Whole-genome sequencing in epidemiology of Campylobacter jejuni infections

Journal of Clinical Microbiology

Volumn 55, Issue 5, 2017, Pages 1269-1275

  Llarena, Ann Katrin ^a   Taboada, Eduardo ^b   Rossi, Mirko ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b PUBLIC HEALTH AGENCY OF CANADA   (Canada)

Author keywords

Foodborne pathogens; Genome analysis; Molecular subtyping; Surveillance studies

Indexed keywords

CAMPYLOBACTER ENTERITIS; DISEASE SURVEILLANCE; EVOLUTIONARY ADAPTATION; FOOD POISONING; FRAMESHIFT MUTATION; GENETIC VARIABILITY; HEALTH CARE PLANNING; HUMAN; KNOWLEDGE; MOLECULAR BIOLOGY; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; RESEARCH; REVIEW; SEQUENCE ANALYSIS; WHOLE GENOME SEQUENCING; BACTERIAL GENOME; CAMPYLOBACTER INFECTIONS; CAMPYLOBACTER JEJUNI; EPIDEMIC; FOODBORNE DISEASES; GASTROENTERITIS; GENETIC VARIATION; GENETICS; MICROBIOLOGY; MOLECULAR EPIDEMIOLOGY; MOLECULAR TYPING; PROCEDURES;

CAMPYLOBACTER INFECTIONS; CAMPYLOBACTER JEJUNI; DISEASE OUTBREAKS; FOODBORNE DISEASES; GASTROENTERITIS; GENETIC VARIATION; GENOME, BACTERIAL; HUMANS; MOLECULAR EPIDEMIOLOGY; MOLECULAR TYPING;

EID: 85018366705     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.00017-17     Document Type: Review

References (31)

