Interpreting whole genome sequencing for investigating tuberculosis transmission: A systematic review

BMC Medicine

Volumn 14, Issue 1, 2016, Pages

  Hatherell, Hollie Ann ^a   Colijn, Caroline ^b   Stagg, Helen R ^a   Jackson, Charlotte ^a   Winter, Joanne R ^a   Abubakar, Ibrahim ^a,c  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c MEDICAL RESEARCH COUNCIL   (United Kingdom)

Author keywords

Systematic review; Transmission; Tuberculosis; Whole genome sequencing

Indexed keywords

ARTICLE; BACTERIAL STRAIN; BACTERIAL TRANSMISSION; DATA ANALYSIS; GENETIC VARIABILITY; HUMAN; INFORMATION RETRIEVAL; MIXED INFECTION; NONHUMAN; POSTPRIMARY TUBERCULOSIS; RELAPSE; SELECTIVE SWEEP; SYSTEMATIC REVIEW; TUBERCULOSIS; WHOLE GENOME SEQUENCING; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIATION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; MYCOBACTERIUM TUBERCULOSIS; PROCEDURES; RECURRENT DISEASE; TRANSMISSION;

BACTERIAL TYPING TECHNIQUES; GENETIC VARIATION; GENOME, BACTERIAL; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MYCOBACTERIUM TUBERCULOSIS; RECURRENCE; SEQUENCE ANALYSIS, DNA; TUBERCULOSIS;

EID: 85007418308     PISSN: None     EISSN: 17417015     Source Type: Journal    
DOI: 10.1186/s12916-016-0566-x     Document Type: Article

References (75)

