprises 5 'TAAATATAAATGCAAACGATGAAAACTTTGC 3' (SEQ ID NO:3) or a complement thereof.

59. The method of any one of claims 52-58, wherein the oligonucleotide probe specifically hybridizes to a 16S rRNA amplification product, and wherein the oligonucleotide probe comprises 5 'CCAGCATGTGATGGTGGGGACTCTA 3' (SEQ ID NO:6) or a complement thereof.

60. The method of any one of claims 44-59, further comprising mixing an exogenous control DNA with the biological sample.

61. The method of claim 60, further comprising contacting the biological sample with a third primer pair suitable for amplifying an exogenous control target nucleic acid, and amplifying the exogenous control target nucleic acid.

62. The method of claim 61, wherein the exogenous control target nucleic acid comprises SEQ ID NO 20.

63. The method of claim 62, wherein the third primer pair consists of a third forward primer comprising 5 'GCTTCAGTACCTTCGGCTTG 3' (SEQ ID NO:17) and a third reverse primer comprising 5 'TTGCAGGCATCTCTGACAAC 3' (SEQ ID NO: 18).

64. The method of claim 61 or 62, further comprising contacting the biological sample with a third oligonucleotide probe, wherein the third oligonucleotide probe is detectably labeled and comprises 5 'TGGCTCTTGGCGGTCCAGATG 3' (SEQ ID NO: 19).

65. The method of any one of claims 44-64, wherein real-time PCR amplification is performed in a direct amplification dish in cooperation with an integrated thermal cycler.

66. The method of any one of claims 44-65, wherein the biological sample is a bronchoalveolar lavage fluid sample, a bronchial wash sample, a sputum sample, a Nasopharyngeal (NP) aspirate or wash sample, a nasal swab, or a bacterial isolate.

67. The method of any one of claims 44-66, wherein the therapeutic agent that inhibits Legionella pneumophila is one or more agents selected from the group consisting of: fluoroquinolones, carbapenems, macrolide antibiotics, trimethoprim-sulfamethoxazole, legionella pneumophila specific antibodies and legionella pneumophila specific vaccines.

68. The method of claim 67, wherein the fluoroquinolone is selected from the group consisting of ciprofloxacin, gemifloxacin, levofloxacin, norfloxacin, ofloxacin, lovastatin, gatifloxacin, grepafloxacin, temafloxacin, lomefloxacin, sparfloxacin, enoxacin, and moxifloxacin.

69. The method of claim 67, wherein the carbapenem is selected from the group consisting of imipenem, meropenem, ertapenem, doripenem, panipenem, biapenem, lazupenem (PZ-601), tebipenem, lenapenem, cephalopenem, and texapenem (thienamycin).

70. The method according to claim 67, wherein the Legionella pneumophila-specific vaccine is selected from the group consisting of a whole cell (wP) Legionella pneumophila vaccine and a cell-free Legionella pneumophila vaccine.

71. The method according to claim 67, wherein the macrolide antibiotic is selected from the group consisting of azithromycin (Shsumet), clarithromycin (bixin), erythromycin (E-Mycin, Eryc, Ery-Tab, PCE, erythromycin ethylsuccinate, ilong), and roxithromycin.

Technical Field

The present disclosure provides methods for determining whether a patient exhibiting pneumonic symptoms will benefit from treatment with a therapeutic agent that inhibits Legionella species (Legionella sp.) and/or Legionella pneumophila. These methods are based on the detection of legionella species and legionella pneumophila in a biological sample by determining the presence of ssrA gene and 16S gene, respectively. Kits for practicing the methods are also provided.

Background

The following description of the background of the disclosure is provided merely to aid the reader in understanding the disclosure and is not an admission that the description describes or constitutes prior art with respect to the disclosure.

Legionella (legionella) is a facultative intracellular gram-negative bacterium found in soil and water environments where they can parasitize and proliferate within protozoa. As a result, they are a common contaminant of artificial water systems, including air conditioning systems, cooling towers, and hot water bathtubs. Legionella is also capable of replication in mammalian alveolar macrophages and epithelial cells. Once aerosolized, the bacteria enter the human respiratory tract and cause community-, travel-, and hospital-acquired pneumonia. In some cases, legionella can cause Legionnaires' disease (a severe form of pneumonia) or pointiac fever (Pontiac lever) (a milder flu-like illness).

Currently, there are 50 known species in the genus Legionella (Legionella), which contain about 70 different serogroups. Legionella pneumophila serogroup 1 accounts for the majority of human infections, but associations with human disease have been reported for more than 20 species within this genus. Identification of infections caused by legionella pneumophila (l.pneumophila) is of particular importance, since this legionella species is associated with diseases that lead to severe morbidity and mortality.

Culture is considered as the "gold standard" for the detection of legionella. However, legionella is a slow growing and critical organism. Serological diagnosis is also common; however, serological diagnosis can only be performed retrospectively, and patient treatment is rarely affected. The urine antigen test is a rapid test for the diagnosis of legionnaires disease, but is limited by its ability to detect only a limited number of serogroups of legionella pneumophila. Existing nucleic acid amplification tests are readily able to detect non-legionella bacteria, including Pseudomonas (Pseudomonas) species and Enterobacter (Enterobacter) species.

Therefore, a more robust, sensitive and specific method that can rapidly detect and distinguish between legionella species and legionella pneumophila in a single biological sample is highly desirable.

Disclosure of Invention

The present disclosure provides compositions and methods for detecting and differentiating legionella species and legionella pneumophila in a single biological sample. In another aspect, the methods and compositions of the present technology can be used to select an optimal treatment regimen for a subject exhibiting pertussis-like symptoms. Nucleic acid amplification tests, including assays using real-time PCR, are attractive tools for detecting legionella in clinical specimens because they are able to detect all legionella and provide rapid results. These tests also enable to distinguish between legionella pneumophila and non legionella pneumophila species. This is important given the more severe morbidity and mortality that has been observed in the case of legionella pneumophila.

Accordingly, in some aspects, provided herein is a method for detecting the presence of at least one legionella species in a biological sample, the method comprising, consisting of or consisting essentially of: (a) providing a first primer pair suitable for amplifying a ssrA target nucleic acid; providing a second primer pair suitable for amplifying the 16S rRNA target nucleic acid; amplifying the ssrA target nucleic acid and the 16S rRNA target nucleic acid, if present; and detecting one or more amplification products produced in step (c); wherein the presence of the ssrA target nucleic acid identifies the presence of at least one Legionella species, and the presence of the 16S rRNA target nucleic acid identifies the presence of Legionella pneumophila.

In some embodiments of the methods provided herein, the first primer pair comprises at least one degenerate primer. In some embodiments, the first primer pair comprises a first forward primer comprising 5 'TCGACGTGGGTTGCRAAACG 3' (SEQ ID NO:1) or a complement thereof. The method of any one of the preceding claims, wherein the first primer pair comprises a first reverse primer comprising 5 'TATGACCGTTGATTCGATACC 3' (SEQ ID NO:2) or a complement thereof. In some embodiments, the second primer pair comprises at least one degenerate primer. In some embodiments, the second primer pair comprises a second forward primer comprising 5 'TACCTACCCTTGACATACAGTG 3' (SEQ ID NO:4) or a complement thereof. In some embodiments, the second primer pair comprises a second reverse primer comprising 5 'CTTCCTCCGGTTTGTCAC 3' (SEQ ID NO:5) or a complement thereof.

In some embodiments, the method further comprises contacting the biological sample with one or more oligonucleotide probes capable of specifically hybridizing to the amplification products or their complements. In some embodiments, the oligonucleotide probe is detectably labeled. In some embodiments, the detectable label is a fluorescent label. In some embodiments, the fluorescent label is selected from the group consisting of fluorescein, Cy3, Cy5, Cy5.5, tetrachloro-6-carboxyfluorescein, 2, 7-dimethoxy-4, 5-dichloro-6-carboxy-fluorescein, yagewasabi (yakia Yellow), texas red, TYE 563, ROX, TEX 615, TYE 665, TYE 705, and hexachloro-6-carboxyfluorescein. In some embodiments, the oligonucleotide probe further comprises at least one quencher. In some embodiments, the quencher is selected from the group consisting of TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa Black FQ, Iowa Black RQ, and DABCYL. In some embodiments, the oligonucleotide probe specifically hybridizes to an ssrA amplification product, and wherein the oligonucleotide probe comprises 5 'TAAATATAAATGCAAACGATGAAAACTTTGC 3' (SEQ ID NO:3) or a complement thereof. In some embodiments, the oligonucleotide probe specifically hybridizes to a 16S rRNA amplification product, and wherein the oligonucleotide probe comprises 5 'CCAGCATGTGATGGTGGGGACTCTA 3' (SEQ ID NO:6) or a complement thereof.

In some embodiments, the method further comprises mixing an exogenous control DNA with the biological sample. In some embodiments, the method further comprises contacting the biological sample with a third primer pair suitable for amplifying the exogenous control target nucleic acid, and amplifying the exogenous control target nucleic acid. In some embodiments, the exogenous control target nucleic acid comprises SEQ ID NO. 20. In some embodiments, the third primer pair consists of a third forward primer comprising 5 'GCTTCAGTACCTTCGGCTTG 3' (SEQ ID NO:17) and a third reverse primer comprising 5 'TTGCAGGCATCTCTGACAAC 3' (SEQ ID NO: 18). In some embodiments, the method further comprises contacting the biological sample with a third oligonucleotide probe, wherein the third oligonucleotide probe is detectably labeled and comprises 5 'TGGCTCTTGGCGGTCCAGATG 3' (SEQ ID NO: 19).

In some embodiments of the methods provided herein, the real-time PCR amplification is performed in a direct amplification dish in cooperation with an integrated thermal cycler.

In some embodiments of the methods provided herein, the biological sample is a bronchoalveolar lavage fluid sample, a bronchial wash sample, a sputum sample, a Nasopharyngeal (NP) aspirate or wash sample, a nasal swab, or a bacterial isolate.

In another aspect, provided herein is a kit for detecting the presence of at least one legionella species in a biological sample, the kit comprising, consisting or consisting essentially of: (a) a first primer pair for amplifying the ssrA target nucleic acid; (b) a second primer pair for amplifying the 16S rRNA target nucleic acid; (c) a first oligonucleotide probe capable of specifically hybridizing to a segment of the ssrA target nucleic acid; and (d) a second oligonucleotide probe capable of specifically hybridizing to a segment of the 16S rRNA target nucleic acid; wherein the first oligonucleotide probe and the second oligonucleotide probe are detectably labeled.

In some embodiments of the kits provided herein, the kit further comprises a third primer pair that amplifies a control target nucleic acid. In some embodiments, the first primer pair is capable of specifically hybridizing to an ssrA target nucleic acid comprising at least 85% -95% identical nucleotides to SEQ ID NO. 7 or its complement. In some embodiments, the second primer pair is capable of specifically hybridizing to a 16S rRNA target nucleic acid comprising at least 85% -95% identical nucleotides to SEQ ID No. 8 or its complement.

