The application of genomics to tracing bacterial pathogen transmission

Current Opinion in Microbiology

Volumn 23, Issue , 2015, Pages 62-67

  Croucher, Nicholas J ^a   Didelot, Xavier ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; BACTERIAL INFECTION; BACTERIAL TRANSMISSION; CHOLERA; CLOSTRIDIUM DIFFICILE; EPIDEMIOLOGICAL DATA; ESCHERICHIA COLI; GENETIC DISTANCE; GENETIC VARIABILITY; GENOMICS; HETEROSEXUALITY; HUMAN; INFECTION CONTROL; KLEBSIELLA PNEUMONIAE; MEN WHO HAVE SEX WITH MEN; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; MYCOBACTERIUM ABSCESSUS; MYCOBACTERIUM TUBERCULOSIS; PHYLOGENY; REVIEW; SALMONELLA TYPHIMURIUM; SINGLE NUCLEOTIDE POLYMORPHISM; STREPTOCOCCUS PYOGENES; VIBRIO CHOLERAE; BACTERIUM; DISEASE TRANSMISSION; GENETICS; MICROBIOLOGY; MOLECULAR EPIDEMIOLOGY; PROCEDURES; TRANSMISSION;

BACTERIA (MICROORGANISMS);

BACTERIA; BACTERIAL INFECTIONS; DISEASE TRANSMISSION, INFECTIOUS; GENOMICS; HUMANS; MOLECULAR EPIDEMIOLOGY;

EID: 84919359586     PISSN: 13695274     EISSN: 18790364     Source Type: Journal    
DOI: 10.1016/j.mib.2014.11.004     Document Type: Review

References (57)

