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Genomic analysis of Shiga toxin-producing Escherichia coli O157:H7 from cattle and pork-production related environments

  • 1.

    Gill, A. et al. Review of the state of knowledge on verotoxigenic Escherichia coli and the role of whole genome sequencing as an emerging technology supporting regulatory food safety in Canada. (2020).

  • 2.

    Thorpe, C. M. Shiga toxin-producing Escherichia coli infection. Clin. Infect. Dis. 38, 1298–1303 (2004).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 3.

    Valilis, E., Ramsey, A., Sidiq, S. & DuPont, H. L. Non-O157 Shiga toxin-producing Escherichia coli-A poorly appreciated enteric pathogen: systematic review. Int. J. Infect. Dis. 76, 82–87 (2018).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 4.

    Karmali, M. A., Steele, B. T., Petric, M. & Lim, C. Sporadic cases of haemolytic-uraemic syndrome associated with faecal cytotoxin and cytotoxin-producing Escherichia coli in stools. Lancet 1, 619–620 (1983).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 5.

    O’Brien, A. O., Lively, T. A., Chen, M. E., Rothman, S. W. & Formal, S. B. Escherichia coli O157:H7 strains associated with haemorrhagic colitis in the United States produce a Shigella dysenteriae 1 (SHIGA) like cytotoxin. Lancet 1, 702 (1983).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 6.

    Gill, A. & Gill, C. O. Non-O157 verotoxigenic Escherichia coli and beef: a Canadian perspective. Can. J. Vet. Res 74, 161–169 (2010).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 7.

    Heiman, K. E., Mody, R. K., Johnson, S. D., Griffin, P. M. & Gould, L. H. Escherichia coli O157 outbreaks in the United States, 2003–2012. Emerg. Infect. Dis. 21, 1293–1301 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 8.

    Callaway, T. R., Carr, M. A., Edrington, T. S., Anderson, R. C. & Nisbet, D. J. Diet, Escherichia coli O157:H7, and cattle: a review after 10 years. Curr. Issues Mol. Biol. 11, 67–79 (2009).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 9.

    Tseng, M., Fratamico, P. M., Manning, S. D. & Funk, J. A. Shiga toxin-producing Escherichia coli in swine: the public health perspective. Anim. Health Res. Rev. 15, 63–75 (2014).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 10.

    Waddell, T. E., Coomber, B. L. & Gyles, C. L. Localization of potential binding sites for the edema disease verotoxin (VT2e) in pigs. Can. J. Vet. Res. 62, 81–86 (1998).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 11.

    Omer, M. K. et al. A systematic review of bacterial foodborne outbreaks related to red meat and meat products. Foodborne Pathog. Dis. 15, 598–611 (2018).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 12.

    Honish, L. et al. Escherichia coli O157:H7 infections associated with contaminated pork products – Alberta, Canada, July–October 2014. Mmwr. Morbidity Mortal. Wkly. Rep. 65, 1477–1481 (2017).

    Article 

    Google Scholar 

  • 13.

    AHS. E. coli outbreak linked to certain pork products in Alberta declared over, https://www.albertahealthservices.ca/news/releases/2018/Page14457.aspx (2018).

  • 14.

    News, F. S. Alberta outbreak prompts raw pork and pork organ recall, https://www.foodsafetynews.com/2016/02/alberta-e-coli-outbreak-prompts-raw-pork-and-pork-organ-recall/ (2016).

  • 15.

    Essendoubi, S. et al. Prevalence and characterization of Escherichia coli O157:H7 on pork carcasses and in swine colon content from provincially-licensed abattoirs in Alberta, Canada. J Food Prot, (2020).

  • 16.

    Colello, R. et al. From farm to table: follow-up of Shiga toxin-producing Escherichia coli throughout the pork production chain in Argentina. Front Microbiol. 7, 93 (2016).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 17.

    Tseng, M., Fratamico, P. M., Bagi, L., Manzinger, D. & Funk, J. A. Shiga toxin-producing E. coli (STEC) in swine: prevalence over the finishing period and characteristics of the STEC isolates. Epidemiol. Infect. 143, 505–514 (2015).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 18.

    Rajkhowa, S. & Sarma, D. K. Prevalence and antimicrobial resistance of porcine O157 and non-O157 Shiga toxin-producing Escherichia coli from India. Trop. Anim. Health Prod. 46, 931–937 (2014).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 19.

    Meng, Q. et al. Characterization of Shiga toxin-producing Escherichia coli isolated from healthy pigs in China. BMC Microbiol 14, 5 (2014).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 20.

    Ho, W. S., Tan, L. K., Ooi, P. T., Yeo, C. C. & Thong, K. L. Prevalence and characterization of verotoxigenic-Escherichia coli isolates from pigs in Malaysia. BMC Vet. Res. 9, 109 (2013).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 21.

    Choi, Y. M. et al. Changes in microbial contamination levels of porcine carcasses and fresh pork in slaughterhouses, processing lines, retail outlets, and local markets by commercial distribution. Res. Vet. Sci. 94, 413–418 (2013).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 22.

