1887
Research article Open Access
Like 0

Abstract

A standardised method for determining O157:H7 strain relatedness using whole genome sequencing or virulence gene profiling is not yet established. We sought to assess the capacity of either high-throughput polymerase chain reaction (PCR) of 49 virulence genes, core-genome single nt variants (SNVs) or -mer clustering to discriminate between outbreak-associated and sporadic O157:H7 isolates. Three outbreaks and multiple sporadic isolates from the province of Alberta, Canada were included in the study. Two of the outbreaks occurred concurrently in 2014 and one occurred in 2012. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA) were employed as comparator typing methods. The virulence gene profiles of isolates from the 2012 and 2014 Alberta outbreak events and contemporary sporadic isolates were mostly identical; therefore the set of virulence genes chosen in this study were not discriminatory enough to distinguish between outbreak clusters. Concordant with PFGE and MLVA results, core genome SNV and -mer phylogenies clustered isolates from the 2012 and 2014 outbreaks as distinct events. -mer phylogenies demonstrated increased discriminatory power compared with core SNV phylogenies. Prior to the widespread implementation of whole genome sequencing for routine public health use, issues surrounding cost, technical expertise, software standardisation, and data sharing/comparisons must be addressed.

Loading

Article metrics loading...

/content/10.2807/1560-7917.ES.2015.20.47.30073
2015-11-26
2017-11-19
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2015.20.47.30073
Loading
Loading full text...

Full text loading...

/deliver/fulltext/eurosurveillance/20/47/eurosurv-20-47-3.html?itemId=/content/10.2807/1560-7917.ES.2015.20.47.30073&mimeType=html&fmt=ahah