1. Loman N.J., Misra R.V., Dallman T.J., Constantinidou C., Gharbia S.E., Wain J., Pallen M.J. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 2012, 30:434-439.
2. Quail M.A., Smith M., Coupland P., Otto T.D., Harris S.R., Connor T.R., Bertoni A., Swerdlow H.P., Gu Y. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012, 13:341.
3. Eyre D.W., Golubchik T., Gordon N.C., Bowden R., Piazza P., Batty E.M., Ip C.L.C., Wilson D.J., Didelot X., O'Connor L., et al. A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open 2012, 2:e001124.
4. Didelot X., Bowden R., Wilson D.J., Peto T.E.A., Crook D.W. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 2012, 13:601-612.
5. Bryant J.M., Grogono D.M., Greaves D., Foweraker J., Roddick I., Inns T., Reacher M., Haworth C.S., Curran M.D., Harris S.R. Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet 2013, 381:1551-1560.
6. Walker T.M., Lalor M.K., Broda A., Ortega L.S., Morgan M., Parker L., Churchill S., Bennett K., Golubchik T., Giess A.P., 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.
7. Eyre D.W., Cule M.L., Wilson D.J., Griffiths D., Vaughan A., O'Connor L., Ip C.L.C., Golubchik T., Batty E.M., Finney J.M., et al. Diverse sources of C. difficile infection identified on whole-genome sequencing. N Engl J Med 2013, 369:1195-1205.
8. Walker T.M., Ip C.L.C., Harrell R.H., Evans J.T., Kapatai G., Dedicoat M.J., Eyre D.W., Wilson D.J., Hawkey P.M., Crook D.W., et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis 2013, 13:137-146.
9. Török M.E., Reuter S., Bryant J., Köser C.U., Stinchcombe S.V., Nazareth B., Ellington M.J., Bentley S.D., Smith G.P., Parkhill J., et al. Rapid whole-genome sequencing for the investigation of a suspected tuberculosis outbreak. J Clin Microbiol 2013, 51:611-614.
10. Gardy J.L., Johnston J.C., Ho Sui S.J., Cook V.J., Shah L., Brodkin E., Rempel S., Moore R., Zhao Y., Holt R., et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 2011, 364:730-739.
11. Didelot X., Eyre D.W., Cule M., Ip C.L., Ansari M.A., Griffiths D., Vaughan A., O'Connor L., Golubchik T., Batty E.M., et al. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol 2012, 13:R118.
12. Didelot X., Nell S., Yang I., Woltemate S., van der Merwe S., Suerbaum S. Genomic evolution and transmission of Helicobacter pylori in two South African families. Proc Natl Acad Sci 2013, 110:13880-13885.
13. Harris S.R., Cartwright E.J.P., Török M.E., Holden M.T.G., Brown N.M., Ogilvy-Stuart A.L., Ellington M.J., Quail M.A., Bentley S.D., Parkhill J., et al. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis 2013, 13:130-136.
14. Didelot X., Gardy J., Colijn C. Bayesian inference of infectious disease transmission from whole genome sequence data. Mol Biol Evol 2014, 31:1869-1879.
15. Worby C.J., Lipsitch M., Hanage W.P. Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data. PLoS Comput Biol 2014, 10:e1003549.
16. Snitkin E.S., Zelazny A.M., Thomas P.J., Stock F., Henderson D.K., Palmore T.N., Segre J.A. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 2012, 4. 148ra116.
17. Okoro C.K., Kingsley R.A., Quail M.A., Kankwatira A.M., Feasey N.A., Parkhill J., Dougan G., Gordon M.A. High-resolution single nucleotide polymorphism analysis distinguishes recrudescence and reinfection in recurrent invasive nontyphoidal Salmonella typhimurium disease. Clin Infect Dis 2012, 54:955-963.
18. Lieberman T.D., Michel J.-B., Aingaran M., Potter-Bynoe G., Roux D., Davis M.R., Skurnik D., Leiby N., LiPuma J.J., Goldberg J.B., et al. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nat Genet 2011, 43:1275-1280.
19. 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:e1003457.
20. Köser C.U., Holden M.T.G., Ellington M.J., Cartwright E.J.P., Brown N.M., Ogilvy-Stuart A.L., Hsu L.Y., Chewapreecha C., Croucher N.J., Harris S.R., et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med 2012, 366:2267-2275.
21. Nübel U., Nachtnebel M., Falkenhorst G., Benzler J., Hecht J., Kube M., Bröcker F., Moelling K., Bührer C., Gastmeier P., et al. MRSA transmission on a neonatal intensive care unit: epidemiological and genome-based phylogenetic analyses. PLoS One 2013, 8:e54898.