In some embodiments of the kits provided herein, the first primer pair comprises at least one degenerate primer. In some embodiments, the first primer pair comprises a first forward primer comprising 5 'TCGACGTGGGTTGCRAAACG 3' (SEQ ID NO:1) or a complement thereof. In some embodiments, the first primer pair comprises a first reverse primer comprising 5 'TATGACCGTTGATTCGATACC 3' (SEQ ID NO:2) or a complement thereof. In some embodiments, the second primer pair comprises at least one degenerate primer. In some embodiments, the second primer pair comprises a second forward primer comprising 5 'TACCTACCCTTGACATACAGTG 3' (SEQ ID NO:4) or a complement thereof. In some embodiments, the second primer pair comprises a second reverse primer comprising 5 'CTTCCTCCGGTTTGTCAC 3' (SEQ ID NO:5) or a complement thereof. In some embodiments, the first nucleic acid probe comprises 5 'TAAATATAAATGCAAACGATGAAAACTTTGC 3' (SEQ ID NO:3) or a complement thereof. In some embodiments, the second nucleic acid probe comprises 5 'CAACCAGCCGCTGCTGACGGTC 3' (SEQ ID NO:9) or a complement thereof.

In some embodiments of the kits provided herein, the detectable label is a fluorescent label. In some embodiments, the fluorescent label is selected from the group consisting of fluorescein, Cy3, Cy5, Cy5.5, tetrachloro-6-carboxyfluorescein, 2, 7-dimethoxy-4, 5-dichloro-6-carboxyfluorescein, jagewasabi, texas red, TYE 563, ROX, TEX 615, TYE 665, TYE 705, and hexachloro-6-carboxyfluorescein. In some embodiments, the at least one oligonucleotide probe further comprises at least one quencher. In some embodiments, the oligonucleotide probe comprises two quenchers. In some embodiments, the quencher is selected from the group consisting of TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa Black FQ, Iowa Black RQ, and DABCYL.

In one aspect, provided herein is a composition comprising a detectably labeled oligonucleotide probe comprising 5 'TAAATATAAATGCAAACGATGAAAACTTTGC 3' (SEQ ID NO: 3). In some embodiments, the detectable label is a fluorescent label. In some embodiments, the fluorescent label is selected from the group consisting of fluorescein, Cy3, Cy5, Cy5.5, tetrachloro-6-carboxyfluorescein, 2, 7-dimethoxy-4, 5-dichloro-6-carboxyfluorescein, jagewasabi, texas red, TYE 563, ROX, TEX 615, TYE 665, TYE 705, and hexachloro-6-carboxyfluorescein. In some embodiments, the oligonucleotide probe further comprises at least one quencher. In some embodiments, the quencher is selected from the group consisting of TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa Black FQ, Iowa Black RQ, and DABCYL.

Also provided herein are methods for selecting a subject exhibiting pneumonic-like symptoms for treatment with a therapeutic agent that inhibits legionella pneumophila, the method comprising, consisting of, or consisting essentially of: (a) contacting a sample isolated from the subject with a first primer pair suitable for amplifying an ssrA target nucleic acid; (b) contacting the sample with a second primer pair suitable for amplifying the 16S rRNA target nucleic acid; (c) amplifying the ssrA target nucleic acid and the 16S rRNA target nucleic acid, if present; and (d) detecting one or more amplification products produced in step (c); and (e) selecting the subject for treatment with a therapeutic agent that inhibits legionella pneumophila if an amplification product of the 16S rRNA target nucleic acid is detected.

In some aspects, provided herein is a method of treating a subject having a legionella pneumophila infection, the method comprising administering, consisting of or consisting essentially of a therapeutic agent that inhibits legionella pneumophila to a subject selected by a method comprising, consisting of, or consisting essentially of: (a) contacting a sample isolated from the subject with a first primer pair suitable for amplifying an ssrA target nucleic acid; (b) contacting the sample with a second primer pair suitable for amplifying the 16S rRNA target nucleic acid; (c) amplifying the ssrA target nucleic acid and the 16S rRNA target nucleic acid, if present; and (d) detecting one or more amplification products produced in step (c); and (e) selecting the subject for treatment with a therapeutic agent that inhibits legionella pneumophila if an amplification product of the 16S rRNA target nucleic acid is detected.

In some embodiments of the methods provided herein, the first primer pair comprises at least one degenerate primer. In some embodiments, the first primer pair comprises a first forward primer comprising 5 'TCGACGTGGGTTGCRAAACG 3' (SEQ ID NO:1) or a complement thereof. The method of any one of the preceding claims, wherein the first primer pair comprises a first reverse primer comprising 5 'TATGACCGTTGATTCGATACC 3' (SEQ ID NO:2) or a complement thereof. In some embodiments, the second primer pair comprises at least one degenerate primer. In some embodiments, the second primer pair comprises a second forward primer comprising 5 'TACCTACCCTTGACATACAGTG 3' (SEQ ID NO:4) or a complement thereof. In some embodiments, the second primer pair comprises a second reverse primer comprising 5 'CTTCCTCCGGTTTGTCAC 3' (SEQ ID NO:5) or a complement thereof.

In some embodiments, the method further comprises contacting the biological sample with one or more oligonucleotide probes capable of specifically hybridizing to the amplification products or their complements. In some embodiments, the oligonucleotide probe is detectably labeled. In some embodiments, the detectable label is a fluorescent label. In some embodiments, the fluorescent label is selected from the group consisting of fluorescein, Cy3, Cy5, Cy5.5, tetrachloro-6-carboxyfluorescein, 2, 7-dimethoxy-4, 5-dichloro-6-carboxyfluorescein, jagewasabi, texas red, TYE 563, ROX, TEX 615, TYE 665, TYE 705, and hexachloro-6-carboxyfluorescein. In some embodiments, the oligonucleotide probe further comprises at least one quencher. In some embodiments, the quencher is selected from the group consisting of TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa Black FQ, Iowa Black RQ, and DABCYL. In some embodiments, the oligonucleotide probe specifically hybridizes to an ssrA amplification product, and wherein the oligonucleotide probe comprises 5 'TAAATATAAATGCAAACGATGAAAACTTTGC 3' (SEQ ID NO:3) or a complement thereof. In some embodiments, the oligonucleotide probe specifically hybridizes to a 16S rRNA amplification product, and wherein the oligonucleotide probe comprises 5 'CCAGCATGTGATGGTGGGGACTCTA 3' (SEQ ID NO:6) or a complement thereof.

In some embodiments, the method further comprises mixing an exogenous control DNA with the biological sample. In some embodiments, the method further comprises contacting the biological sample with a third primer pair suitable for amplifying the exogenous control target nucleic acid, and amplifying the exogenous control target nucleic acid. In some embodiments, the exogenous control target nucleic acid comprises SEQ ID NO. 20. In some embodiments, the third primer pair consists of a third forward primer comprising 5 'GCTTCAGTACCTTCGGCTTG 3' (SEQ ID NO:17) and a third reverse primer comprising 5 'TTGCAGGCATCTCTGACAAC 3' (SEQ ID NO: 18). In some embodiments, the method further comprises contacting the biological sample with a third oligonucleotide probe, wherein the third oligonucleotide probe is detectably labeled and comprises 5 'TGGCTCTTGGCGGTCCAGATG 3' (SEQ ID NO: 19).

In some embodiments of the methods provided herein, the real-time PCR amplification is performed in a direct amplification dish in cooperation with an integrated thermal cycler.

In some embodiments of the methods provided herein, the biological sample is a bronchoalveolar lavage fluid sample, a bronchial wash sample, a sputum sample, a Nasopharyngeal (NP) aspirate or wash sample, a nasal swab, or a bacterial isolate.

In some embodiments of the methods provided herein, the therapeutic agent that inhibits legionella pneumophila is one or more agents selected from the group consisting of: fluoroquinolones, carbapenems, macrolide antibiotics, trimethoprim-sulfamethoxazole, legionella pneumophila specific antibodies and legionella pneumophila specific vaccines. In some embodiments of the methods provided herein, the fluoroquinolone is selected from the group consisting of ciprofloxacin, gemifloxacin, levofloxacin, norfloxacin, ofloxacin, lovastatin (rovafloxacin), gatifloxacin, grepafloxacin, temafloxacin, lomefloxacin, sparfloxacin, enoxacin, and moxifloxacin. In some embodiments of the methods provided herein, the carbapenem is selected from imipenem, meropenem, ertapenem, doripenem, panipenem, biapenem, lazupenem (razapeem) (PZ-601), tebipenem, lenapenem, cephalopenem, and sienpenem (thienpenem) (thienamycin). In some embodiments of the methods provided herein, the legionella pneumophila-specific vaccine is selected from the group consisting of a whole cell (wP) legionella pneumophila vaccine and a cell-free legionella pneumophila vaccine. In some embodiments of the methods provided herein, the macrolide antibiotic is selected from the group consisting of azithromycin (shisumax), clarithromycin (Biaxin), erythromycin (E-Mycin, Eryc, Ery-Tab, PCE, erythromycin succinylate (Pediazole), Ilosone (Ilosone), and roxithromycin.

Detailed Description

The present disclosure provides methods for determining whether a patient exhibiting pneumonic symptoms will benefit from treatment with a therapeutic agent that inhibits legionella species and/or legionella pneumophila. These methods are based on the detection of legionella species and/or legionella pneumophila in biological samples by determining the presence of ssrA and 16S rRNA target nucleic acids, respectively, using real-time PCR. In some embodiments, the method comprises: (a) providing a first primer pair suitable for amplifying a ssrA target nucleic acid; providing a second primer pair suitable for amplifying the 16S rRNA target nucleic acid; amplifying the ssrA target nucleic acid and the 16S rRNA target nucleic acid, if present; and detecting one or more amplification products produced in step (c); wherein the presence of ssrA target nucleic acid identifies the presence of at least one Legionella species, and the presence of 16S rRNA target nucleic acid identifies the presence of Legionella pneumophila. Kits for practicing the methods are also provided.

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 this invention belongs.

As used herein, the singular forms "a", "an" and "the" include plural references unless otherwise specified. Thus, for example, reference to "an oligonucleotide" includes a plurality of oligonucleotide molecules, and reference to "a nucleic acid" is a reference to one or more nucleic acids.

As used herein, the term "about" with respect to a number is generally considered to include numbers that fall within a range of 1% -10% of either direction (greater or less) of the number, unless otherwise indicated or otherwise evident from the context.

As used herein, the terms "amplification" or "amplification" with respect to a nucleic acid sequence refer to a method of increasing the expression of a population of nucleic acid sequences in a sample. Copies of a particular target nucleic acid sequence produced in vitro in an amplification reaction are referred to as "amplicons" or "amplification products. Amplification may be exponential or linear. The target nucleic acid may be DNA (such as genomic DNA and cDNA, for example) or RNA. Although the exemplary methods described below involve amplification using the Polymerase Chain Reaction (PCR), the skilled artisan is familiar with a variety of other methods, such as isothermal methods, rolling circle methods, and the like. The skilled artisan will appreciate that these other methods may be used in place of or in addition to the PCR method. See, e.g., Saiki, "Amplification of Genomic DNA", PCR Protocols, edited by Innis et al, Academic Press, San Diego, CA 1990, pages 13-20; wharam et al, Nucleic Acids Res.29(11): E54-E54 (2001).

An "amplification mixture" as used herein is a mixture of reagents for a nucleic acid amplification reaction, but without primers or sample. The amplification mixture comprises buffer, dntps and DNA polymerase. The amplification mixture may further comprise MgCl₂KCl, nonionic and ionic detergents (including cationic detergents).

An "amplification master mix" comprises an amplification mix and primers for amplifying one or more target nucleic acids, but does not contain the sample to be amplified.