    Farzan, A., Friendship, R. M., Cook, A. & Pollari, F. Occurrence of Salmonella, Campylobacter, Yersinia enterocolitica, Escherichia coli O157 and Listeria monocytogenes in swine. Zoonoses Public Health 57, 388–396 (2010).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 23.

    Lenahan, M. et al. The potential use of chilling to control the growth of Enterobacteriaceae on porcine carcasses and the incidence of E. coli O157:H7 in pigs. J. Appl. Microbiol. 106, 1512–1520 (2009).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 24.

    Milnes, A. S. et al. Factors related to the carriage of Verocytotoxigenic E. coli, Salmonella, thermophilic Campylobacter and Yersinia enterocolitica in cattle, sheep and pigs at slaughter. Epidemiol. Infect. 137, 1135–1148 (2009).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 25.

    Kaufmann, M. et al. Escherichia coli O157 and non-O157 Shiga toxin-producing Escherichia coli in fecal samples of finished pigs at slaughter in Switzerland. J. Food Prot. 69, 260–266 (2006).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 26.

    Fratamico, P. M., Bagi, L. K., Bush, E. J. & Solow, B. T. Prevalence and characterization of Shiga toxin-producing Escherichia coli in swine feces recovered in the National Animal Health Monitoring System’s Swine 2000 study. Appl Environ. Microbiol 70, 7173–7178 (2004).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 27.

    Bonardi, S. et al. Detection of Salmonella spp., Yersinia enterocolitica and verocytotoxin-producing Escherichia coli O157 in pigs at slaughter in Italy. Int J. Food Microbiol 85, 101–110 (2003).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 28.

    Eriksson, E., Nerbrink, E., Borch, E., Aspan, A. & Gunnarsson, A. Verocytotoxin-producing Escherichia coli O157:H7 in the Swedish pig population. Vet. Rec. 152, 712–717 (2003).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 29.

    Feder, I. et al. Isolation of Escherichia coli O157:H7 from intact colon fecal samples of swine. Emerg. Infect. Dis. 9, 380–383 (2003).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 30.

    Johnsen, G., Wasteson, Y., Heir, E., Berget, O. I. & Herikstad, H. Escherichia coli O157:H7 in faeces from cattle, sheep and pigs in the southwest part of Norway during 1998 and 1999. Int J. Food Microbiol 65, 193–200 (2001).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 31.

    Leung, P. H., Yam, W. C., Ng, W. W. & Peiris, J. S. The prevalence and characterization of verotoxin-producing Escherichia coli isolated from cattle and pigs in an abattoir in Hong Kong. Epidemiol. Infect. 126, 173–179 (2001).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 32.

    Nakazawa, M. & Akiba, M. Swine as a potential reservoir of Shiga toxin-producing Escherichia coli O157:H7 in Japan. Emerg. Infect. Dis. 5, 833–834 (1999).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 33.

    Chapman, P. A., Siddons, C. A., Gerdan Malo, A. T. & Harkin, M. A. A 1-year study of Escherichia coli O157 in cattle, sheep, pigs and poultry. Epidemiol. Infect. 119, 245–250 (1997).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 34.

    Tang, S. et al. Assessment and comparison of molecular subtyping and characterization methods for Salmonella. Front Microbiol. 10, 1591 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 35.

    Schurch, A. C., Arredondo-Alonso, S., Willems, R. J. L. & Goering, R. V. Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches. Clin. Microbiol Infect. 24, 350–354 (2018).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 36.

    McNally, A. et al. Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations. PLoS Genet. 12, e1006280 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 37.

    Kaas, R. S., Friis, C., Ussery, D. W. & Aarestrup, F. M. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. BMC Genomics 13, 577 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 38.

    Rusconi, B. et al. Whole genome sequencing for genomics-guided investigations of Escherichia coli O157:H7 outbreaks. Front Microbiol 7, 985 (2016).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 39.

    Rumore, J. et al. Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective. BMC Genomics 19, 870 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 40.

    Manning, S. D. et al. Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc. Natl Acad. Sci. USA 105, 4868–4873 (2008).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 41.

    Yang, Z. et al. Identification of common subpopulations of non-sorbitol-fermenting, beta-glucuronidase-negative Escherichia coli O157:H7 from bovine production environments and human clinical samples. Appl Environ. Microbiol. 70, 6846–6854 (2004).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 42.

    Clermont, O., Christenson, J. K., Denamur, E. & Gordon, D. M. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ. Microbiol Rep. 5, 58–65 (2013).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 43.

    Latif, H., Li, H. J., Charusanti, P., Palsson, B. O. & Aziz, R. K. A gapless, unambiguous genome sequence of the enterohemorrhagic Escherichia coli O157:H7 strain EDL933. Genome Announc. 2, e00821-14 (2014).

  • 44.

    Sokal, R. R. & Rohlf, F. J. The comparison of dendrograms by objective methods. Taxon 11, 33–40, (1962).

  • 45.