22. Harris S.R., Feil E.J., Holden M.T., Quail M.A., Nickerson E.K., Chantratita N., Gardete S., Tavares A., Day N., Lindsay J.A., et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327:469-474.
23. Miller R.M., Price J.R., Batty E.M., Didelot X., Wyllie D., Golubchik T., Crook D.W., Paul J., Peto T.E.A., Wilson D.J., et al. Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone. J Hosp Infect 2014, 86:83-89.
24. Mellmann A., Harmsen D., Cummings C.A., Zentz E.B., Leopold S.R., Rico A., Prior K., Szczepanowski R., Ji Y., Zhang W., et al. Prospective genomic characterization of the german enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 2011, 6:e22751.
25. Rasko D.A., Webster D.R., Sahl J.W., Bashir A., Boisen N., Scheutz F., Paxinos E.E., Sebra R., Chin C.-S., Iliopoulos D., et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011, 365:709-717.
26. Rohde H., Qin J., Cui Y., Li D., Loman N.J., Hentschke M., Chen W., Pu F., Peng Y., Li J., et al. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 2011, 365:718-724.
27. Grad Y.H., Lipsitch M., Feldgarden M., Arachchi H.M., Cerqueira G.C., Fitzgerald M., Godfrey P., Haas B.J., Murphy C.I., Russ C., et al. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci USA 2012, 109:3065-3070.
28. Grad Y.H., Godfrey P., Cerquiera G.C., Mariani-Kurkdjian P., Gouali M., Bingen E., Shea T.P., Haas B.J., Griggs A., Young S., et al. Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen. MBio 2013, 4:e00452-e512.
29. Chin C.S., Sorenson J., Harris J.B., Robins W.P., Charles R.C., Jean-Charles R.R., Bullard J., Webster D.R., Kasarskis A., Peluso P., et al. The origin of the Haitian cholera outbreak strain. N Engl J Med 2011, 364:33-42.
30. Mutreja A., Kim D.W., Thomson N.R., Connor T.R., Lee J.H., Kariuki S., Croucher N.J., Choi S.Y., Harris S.R., Lebens M., et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 2011, 477:462-465.
31. Katz L.S., Petkau A., Beaulaurier J., Tyler S., Antonova E.S., Turnsek M.A., Guo Y., Wang S., Paxinos E.E., Orata F., et al. Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. MBio 2013, 4:e00398-e413.
32. Hendriksen R.S., Price L.B., Schupp J.M., Gillece J.D., Kaas R.S., Engelthaler D.M., Bortolaia V., Pearson T., Waters A.E., Prasad Upadhyay B., et al. Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the haitian outbreak. MBio 2011, 2:e00157-e211.
33. Ypma R.J.F., van Ballegooijen W.M., Wallinga J. Relating phylogenetic trees to transmission trees of infectious disease outbreaks. Genetics 2013, 195:1055-1062.
34. Comas I., Coscolla M., Luo T., Borrell S., Holt K.E., Kato-Maeda M., Parkhill J., Malla B., Berg S., Thwaites G., et al. Out-of-Africa migration and neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet 2013, 45:1176-1182.
35. Yahara K., Furuta Y., Oshima K., Yoshida M., Azuma T., Hattori M., Uchiyama I., Kobayashi I. Chromosome painting in silico in a bacterial species reveals fine population structure. Mol Biol Evol 2013, 30:1454-1464.
36. Beres S.B., Carroll R.K., Shea P.R., Sitkiewicz I., Martinez-Gutierrez J.C., Low D.E., McGeer A., Willey B.M., Green K., Tyrrell G.J., et al. Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics. Proc Natl Acad Sci U S A 2010, 107:4371-4376.
37. Nasser W., Beres S.B., Olsen R.J., Dean M.A., Rice K.A., Long S.W., Kristinsson K.G., Gottfredsson M., Vuopio J., Raisanen K., et al. Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences. Proc Natl Acad Sci 2014, 111:E1768-E1776.
38. Okoro C.K., Kingsley R.A., Connor T.R., Harris S.R., Parry C.M., Al-Mashhadani M.N., Kariuki S., Msefula C.L., Gordon M.A., de Pinna E. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet 2012, 44:1215-1221.
39. Holden M.T.G., Hsu L.-Y., Kurt K., Weinert L.A., Mather A.E., Harris S.R., Strommenger B., Layer F., Witte W., de Lencastre H., et al. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res 2013, 23:653-664.
40. Uhlemann A.-C., Hafer C., Miko B.A., Sowash M.G., Sullivan S.B., Shu Q., Lowy F.D. Emergence of sequence Type 398 as a community- and healthcare-associated methicillin-susceptible Staphylococcus aureus in Northern Manhattan. Clin Infect Dis 2013, 57:700-703.