The terms "complement", "complementary" or "complementarity" as used herein with respect to a polynucleotide (i.e., a nucleotide sequence, such as an oligonucleotide or a target nucleic acid) refer to the Watson/Crick base pairing rules. The complement of a nucleic acid sequence as used herein refers to an oligonucleotide that is in "antiparallel association" when aligned with a nucleic acid sequence such that the 5 'end of one sequence is aligned with the 3' end of another sequence. For example, the sequence "5 '-A-G-T-3'" is complementary to the sequence "3 '-T-C-A-5'". Certain bases that are not normally found in naturally occurring nucleic acids may be included in the nucleic acids described herein. These bases include, for example, inosine, 7-deazaguanine, Locked Nucleic Acid (LNA), and Peptide Nucleic Acid (PNA). Complementarity need not be perfect; the stable duplex may contain mismatched base pairs, denatured or mismatched bases. One skilled in the art of nucleic acid technology can empirically determine duplex stability after considering a number of variables including, for example, the length of the oligonucleotide, the base composition and sequence of the oligonucleotide, ionic strength, and the incidence of mismatched base pairs. The complement sequence may also be an RNA sequence complementary to a DNA sequence or its complement sequence, and may also be a cDNA.

The term "substantially complementary" as used herein means that two sequences hybridize under stringent hybridization conditions. The skilled artisan will appreciate that substantially complementary sequences need not hybridize along their entire length. In particular, the substantially complementary sequence may comprise a contiguous base sequence that does not hybridize to the target sequence, positioned 3 'or 5' to a contiguous base sequence that hybridizes to the target sequence under stringent hybridization conditions.

As used herein, the "cycle threshold" (Ct) of an analyte is the PCR cycle at which the fluorescence signal crosses a specified fluorescence threshold. The Ct depends on the amplification reaction efficiency, including starting template copy number, organism lysis, PCR amplification, hybridization or cleavage of fluorescent probes, and detection sensitivity. The Ct provides a relative measure of the concentration of the target nucleic acid in the PCR reaction. Many factors other than target nucleic acid concentration can affect the absolute value of Ct. However, artifacts from fluorescence measurements that alter the reaction mixture or instrument in relation to the Ct calculation will result in template-independent changes in Ct values.

The term "detecting" as used herein refers to determining the presence of a target nucleic acid in a sample. The detection does not require the method to provide 100% sensitivity and/or 100% specificity.

As used herein, the term "direct amplification" refers to a nucleic acid amplification reaction in which a target nucleic acid is amplified from a sample without prior purification, extraction, or concentration.

As used herein, the term "extraction" refers to any action taken to remove nucleic acids from other (non-nucleic acid) material present in a sample. The term extraction includes mechanical or chemical cleavage, addition of detergents or proteases, or precipitation and removal of non-nucleic acids (e.g., proteins).

The term "fluorophore" as used herein refers to a molecule that absorbs light of a particular wavelength (excitation frequency) and subsequently emits light of a longer wavelength (emission frequency). The term "donor fluorophore" as used herein means a fluorophore that, when in close proximity to a quencher moiety, contributes or transfers emission energy to the quencher. Since energy is contributed to the quencher moiety, the donor fluorophore itself will emit less light at a particular emission frequency than light emitted in the absence of a tightly localized quencher moiety.

The term "hybridize" as used herein refers to the process of two substantially complementary nucleic acid strands (at least about 65% complementary, at least about 75% complementary, or at least about 90% complementary over an extension of at least 14 to 25 nucleotides) annealing to each other under conditions of appropriate stringency to form a duplex or heteroduplex by forming hydrogen bonds between complementary base pairs. Hybridization is typically and preferably performed with nucleic acid molecules of probe length, preferably 15-100 nucleotides in length, more preferably 18-50 nucleotides in length. Nucleic acid hybridization techniques are well known in the art. See, e.g., Sambrook et al, 1989, Molecular Cloning: A Laboratory Manual, second edition, Cold Spring Harbor Press, Plainview, N.Y.. Hybridization and hybridization intensity (i.e., strength of association between nucleic acids) are affected by factors such as the degree of complementarity between nucleic acids, the stringency of the conditions involved, and the thermal melting point (T) of the hybrids formed_m) Etc. One skilled in the art knows how to estimate and adjust the stringency of hybridization conditions such that sequences with at least the desired level of complementarity will stably hybridize, while sequences with lower complementarity will not hybridize. For examples of hybridization conditions and parameters, see, e.g., Sambrook et al, 1989, Molecular Cloning, A Laboratory Manual, second edition, Cold Spring Harbor Press, Plainview, N.Y.; ausubel, F.M. et al 1994, Current Protocols in Molecular Biology, John Wiley&Sons, Secaucus, n.j. In some embodiments, specific hybridization occurs under stringent hybridization conditions. Specific for target nucleic acidWill "hybridize" to the target nucleic acid under suitable conditions.

As used herein, the term "individual", "patient" or "subject" can be an individual organism, vertebrate, mammal, or human. In a preferred embodiment, the individual, patient or subject is a human.

As used herein, the term "multiplex PCR" refers to the simultaneous production of two or more PCR products or amplicons within the same reaction vessel. Each PCR product was primed using a different primer pair. The multiplex reaction may further comprise a probe specific for each product, the probe being labeled with a different detectable moiety.

As used herein, "oligonucleotide" refers to a molecule having a sequence of nucleobases on a backbone comprising predominantly the same monomeric units at defined intervals. The bases are arranged on the backbone in such a way that they can bind to nucleic acids having a base sequence complementary to the bases of the oligonucleotide. Most commonly oligonucleotides have a backbone of phosphate sugar units. Oligodeoxyribonucleotides without a hydroxyl group at the 2 'position can be distinguished from oligoribonucleotides with a hydroxyl group at the 2' position. Oligonucleotides may also include derivatives in which the hydrogen in the hydroxyl group is replaced with an organic group (e.g., allyl). Oligonucleotides useful as primers or probes are typically at least about 10-15 nucleotides in length, or up to about 70, 100, 110, 150, or 200 nucleotides in length, more preferably at least about 15 to 25 nucleotides in length. Oligonucleotides used as primers or probes for specific amplification or specific detection of a particular target nucleic acid are generally capable of specifically hybridizing to the target nucleic acid.

As used herein, "Legionella species (Legionella species)" or "Legionella species (Legionella sp.)" refers to any microbial organism of the Legionella genus. In some embodiments, the legionella species is pathogenic and is capable of causing pneumonia, legionnaires disease, pointiac fever, or related disorders in a subject (e.g., a human). Specific pathogens include, for example, legionella anisum (l.anisa), legionella berminghalensis (l.birminghaensis), legionella boltzeri (l.bozemanii) (serogroup 1), legionella boltzeri (serogroup 2), legionella cadicaria (l.cadiacea), legionella chester (l.cherrii), legionella cincinnati (l.cincinninatiensis), legionella cleavana (l.clemsoniensis), legionella dum (l.dumomoffii), legionella philippinensis (l.feleii) (serogroup 1), legionella philippinensis (serogroup 2), legionella gordonii (l.goremanniani), legionella kazakii (l.halclaiera), legionella anserina (l.gordonii) (serogroup 1), legionella kesii serogroup 2), legionella (l.zoea), legionella longella (l.l.l.jejunipes), legionella (l.la) Legionella pneumophila (Philadelphia 1), Legionella pneumophila (Nockverl 1), Legionella pneumophila (Benydomum 030E), Legionella pneumophila (France 5811), Legionella pneumophila (Allen 1), Legionella pneumophila (OLDA), Legionella pneumophila (Oxford 4032E), Legionella pneumophila (Bellingham), Legionella pneumophila (Shexin 1), Legionella pneumophila (Campton 1), Legionella pneumophila (Togus)1), Legionella pneumophila (Blumeton 2), Legionea Legionella pneumophila (Logania), Legionella pneumophila (Portland 1), Legionella pneumophila (Dallas 1E), Legionella pneumophila (Cambridge 1), Legionella pneumophila (Chicago 1), Legionella pneumophila (C8), Legionella pneumophila (IN 3), Legionella pneumophila (C-2), Legionella pneumophila (C-1), Legionella pneumophila (797-PA-H), legionella pneumophila (570-CO-H), legionella pneumophila (82A3105), legionella pneumophila (1169-MN-H), legionella pneumophila (Lanxin 3), legionella rubra (L.rubrilucts), legionella saintensis (L.saintenhelensi) (serogroup 1), legionella saint hernana (serogroup 2), legionella tucsense (L.tucsonensis) and legionella farezii (L.wadswordworthii).

As used herein, a "positive control nucleic acid" or "internal positive amplification control" is a nucleic acid that is known to be present in a sample at an amount or level. In some embodiments, in the disclosed methods for detecting the presence of a pathogenic legionella species in a sample, the positive control nucleic acid is not naturally present in the sample, but is added to the sample prior to subjecting the reaction-sample mixture to a real-time polymerase chain reaction.

As used herein, the term "primer" refers to an oligonucleotide that is capable of acting as a point of initiation of nucleic acid sequence synthesis when placed under conditions that induce synthesis of a primer extension product that is complementary to a target nucleic acid strand, i.e., in the presence of different nucleotide triphosphates and a polymerase in an appropriate buffer (a "buffer" includes pH, ionic strength, cofactors, etc.) and at an appropriate temperature. One or more nucleotides in the primer may be modified, for example, by the addition of methyl, biotin or digoxigenin moieties, fluorescent tags or by the use of radionucleotides. The primer sequence need not reflect the exact sequence of the template. For example, a non-complementary nucleotide fragment may be attached to the 5' end of a primer, with the remainder of the primer sequence being substantially complementary to the strand. The term primer as used herein includes all primer forms that can be synthesized, including peptide nucleic acid primers, locked nucleic acid primers, phosphorothioate modified primers, labeled primers, and the like. The term "forward primer" as used herein means a primer that anneals to the antisense strand of double-stranded dna (dsdna). The "reverse primer" anneals to the sense strand of dsDNA.

Primers are typically at least 10, 15, 18, or 30 nucleotides in length, or up to about 100, 110, 125, or 200 nucleotides in length. In some embodiments, the primer is preferably between about 15 to about 60 nucleotides in length, most preferably between about 25 to about 40 nucleotides in length. In some embodiments, the primer is 15 to 35 nucleotides in length. There is no standard length for optimal hybridization or polymerase chain reaction amplification. The optimal length for the Application of a particular primer can be readily determined in the manner described in H.Erlich, PCR Technology, Principles and Application for DNA Amplification, (1989).

"primer extension reaction" refers to a synthesis reaction in which an oligonucleotide primer hybridizes to a target nucleic acid and produces complementary copies of the target nucleic acid by polymerase-dependent 3' addition of individual complementary nucleotides. In some embodiments, the primer extension reaction is PCR.

As used herein, the term "primer pair" refers to a pair of forward and reverse primers (i.e., left and right primer pairs) that can be used together to amplify a given region of a target nucleic acid.

"Probe" as used herein refers to a nucleic acid that interacts with a target nucleic acid via hybridization. The probe may be fully complementary or partially complementary to the target nucleic acid sequence. The level of complementarity will generally depend on many factors based on the function of the probe. The probes may or may not be labeled or modified in any of a variety of ways well known in the art. The probe can specifically hybridize to the target nucleic acid. The probe may be DNA, RNA or RNA/DNA hybrid. The probe may be an oligonucleotide, an artificial chromosome, a fragmented artificial chromosome, a genomic nucleic acid, a fragmented genomic nucleic acid, RNA, a recombinant nucleic acid, a fragmented recombinant nucleic acid, a Peptide Nucleic Acid (PNA), a locked nucleic acid, an oligomer of cyclic heterocycles, or a conjugate of a nucleic acid. Probes may comprise modified nucleobases, modified sugar moieties and modified internucleotide linkages. Probes can be used to detect the presence or absence of a methylated target nucleic acid. Probes are typically at least about 10, 15, 20, 25, 30, 35, 40, 50, 60, 75, 100 nucleotides in length or longer.

