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Abstract

We aim to provide insight and guidance on the utility of whole genome sequencing (WGS) data for investigating food-borne outbreaks of Shiga toxin-producing (STEC) O157:H7 in England between 2013 and 2017. Analysis of WGS data delivered an unprecedented level of strain discrimination when compared with multilocus variable number tandem repeat analysis. The robustness of the WGS method ensured confidence in the microbiological identification of linked cases, even when epidemiological links were obscured. There was evidence that phylogeny derived from WGS data can be used to trace the geographical origin of an isolate. Further analysis of the phylogenetic data provided insight on the evolutionary context of emerging pathogenic strains. Publically available WGS data linked to the clinical, epidemiological and environmental context of the sequenced strain has improved trace back investigations during outbreaks. Expanding the use of WGS-based typing analysis globally will ensure the rapid implementation of interventions to protect public health, inform risk assessment and facilitate the management of national and international food-borne outbreaks of STEC O157:H7.

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/content/10.2807/1560-7917.ES.2019.24.4.1800346
2019-01-24
2019-10-21
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2019.24.4.1800346
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References

  1. Taylor CM, White RH, Winterborn MH, Rowe B. Haemolytic-uraemic syndrome: clinical experience of an outbreak in the West Midlands. Br Med J (Clin Res Ed). 1986;292(6534):1513-6.  https://doi.org/10.1136/bmj.292.6534.1513  PMID: 3087499 
  2. Wall PG, McDonnell RJ, Adak GK, Cheasty T, Smith HR, Rowe B. General outbreaks of vero cytotoxin producing Escherichia coli O157 in England and Wales from 1992 to 1994. Commun Dis Rep CDR Rev. 1996;6(2):R26-33. PMID: 8777442 
  3. Khakhria R, Duck D, Lior H. Extended phage-typing scheme for Escherichia coli O157:H7. Epidemiol Infect. 1990;105(3):511-20.  https://doi.org/10.1017/S0950268800048135  PMID: 2249715 
  4. Willshaw GA, Smith HR, Cheasty T, Wall PG, Rowe B. Vero cytotoxin-producing Escherichia coli O157 outbreaks in England and Wales, 1995: phenotypic methods and genotypic subtyping. Emerg Infect Dis. 1997;3(4):561-5.  https://doi.org/10.3201/eid0304.970422  PMID: 9366610 
  5. Byrne L, Elson R, Dallman TJ, Perry N, Ashton P, Wain J, et al. Evaluating the use of multilocus variable number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 as a routine public health tool in England. PLoS One. 2014;9(1):e85901.  https://doi.org/10.1371/journal.pone.0085901  PMID: 24465775 
  6. Dallman TJ, Byrne L, Ashton PM, Cowley LA, Perry NT, Adak G, et al. Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157. Clin Infect Dis. 2015;61(3):305-12.  https://doi.org/10.1093/cid/civ318  PMID: 25888672 
  7. Butcher H, Elson R, Chattaway MA, Featherstone CA, Willis C, Jorgensen F, et al. Whole genome sequencing improved case ascertainment in an outbreak of Shiga toxin-producing Escherichia coli O157 associated with raw drinking milk. Epidemiol Infect. 2016;144(13):2812-23.  https://doi.org/10.1017/S0950268816000509  PMID: 27338677 
  8. Mikhail AFW, Jenkins C, Dallman TJ, Inns T, Martín AIC, Fox A, et al. An outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with contaminated salad leaves: epidemiological, genomic and food trace back investigations. Epidemiol Infect. 2018;146(2):187-96.  https://doi.org/10.1017/S0950268817002874  PMID: 29248018 
  9. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589-95.  https://doi.org/10.1093/bioinformatics/btp698  PMID: 20080505 
  10. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-303.  https://doi.org/10.1101/gr.107524.110  PMID: 20644199 
  11. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312-3.  https://doi.org/10.1093/bioinformatics/btu033  PMID: 24451623 
  12. Dallman T, Ashton P, Schafer U, Jironkin A, Painset A, Shaaban S, et al. SnapperDB: a database solution for routine sequencing analysis of bacterial isolates. Bioinformatics. 2018;34(17):3028-9.  https://doi.org/10.1093/bioinformatics/bty212  PMID: 29659710 
  13. Ashton PM, Perry N, Ellis R, Petrovska L, Wain J, Grant KA, et al. Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing. PeerJ. 2015;3:e739.  https://doi.org/10.7717/peerj.739  PMID: 25737808 
  14. Sadiq SM, Hazen TH, Rasko DA, Eppinger M. EHEC Genomics: Past, Present, and Future. Microbiol Spectr. 2014;2(4):0020-2013.
  15. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol. 2014;52(5):1501-10.  https://doi.org/10.1128/JCM.03617-13  PMID: 24574290 
  16. Holmes A, Allison L, Ward M, Dallman TJ, Clark R, Fawkes A, et al. Utility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance. J Clin Microbiol. 2015;53(11):3565-73.  https://doi.org/10.1128/JCM.01066-15  PMID: 26354815 