41. He M., Miyajima F., Roberts P., Ellison L., Pickard D.J., Martin M.J., Connor T.R., Harris S.R., Fairley D., Bamford K.B., et al. Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat Genet 2013, 45:109-113.
42. Holt K.E., Thieu Nga T.V., Thanh D.P., Vinh H., Kim D.W., Vu Tra M.P., Campbell J.I., Hoang N.V.M., Vinh N.T., Minh P Van, et al. Tracking the establishment of local endemic populations of an emergent enteric pathogen. Proc Natl Acad Sci U S A 2013, 110:17522-17527.
43. Croucher N.J., Harris S.R., Fraser C., Quail M.A., Burton J., van der Linden M., McGee L., von Gottberg A., Song J.H., Ko K.S., et al. Rapid pneumococcal evolution in response to clinical interventions. Science 2011, 331:430-434.
44. Croucher N.J., Finkelstein J.A., Pelton S.I., Mitchell P.K., Lee G.M., Parkhill J., Bentley S.D., Hanage W.P., Lipsitch M. Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet 2013, 45:656-663.
45. Bart M.J., Harris S.R., Advani A., Arakawa Y., Bottero D., Bouchez V., Cassiday P.K., Chiang C.-S., Dalby T., Fry N.K., et al. Global population structure and evolution of Bordetella pertussis and their relationship with vaccination. mBio 2014, 5:e01074-e1114.
46. Grad Y.H., Kirkcaldy R.D., Trees D., Dordel J., Harris S.R., Goldstein E., Weinstock H., Parkhill J., Hanage W.P., Bentley S., et al. Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study. Lancet Infect Dis 2014, 14:220-226.
47. Mather A.E., Reid S.W.J., Maskell D.J., Parkhill J., Fookes M.C., Harris S.R., Brown D.J., Coia J.E., Mulvey M.R., Gilmour M.W. Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science 2013, 341:1514-1517.
48. Reuter S., Ellington M.J., Cartwright E.J.P., Köser C.U., Török M.E., Gouliouris T., Harris S.R., Brown N.M., Holden M.T.G., Quail M., et al. Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. JAMA Intern Med 2013, 173:1397-1404.
49. Ford C.B., Lin P.L., Chase M.R., Shah R.R., Iartchouk O., Galagan J., Mohaideen N., Ioerger T.R., Sacchettini J.C., Lipsitch M., et al. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat Genet 2011, 43:482-486.
50. Shea P.R., Beres S.B., Flores A.R., Ewbank A.L., Gonzalez-Lugo J.H., Martagon-Rosado A.J., Martinez-Gutierrez J.C., Rehman H.A., Serrano-Gonzalez M., Fittipaldi N., et al. Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations. Proc Natl Acad Sci U S A 2011, 108:5039-5044.
51. Flores A.R., Sahasrabhojane P., Saldaña M., Galloway-Peña J., Olsen R.J., Musser J.M., Shelburne S.A. Molecular characterization of an invasive phenotype of group A streptococcus arising during human infection using whole genome sequencing of multiple isolates from the same patient. J Infect Dis 2014, 209:1520-1523.
52. Young B.C., Golubchik T., Batty E.M., Fung R., Larner-svensson H., Votintseva A.A., Miller R.R., Godwin H., Knox K., Everitt R.G., et al. Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. Proc Natl Acad Sci U S A 2012, 109:4550-4555.
53. Golubchik T., Batty E.M., Miller R.R., Farr H., Young B.C., Larner-Svensson H., Fung R., Godwin H., Knox K., Votintseva A., et al. Within-host evolution of Staphylococcus aureus during asymptomatic carriage. PLoS One 2013, 8:e61319.
54. Croucher N.J., Mitchell A.M., Gould K.A., Inverarity D., Barquist L., Feltwell T., Fookes M.C., Harris S.R., Dordel J., Salter S.J., et al. Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection. PLoS Genet 2013, 9:e1003868.
55. Casali N., Nikolayevskyy V., Balabanova Y., Ignatyeva O., Kontsevaya I., Harris S.R., Bentley S.D., Parkhill J., Nejentsev S., Hoffner S.E., et al. Microevolution of extensively drug-resistant tuberculosis in Russia. Genome Res 2012, 22:735-745.
56. Holt K.E., Baker S., Weill F.-X., Holmes E.C., Kitchen A., Yu J., Sangal V., Brown D.J., Coia J.E., Kim D.W., et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet 2012, 44:1056-1059.
57. Reuter S., Harrison T.G., Köser C.U., Ellington M.J., Smith G.P., Parkhill J., Peacock S.J., Bentley S.D., Török M.E. A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak. BMJ Open 2013, 3:e002175.