1. Kao RR, Haydon DT, Lycett SJ, Murcia PR. Supersize me: how whole-genome sequencing and big data are transforming epidemiology. Trends Microbiol. 2014;22(5):282-91.
2. Grad YH, Lipsitch M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol. 2014;15(11):538.
3. Sreevatsan S, Pan X, Stockbauer KE, Connell ND, Kreiswirth BN, Whittam TS, et al. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci U S A. 1997;94(18):9869-74.
4. Ford C, Yusim K, Ioerger T, Feng S, Chase M, Greene M, et al. Mycobacterium tuberculosis-heterogeneity revealed through whole genome sequencing. Tuberculosis. 2012;92(3):194-201.
5. Walker TM, Monk P, Smith EG, Peto TE. Contact investigations for outbreaks of Mycobacterium tuberculosis: advances through whole genome sequencing. Clin Microbiol Infect. 2013;19(9):796-802.
6. Robinson ER, Walker TM, Pallen MJ. Genomics and outbreak investigation: from sequence to consequence. Genome Med. 2013;5(4):36.
7. Wilson DJ. Insights from genomics into bacterial pathogen populations. PLoS Pathog. 2012;8(9):e1002874.
8. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson N. Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. PLoS Comput Biol. 2014;10(1):e1003457.
9. K�ser CU, Holden MTG, Ellington MJ, Cartwright EJP, Brown NM, Ogilvy-Stuart AL, et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med. 2012;366(24):2267-75.
10. Knetsch CW, Connor TR, Mutreja A, van Dorp SM, Sanders IM, Browne HP, et al. Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011 Euro Surveill. 2014;19(45):20954.
11. Field N, Cohen T, Struelens MJ, Palm D, Cookson B, Glynn JR, et al. Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID): an extension of the STROBE statement. Lancet Infect Dis. 2014;14(4):341-52.
12. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, et al. Wholegenome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med. 2011;364(8):730-9.
13. 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(11):e112928.
14. Roetzer A, Diel R, Kohl TA, Ruckert C, Nubel 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(2):e1001387.
15. Bryant JM, Schurch 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.
16. Luo T, Yang C, Peng Y, Lu L, Sun G, Wu J, et al. Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis. Tuberculosis. 2014;94(4):434-40.
17. Lee RS, Radomski N, Proulx JF, Manry J, McIntosh F, Desjardins F, et al. Re-emergence and amplification of tuberculosis in the Canadian arctic. J Infect Dis. 2015;211(12):1905-14.
18. Guerra-Assun��o JA, Crampin AC, Houben R, Mzembe T, Mallard K, Coll F, et al. Large-scale whole genome sequencing of M-tuberculosis provides insights into transmission in a high prevalence area. eLife. 2015;4. doi:10.7554/eLife.05166.
19. Witney AA, Gould KA, Arnold A, Coleman D, Delgado R, Dhillon J, et al. Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases. J Clin Microbiol. 2015;53(5):1473-83.
20. Martin Williams O, Abeel T, Casali N, Cohen K, Pym AS, Mungall SB, et al. Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing. Emerg Infect Dis. 2015;21(6):1082-4.
21. Walker TM, Ip CL, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, et al. Wholegenome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis. 2013;13(2):137-46.
22. 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(4):285-92.
23. Clark TG, Mallard K, Coll F, Preston M, Assefa S, Harris D, et al. Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. PLoS One. 2013;8(12):e83012.
24. Sch�rch AC, Kremer K, Daviena O, Kiers A, Boeree MJ, Siezen RJ, et al. Highresolution typing by integration of genome sequencing data in a large tuberculosis cluster. J Clin Microbiol. 2010;48(9):3403-6.
25. Didelot X, Gardy J, Colijn C. Bayesian inference of infectious disease transmission from whole-genome sequence data. Mol Biol Evol. 2014;31(7):1869-79.
26. Kato-Maeda M, Ho C, Passarelli B, Banaei N, Grinsdale J, Flores L, et al. Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak. PLoS One. 2013;8(3):e58235.
27. Smit PW, Vasankari T, Aaltonen H, Haanpera M, Casali N, Marttila H, et al. Enhanced tuberculosis outbreak investigation using whole genome sequencing and IGRA. Eur Respir J. 2015;45(1):276-9.