As used herein, "probe element" refers to an extension of nucleotides that (a) is associated with a primer, wherein the extension is linked to or positioned adjacent to a primer nucleic acid sequence, and (b) specifically hybridizes under stringent conditions to a target nucleic acid sequence to be detected.

As used herein, the term "primer-probe detection system" refers to a method for real-time PCR. In some embodiments, the system is a Taqman-based PCR system and/or a SCORPION-based PCR system. In some embodiments, the primer-probe detection system comprises at least one forward primer, at least one reverse primer, and at least one oligonucleotide probe. In some embodiments, the oligonucleotide probe is detectably labeled. In some embodiments, the oligonucleotide probe comprises a detectable label and a quencher moiety.

The term "quencher moiety" as used herein means a molecule in close proximity to a donor fluorophore that absorbs the emission energy generated by the donor and causes the energy to be shaped into heatThe formula dissipates or emits light at a wavelength longer than the emission wavelength of the donor. In the latter case, the quencher is considered to be an acceptor fluorophore. Quenching moieties may be quenched via proximity (i.e., collision) or byOr fluorescence resonance energy transfer ("FRET"). Quenching by FRET is commonly usedIn probes, while proximity quenching is used for molecular beacons and Scorpion^TMIn type probes. Non-limiting examples of quenchers include TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa Black FQ, Iowa Black RQ, and DABCYL.

As used herein, a "reaction-sample mixture" refers to a mixture containing an amplification master mixture and a sample.

As used herein, the term "sample" refers to a clinical sample obtained from a patient or an isolated microorganism. In a preferred embodiment, the sample is obtained from a biological source (i.e., a "biological sample"), such as a tissue, body fluid, or microorganism collected from a subject. Sample sources include, but are not limited to, mucus, sputum (treated or untreated), bronchoalveolar lavage (BAL), bronchial lavage (BW), blood, bodily fluids, cerebrospinal fluid (CSF), urine, plasma, serum, or tissue (e.g., biopsy material). Preferred sample sources include BAL, BW, and/or a pharyngeal swab or nasal wash.

The term "sensitivity" as used herein with respect to the methods of the present technology is a measure of the ability of the method to detect a preselected sequence variant in a heterogeneous population of sequences. The method has a sensitivity of S% for variants of F% if the preselected sequence variant in a given sample is present at least F% of the sequence in the sample, the preselected sequence being detectable by the method S% of the times at a preselected confidence of C%. For example, if a preselected variant sequence in a given sample is present in at least 5% of the sequences in the sample, the method can detect the preselected sequence 10 times with a preselected confidence of 99% (F5%; C99%; S90%), then the method has a sensitivity of 90% for 5% of the variants. Exemplary sensitivities include at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, and 99%.

The term "specific" as used herein with respect to an oligonucleotide primer means that the nucleotide sequence of the primer has at least 12 bases of sequence identity with a portion of the nucleic acid to be amplified when aligning the oligonucleotide with the nucleic acid. Oligonucleotide primers specific for nucleic acids are primers that are capable of hybridizing to a target of interest under stringent hybridization or wash conditions and do not substantially hybridize to non-target nucleic acids. Higher levels of sequence identity are preferred and include at least 75%, at least 80%, at least 85%, at least 90%, at least 85% -95%, more preferably at least 98% sequence identity. Sequence identity can be determined using a commercially available computer program employing algorithms well known in the art, with default settings. As used herein, a sequence having "high sequence identity" has identical nucleotides at least at about 50% of the aligned nucleotide positions, preferably at least about 60% of the aligned nucleotide positions, more preferably at least about 75% of the aligned nucleotide positions.

As used herein, "specificity" is a measure of the ability of a method to distinguish between a truly present preselected sequence variant and sequencing artifacts or other closely related sequences. It is the ability to avoid false positive detection. False positive detection may result from: errors introduced into the target sequence during sample preparation, sequencing errors, or inadvertent sequencing of closely related sequences (e.g., pseudogenes or gene family members). If it is applied to N_{General assembly}A sample set of sequences, wherein X_{Reality (reality)}The sequence is a true variant and X_{Is not real}Non-authentic variants, the method selecting at least X% of the non-authentic variants as non-variants, the method having a specificity of X%. For example, if the method selects 90% of the 500 unreal variant sequences to be non-variant when applied to a sample set of 1,000 sequences, 500 of which are authentic variants and 500 are non-authentic variants, the method has a specificity of 90%. Exemplary specificities include at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, and99％。

the term "stringent hybridization conditions" as used herein refers to hybridization conditions that are at least as stringent as: in 50% formamide, 5 XSSC, 50mM NaH₂PO4(pH 6.8), 0.5% SDS, 0.1mg/mL sonicated salmon sperm DNA and 5 XDenhart's solution at 42 ℃ for overnight; wash with 2x SSC, 0.1% SDS at 45 ℃; and washed with 0.2x SSC, 0.1% SDS at 45 ℃. In another example, stringent hybridization conditions should not allow hybridization of two nucleic acids that differ by more than two bases over an extension of 20 contiguous nucleotides.

As used herein,' A "PCR detection system "refers to a method for real-time PCR. In this method, the amplified nucleic acid segments are included in the amplification master mixAnd (3) a probe.The probe comprises a donor and a quencher fluorophore on either end of the probe that are sufficiently close to each other that the quencher absorbs fluorescence of the donor. However, upon hybridization of the probe to the amplified segment, the 5' -exonuclease activity of the Taq polymerase cleaves the probe, allowing the donor fluorophore to emit fluorescence that can be detected.

The term "target nucleic acid" or "target sequence" as used herein refers to a nucleic acid sequence of interest to be detected and/or quantified in a sample to be analyzed. The target nucleic acid can be composed of: a chromosomal segment, a complete gene with or without intergenic sequence, a segment or portion of a gene with or without intergenic sequence, or a nucleic acid sequence for which probes or primers are designed. The target nucleic acid may comprise one or more wild-type sequences, mutations, deletions, insertions or repeats, tandem repeat elements, the gene of interest, a region of the gene of interest, or any upstream or downstream region of said region. The target nucleic acid can represent an alternative sequence or allele of a particular gene. The target nucleic acid may be derived from genomic DNA, cDNA or RNA.

Biological sample collection and preparation

The methods and compositions of the present technology can be used to detect pathogenic legionella species by determining target nucleic acid sequences corresponding to the ssrA gene and the 16S rRNA gene in a biological sample obtained from a subject. Samples for pathogenic legionella species detection may also include cultures of bacterial isolates grown on appropriate media to form colonies, wherein the cultures are prepared from biological samples obtained from the subject.

The methods disclosed herein can be used to detect and quantify pathogenic legionella species in biological samples derived from sterile and/or non-sterile sites. "sterile site" includes bodily fluids such as whole blood, plasma, acellular plasma, urine, cerebrospinal fluid, synovial fluid, pleural fluid, pericardial fluid, ocular fluid, tissue biopsy, or endotracheal aspirates. As used herein, "cell-free plasma" refers to plasma containing less than 1% cells by volume. "non-sterile sites" include sputum, feces, skin swabs, groin swabs, nasal swabs, and pharyngeal swabs. In some embodiments, the biological sample comprises a Nasopharyngeal (NP) aspirate or swab or a nasal wash. In other embodiments, the biological sample comprises a culture of isolated bacteria grown on a suitable medium to form colonies. The sample may also include bacterial isolates.

In some embodiments, the sample is transported or stored in a sterile vial containing VCM or M4 medium. The VCM medium comprises hank's balanced salts, bovine serum albumin, L-cysteine, gelatin, sucrose, L-glutamic acid, HEPES buffer, vancomycin, amphotericin B, colistin, and optionally phenol red. M4 medium contained gelatin, vancomycin, amphotericin B, and colistin.

The biological sample may be suspected of containing nucleic acid of a pathogenic legionella species and/or one or more pathogenic legionella species. Additionally, the biological sample may be obtained from a subject suspected of being infected with one or more pathogenic legionella species. The biological sample may be contacted with an amplification master mix for a microfluidic/microelectronic centrifugation platform.

In some embodiments, the disclosed methods employ untreated biological samples, thereby resulting in a direct, simplified sample-to-result process. In other embodiments, the detection methods disclosed herein will be effective if used for isolated nucleic acids (DNA or RNA) purified from a biological sample according to any method well known to those skilled in the art. The sample may be collected or concentrated by centrifugation or the like, if desired. The cells of the sample may be lysed, such as by enzymatic treatment, thermal surfactant treatment, sonication, or a combination thereof. Alternatively, a biological sample can be processed using a commercially available nucleic acid extraction kit.

In some embodiments, one or more primer pairs are present in the amplification master mix prior to contacting with the biological sample, the amplification master mix further comprising a DNA polymerase, dntps, and a PCR buffer. Amplification of the ssrA gene and the 16S rRNA gene preferably occurs in multiplex format. Alternatively, it is also possible to use individual PCR reactions for each target sequence. The biological sample may be contacted with the one or more primer pairs and/or with the amplification master mix in a direct amplification dish to form a reaction-sample mixture. For example, a biological sample can be contacted with the amplification master mix in a direct amplification dish (such as that sold by Focus Diagnostics, Inc. (Seplacian, Calif.), as part of a SIMPLEXA direct real-time PCR assay, to contact 3M^TMThe integrated circulator works in a coordinated manner. The direct amplification disk is a circular thin disk containing a plurality of designated regions, each designated region containing a well for receiving an amplification master mix and an associated well for receiving an untreated patient sample. The sample-reaction mixture is generated in the direct amplification dish either at the time of addition of the amplification master mix and the sample or after addition.

In some embodiments, the biological sample is isolated from a subject. In some embodiments, the subject is a mammal. In some embodiments, the mammal is a bovine, equine, porcine, feline, canine, murine, simian, rat, or human. In some embodiments, the subject is a human. In particular embodiments, the subject is a human patient with one or more pneumonic symptoms.

Real-time PCR

Amplification of a target nucleic acid can be detected by any of a variety of methods well known in the art, such as gel electrophoresis, column chromatography, hybridization to probes, sequencing, melt curve analysis, or "real-time" detection.

For real-time detection, the primers and/or probes may be detectably labeled to allow for differences in fluorescence to be found in an instrument capable of monitoring changes in fluorescence during the reaction, either upon incorporation of the primers or upon hybridization and amplification of the probes, for example. Real-time detection methods for nucleic acid amplification are well known and include, for exampleSystem, Scorpion^TMPrimer systems and the use of intercalating dyes for double-stranded nucleic acids.

In real-time quantitative PCR, the accumulation of amplified products is measured continuously in both standard dilutions of target DNA and samples containing unknown amounts of target DNA. By comparing the initial template concentration in the standard sample to the PCR required to produce a product of a particular threshold concentration^TMCycle (Ct) numbers were correlated to construct a standard curve. In the test samples, target PCR was measured after the same Ct^TMProduct accumulation, which allows interpolation of target DNA concentration from the standard curve.