References

  1. Chekabab SM, Paquin-Veillette J, Dozois CM, Harel J. The ecological habitat and transmission of Escherichia coli O157:H7. FEMS Microbiol Lett. 2013;341(1):1-12.  https://doi.org/10.1111/1574-6968.12078  PMID: 23305397 
  2. Rangel JM, Sparling PH, Crowe C, Griffin PM, Swerdlow DL. Epidemiology of Escherichia coli O157:H7 outbreaks, United States, 1982-2002. Emerg Infect Dis. 2005;11(4):603-9.  https://doi.org/10.3201/eid1104.040739  PMID: 15829201 
  3. Mead PS, Griffin PM. Escherichia coli O157:H7. Lancet. 1998;352(9135):1207-12.  https://doi.org/10.1016/S0140-6736(98)01267-7  PMID: 9777854 
  4. Clark WF, Sontrop JM, Macnab JJ, Salvadori M, Moist L, Suri R, et al. Long term risk for hypertension, renal impairment, and cardiovascular disease after gastroenteritis from drinking water contaminated with Escherichia coli O157:H7: a prospective cohort study. BMJ. 2010;341(nov17 2):c6020.  https://doi.org/10.1136/bmj.c6020  PMID: 21084368 
  5. Karch H, Tarr PI, Bielaszewska M. Enterohaemorrhagic Escherichia coli in human medicine. Int J Med Microbiol. 2005;295(6-7):405-18.  https://doi.org/10.1016/j.ijmm.2005.06.009  PMID: 16238016 
  6. MacCannell D. Bacterial strain typing. Clin Lab Med. 2013;33(3):629-50.  https://doi.org/10.1016/j.cll.2013.03.005  PMID: 23931842 
  7. Sabat AJ, Budimir A, Nashev D, Sá-Leão R, van Dijl Jm, Laurent F, et al. . Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill. 2013;18(4):20380. PMID: 23369389 
  8. Ranjbar R, Karami A, Farshad S, Giammanco GM, Mammina C. Typing methods used in the molecular epidemiology of microbial pathogens: a how-to guide. New Microbiol. 2014;37(1):1-15. PMID: 24531166 
  9. Chui L, Lee M-C, Allen R, Bryks A, Haines L, Boras V. Comparison between ImmunoCard STAT!(®) and real-time PCR as screening tools for both O157:H7 and non-O157 Shiga toxin-producing Escherichia coli in Southern Alberta, Canada. Diagn Microbiol Infect Dis. 2013;77(1):8-13.  https://doi.org/10.1016/j.diagmicrobio.2013.05.015  PMID: 23810166 
  10. Chui L, Couturier MR, Chiu T, Wang G, Olson AB, McDonald RR, et al. Comparison of Shiga toxin-producing Escherichia coli detection methods using clinical stool samples. J Mol Diagn. 2010;12(4):469-75.  https://doi.org/10.2353/jmoldx.2010.090221  PMID: 20466837 
  11. Scheutz F, Teel LD, Beutin L, Piérard D, Buvens G, Karch H, et al. Multicenter evaluation of a sequence-based protocol for subtyping Shiga toxins and standardizing Stx nomenclature. J Clin Microbiol. 2012;50(9):2951-63.  https://doi.org/10.1128/JCM.00860-12  PMID: 22760050 
  12. Bugarel M, Beutin L, Scheutz F, Loukiadis E, Fach P. Identification of genetic markers for differentiation of Shiga toxin-producing, enteropathogenic, and avirulent strains of Escherichia coli O26. Appl Environ Microbiol. 2011;77(7):2275-81.  https://doi.org/10.1128/AEM.02832-10  PMID: 21317253 
  13. Feng PCH, Delannoy S, Lacher DW, Dos Santos LF, Beutin L, Fach P, et al. Genetic diversity and virulence potential of shiga toxin-producing Escherichia coli O113:H21 strains isolated from clinical, environmental, and food sources. Appl Environ Microbiol. 2014;80(15):4757-63.  https://doi.org/10.1128/AEM.01182-14  PMID: 24858089 
  14. Bugarel M, Beutin L, Martin A, Gill A, Fach P. Micro-array for the identification of Shiga toxin-producing Escherichia coli (STEC) seropathotypes associated with Hemorrhagic Colitis and Hemolytic Uremic Syndrome in humans. Int J Food Microbiol. 2010;142(3):318-29.  https://doi.org/10.1016/j.ijfoodmicro.2010.07.010  PMID: 20675003 
  15. Chui L, Li V, Fach P, Delannoy S, Malejczyk K, Patterson-Fortin L, et al. Molecular profiling of Escherichia coli O157:H7 and non-O157 strains isolated from humans and cattle in Alberta, Canada. J Clin Microbiol. 2015;53(3):986-90.  https://doi.org/10.1128/JCM.03321-14  PMID: 25540392 
  16. Tseng M, Fratamico PM, Bagi L, Delannoy S, Fach P, Manning SD, et al. Diverse virulence gene content of Shiga toxin-producing Escherichia coli from finishing swine. Appl Environ Microbiol. 2014;80(20):6395-402.  https://doi.org/10.1128/AEM.01761-14  PMID: 25107960 
  17. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455-77.  https://doi.org/10.1089/cmb.2012.0021  PMID: 22506599 
  18. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068-9.  https://doi.org/10.1093/bioinformatics/btu153  PMID: 24642063 
  19. Petkau A, Van Domselaar G, Mabon P, Katz L. apetkau/core-phylogenomics · GitHub [Accessed 5 Feb 2015]. Available from: https://github.com/apetkau/core-phylogenomics
  20. Ponstingl H. SMALT efficiently aligns DNA sequencing reads with a reference genome. Wellcome Trust Sanger Institute, Hinxton, United Kingdom. Current version-SMALT v0. 7.5. Released 16 July 2013. [Accessed 24 Nov 2015]. Available from: http://www.sanger.ac.uk/science/tools/smalt-0
  21. Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv. 2012; arXiv:1207.3907 [q-bio.GN].
  22. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9.  https://doi.org/10.1093/bioinformatics/btp352  PMID: 19505943 
  23. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59(3):307-21.  https://doi.org/10.1093/sysbio/syq010  PMID: 20525638 
  24. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE. 2010;5(6):e11147.  https://doi.org/10.1371/journal.pone.0011147  PMID: 20593022 
  25. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res. 2011;39(Web Server issue):W347-52.
  26. Langille MGI, Brinkman FSL. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics. 2009;25(5):664-5.  https://doi.org/10.1093/bioinformatics/btp030  PMID: 19151094 
  27. Francisco AP, Bugalho M, Ramirez M, Carriço JA. Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinformatics. 2009;10(1):152.  https://doi.org/10.1186/1471-2105-10-152  PMID: 19450271 
  28. Sims GE, Jun SR, Wu GA, Kim SH. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci USA. 2009;106(8):2677-82.  https://doi.org/10.1073/pnas.0813249106  PMID: 19188606 
  29. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6 [Internet]. Distributed by author. University of Washington, Seattle, WA. 2005. [Accessed 7 Feb 2015]. Available from: http://evolution.genetics.washington.edu/phylip.html
  30. ProMED-mail. E. coli EHEC - Canada (04): (AB) O157, pork products, recall. Archive Number: 20140909.2759887. 9 Sep 2014. Available from: http://www.promedmail.org/
  31. Public Health Agency of Canada. Public Health Notice: E. coli O157 illness related to beef. 21 Dec 2013. [Accessed 4 Mar 2015]. Available from: http://www.phac-aspc.gc.ca/fs-sa/phn-asp/ecoli-1012-eng.php
  32. Dowd SE, Ishizaki H. Microarray based comparison of two Escherichia coli O157:H7 lineages. BMC Microbiol. 2006;6(1):30.  https://doi.org/10.1186/1471-2180-6-30  PMID: 16539702 
  33. Bielaszewska M, Köck R, Friedrich AW, von Eiff C, Zimmerhackl LB, Karch H, et al. Shiga toxin-mediated hemolytic uremic syndrome: time to change the diagnostic paradigm? PLoS ONE. 2007;2(10):e1024.  https://doi.org/10.1371/journal.pone.0001024  PMID: 17925872 
  34. van Belkum A, Tassios PT, Dijkshoorn L, Haeggman S, Cookson B, Fry NK, et al. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin Microbiol Infect. 2007;13(Suppl 3):1-46.  https://doi.org/10.1111/j.1469-0691.2007.01786.x  PMID: 17716294 
  35. Sherry NL, Porter JL, Seemann T, Watkins A, Stinear TP, Howden BP. Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J Clin Microbiol. 2013;51(5):1396-401.  https://doi.org/10.1128/JCM.03332-12  PMID: 23408689 
  36. 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 
  37. 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 
  38. 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 
  39. Gilmour MW, Graham M, Van Domselaar G, Tyler S, Kent H, Trout-Yakel KM, et al. High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics. 2010;11(1):120.  https://doi.org/10.1186/1471-2164-11-120  PMID: 20167121 
/content/10.2807/1560-7917.ES.2015.20.47.30073
Loading

Data & Media loading...

Comment has been disabled for this content
Submit comment
Close
Comment moderation successfully completed
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error