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Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study


In this retrospective observational study, Francis Drobniewski and colleagues assess the power and value of whole genome sequencing to resolve transmission network of a large tuberculosis outbreak.


Vyšlo v časopise: Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study. PLoS Med 13(10): e32767. doi:10.1371/journal.pmed.1002137
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pmed.1002137

Souhrn

In this retrospective observational study, Francis Drobniewski and colleagues assess the power and value of whole genome sequencing to resolve transmission network of a large tuberculosis outbreak.


Zdroje

1. Ruddy MC, Davies AP, Yates MD, Yates S, Balasegaram S, Drabu Y, et al. Outbreak of isoniazid resistant tuberculosis in north London. Thorax. 2004;59: 279–285. doi: 10.1136/thx.2003.010405 15047945

2. Health Protection Agency. Isoniazid Resistant TB outbreak in London 2000 to 2008: Progress report for TB professionals across London. 2008.

3. Public Health England. Tuberculosis in London: Annual review (2013 data). 2014.

4. Maguire H, Brailsford S, Carless J, Yates M, Altass L, Yates S, et al. Large outbreak of isoniazid-monoresistant tuberculosis in London, 1995 to 2006: case-control study and recommendations. Euro Surveill. 2011;16.

5. Anderson C, Story A, Brown T, Drobniewski F, Abubakar I. Tuberculosis in UK prisoners: a challenge for control. J Epidemiol Community Health. 2010; doi: 10.1136/jech.2009.094375

6. Neely F, Maguire H, Brun FL, Davies A, Gelb D, Yates S. High rate of transmission among contacts in large London outbreak of isoniazid mono-resistant tuberculosis. J Public Health. 2010;32: 44–51. doi: 10.1093/pubmed/fdp056

7. Grad YH, Lipsitch M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol. 2014;15: 538. doi: 10.1186/s13059-014-0538-4 25418119

8. van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B, et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol. 1993;31: 406–409. 8381814

9. Brown TJ, Nikolayevskyy VN, Drobniewski FA. Typing Mycobacterium tuberculosis using variable number tandem repeat analysis. Methods Mol Biol. 2009;465: 371–394. doi: 10.1007/978-1-59745-207-6_25 20560063

10. Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 1997;35: 907–914. 9157152

11. Collins CH, Grange JM, Yates MD. Drug susceptibility testing. Tuberculosis bacteriology: Organization and practice. 2nd ed. Oxford, United Kingdom: Butterworth-Heinemann; 1997. pp. 98–109.

12. Casali N, Nikolayevskyy V, Balabanova Y, Ignatyeva O, Kontsevaya I, Harris SR, et al. Microevolution of extensively drug-resistant tuberculosis in Russia. Genome Res. 2012;22: 735–745. doi: 10.1101/gr.128678.111 22294518

13. SMALT [Internet]. Available: http://www.sanger.ac.uk/resources/software/smalt/

14. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25: 2078–2079. doi: 10.1093/bioinformatics/btp352 19505943

15. Stamatakis A, Ludwig T, Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics. 2005;21: 456–463. doi: 10.1093/bioinformatics/bti191 15608047

16. FigTree [Internet]. http://tree.bio.ed.ac.uk/software/figtree

17. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25: 2865–2871. doi: 10.1093/bioinformatics/btp394 19561018

18. Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics. 2012;28: 464–469. doi: 10.1093/bioinformatics/btr703 22199388

19. Coll F, Mallard K, Preston MD, Bentley S, Parkhill J, McNerney R, et al. SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics. 2012;28: 2991–2993. doi: 10.1093/bioinformatics/bts544 23014632

20. Heep M, Rieger U, Beck D, Lehn N. Mutations in the beginning of the rpoB gene can induce resistance to rifamycins in both Helicobacter pylori and Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2000;44: 1075–1077. doi: 10.1128/AAC.44.4.1075–1077.2000 10722516

21. Jenkins C, Claxton Alleyna P., Shorten Robert J., McHugh Timothy D., Gillespie Stephen H. Rifampicin resistance in tuberculosis outbreak, London, England. Emerg Infect Dis. 2005;11: 931–934. doi: 10.3201/eid1106.041262 15963290

22. Heep M, Brandstätter B, Rieger U, Lehn N, Richter E, Rüsch-Gerdes S, et al. Frequency of rpoB mutations inside and outside the cluster I region in rifampin-resistant clinical Mycobacterium tuberculosis isolates. J Clin Microbiol. 2001;39: 107–110. doi: 10.1128/JCM.39.1.107–110.2001 11136757

23. Casali N, Nikolayevskyy V, Balabanova Y, Harris SR, Ignatyeva O, Kontsevaya I, et al. Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat Genet. 2014;46: 279–286. doi: 10.1038/ng.2878 24464101