In some embodiments, the amplified nucleic acid is detected by hybridization to a specific probe. The amplified fragments can be detected using a probe oligonucleotide that is complementary to a portion of the amplified target sequence. In some embodiments, hybridization can be detected in real time. In an alternative embodiment, hybridization is not detected in real time. The amplified nucleic acids in each target sequence can be detected simultaneously (i.e., in the same reaction vessel, such as a multiplex PCR) or separately (i.e., in separate reaction vessels). In certain embodiments, multiple target nucleic acids are detected simultaneously using two or more gene-specific oligonucleotide probes that are distinguishable labels (e.g., via different detectable moieties, such as color), wherein one probe hybridizes to a first target sequence and the other probe hybridizes to a second target sequence.

In some embodiments, different primer pairs are labeled with different distinguishable detectable moieties. Thus, for example, HEX and FAM fluorescent dyes can be present on different primer pairs in a multiplex PCR and associated with the resulting amplicons. In other embodiments, the forward primer is labeled with one detectable moiety and the reverse primer is labeled with a different detectable moiety, e.g., a FAM dye is used for the forward primer and a HEX dye is used for the reverse primer. The use of different detectable moieties can be used to distinguish between amplified products of the same or very similar length.

For sequence-modified nucleic acids, the target may be independently selected from the top strand or the bottom strand. Thus, all targets to be detected may comprise the top strand, the bottom strand, or a combination of top and bottom strand targets.

A common method for real-time PCR uses fluorescent probes, e.g.Probes, molecular beacons and Scorpion primer-probes. Real-time PCR quantifies the initial amount of template with greater specificity, sensitivity, and reproducibility than other forms of quantitative PCR that detect the amount of amplified end product. Real-time PCR does not detect the size of the amplicon. Scorpion^TMAndthe probes employed in the art are based on the principle of fluorescence quenching and involve a donor fluorophore and a quenching moiety.

Real-time PCR is performed using any suitable instrument capable of detecting the accumulation of PCR amplification products. Most typically, the instrument is capable of detecting fluorescence from one or more fluorescent labels. For example, instruments (e.g., ABI real-time PCR System)Sequence detector) monitor fluorescence during each PCR cycle and calculateReporting the measured value or Rn value of the signal. The threshold cycle or Ct value is the cycle at which fluorescence crosses the threshold. The threshold may be determined by the sequence detection system software or manually.

In some embodiments, the probe employed is detectably labeled, and detection is accomplished by probe labeling that detects each amplification product. The quencher may further be associated with a detectable label, which prevents detection of the label prior to target amplification of the probe.Probes are examples of such probes.

The probe (Heid et al, Genome Res.6: 986-.The probe is an oligonucleotide containing a donor fluorophore, usually at or near the 5 'base, and a quencher moiety, typically at or near the 3' base. The quencher moiety may be a dye, such as TAMRA; or may be a non-fluorescent molecule such as 4- (4-dimethylaminophenylazo) benzoic acid (DABCYL). See Tyagi et al, 16Nature Biotechnology 49-53 (1998). When irradiated, the excited fluorescence donor transfers energy to a nearby quenching moiety via FRET rather than fluorescence. Thus, the close proximity of the donor to the quencher prevents emission of donor fluorescence when the probe is intact.

The probe is designed to anneal to an internal region of the PCR product. Replication in polymeraseWhen the probe binds to the template, its 5' exonuclease activity cleaves the probe. This terminates the activity of the quencher (none)FRET), and the donor fluorophore begins to emit fluorescence, which increases in each cycle in proportion to the rate of probe cleavage. Accumulation of PCR products was detected by monitoring the increase in fluorescence of the reporter dye. If the quencher is an acceptor fluorophore, accumulation of the PCR product can be detected by monitoring the decrease in fluorescence of the acceptor fluorophore.

In certain embodiments, a bifunctional primer-probe detection system (e.g., Scorpion) is used^TMPrimers) to perform real-time PCR. In the case of the Scorpion primer, sequence-specific priming and PCR product detection was achieved using a single molecule. The Scorpion primer maintains a stem-loop configuration in an unhybridized state. The fluorophore is attached to the 5 'end and quenched by a moiety coupled to the 3' end, but in certain embodiments, this arrangement can be switched. The 3 'portion of the stem and/or loop also contains a sequence that is complementary to the extension product of the primer and is linked to the 5' end of the specific primer via a non-amplifiable monomer. After partial extension of the primer, the specific probe sequence is able to bind its complement within the extended amplicon, thereby opening the hairpin loop. This prevents the fluorescence from being quenched and a signal is observed. By reverse primer and Scorpion^TMThe primer portion of the primer amplifies the specific target, thereby generating an extension product. Due to the passing of Scorpion^TMThe fluorophore is separated from the quencher by binding of the probe element of the primer to the extension product, and a fluorescent signal is generated.

In some embodiments, the Probes employed in the disclosed methods comprise or consist of short fluorescently labeled DNA sequences designed to detect DNA sequence segments with genetic variation, such as the Probes disclosed in French et al, Mol Cell Probes,5(6):363-74(2001) (incorporated herein by reference in its entirety).Are examples of such probes.

In some embodiments of the methods, at least one primer or at least one probe of each primer pair in the amplification reaction comprises a detectable moiety. Alternatively, the detectable moiety may be on a probe attached to a primer, e.g., with a primer-probeThe needles together. In some embodiments, the detectable moiety or label is a fluorophore. Suitable fluorescent moieties include, but are not limited to, the following fluorophores: 4-acetamido-4 '-isothiocyanatostilbene-2, 2' -disulfonic acid, acridine and derivatives (acridine, acridine isothiocyanate), Alexa Fluor (Alexa350、Alexa488、Alexa546、Alexa555、Alexa568、Alexa594、Alexa647(Molecular Probes)), 5- (2' -aminoethyl) aminonaphthalene-1-sulfonic acid (EDANS), 4-amino-N- [ 3-vinylsulfonyl) phenyl]Naphthalimide-3, 5-disulfonate (firefly yellow VS), N- (4-anilino-1-naphthyl) maleimide, anthranilamide,R-6G、530/550、FL, Bright yellow, Cal Fluor Red(CFR610), coumarins and derivatives (coumarin, 7-amino-4-methylcoumarin (AMC, coumarin 120), 7-amino-4-trifluoromethylcoumarin (coumarin 151)),tetrachlorotetrabromo fluorescein sodium (cyanosine), 4', 6-diamidino-2-phenylindole (DAPI), 5' -dibromopyrogallol-sulfonphthalein (bromopyrogallol red), 7-diethylamino-3- (4' -isothiocyanatophenyl) -4-methylcoumarin, diethylenetriamine pentaacetate, 4' -diisothiocyanatodihydro-stilbene-2, 2' -disulfonic acid, 4' -diisothiocyanatostilbene-2, 2' -disulfonic acid, 5- [ dimethylamino ] dimethyl-amino]Naphthalene-1-sulfonyl chloride (DNS, dansyl chloride), 4- (4 '-dimethylaminophenylazo) benzoic acid (DABCYL), 4-dimethylaminophenylazophenyl-4' -isothiocyanate (DABITC), eclipse (TM) (Epoch Biosciences Inc.), eosin and derivatives (eosin, eosin isothiocyanate), erythrosin and derivatives (erythrosin B, erythrosin isothiocyanate), ethidium, fluorescein and derivatives (5-carboxyfluorescein (FAM), 5- (4, 6-dichlorotriazin-2-yl) aminofluorescein (DTAF), 2',7' -dimethoxy-4 '5' -dichloro-6-carboxyfluorescein (JOE), Fluorescein Isothiocyanate (FITC), hexachloro-6-carboxyfluorescein (HEX), QFITC (XRITC), tetrachlorofluorescein (TET)), fluorescamine, IR144, IR1446, lanthanide phosphor, malachite green isothiocyanate, 4-methylumbelliferone, o-cresolphthalein, nitrotyrosine, pararosaniline, phenol red, B-phycoerythrin, R-phycoerythrin, allophycocyanin, o-phthaldehyde, OregonPropidium iodide, pyrene and derivatives (pyrene, pyrene butyrate, 1-pyrenebutanoic acid succinimidyl ester),7、9、21、35(Molecular Probes), reactive Red 4: (B)Brilliant red 3B-A), rhodamine and derivatives (6-carboxy-X-Rhodamine (ROX), 6-carboxyrhodamine (R6G), lissamine rhodamine B sulfonyl chloride, rhodamine (Rhod), rhodamine B, rhodamine 123, rhodamine green, rhodamine X isothiocyanate, sulforhodamine B, sulforhodamine 101, sulfonyl rhodamine 101 sulfonyl chloride derivatives of sulforhodamine 101 (Texas Red), N, N, N ', N' -tetramethyl-6-carboxyrhodamine (TAMRA), tetramethylrhodamine isothiocyanate (TRITC)), riboflavin, rhodizonic acid, terbium chelate derivatives, QuasarAnd

the appropriate quencher is selected based on the fluorescence spectrum of the particular fluorophore. Useful quenchers include, for example, Black Hole^TMQuenchers BHQ-1, BHQ 2 and BHQ-3(Biosearch Technologies, Inc.) and ATTO series quenchers (ATTO 540Q, ATTO 580Q and ATTO 612Q; ATTO-Tec GmbH).

In some embodiments of the methods, the reaction-sample mixture is subjected to real-time Polymerase Chain Reaction (PCR) conditions under which amplification of each target nucleic acid present in the biological sample occurs, and the one or more amplification products are detected and measured. In some embodiments, the biological sample is loaded directly into a direct amplification disc without separate front end standard preparation, followed by real-time PCR detection and differentiation of the target analyte in the same disc. In certain embodiments, amplification is performed in a direct amplification disc (8-well disc, from Focus Diagnostics, Inc.). In some embodiments, real-time PCR amplification is performed on direct amplification discs using the simple direct assayAn integrated thermal cycler (e.g., 3M sold by 3M (St. Paul, Minn.) was added and used^TMIntegrated cycler) for detection. 3M^TMThe integrated cycler can receive direct amplification discs and can perform multiple assays on each disc. Such a device may be of the kind described in>Heating at 5 deg.C/sec and heating at>Cooling at 4 deg.C/sec. The cycling parameters may vary depending on the length of the amplification product to be extended. In certain embodiments, an internal positive amplification control (IPC) may be included in the sample, utilizing oligonucleotide primers, probes, and/or primer-probes.

Alternative methods for detecting target nucleic acids

Alternatively, detection of the target nucleic acid can be performed by measuring the end point of the reaction. In end-point detection, the one or more amplicons may be detected by: the amplicons are first size separated and then the size separated amplicons are detected. Separation of amplicons of different sizes may be accomplished by gel electrophoresis, column chromatography, capillary electrophoresis, or other separation methods known in the art.

The detectable label may be incorporated into, associated with, or conjugated to the nucleic acid. The labels may be attached by spacer arms of different lengths to reduce potential steric hindrance or impact on other useful or desired properties. See, e.g., Mansfield,9mol. cell. probes 145-156 (1995). Incorporation of the detectable label into the nucleic acid can be by covalent or non-covalent means (e.g., by transcription, such as by random primer labeling using Klenow polymerase, or nick translation, or amplification or equivalent means as known in the art). For example, a nucleotide base is conjugated to a detectable moiety (e.g., a fluorescent dye) and then incorporated into nucleic acid during nucleic acid synthesis or amplification.

Examples of other useful labels to aid in the detection of target nucleic acids include radioisotopes (e.g.,³²P、³⁵S、³H、¹⁴C、¹²⁵I、¹³¹I) electron dense reagents (e.g., gold), enzymes (e.g., horseradish peroxidase, beta-galactosidase, luciferase, alkaline phosphatase), colorimetric labels (e.g., colloidal gold), magneticSex markers (e.g., Dynabeads)^TM) Biotin, digoxin or haptens and proteins from which antisera or monoclonal antibodies are available. Other labels include ligands or oligonucleotides capable of forming complexes with the corresponding receptor or oligonucleotide complement, respectively. The label may be incorporated directly into the nucleic acid to be detected, or may be attached to a probe (e.g., an oligonucleotide) or antibody that hybridizes or binds to the nucleic acid to be detected.