  17. Ferdous M, Friedrich AW, Grundmann H, de Boer RF, Croughs PD, Islam MA, et al. Molecular characterization and phylogeny of Shiga toxin-producing Escherichia coli isolates obtained from two Dutch regions using whole genome sequencing. Clin Microbiol Infect. 2016;22(7):642.e1-9.  https://doi.org/10.1016/j.cmi.2016.03.028  PMID: 27058887 
  18. Parsons BD, Zelyas N, Berenger BM, Chui L. Detection, Characterization, and Typing of Shiga Toxin-Producing Escherichia coli. Front Microbiol. 2016;7:478.  https://doi.org/10.3389/fmicb.2016.00478  PMID: 27148176 
  19. Rusconi B, Sanjar F, Koenig SS, Mammel MK, Tarr PI, Eppinger M. Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks. Front Microbiol. 2016;7:985.  https://doi.org/10.3389/fmicb.2016.00985  PMID: 27446025 
  20. Gilchrist CA, Turner SD, Riley MF, Petri WA Jr, Hewlett EL. Whole-genome sequencing in outbreak analysis. Clin Microbiol Rev. 2015;28(3):541-63.  https://doi.org/10.1128/CMR.00075-13  PMID: 25876885 
  21. Byrne L, Jenkins C, Launders N, Elson R, Adak GK. The epidemiology, microbiology and clinical impact of Shiga toxin-producing Escherichia coli in England, 2009-2012. Epidemiol Infect. 2015;143(16):3475-87.  https://doi.org/10.1017/S0950268815000746  PMID: 25920912 
  22. Byrne L, Adams N, Glen K, Dallman TJ, Kar-Purkayastha I, Beasley G, et al. Epidemiological and Microbiological Investigation of an Outbreak of Severe Disease from Shiga Toxin-Producing Escherichia coli O157 Infection Associated with Consumption of a Slaw Garnish. J Food Prot. 2016;79(7):1161-8.  https://doi.org/10.4315/0362-028X.JFP-15-580  PMID: 27357035 
  23. Buchholz U, Bernard H, Werber D, Böhmer MM, Remschmidt C, Wilking H, et al. German outbreak of Escherichia coli O104:H4 associated with sprouts. N Engl J Med. 2011;365(19):1763-70.  https://doi.org/10.1056/NEJMoa1106482  PMID: 22029753 
  24. Wilson D, Dolan G, Aird H, Sorrell S, Dallman TJ, Jenkins C, et al. Farm-to-fork investigation of an outbreak of Shiga toxin-producing Escherichia coli O157. Microb Genom. 2018;4(3):e000160.  PMID: 29488865 
  25. Rowell S, King C, Jenkins C, Dallman TJ, Decraene V, Lamden K, et al. An outbreak of Shiga toxin-producing Escherichia coli serogroup O157 linked to a lamb-feeding event. Epidemiol Infect. 2016;144(12):2494-500.  https://doi.org/10.1017/S0950268816001229  PMID: 27297133 
  26. Strachan NJ, Rotariu O, Lopes B, MacRae M, Fairley S, Laing C, et al. Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association. Sci Rep. 2015;5(1):14145.  https://doi.org/10.1038/srep14145  PMID: 26442781 
  27. Underwood AP, Dallman T, Thomson NR, Williams M, Harker K, Perry N, et al. Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak. J Clin Microbiol. 2013;51(1):232-7.  https://doi.org/10.1128/JCM.01696-12  PMID: 23135946 
  28. Jenkins C, Dallman TJ, Launders N, Willis C, Byrne L, Jorgensen F, et al. Public Health Investigation of Two Outbreaks of Shiga Toxin-Producing Escherichia coli O157 Associated with Consumption of Watercress. Appl Environ Microbiol. 2015;81(12):3946-52.  https://doi.org/10.1128/AEM.04188-14  PMID: 25841005 
  29. Launders N, Locking ME, Hanson M, Willshaw G, Charlett A, Salmon R, et al. A large Great Britain-wide outbreak of STEC O157 phage type 8 linked to handling of raw leeks and potatoes. Epidemiol Infect. 2016;144(1):171-81.  https://doi.org/10.1017/S0950268815001016  PMID: 26041509 
  30. Sinclair C, Jenkins C, Warburton F, Adak GK, Harris JP. Investigation of a national outbreak of STEC Escherichia coli O157 using online consumer panel control methods: Great Britain, October 2014. Epidemiol Infect. 2017;145(5):864-71.  https://doi.org/10.1017/S0950268816003009  PMID: 27964764 
  31. Gobin M, Hawker J, Cleary P, Inns T, Gardiner D, Mikhail A, et al. National outbreak of Shiga toxin-producing Escherichia coli O157:H7 linked to mixed salad leaves, United Kingdom, 2016. Euro Surveill. 2018;23(18):17-00197.  https://doi.org/10.2807/1560-7917.ES.2018.23.18.17-00197  PMID: 29741151 
  32. Cowley LA, Dallman TJ, Fitzgerald S, Irvine N, Rooney PJ, McAteer SP, et al. Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks. Microb Genom. 2016;2(9):e000084. PMID: 28348875 
  33. Franz E, Delaquis P, Morabito S, Beutin L, Gobius K, Rasko DA, et al. Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems. Int J Food Microbiol. 2014;187:57-72.  https://doi.org/10.1016/j.ijfoodmicro.2014.07.002  PMID: 25051454 
  34. Allard MW, Bell R, Ferreira CM, Gonzalez-Escalona N, Hoffmann M, Muruvanda T, et al. Genomics of foodborne pathogens for microbial food safety. Curr Opin Biotechnol. 2018;49:224-9.  https://doi.org/10.1016/j.copbio.2017.11.002  PMID: 29169072 
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