Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Outbreak: A Longitudinal Molecular Epidemiological Study

English version České info

Background:
Understanding Mycobacterium tuberculosis (Mtb) transmission is essential to guide efficient tuberculosis control strategies. Traditional strain typing lacks sufficient discriminatory power to resolve large outbreaks. Here, we tested the potential of using next generation genome sequencing for identification of outbreak-related transmission chains.

Methods and Findings:
During long-term (1997 to 2010) prospective population-based molecular epidemiological surveillance comprising a total of 2,301 patients, we identified a large outbreak caused by an Mtb strain of the Haarlem lineage. The main performance outcome measure of whole genome sequencing (WGS) analyses was the degree of correlation of the WGS analyses with contact tracing data and the spatio-temporal distribution of the outbreak cases. WGS analyses of the 86 isolates revealed 85 single nucleotide polymorphisms (SNPs), subdividing the outbreak into seven genome clusters (two to 24 isolates each), plus 36 unique SNP profiles. WGS results showed that the first outbreak isolates detected in 1997 were falsely clustered by classical genotyping. In 1998, one clone (termed “Hamburg clone”) started expanding, apparently independently from differences in the social environment of early cases. Genome-based clustering patterns were in better accordance with contact tracing data and the geographical distribution of the cases than clustering patterns based on classical genotyping. A maximum of three SNPs were identified in eight confirmed human-to-human transmission chains, involving 31 patients. We estimated the Mtb genome evolutionary rate at 0.4 mutations per genome per year. This rate suggests that Mtb grows in its natural host with a doubling time of approximately 22 h (400 generations per year). Based on the genome variation discovered, emergence of the Hamburg clone was dated back to a period between 1993 and 1997, hence shortly before the discovery of the outbreak through epidemiological surveillance.

Conclusions:
Our findings suggest that WGS is superior to conventional genotyping for Mtb pathogen tracing and investigating micro-epidemics. WGS provides a measure of Mtb genome evolution over time in its natural host context.

Please see later in the article for the Editors' Summary

Vyšlo v časopise: Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Outbreak: A Longitudinal Molecular Epidemiological Study. PLoS Med 10(2): e32767. doi:10.1371/journal.pmed.1001387
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pmed.1001387

Souhrn

Zdroje

1. DyeC, WilliamsBG (2010) The population dynamics and control of tuberculosis. Science 328: 856–861 doi:10.1126/science.1185449.

2. World Health Organization (2012) Global tuberculosis report 2012. Available: http://www.who.int/tb/publications/global_report/en/index.html. Accessed 8 January 2013.

3. ReadAF (1994) The evolution of virulence. Trends Microbiol 2: 73–76.

4. van EmbdenJD, CaveMD, CrawfordJT, DaleJW, EisenachKD, et al. (1993) Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 31: 406–409.

5. KamerbeekJ, SchoulsL, KolkA, van AgterveldM, van SoolingenD, et al. (1997) Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 35: 907–914.

6. SupplyP, AllixC, LesjeanS, Cardoso-OelemannM, Rüsch-GerdesS, et al. (2006) Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 44: 4498–4510 doi:10.1128/JCM.01392-06.

7. Cardoso OelemannM, GomesHM, WilleryE, PossueloL, Batista LimaKV, et al. (2011) The forest behind the tree: phylogenetic exploration of a dominant Mycobacterium tuberculosis strain lineage from a high tuberculosis burden country. PLoS ONE 6: e18256 doi:10.1371/journal.pone.0018256.

8. DielR, SchneiderS, Meywald-WalterK, RufC-M, Rüsch-GerdesS, et al. (2002) Epidemiology of tuberculosis in Hamburg, Germany: long-term population-based analysis applying classical and molecular epidemiological techniques. J Clin Microbiol 40: 532–539.

9. SchürchAC, van SoolingenD (2012) DNA fingerprinting of Mycobacterium tuberculosis: from phage typing to whole-genome sequencing. Infect Genet Evol 12: 602–609 doi:10.1016/j.meegid.2011.08.032.

10. DielR, Rüsch-GerdesS, NiemannS (2004) Molecular epidemiology of tuberculosis among immigrants in Hamburg, Germany. J Clin Microbiol 42: 2952–2960 doi:10.1128/JCM.42.7.2952-2960.2004.

11. RoetzerA, SchubackS, DielR, GasauF, UbbenT, et al. (2011) Evaluation of Mycobacterium tuberculosis typing methods in a 4-year study in Schleswig-Holstein, Northern Germany. J Clin Microbiol 49: 4173–4178 doi:10.1128/JCM.05293-11.

12. NiemannS, KöserCU, GagneuxS, PlinkeC, HomolkaS, et al. (2009) Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints. PLoS ONE 4: e7407 doi:10.1371/journal.pone.0007407.

13. GardyJL, JohnstonJC, Ho SuiSJ, CookVJ, ShahL, et al. (2011) Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 364: 730–739 doi:10.1056/NEJMoa1003176.