In other embodiments, nucleic acids can be labeled using fluorescent nucleotide analogs, see, e.g., Jameson, methods, enzymol.278: 363-; zhu, Nucl. acids Res.22:3418-3422 (1994). U.S. Pat. nos. 5,652,099 and 6,268,132 also describe nucleoside analogs for incorporation into nucleic acids (e.g., DNA and/or RNA) or oligonucleotides via enzymatic or chemical synthesis to produce fluorescent oligonucleotides. U.S. patent No. 5,135,717 describes phthalocyanine and tetraphenyltriazaporphyrin reagents for use as fluorescent labels.

In some embodiments, detectably labeled probes can be used in hybridization assays, including but not limited to northern blots, southern blots, microarrays, dot or slot blots, and in situ hybridization assays, such as Fluorescence In Situ Hybridization (FISH), to detect target nucleic acid sequences within a biological sample. Certain embodiments may employ hybridization methods for measuring the expression of a polynucleotide gene product (e.g., mRNA). Methods for performing polynucleotide hybridization assays have been well developed in the art. Hybridization assay procedures and conditions will vary depending on the application and are selected according to known general binding methods, including those mentioned in the following references: maniatis et al Molecular Cloning, laboratory Manual (Cold Spring Harbor 2 nd edition, N.Y., 1989); berger and Kimmel Methods in Enzymology, Vol.152, Guide to Molecular Cloning technologies (Academic Press, Inc., San Diego, Calif., 1987); young and Davis, PNAS.80:1194 (1983).

Legionella screening assay of the present technology

In various embodiments of the disclosure, primers and probes are used in the methods described herein to amplify and detect target nucleic acid sequences of pathogenic legionella species. In certain embodiments, the target nucleic acid may include ssrA genes from all legionella species and the 16S rRNA gene from legionella pneumophila. In addition, primers can also be used to amplify one or more control nucleic acid sequences.

The primers and probes of the present technology are used in the methods described herein to amplify and detect the target nucleic acid comprising SEQ ID NO. 7 corresponding to the ssrA gene and the target nucleic acid comprising SEQ ID NO. 8 corresponding to the 16S rRNA gene. In one embodiment, the method involves the use of primer pairs specific for the ssrA and 16S rRNA genes. The target nucleic acids described herein can be detected individually or in multiplex format using individual labels for each target.

Specific primers, probes and primer-probes for amplification and detection of all or a fragment of a marker gene specific for legionella pneumophila include those directed against sequences present in legionella pneumophila but not present in other legionella species. Detection of a legionella pneumophila specific gene helps to distinguish between a sample containing legionella pneumophila and a sample that may contain another legionella pathogenic species.

A suitable marker gene is the 16S rRNA gene (see, e.g., GenBank accession No. NC _002942.5), and is shown below.

AACTGAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGCAGCATTGTCTAGCTTGCTAGACAGATGGCGAGTGGCGAACGGGTGAGTAACGCGTAGGAATATGCCTTGAAGAGGGGGACAACTTGGGGAAACTCAAGCTAATACCGCATAATGTCTGAGGACGAAAGCTGGGGACCTTCGGGCCTGGCGCTTTAAGATTAGCCTGCGTCCGATTAGCTAGTTGGTGGGGTAAGGGCCTACCAAGGCGACGATCGGTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGAGGGTTGTAAAGCACTTTCAGTGGGGAGGAGGGTTGATAGGTTAAGAGCTGATTAACTGGACGTTACCCACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGGGTGCGTAGGTGGTTGATTAAGTTATCTGTGAAATTCCTGGGCTTAACCTGGGACGGTCAGATAATACTGGTTGACTCGAGTATGGGAGAGGGTAGTGGAATTTCCGGTGTAGCGGTGAAATGCGTAGAGATCGGAAGGAACACCAGTGGCGAAGGCGGCTACCTGGCCTAATACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGTCAACTAGCTGTTGGTTATATGAAAATAATTAGTGGCGCAGCAAACGCGATAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTACCCTTGACATACAGTGAATTTTGCAGAGATGCATTAGTGCCTTCGGGAACACTGATACAGGTGCTGCAT GGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGTAACGAGCGCAACCCTTATCCTTAGTTGCCAGC ATGTGATGGTGGGGACTCTAAGGAGACTGCCGGTGACAAACCGGAGGAAGGCGGGGATGACGTCAAGTCATCATGGCCCTTACGGGTAGGGCTACACACGTGCTACAATGGCCGATACAGAGGGCGGCGAAGGGGCGACCTGGAGCAAATCCTTAAAAGTCGGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGCGAATCAGCATGTCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCACCAGAAGTAGATAGTCTAACCTTCGGGGGGACGTTTACCACGGTGT(SEQ ID NO:8)

The nucleic acid sequence of the 16S rRNA amplicon generated using the methods disclosed herein is underlined.

In some embodiments, the 16S rRNA target nucleic acid comprises 5 'TACCTACCCTTGACATACAGTGAATTTTGCAGAGATGCATTAGTGCCTTCGGGAACACTGATACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGTAACGAGCGCAACCCTTATCCTTAGTTGCCAGCATGTGATGGTGGGGACTCTAAGGAGACTGCCGGTGACAAACCGGAGGAAG 3' (SEQ ID NO:9) or a fragment thereof.

Exemplary primers and labeled probe sequences for amplification and detection of 16S rRNA elements include:

the ssrA gene encodes a tmRNA-binding protein and is present in all Legionella species. Non-limiting exemplary nucleotide sequences of ssrA are provided under GenBank accession AE017354.1 (bp 3213808 to 3214278) and are shown below. The nucleic acid sequence of the ssrA amplicon generated using the methods disclosed herein is underlined:

ATGTGGGCAGAAGTATTATCCAGCGATGCCTTTGCGCGCTTTGAGGAGGAAGGTATTTTCAACCCCAAAACTGGACATGACTTTTTAAAATCCATTCTGGAGGTAGGCGGCTCAAGAAAAGCAGCCGATGCTTTTGTTGAATTCAGAGGAAGACCCGCGACGATTGATGCCTTGCTGCGCCATAACGGGATTTTATAAAAACAGGACTTGCGCCCCCCAATCCTCTCGGTAAAACATTTTTTGCCTTGACCTTGGGGTTTTCCGTAAGTCCTGAAAATATATTCGGTATGCTGGCGGGATTTTGCTTACATGCCGGCATTTTATGTTATAATTAAAGTGTACAGAATGGGGGGCGACCTGGCTTCGACGTGG GTTGCAAAACCGGAAGTGCATGCCGAGAAGGAGATCTCTCGTAAATAAGACTCAATTAAATATAAATGCAAACGAT GAAAACTTTGCTGGTGGGGAAGCTATCGCTGCCTAATAAGCACTTTAGTTAAACCATCACTGTGTACTGGCCAATA AACCCAGTATCCCGTTCGACCGAGCCCGCTTATCGGTATCGAATCAACGGTCATAAGAGATAAGCTAGCGTCCTAATCTATCCCGGGTTATGGCGCGAAACTCAGGGAATCGCTGTGTATCATCCTGCCCGTCGGAGGAGCCACAGTTAAATTCAAAAGACAAGGCTATGCATGTAGAGCTAAAGGCAGAGGACTTGCGGACGCGGGTTCGATTCCCGCCGCCTCCACCAATTCATTATCCGATACAGTCCAATACCGGGTCTTTCCCAAATACCTGAATCTTCTACACATCTTGTTTATTCCAAACAAACATGATCAAATCACCTCTTTTTGAGGTATGTATGGACTTAGCAGTTGAAGATACTACAGCATGGTCGGAAGCTATTTTTGGTTCAGTTGCTTTAGGGGATAAACGACTTACTCGTCGGTTAATTCAAATAGGCAAACAATTATCATCGACGCCTGGTGGTTCTCTTTCAGGAAGTTGTGGAGGGCAGGATGCGCTTATAGAAGGTAGTTATCGTTTTTTACGAAACAAACGAGTCACAGCGAATCAAATTGCAGAGGGTGGTT(SEQ ID NO:7)

in some embodiments, the ssrA target nucleic acid comprises 5 'TCGACGTGGGTTGCAAAACCGGAAGTGCATGCCGAGAAGGAGATCTCTCGTAAATAAGACTCAATTAAATATAAATGCAAACGATGAAAACTTTGCTGGTGGGGAAGCTATCGCTGCCTAATAAGCACTTTAGTTAAACCATCACTGTGTACTGGCCAATAAACCCAGTATCCCGTTCGACCGAGCCCGCTTATCGGTATCGAATCAACGGTCATA 3' (SEQ ID NO:10) or a fragment thereof.

Exemplary primers and labeled probe sequences for amplification and detection of ssrA target sequences include:

in some embodiments, the ssrA detection assay does not detect bacteria of non-legionella species. For example, in some embodiments, the ssrA assay comprises PCR primers and probes specific for legionella species without amplifying nucleic acids derived from one or more of: bacillus cereus (Bacillus cereus), Chlamydophila pneumoniae (Chlamydophila pneumoniae), Haemophilus influenzae (Haemophilus influenzae), Klebsiella pneumoniae (Klebsiella pneumoniae), RSV B, Mycoplasma pneumoniae (Mycoplasma pneumoniae), Streptococcus pneumoniae (Streptococcus pneumoniae), Staphylococcus aureus (Staphylococcus aureus), Moraxella catarrhalis (Moraxella catarrhalis), Influenza A virus (Influenza A), Influenza B virus (Influenza B), Pseudomonas sp, and Enterobacter sp.

Qualitative detection and differentiation of legionella species and legionella pneumophila using the disclosed methods can utilize primer pairs, labeled probes, and real-time PCR to amplify and detect ssrA and 16S rRNA genes on a direct amplification dish with an integrated cycler system. Using this method, the target genomic DNA is specifically amplified and simultaneously detected in the same reaction by a fluorescently labeled probe.

In some embodiments, one or more primers and/or probes used herein are degenerate primers or probes, meaning a mixture of oligonucleotide sequences, wherein some positions contain multiple possible bases, resulting in a population of primers with similar sequences covering all possible nucleotide combinations of a given protein sequence. Degenerate nucleotides are designated by R. A non-limiting example of a degenerate primer is SEQ ID NO 1.

In some embodiments, a positive control comprising nucleic acid derived from a legionella pneumophila elite organism is used in the screening assay. For example, suitable control DNA is available from microbiology (Cat. No. 0211P). In some embodiments, the positive control is diluted in a buffer (e.g., TE buffer or water). In some embodiments, the dilution in the buffer is about 1:1,000, 1:10,000, 1:100,000, 1:1,000,000, or 1:10,000,000.

In some embodiments, an amplification or extraction control comprising an exogenous nucleic acid is used in the screening assay. In some embodiments, the amplification or extraction control sample does not comprise nucleic acids derived from a legionella species. For example, suitable control DNA may be obtained from Diasorin (catalog number 151599). In some embodiments, the amplification or extraction control is diluted in a buffer (e.g., TE buffer or water). In some embodiments, the dilution in the buffer is about 1:1,000, 1:10,000, 1:100,000, 1:1,000,000, or 1:10,000,000. In some embodiments, the amplified or extracted control sample is mixed with the biological sample prior to amplification of the target nucleic acid.