1. Carrillo CD, Kruczkiewicz P, Mutschall S, Tudor A, Clark C, Taboada EN. 2012. A framework for assessing the concordance of molecular typing methods and the true strain phylogeny of Campylobacter jejuni and C. coli using draft genome sequence data. Front Cell Infect Microbiol 2:57.
2. Köser CU, Ellington MJ, Cartwright EJP, Gillespie SH, Brown NM, Farrington M, Holden MTG, Dougan G, Bentley SD, Parkhill J, Peacock SJ. 2012. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 8:e1002824. https://doi.org/10.1371/journal.ppat.1002824.
3. Inns T, Ashton PM, Herrera-Leon S, Lighthill J, Foulkes S, Jombart T, Rehman Y, Fox A, Dallman T, Pinna ED, Browning L, Coia JE, Edeghere O, Vivancos R. 2017. Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis. Epidemiol Infect 145:289-298. https://doi.org/10.1017/S0950268816001941.
4. Kaakoush NO, Castaño-Rodríguez N, Mitchell HM, Man SM. 2015. Global epidemiology of Campylobacter infection. Clin Microbiol Rev 28: 687-720. https://doi.org/10.1128/CMR.00006-15.
5. Biggs PJ, Fearnhead P, Hotter G, Mohan V, Collins-Emerson J, Kwan E, Besser TE, Cookson A, Carter PE, French NP. 2011. Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage. PLoS One 6:e27121. https://doi.org/10.1371/journal.pone.0027121.
6. Llarena AK, Zhang J, Vehkala M, Välimäki N, Hakkinen M, Hänninen ML, Roasto M, Mäesaar M, Taboada EN, Barker D, Garfolo G, Cammà C, Di Giannatale ED, Corander J, Rossi M. 2016. Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion. Microb Genomics 10:2.
7. Revez J, Llarena AK, Schott T, Kuusi M, Hakkinen M, Kivistö R, Hänninen ML, Rossi M. 2014. Genome analysis of Campylobacter jejuni strains isolated from a waterborne outbreak. BMC Genomics 15:768. https://doi.org/10.1186/1471-2164-15-768.
8. Kovanen S, Kivistö R, Rossi M, Schott T, Kärkkäinen UM, Tuuminen T, Uksila J, Rautelin H, Hänninen ML. 2014. Multilocus sequence typing (MLST) and whole-genome MLST of Campylobacter jejuni isolates from human infections in three districts during a seasonal peak in Finland. J Clin Microbiol 52:4147-4154. https://doi.org/10.1128/JCM.01959-14.
9. Wu Z, Periaswamy B, Sahin O, Yaeger M, Plummer P, Zhai W, Shen Z, Dai L, Chen SL, Zhang Q. 2016. Point mutations in the major outer membrane protein drive hypervirulence of a rapidly expanding clone of Campylobacter jejuni. Proc Natl Acad Sci U S A 113:10690-10695. https://doi.org/10.1073/pnas.1605869113.
10. Bayliss CD, Bidmos FA, Anjum A, Manchev VT, Richards RL, Grossier J-P, Wooldridge KG, Ketley JM, Barrow PA, Jones MA, Tretyakov MV. 2012. Phase variable genes of Campylobacter jejuni exhibit high mutation rates and specific mutational patterns but mutability is not the major determinant of population structure during host colonization. Nucleic Acids Res 40:5876-5889. https://doi.org/10.1093/nar/gks246.
11. Revez J, Schott T, Llarena AK, Rossi M, Hänninen ML. 2013. Genetic heterogeneity of Campylobacter jejuni NCTC 11168 upon human infection. Infect Genet Evol 16:305-309. https://doi.org/10.1016/j.meegid.2013.03.009.
12. Thomas DK, Lone AG, Selinger LB, Taboada EN, Uwiera RRE, Abbott DW, Inglis GD. 2014. Comparative variation within the genome of Campylobacter jejuni NCTC 11168 in human and murine hosts. PLoS One 9:e88229. https://doi.org/10.1371/journal.pone.0088229.
13. Jerome JP, Bell JA, Plovanich-Jones AE, Barrick JE, Brown CT, Mansfield LS. 2011. Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host. PLoS One 6:e16399. https://doi.org/10.1371/journal.pone.0016399.
14. Kim JS, Artymovich KA, Hall DF, Smith EJ, Fulton R, Bell J, Dybas L, Mansfield LS, Tempelman R, Wilson DL, Linz JE. 2012. Passage of Campylobacter jejuni through the chicken reservoir or mice promotes phase variation in contingency genes Cj0045 and Cj0170 that strongly associates with colonization and disease in a mouse model. Microbiology 158:1304-1316. https://doi.org/10.1099/mic.0.057158-0.
15. Revez J, Zhang J, Schott T, Kivistö R, Rossi M, Hänninen ML. 2014. Genomic variation between Campylobacter jejuni isolates associated with milk-borne-disease outbreaks. J Clin Microbiol 52:2782-2786. https://doi.org/10.1128/JCM.00931-14.
16. Kovanen S, Kivistö R, Llarena AK, Zhang J, Kärkkäinen UM, Tuuminen T, Uksila J, Hakkinen M, Rossi M, Hänninen ML. 2016. Tracing isolates from domestic human Campylobacter jejuni infections to chicken slaughter batches and swimming water using whole-genome multilocus sequence typing. Int J Food Microbiol 226:53-60. https://doi.org/10.1016/j.ijfoodmicro.2016.03.009.
17. Zhang J, Halkilahti J, Hänninen ML, Rossi M. 2015. Refinement of wholegenome multilocus sequence typing analysis by addressing gene paralogy. J Clin Microbiol 53:1765-1767. https://doi.org/10.1128/JCM.00051-15.
18. Lahti E, Löfdahl M, Agren J, Hansson I, Olsson Engvall E. 2017. Confirmation of a campylobacteriosis outbreak associated with chicken liver pâté using PFGE and WGS. Zoonoses Public Health 64:14-20. https://doi.org/10.1111/zph.12272.
19. Clark CG, Berry C, Walker M, Petkau A, Barker DOR, Guan C, Reimer A, Taboada EN. 2016. Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population. BMC Genomics 17:990. https://doi.org/10.1186/s12864-016-3340-8.
20. Moffatt CRM, Greig A, Valcanis M, Gao W, Seemann T, Howden BP, Kirk MD. 2016. A large outbreak of Campylobacter jejuni infection in a university college caused by chicken liver pâté, Australia, 2013. Epidemiol Infect 144:2971-2978. https://doi.org/10.1017/S0950268816001187.
21. Jonsson ME, Heier BT, Norström M, Hofshagen M. 2010. Analysis of simultaneous space-time clusters of Campylobacter spp. in humans and in broiler flocks using a multiple dataset approach. Int J Health Geogr 9:48. https://doi.org/10.1186/1476-072X-9-48.
22. Strachan NJC, Forbes KJ. 2014. Extensive spatial and temporal clustering of Campylobacter infections evident in high-resolution genotypes, p 253-263. In Sheppard SK, Meric G (ed), Campylobacter ecology and evolution, 1st ed. Caister Academic Press, Norfolk, UK.
23. Castrodale LJ, Provo GM, Xavier CM, McLaughlin JB. 2016. Calling all Campy: how routine investigation and molecular characterization impacts the understanding of campylobacteriosis epidemiology: Alaska, United States, 2004-2013. Epidemiol Infect 144:265-267. https://doi.org/10.1017/S0950268815001466.
24. Maiden MCJ, Jansen van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND. 2013. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol 11:728-736. https://doi.org/10.1038/nrmicro3093.
25. Cody AJ, McCarthy ND, van Rensburg MJ, Isinkaye T, Bentley SD, Parkhill J, Dingle KE, Bowler ICJW, Jolley KA, Maiden MCJ. 2013. Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing. J Clin Microbiol 51:2526-2534. https://doi.org/10.1128/JCM.00066-13.
26. Jolley KA, Maiden MC. 2010. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:595. https://doi.org/10.1186/1471-2105-11-595.
27. Fernandes AM, Balasegaram S, Willis C, Wimalarathna HML, Maiden MC, McCarthy ND. 2015. Partial failure of milk pasteurization as a risk for the transmission of Campylobacter from cattle to humans. Clin Infect Dis 61:903-909. https://doi.org/10.1093/cid/civ431.
28. Mullner P, Spencer SEF, Wilson DJ, Jones G, Noble AD, Midwinter AC, Collins-Emerson JM, Carter P, Hathaway S, French NP. 2009. Assigning the source of human campylobacteriosis in New Zealand: a comparative genetic and epidemiological approach. Infect Genet Evol 9:1311-1319. https://doi.org/10.1016/j.meegid.2009.09.003.
29. Sheppard SK, Didelot X, Meric G, Torralbo A, Jolley KA, Kelly DJ, Bentley SD, Maiden MCJ, Parkhill J, Falush D. 2013. Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. Proc Natl Acad Sci U S A 110:11923-11927. https://doi.org/10.1073/pnas.1305559110.
30. Morley L, McNally A, Paszkiewicz K, Corander J, Méric G, Sheppard SK, Blom J, Manning G. 2015. Gene loss and lineage-specific restrictionmodification systems associated with niche differentiation in the Campylobacter jejuni sequence type 403 clonal complex. Appl Environ Microbiol 81:3641-3647. https://doi.org/10.1128/AEM.00546-15.
31. Dearlove BL, Cody AJ, Pascoe B, Méric G, Wilson DJ, Sheppard SK. 2016. Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections. ISME J 10:721-729. https://doi.org/10.1038/ismej.2015.149.