28. Stucki D, Ballif M, Bodmer T, Coscolla M, Maurer AM, 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. 2015;211(8):1306-16.
29. Guerra-Assun��o JA, Houben RM, Crampin AC, Mzembe T, Mallard K, Coll F, et al. Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, populationbased cohort with a high HIV infection prevalence and active follow-up. J Infect Dis. 2015;211(7):1154-63.
30. 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(10):786-92.
31. P�rez-Lago L, Comas I, Navarro Y, Gonzalez-Candelas F, Herranz M, Bouza E, et al. Whole genome sequencing analysis of intrapatient microevolution in Mycobacterium tuberculosis: potential impact on the inference of tuberculosis transmission. J Infect Dis. 2014;209(1):98-108.
32. 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(3):279-86.
33. Ioerger TR, Feng Y, Chen X, Dobos KM, Victor TC, Streicher EM, et al. The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa. BMC Genomics. 2010;11(1):670.
34. Lanzas F, Karakousis PC, Sacchettini JC, Ioerger TR. Multidrug-resistant tuberculosis in panama is driven by clonal expansion of a multidrugresistant mycobacterium tuberculosis strain related to the KZN extensively drug-resistant m. tuberculosis strain from South Africa. J Clin Microbiol. 2013;51(10):3277-85.
35. Regmi SM, Chaiprasert A, Kulawonganunchai S, Tongsima S, Coker OO, Prammananan T, et al. Whole genome sequence analysis of multidrugresistant Mycobacterium tuberculosis Beijing isolates from an outbreak in Thailand. Mol Genet Genomics. 2015;290(5):1933-41.
36. Ocheretina O, Shen L, Escuyer VE, Mabou MM, Royal-Mardi G, Collins SE, et al. Whole genome sequencing investigation of a tuberculosis outbreak in Port-au-Prince, Haiti caused by a strain with a "low-level" rpoB mutation L511P-insights into a mechanism of resistance escalation. PLoS One. 2015;10(6):e0129207.
37. Niemann S, Koser CU, Gagneux S, Plinke C, Homolka S, Bignell H, et al. Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints. PLoS One. 2009;4(10):e7407.
38. Ypma RJF, van Ballegooijen WM, Wallinga J. Relating phylogenetic trees to transmission trees of infectious disease outbreaks. Genetics. 2013;195(3):1055-62.
39. Lambert ML, Hasker E, Van Deun A, Roberfroid D, Boelaert M, Van der Stuyft P. Recurrence in tuberculosis: relapse or reinfection? Lancet Infect Dis. 2003;3(5):282-7.
40. Gillespie SH, Crook AM, McHugh TD, Mendel CM, Meredith SK, Murray SR, et al. Four-month moxifloxacin-based regimens for drug-sensitive tuberculosis. N Engl J Med. 2014;371(17):1577-87.
41. Wlodarska M, Johnston JC, Gardy JL, Tang P. A microbiological revolution meets an ancient disease: improving the management of tuberculosis with genomics. Clin Microbiol Rev. 2015;28(2):523-39.
42. Kato-Maeda M, Metcalfe JZ, Flores L. Genotyping of Mycobacterium tuberculosis: application in epidemiologic studies. Future Microbiol. 2011;6(2):203-16.
43. Drobniewski F, Nikolayevskyy V, Maxeiner H, Balabanova Y, Casali N, Kontsevaya I, et al. Rapid diagnostics of tuberculosis and drug resistance in the industrialized world: clinical and public health benefits and barriers to implementation. BMC Med. 2013;11(1):190.
44. Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, et al. A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform. 2014;15(2):256-78.
45. Pirooznia M, Kramer M, Parla J, Goes FS, Potash JB, McCombie WR, et al. Validation and assessment of variant calling pipelines for next-generation sequencing. Hum Genomics. 2014;8(1):14-4.
46. Zhang J, Chiodini R, Badr A, Zhang G. The impact of next-generation sequencing on genomics. J Genet Genomics. 2011;38(3):95-109.
47. Quail M, Smith M, Coupland P, Otto T, Harris S, Connor T, et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13:341.
48. Fitzpatrick LK, Hardacker JA, Heirendt W, Agerton T, Streicher A, Melnyk H, et al. A preventable outbreak of tuberculosis investigated through an intricate social network. Clin Infect Dis. 2001;33(11):1801-6.
49. Worby CJ, Chang HH, Hanage WP, Lipsitch M. The distribution of pairwise genetic distances: a tool for investigating disease transmission. Genetics. 2014;198(4):1395-404.
50. Barton NH. Genetic hitchhiking. Philos Trans R Soc Lond B Biol Sci. 2000;355(1403):1553-62.