In some embodiments, the control nucleic acid sequence comprises 5' TAACCCCGCGATAAAGACAGAAGATTATGCATACGAGATCAAAGGAGCCGGCCTTTTCTCTAGAGATCTCTTATTTTCCTTGAAGTCACCTGTTTATGTTAAAGCAGGTGAGCAGGTATACATTCAGTACGATCTGAACAAAAGCAATGCAGAACTTGCTCTCGACTATGGTTTTGTGGAATCAAACCCTAAACGGAACTCATATACTTTAACAATAGAGATACCAGAATCAGACCCATTCTTTGGGGATAAGTTGGATATTGCTGAGAGTAACAAGATGGGTGAGACCGGATACTTTGACATAGTAGACGGCCAGACTCTTCCCGCTGGTATGCTT CAGTACCTTCGGCTTGTGGCTCTTGGCGGTCCAGATGCTTTCTTATTAGAATCTATCTTCAATAACACCATATGGG GTCATCTTGAATTGCCTGTAAGTCGTACAAACGAGGAACTCATATGCCGTGTTGTCAGAGATGCCTGCAAATCTGCTCTGTCTGGTTTTGATACGACCATTGAAGAGGATGAGAAGCTTCTGGACAAAGGAAAGCTTGAGCCTAGGTTGGAAATGGCTCTCAAG 3' (SEQ ID NO:13), and amplifying the control nucleic acid sequence using a forward primer comprising 5' GCTTCAGTACCTTCGGCTTG 3' (SEQ ID NO:17), a reverse primer comprising 5' TTGCAGGCATCTCTGACAAC 3' (SEQ ID NO:18) and a detectably labeled nucleic acid probe comprising 5' TGGCTCTTGGCGGTCCAGATG 3' (SEQ ID NO: 19).

In some embodiments, the control target nucleic acid comprises 5 'GCTTCAGTACCTTCGGCTTGTGGCTCTTGGCGGTCCAGATGCTTTCTTATTAGAATCTATCTTCAATAACACCATATGGGGTCATCTTGAATTGCCTGTAAGTCGTACAAACGAGGAACTCATATGCCGTGTTGTCAGAGATGCCTGCAA 3' (SEQ ID NO: 20).

In some embodiments, a negative control that does not comprise a nucleic acid derived from a legionella species is used in the screening assay. Non-limiting examples of suitable negative controls include nuclease-free water, sterile nuclease-free water, and TE buffer.

Accordingly, in some aspects, provided herein is a method for detecting the presence of at least one legionella species in a biological sample, the method comprising, consisting of or consisting essentially of: (a) providing a first primer pair suitable for amplifying a ssrA target nucleic acid; providing a second primer pair suitable for amplifying the 16S rRNA target nucleic acid; amplifying the ssrA target nucleic acid and the 16S rRNA target nucleic acid, if present; and detecting one or more amplification products produced in step (c); wherein the presence of ssrA target nucleic acid identifies the presence of at least one Legionella species, and the presence of 16S rRNA target nucleic acid identifies the presence of Legionella pneumophila.

Treatment of legionella infections

Disclosed herein are methods for determining whether a patient exhibiting pneumonic symptoms will benefit from treatment with a therapeutic agent that inhibits a legionella species and/or legionella pneumophila.

Accordingly, provided herein is a method for selecting a subject exhibiting pneumonic symptoms for treatment with a therapeutic agent that inhibits legionella pneumophila, the method comprising, consisting or consisting essentially of: (a) contacting a sample isolated from the subject with a first primer pair suitable for amplifying an ssrA target nucleic acid; (b) contacting the sample with a second primer pair suitable for amplifying the 16S rRNA target nucleic acid; (c) amplifying the ssrA target nucleic acid and the 16S rRNA target nucleic acid, if present; and (d) detecting one or more amplification products produced in step (c); and (e) selecting the subject for treatment with a therapeutic agent that inhibits legionella pneumophila if an amplification product of the 16S rRNA target nucleic acid is detected.

Also provided herein is a method of treating a subject having a legionella pneumophila infection, the method comprising administering, consisting of or consisting essentially of a therapeutic agent that inhibits legionella pneumophila to a subject selected by a method comprising, consisting of, or consisting essentially of: (a) contacting a sample isolated from the subject with a first primer pair suitable for amplifying an ssrA target nucleic acid; (b) contacting the sample with a second primer pair suitable for amplifying the 16S rRNA target nucleic acid; (c) amplifying the ssrA target nucleic acid and the 16S rRNA target nucleic acid, if present; and (d) detecting one or more amplification products produced in step (c); and (e) selecting the subject for treatment with a therapeutic agent that inhibits legionella pneumophila if an amplification product of the 16S rRNA target nucleic acid is detected.

In some embodiments of the methods provided herein, the first primer pair comprises at least one degenerate primer. In some embodiments, the first primer pair comprises a first forward primer comprising 5 'TCGACGTGGGTTGCRAAACG 3' (SEQ ID NO:1) or a complement thereof. The method of any one of the preceding claims, wherein the first primer pair comprises a first reverse primer comprising 5 'TATGACCGTTGATTCGATACC 3' (SEQ ID NO:2) or a complement thereof. In some embodiments, the second primer pair comprises at least one degenerate primer. In some embodiments, the second primer pair comprises a second forward primer comprising 5 'TACCTACCCTTGACATACAGTG 3' (SEQ ID NO:4) or a complement thereof. In some embodiments, the second primer pair comprises a second reverse primer comprising 5 'CTTCCTCCGGTTTGTCAC 3' (SEQ ID NO:5) or a complement thereof.

In some embodiments, the method further comprises contacting the biological sample with one or more oligonucleotide probes capable of specifically hybridizing to the amplification products or their complements. In some embodiments, the oligonucleotide probe is detectably labeled. In some embodiments, the detectable label is a fluorescent label. In some embodiments, the fluorescent label is selected from the group consisting of fluorescein, Cy3, Cy5, Cy5.5, tetrachloro-6-carboxyfluorescein, 2, 7-dimethoxy-4, 5-dichloro-6-carboxyfluorescein, jagewasabi, texas red, TYE 563, ROX, TEX 615, TYE 665, TYE 705, and hexachloro-6-carboxyfluorescein. In some embodiments, the oligonucleotide probe further comprises at least one quencher. In some embodiments, the quencher is selected from the group consisting of TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa Black FQ, Iowa Black RQ, and DABCYL. In some embodiments, the oligonucleotide probe specifically hybridizes to the ssrA amplification product, and wherein the oligonucleotide probe comprises 5 'TAAATATAAATGCAAACGATGAAAACTTTGC 3' (SEQ ID NO:3) or a complement thereof. In some embodiments, the oligonucleotide probe specifically hybridizes to a 16S rRNA amplification product, and wherein the oligonucleotide probe comprises 5 'CCAGCATGTGATGGTGGGGACTCTA 3' (SEQ ID NO:6) or a complement thereof.

In some embodiments, the method further comprises mixing the exogenous control DNA with the biological sample. In some embodiments, the method further comprises contacting the biological sample with a third primer pair suitable for amplifying the exogenous control target nucleic acid, and amplifying the exogenous control target nucleic acid. In some embodiments, the exogenous control target nucleic acid comprises SEQ ID NO. 20. In some embodiments, the third primer pair consists of a third forward primer comprising 5 'GCTTCAGTACCTTCGGCTTG 3' (SEQ ID NO:17) and a third reverse primer comprising 5 'TTGCAGGCATCTCTGACAAC 3' (SEQ ID NO: 18). In some embodiments, the method further comprises contacting the biological sample with a third oligonucleotide probe, wherein the third oligonucleotide probe is detectably labeled and comprises 5 'TGGCTCTTGGCGGTCCAGATG 3' (SEQ ID NO: 19).

In some embodiments of the methods provided herein, the real-time PCR amplification is performed in a direct amplification dish in cooperation with an integrated thermal cycler.

In some embodiments of the methods provided herein, the biological sample is a bronchoalveolar lavage fluid sample, a bronchial wash sample, a sputum sample, a Nasopharyngeal (NP) aspirate or wash sample, a nasal swab, or a bacterial isolate.

Examples of therapeutic agents that inhibit legionella species and/or legionella pneumophila include fluoroquinolones, carbapenems, trimethoprim-sulfamethoxazole (e.g., sulfamethoxazole (Bactrim), sulfamethoxazole (Septra)), and legionella pneumophila-specific antibodies. In some embodiments, the fluoroquinolone is selected from the group consisting of ciprofloxacin, gemifloxacin, levofloxacin, norfloxacin, ofloxacin, lovastatin, gatifloxacin, grepafloxacin, temafloxacin, lomefloxacin, sparfloxacin, enoxacin, and moxifloxacin. In certain embodiments, the carbapenem is selected from the group consisting of imipenem, meropenem, ertapenem, doripenem, panipenem, biapenem, lazupenem (PZ-601), tebipenem, lenapenem, cephalopenem, and cepenem (thienamycin).

Examples of therapeutic agents that inhibit legionella species and/or legionella pneumophila include whole cell (wP) legionella species and/or legionella pneumophila vaccines, acellular legionella species and/or legionella pneumophila vaccines, trimethoprim-sulfamethoxazole (e.g., sulfamethoxazole), telithromycin, and macrolide antibiotics. In some embodiments, the macrolide antibiotic is selected from the group consisting of azithromycin (shisumet), clarithromycin (bixin), erythromycin (E-Mycin, Eryc, Ery-Tab, PCE, erythromycin ethylsuccinate, iloson), and roxithromycin.

Examples of additional therapeutic agents that inhibit legionella species and/or legionella pneumophila include trimethoprim-sulfamethoxazole (e.g., sulfamethoxazole), ciprofloxacin, gemifloxacin, levofloxacin, norfloxacin, ofloxacin, lovastatin, gatifloxacin, grepafloxacin, temafloxacin, lomefloxacin, sparfloxacin, enoxacin, and moxifloxacin.

Pneumonic symptoms include, but are not limited to, chest pain, confusion, altered mental consciousness, coughing, sputum, fatigue, fever, sweating, shivering, chills, hypothermia, nausea, vomiting, diarrhea, shortness of breath, lung inflammation, and fluid in the lungs.

In some embodiments, the subject is a mammal. In some embodiments, the mammal is a bovine, equine, porcine, feline, canine, murine, simian, rat, or human. In some embodiments, the subject is a human. In particular embodiments, the subject is a human patient with one or more pneumonic symptoms.

Interpretation of results

After real-time PCR of the sample-reaction mixture and detection and measurement of the fluorescent signals associated with the amplified ssrA, 16S rRNA and control target sequences, the methods of the present technology also provide an algorithm for determining the presence of one or more related pathogenic legionella species that provides a final result by matching the cycle threshold (Ct) from the amplified target nucleic acid sequences.

In some embodiments, a positive Ct is a Ct less than or equal to about 35, about 36, about 37, about 38, about 39, or about 40 for a reaction comprising 40 cycles. In some embodiments, a negative Ct is a Ct greater than about 35, about 36, about 37, or about 38, about 39, or about 40 for a reaction comprising 40 cycles. In some embodiments, a positive Ct is a Ct less than or equal to about 40, about 41, about 42, about 43, about 44, or about 45 for a reaction comprising 45 cycles. In some embodiments, a negative Ct is a Ct greater than about 40, about 41, about 42, about 43, or about 44, or a Ct of about 45 for a reaction comprising 45 cycles. In some embodiments, a positive Ct is a Ct less than or equal to about 45, about 46, about 47, about 48, about 49, or about 50 for a reaction comprising 50 cycles. In some embodiments, a negative Ct is a Ct greater than about 45, about 46, about 47, about 48, or about 49, or a Ct of about 50, for a reaction comprising 50 cycles.