14. BakerS, HanageWP, HoltKE (2010) Navigating the future of bacterial molecular epidemiology. Curr Opin Microbiol 13: 640–645 doi:10.1016/j.mib.2010.08.002.

15. BravoLTC, ProcopGW (2009) Recent advances in diagnostic microbiology. Semin Hematol 46: 248–258 doi:10.1053/j.seminhematol.2009.03.009.

16. SchürchAC, KremerK, HendriksACA, FreyeeB, McEvoyCRE, et al. (2011) SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes. PLoS ONE 6: e28365 doi:10.1371/journal.pone.0028365.

17. MeyerF, GoesmannA, McHardyAC, BartelsD, BekelT, et al. (2003) GenDB—an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31: 2187–2195.

18. ColeST, BroschR, ParkhillJ, GarnierT, ChurcherC, et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537–544 doi:10.1038/31159.

19. DarlingACE, MauB, BlattnerFR, PernaNT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394–1403 doi:10.1101/gr.2289704.

20. BlomJ, JakobiT, DoppmeierD, JaenickeS, KalinowskiJ, et al. (2011) Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics 27: 1351–1358 doi:10.1093/bioinformatics/btr151.

21. DrummondAJ, RambautA (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214 doi:10.1186/1471-2148-7-214.

22. NübelU, DordelJ, KurtK, StrommengerB, WesthH, et al. (2010) A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus. PLoS Pathog 6: e1000855 doi:10.1371/journal.ppat.1000855.

23. Birren B, Lander E, Galagan J, Devon K, Nusbaum C, et al.. (2007) Mycobacterium tuberculosis F11 chromosome, complete genome. Available: http://www.ncbi.nlm.nih.gov/nucleotide/148821191/. Accessed 8 January 2013.

24. FleischmannRD, AllandD, EisenJA, CarpenterL, WhiteO, et al. (2002) Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol 184: 5479–5490.

25. TekaiaF, GordonSV, GarnierT, BroschR, BarrellBG, et al. (1999) Analysis of the proteome of Mycobacterium tuberculosis in silico. Tuber Lung Dis 79: 329–342 doi:10.1054/tuld.1999.0220.

26. DielR, Meywald-WalterK, GottschalkR, Rüsch-GerdesS, NiemannS (2004) Ongoing outbreak of tuberculosis in a low-incidence community: a molecular-epidemiological evaluation. Int J Tuberc Lung Dis 8: 855–861.

27. ComasI, ChakravarttiJ, SmallPM, GalaganJ, NiemannS, et al. (2010) Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet 42: 498–503 doi:10.1038/ng.590.

28. CroucherNJ, HarrisSR, FraserC, QuailMA, BurtonJ, et al. (2011) Rapid pneumococcal evolution in response to clinical interventions. Science 331: 430–434 doi:10.1126/science.1198545.

29. HarrisSR, FeilEJ, HoldenMTG, QuailMA, NickersonEK, et al. (2010) Evolution of MRSA during hospital transmission and intercontinental spread. Science 327: 469–474 doi:10.1126/science.1182395.

30. FordCB, LinPL, ChaseMR, ShahRR, IartchoukO, et al. (2011) Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat Genet 43: 482–486 doi:10.1038/ng.811.

31. Gutierrez-VazquezJ (1956) Studies on the rate of growth of mycobacteria. I. Generation time of Mycobacterium tuberculosis on several solid and liquid media and effects exerted by glycerol and malachite green. Am Rev Tuberc 74: 50–58.

32. HoSYW, PhillipsMJ, CooperA, DrummondAJ (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol 22: 1561–1568 doi:10.1093/molbev/msi145.

33. FennellyKP, Jones-LópezEC, AyakakaI, KimS, MenyhaH, et al. (2012) Variability of infectious aerosols produced during coughing by patients with pulmonary tuberculosis. Am J Respir Crit Care Med 186: 450–457 doi:10.1164/rccm.201203-0444OC.

34. CohenT, MurrayM (2004) Modeling epidemics of multidrug-resistant M. tuberculosis of heterogeneous fitness. Nat Med 10: 1117–1121 doi:10.1038/nm1110.

35. HomolkaS, NiemannS, RussellDG, RohdeKH (2010) Functional genetic diversity among Mycobacterium tuberculosis complex clinical isolates: delineation of conserved core and lineage-specific transcriptomes during intracellular survival. PLoS Pathog 6: e1000988 doi:10.1371/journal.ppat.1000988.

36. MathemaB, KurepinaN, YangG, ShashkinaE, MancaC, et al. (2012) Epidemiologic consequences of microvariation in Mycobacterium tuberculosis. J Infect Dis 205: 964–974 doi:10.1093/infdis/jir876.

37. KöserCU, EllingtonMJ, CartwrightEJP, GillespieSH, BrownNM, et al. (2012) Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 8: e1002824 doi:10.1371/journal.ppat.1002824.

38. TsolakiAG, HirshAE, DeRiemerK, EncisoJA, WongMZ, et al. (2004) Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains. Proc Natl Acad Sci U S A 101: 4865–4870 doi:10.1073/pnas.0305634101.