51. Al-Hajoj SA, Akkerman O, Parwati I, al-Gamdi S, Rahim Z, van Soolingen D, et al. Microevolution of Mycobacterium tuberculosis in a tuberculosis patient. J Clin Microbiol. 2010;48(10):3813-6.
52. Eldholm V, Norheim G, von der Lippe B, Kinander W, Dahle UR, Caugant DA, et al. Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient. Genome Biol. 2014;15(11):490.
53. Sun G, Luo T, Yang C, Dong X, Li J, Zhu Y, et al. Dynamic population changes in Mycobacterium tuberculosis during acquisition and fixation of drug resistance in patients. J Infect Dis. 2012;206(11):1724-33.
54. Merker M, Kohl TA, Roetzer A, Truebe L, Richter E, R�sch-Gerdes S, et al. Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients. PLoS One. 2013;8(12):e82551.
55. Saunders NJ, Trivedi U, Thomson M, Doig C, Laurenson IF, Blaxter ML. Deep resequencing of serial sputum isolates of Mycobacterium tuberculosis during therapeutic failure due to poor compliance reveals stepwise mutation of key resistance genes on an otherwise stable genetic background. J Infect. 2011;62(3):212-7.
56. Rad ME, Bifani P, Martin C, Kremer K, Samper S, Rauzier J, et al. Mutations in putative mutator genes of Mycobacterium tuberculosis strains of the W-Beijing family. Emerg Infect Dis. 2003;9(7):838-45.
57. Colangeli R, Arcus VL, Cursons RT, Ruthe A, Karalus N, Coley K, et al. Whole genome sequencing of Mycobacterium tuberculosis reveals slow growth and low mutation rates during latent infections in humans. PLoS One. 2014;9(3):e91024.
58. Ford CB, Lin PL, Chase MR, Shah RR, Iartchouk O, Galagan J, et al. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat Genet. 2011;43(5):482-6.
59. Jombart T, Eggo RM, Dodd PJ, Balloux F. Reconstructing disease outbreaks from genetic data: a graph approach. Heredity (Edinb). 2011;106(2):383-90.
60. Liu XM, Gutacker MM, Musser JM, Fu YX. Evidence for recombination in Mycobacterium tuberculosis. J Bacteriol. 2006;188(23):8169-77.
61. Liu Q, Guo Y, Li J, Long JR, Zhang B, Shyr Y. Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data. BMC Genomics. 2012;13(8):S8.
62. Comas I, Homolka S, Niemann S, Gagneux S. Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS One. 2009;4(11):e7815.
63. David HL. Probability distribution of drug-resistant mutants in unselected populations of Mycobacterium tuberculosis. Appl Microbiol. 1970;20(5):810-4.
64. Kaplan G, Post FA, Moreira AL, Wainwright H, Kreiswirth BN, Tanverdi M, et al. Mycobacterium tuberculosis growth at the cavity surface: a microenvironment with failed immunity. Infect Immun. 2003;71(12):7099-108.
65. van den Berg RH. Communicable medical diseases: a holistic and social medicine perspective for healthcare providers. Bloomington, IN: Balboa Press; 2014.
66. Worby CJ, Lipsitch M, Hanage WP. Shared genomic variants: identification of transmission routes using pathogen deep sequence data. bioRxiv. 2015. doi:http://dx.doi.org/10.1101/032458.
67. Warner DF, Koch A, Mizrahi V. Diversity and disease pathogenesis in Mycobacterium tuberculosis. Trends Microbiol. 2015;23(1):14-21.
68. Cohen T, van Helden PD, Wilson D, Colijn C, McLaughlin MM, Abubakar I, et al. Mixed-strain mycobacterium tuberculosis infections and the implications for tuberculosis treatment and control. Clin Microbiol Rev. 2012;25(4):708-19.
69. Black PA, de Vos M, Louw GE, van der Merwe RG, Dippenaar A, Streicher EM, et al. Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates. BMC Genomics. 2015;16(1):857.
70. Liu Q, Via LE, Luo T, Liang L, Liu X, Wu S, et al. Within patient microevolution of Mycobacterium tuberculosis correlates with heterogeneous responses to treatment. Sci Rep. 2015;5:17507.
71. Galagan JE. Genomic insights into tuberculosis. Nat Rev Genet. 2014;15(5):307-20.
72. Takiff HE, Feo O. Clinical value of whole-genome sequencing of Mycobacterium tuberculosis. Lancet Infect Dis. 2015;15(9):1077-90.
73. Croucher NJ, Didelot X. The application of genomics to tracing bacterial pathogen transmission. Curr Opin Microbiol. 2015;23:62-7.
74. Le VT, Diep BA. Selected insights from application of whole-genome sequencing for outbreak investigations. Curr Opin Crit Care. 2013;19(5):432-9.
75. Bull RA, Luciani F, McElroy K, Gaudieri S, Pham ST, Chopra A, et al. Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLoS Pathog. 2011;7(9):e1002243.