Legionella species algorithm specifies:

negative control

Positive control

Thus, the presence or absence of pathogenic legionella species in a biological sample can be determined according to:

kits and compositions

The present disclosure also provides kits for detecting a target nucleic acid sequence corresponding to a pathogenic legionella species.

Accordingly, provided herein is a kit for detecting the presence of at least one legionella species in a biological sample, the kit comprising, consisting or consisting essentially of: (a) a first primer pair for amplifying the ssrA target nucleic acid; (b) a second primer pair for amplifying the 16S rRNA target nucleic acid; (c) a first oligonucleotide probe capable of specifically hybridizing to a segment of an ssrA target nucleic acid; and (d) a second oligonucleotide probe capable of specifically hybridizing to a segment of the 16S rRNA target nucleic acid; wherein the first oligonucleotide probe and the second oligonucleotide probe are detectably labeled.

In some embodiments of the kits provided herein, the kit further comprises a third primer pair that amplifies a control target nucleic acid. In some embodiments, the first primer pair is capable of specifically hybridizing to an ssrA target nucleic acid comprising at least 85% -95% identical nucleotides to SEQ ID NO. 7 or its complement. In some embodiments, the second primer pair is capable of specifically hybridizing to a 16S rRNA target nucleic acid comprising at least 85% -95% identical nucleotides to SEQ ID No. 8 or its complement.

In some embodiments of the kits provided herein, the first primer pair comprises at least one degenerate primer. In some embodiments, the first primer pair comprises a first forward primer comprising 5 'TCGACGTGGGTTGCRAAACG 3' (SEQ ID NO:1) or a complement thereof. In some embodiments, the first primer pair comprises a first reverse primer comprising 5 'TATGACCGTTGATTCGATACC 3' (SEQ ID NO:2) or a complement thereof. In some embodiments, the second primer pair comprises at least one degenerate primer. In some embodiments, the second primer pair comprises a second forward primer comprising 5 'TACCTACCCTTGACATACAGTG 3' (SEQ ID NO:4) or a complement thereof. In some embodiments, the second primer pair comprises a second reverse primer comprising 5 'CTTCCTCCGGTTTGTCAC 3' (SEQ ID NO:5) or a complement thereof. In some embodiments, the first nucleic acid probe comprises 5 'TAAATATAAATGCAAACGATGAAAACTTTGC 3' (SEQ ID NO:3) or a complement thereof. In some embodiments, the second nucleic acid probe comprises 5 'CAACCAGCCGCTGCTGACGGTC 3' (SEQ ID NO:9) or a complement thereof.

In some embodiments of the kits provided herein, the detectable label is a fluorescent label. In some embodiments, the fluorescent label is selected from the group consisting of fluorescein, Cy3, Cy5, Cy5.5, tetrachloro-6-carboxyfluorescein, 2, 7-dimethoxy-4, 5-dichloro-6-carboxyfluorescein, jagewasabi, texas red, TYE 563, ROX, TEX 615, TYE 665, TYE 705, and hexachloro-6-carboxyfluorescein. In some embodiments, the at least one oligonucleotide probe further comprises at least one quencher. In some embodiments, the oligonucleotide probe comprises two quenchers. In some embodiments, the quencher is selected from the group consisting of TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa Black FQ, Iowa Black RQ, and DABCYL.

The kits of the present technology comprise at least two oligonucleotides that can be used as primers or primer-probes for amplifying ssrA and 16S rRNA target nucleic acid sequences to determine the presence of pathogenic Legionella species in a biological sample.

In some embodiments, the kit comprises a liquid medium containing at least one target-specific nucleic acid probe at a concentration of 250nM or less. Using such a kit, probes are provided in the required amount to perform a reliable multiplex detection reaction according to the present technology. In some embodiments, the target-specific nucleic acid probe is detectably labeled.

In some embodiments, the kit further comprises buffers required to perform an assay or reaction (e.g., amplification and/or detection of a target nucleic acid sequence corresponding to a pathogenic legionella species), an enzyme having polymerase activity and lacking 5'→ 3' exonuclease activity or both 5'→ 3' and 3'→ 5' exonuclease activity, an enzyme cofactor (e.g., magnesium or manganese), a salt, a chain extension nucleotide (e.g., a deoxynucleoside triphosphate (dNTP), a modified dNTP, a nuclease-resistant dNTP, or a labeled dNTP).

In one embodiment, the kits of the present technology further comprise a positive control nucleic acid sequence and a negative control nucleic acid sequence to ensure the integrity of the assay during the experimental run. The kit may further contain means for comparing the copy number of one or more of ssrA and 16S rRNA in the biological sample to a reference nucleic acid sample (e.g., a sample having a known copy number of one or more of ssrA and 16S rRNA). The kit may also contain instructions for use, software for automated analysis, containers, packaging (as is illustrated for commercial sale), and the like.

The kit may further comprise one or more of the following: washing buffers and/or reagents, hybridization buffers and/or reagents, labeling buffers and/or reagents, and detection means. Buffers and/or reagents are typically optimized for the particular amplification/detection technique for which the kit is intended. Protocols for performing the various steps of the procedure using these buffers and reagents may also be included in the kit.

The kit may additionally comprise instructions, such as printed instructions or electronic instructions, for the assay to define the scan card and/or to use the oligonucleotides in the assay. In some embodiments, the kit comprises an amplification reaction mixture or an amplification master mixture. The reagents included in the kit may be contained in one or more containers (e.g., vials).

Primers, probes and/or primer-probes specific for amplification and detection of internal controls of DNA can be included in the amplification master mix as target primer pairs to monitor potential PCR inhibition. The reagents required for amplification and detection of the target and internal controls can be formulated as an all-in-one amplification master mix, which can be provided in the kit as a single reaction aliquot.

In one aspect, provided herein is a composition comprising, consisting or consisting essentially of a detectably labeled oligonucleotide probe comprising 5 'TAAATATAAATGCAAACGATGAAAACTTTGC 3' (SEQ ID NO: 3). In some embodiments, the detectable label is a fluorescent label. In some embodiments, the fluorescent label is selected from the group consisting of fluorescein, Cy3, Cy5, Cy5.5, tetrachloro-6-carboxyfluorescein, 2, 7-dimethoxy-4, 5-dichloro-6-carboxyfluorescein, jagewasabi, texas red, TYE 563, ROX, TEX 615, TYE 665, TYE 705, and hexachloro-6-carboxyfluorescein. In some embodiments, the oligonucleotide probe further comprises at least one quencher. In some embodiments, the quencher is selected from the group consisting of TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa Black FQ, Iowa Black RQ, and DABCYL.

In another aspect, provided herein are compositions comprising a detectably labeled oligonucleotide probe comprising 5 'TAAATATAAATGCAAACGATGAAAACTTTGC 3' (SEQ ID NO: 3). In some embodiments, the detectable label is a fluorescent label. In some embodiments, the fluorescent label is selected from the group consisting of fluorescein, Cy3, Cy5, Cy5.5, tetrachloro-6-carboxyfluorescein, 2, 7-dimethoxy-4, 5-dichloro-6-carboxyfluorescein, jagewasabi, texas red, TYE 563, ROX, TEX 615, TYE 665, TYE 705, and hexachloro-6-carboxyfluorescein. In some embodiments, the oligonucleotide probe further comprises at least one quencher. In some embodiments, the quencher is selected from the group consisting of TAMRA, Black Hole quencher, Deep Dark quencher, ZEN, Iowa B lack FQ, Iowa Black RQ, and DABCYL.

Examples

Example 1: detection of pathogenic legionella species using real-time PCR

A sample of bronchoalveolar lavage fluid is collected from the patient. Prior to extraction, the internal positive control DNA target was added to the external lysis buffer. DNA was extracted using a "DNA/Virus NA SV 2.0" kit using a MagNA Pure 96 instrument. The elution volume was set to 50.

A legionella PCR master mix comprising the following reagents was generated and stored at-10 ℃ to-90 ℃:

real-time PCR was performed using the following conditions: i) the sample was preheated at 50 ℃ for 120 seconds for 1 cycle; ii) polymerase was activated at 95 ℃ for 10 min for 1 cycle; and iii) denaturation at 95 ℃ for 15 seconds and annealing at 60 ℃ for 35 seconds, 40 cycles.

The target genomic DNA is specifically amplified and simultaneously detected in the same reaction by a fluorescently labeled probe. Ct was detected and the results were analyzed according to the following algorithm:

example 2: cross-reactivity of legionella multiplex assays.

For cross-reactivity assays, control nasal swab specimens will incorporate one of the test organisms listed below (each organism n-5).

Bacillus cereus	Chlamydophila pneumoniae
		Haemophilus influenzae	Klebsiella pneumoniae
RSV B	Mycoplasma pneumoniae
		Streptococcus pneumoniae	Staphylococcus aureus
Moraxella catarrhalis	Influenza A virus
		Influenza B virus	Pseudomonas species
Enterobacter species

A legionella multiplex assay will be performed on each sample. In each case, a Ct value of ≦ 40 is interpreted as a positive result for Legionella cross-reactivity, and a Ct value of ≦ 40 is interpreted as a positive result for Legionella cross-reactivity.

It is expected that no cross-reactivity will be observed with any of the above microbial species.

Equivalents of

The present technology is not limited to the specific embodiments described herein, which are intended as single illustrations of individual aspects of the present technology. As will be apparent to those skilled in the art, many modifications and variations can be made to the present technology without departing from the spirit and scope of the present technology. It will be clear to those skilled in the art from the foregoing description that functionally equivalent methods and apparatuses are within the technical scope of the present invention, in addition to those enumerated herein. Such modifications and variations are intended to fall within the scope of the present technology. It is to be understood that the present technology is not limited to particular methods, reagents, compounds, compositions or biological systems, which can, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting.

The terms "comprising," "including," "containing," and the like are to be construed in a broad and non-limiting sense. Additionally, the terms and expressions employed herein have been used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the disclosure claimed.

Further, where features or aspects of the disclosure are described in terms of Markush groups (Markush groups), those skilled in the art will recognize that the disclosure is thus also described in terms of any individual member or subgroup of members of the Markush group.

As will be understood by those skilled in the art, for any and all purposes, particularly in terms of providing a written description, all ranges disclosed herein also encompass any and all possible subranges and combinations of subranges thereof. Any listed range can be readily identified as sufficiently describing the same range and enabling the same range to be broken down into at least equal halves, thirds, quarters, fifths, tenths, etc. As a non-limiting example, each range discussed herein can be readily broken down into a lower third, a middle third, an upper third, and the like. As will also be understood by those skilled in the art, all words such as "up to," "at least," "greater than," "less than," and the like include the stated number and refer to ranges that may be subsequently resolved into subranges as discussed above. Finally, as will be understood by those of skill in the art, a range includes each individual member. Thus, for example, a group having 1-3 cells refers to a group having 1, 2, or 3 cells. Similarly, a group having 1-5 cells refers to a group having 1, 2, 3, 4, or 5 cells, and so forth.

All patents, patent applications, provisional applications, and publications mentioned or cited herein are incorporated by reference in their entirety, including all figures and tables, to the extent they are not inconsistent with the explicit teachings of this specification.