24. Maguire H, Ruddy M, Bothamley G, Patel B, Lipman M, Drobniewski F, et al. Multidrug resistance emerging in North London outbreak. Thorax. 2006;61: 547–548. doi: 10.1136/thx.2005.052423

25. Menzies D, Benedetti A, Paydar A, Royce S, Madhukar P, Burman W, et al. Standardized treatment of active tuberculosis in patients with previous treatment and/or with mono-resistance to isoniazid: a systematic review and meta-analysis. PLoS Med. 6: e1000150. 20101802

26. Shorten RJ, McGregor AC, Platt S, Jenkins C, Lipman MCI, Gillespie SH, et al. When is an outbreak not an outbreak? Fit, divergent strains of Mycobacterium tuberculosis display independent evolution of drug resistance in a large London outbreak. J Antimicrob Chemother. 2013;68: 543–549. doi: 10.1093/jac/dks430 23129727

27. Parida BK, Douglas T, Nino C, Dhandayuthapani S. Interactions of anti-sigma factor antagonists of Mycobacterium tuberculosis in the yeast two-hybrid system. Tuberculosis. 2005;85: 347–355. doi: 10.1016/j.tube.2005.08.001 16263329

28. Walker TM, Ip CL, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis. 2013;13: 137–146. doi: 10.1016/S1473-3099(12)70277-3 23158499

29. Walker TM, Lalor MK, Broda A, Ortega LS, Morgan M, Parker L, et al. Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study. Lancet Respir Med. 2014;2: 285–292. doi: 10.1016/S2213-2600(14)70027-X 24717625

30. Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, et al. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med. 2013;10: e1001387. doi: 10.1371/journal.pmed.1001387 23424287

31. Mehaffy C, Guthrie JL, Alexander DC, Stuart R, Rea E, Jamieson FB. Marked microevolution of a unique Mycobacterium tuberculosis strain in 17 years of ongoing transmission in a high risk population. PLoS ONE. 2014;9: e112928. doi: 10.1371/journal.pone.0112928 25405861

32. Stucki D, Ballif M, Bodmer T, Coscolla M, Maurer A-M, Droz S, et al. Tracking a tuberculosis outbreak over 21 years: strain-specific single nucleotide polymorphism-typing combined with targeted whole genome sequencing. J Infect Dis. 2014;211: 1306–1316. doi: 10.1093/infdis/jiu601 25362193

33. Akhtar P, Srivastava S, Srivastava A, Srivastava M, Srivastava BS, Srivastava R. Rv3303c of Mycobacterium tuberculosis protects tubercle bacilli against oxidative stress in vivo and contributes to virulence in mice. Microbes Infect. 2006;8: 2855–2862. doi: 10.1016/j.micinf.2006.09.004 17097323

34. Akhtar P, Singh S, Bifani P, Kaur S, Srivastava BS, Srivastava R. Variable-number tandem repeat 3690 polymorphism in Indian clinical isolates of Mycobacterium tuberculosis and its influence on transcription. J Med Microbiol. 2009;58: 798–805. doi: 10.1099/jmm.0.002550–0 19429757

35. Geiman DE, Kaushal D, Ko C, Tyagi S, Manabe YC, Schroeder BG, et al. Attenuation of late-stage disease in mice infected by the Mycobacterium tuberculosis mutant lacking the SigF alternate sigma factor and identification of SigF-dependent genes by microarray analysis. Infect Immun. 2004;72: 1733–1745. doi: 10.1128/IAI.72.3.1733–1745.2004 14977982

36. Bryant JM, Schürch AC, van Deutekom H, Harris SR, de Beer JL, de Jager V, et al. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. BMC Infect Dis. 2013;13: 110. doi: 10.1186/1471-2334-13-110 23446317

37. Bryant JM, Harris SR, Parkhill J, Dawson R, Diacon AH, van Helden P, et al. Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study. Lancet Respir Med. 2013;1: 786–792. doi: 10.1016/S2213-2600(13)70231-5 24461758

38. McEvoy CRE, Cloete R, Müller B, Schürch AC, van Helden PD, Gagneux S, et al. Comparative Analysis of Mycobacterium tuberculosis PE and PPE genes reveals high sequence variation and an apparent absence of selective constraints. PLoS ONE. 2012;7: e30593. doi: 10.1371/journal.pone.0030593 22496726

39. Copin R, Coscollá M, Seiffert SN, Bothamley G, Sutherland J, Mbayo G, et al. Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition. mBio. 2014;5: e00960–13. doi: 10.1128/mBio.00960-13 24425732

40. Velji P, Nikolayevskyy V, Brown T, Drobniewski F. Discriminatory ability of hypervariable variable number tandem repeat loci in population-based analysis of Mycobacterium tuberculosis strains, London, UK. Emerg Infect Dis. 2009;15: 1609–1616. doi: 10.3201/eid1510.090463 19861054

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