    Pightling, A. W. et al. Interpreting whole-genome sequence analyses of foodborne bacteria for regulatory applications and outbreak investigations. Front Microbiol. 9, 1482 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 46.

    Galperin, M. Y., Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic acids Res. 43, D261–269 (2015).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 47.

    Batisson, I. et al. Characterization of the novel factor paa involved in the early steps of the adhesion mechanism of attaching and effacing Escherichia coli. Infect. Immun. 71, 4516–4525 (2003).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 48.

    Tatsuno, I. et al. toxB gene on pO157 of enterohemorrhagic Escherichia coli O157:H7 is required for full epithelial cell adherence phenotype. Infect. Immun. 69, 6660–6669 (2001).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 49.

    Wells, T. J. et al. EhaA is a novel autotransporter protein of enterohemorrhagic Escherichia coli O157:H7 that contributes to adhesion and biofilm formation. Environ. Microbiol. 10, 589–604 (2008).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 50.

    Paton, A. W., Srimanote, P., Woodrow, M. C. & Paton, J. C. Characterization of Saa, a novel autoagglutinating adhesin produced by locus of enterocyte effacement-negative Shiga-toxigenic Escherichia coli strains that are virulent for humans. Infect. Immun. 69, 6999–7009 (2001).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 51.

    Galli, L., Torres, A. G. & Rivas, M. Identification of the long polar fimbriae gene variants in the locus of enterocyte effacement-negative Shiga toxin-producing Escherichia coli strains isolated from humans and cattle in Argentina. FEMS Microbiol Lett. 308, 123–129 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 52.

    Tarr, P. I. et al. Iha: a novel Escherichia coli O157:H7 adherence-conferring molecule encoded on a recently acquired chromosomal island of conserved structure. Infect. Immun. 68, 1400–1407 (2000).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 53.

    Stanley, P., Koronakis, V. & Hughes, C. Acylation of Escherichia coli hemolysin: a unique protein lipidation mechanism underlying toxin function. Microbiol Mol. Biol. Rev. 62, 309–333 (1998).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 54.

    Veilleux, S. & Dubreuil, J. D. Presence of Escherichia coli carrying the EAST1 toxin gene in farm animals. Vet. Res 37, 3–13 (2006).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 55.

    Savarino, S. J. et al. Enteroaggregative Escherichia coli heat-stable enterotoxin 1 represents another subfamily of E. coli heat-stable toxin. Proc. Natl Acad. Sci. USA 90, 3093–3097 (1993).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 56.

    Paton, A. W., Srimanote, P., Talbot, U. M., Wang, H. & Paton, J. C. A new family of potent AB(5) cytotoxins produced by Shiga toxigenic Escherichia coli. J. Exp. Med 200, 35–46 (2004).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 57.

    Thomas, C. M. & Summers, D. Encyclopedia of life sciences. (John Wiley & Sons, Ltd, 2008).

  • 58.

    Carattoli, A. et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 3895–3903 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 59.

    Lim, J. Y., Yoon, J. & Hovde, C. J. A brief overview of Escherichia coli O157:H7 and its plasmid O157. J. Microbiol Biotechnol. 20, 5–14 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 60.

    Kim, J. Y. et al. Isolation and identification of Escherichia coli O157:H7 using different detection methods and molecular determination by multiplex PCR and RAPD. J. Vet. Sci. 6, 7–19 (2005).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 61.

    Jaros, P. et al. Geographic divergence of bovine and human Shiga toxin–producing Escherichia coli O157: H7 genotypes. NZ 20, 1980 (2014).

    CAS 

    Google Scholar 

  • 62.

    Mellor, G. E. et al. Geographically distinct Escherichia coli O157 isolates differ by lineage, Shiga toxin genotype, and total shiga toxin production. J. Clin. Micro. 53, 579–586 (2015).

    CAS 
    Article 

    Google Scholar 

  • 63.

    Pianciola, L. & Rivas, M. Genotypic features of clinical and bovine Escherichia coli O157 strains isolated in countries with different associated-disease incidences. Microorganisms 6, 36 (2018).

  • 64.

    Strachan, N. J. et al. Whole genome sequencing demonstrates that geographic variation of Escherichia coli O157 genotypes dominates host association. Sci. Rep. 5, 14145 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 65.

    Touchon, M. et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5, e1000344 (2009).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 66.

    Wochtl, B. et al. Comparison of clinical and immunological findings in gnotobiotic piglets infected with Escherichia coli O104:H4 outbreak strain and EHEC O157:H7. Gut Pathog. 9, 30 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 67.

    Booher, S. L., Cornick, N. A. & Moon, H. W. Persistence of Escherichia coli O157:H7 in experimentally infected swine. Vet. Microbiol. 89, 69–81 (2002).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 68.

    Moxley, R. A. Edema disease. Vet. Clin. North Am. Food Anim. Pr. 16, 175–185 (2000).

    CAS 
    Article 

    Google Scholar 

  • 69.

    Melton-Celsa, A. R. Shiga toxin (Stx) classification, structure, and function. Microbiol Spectr. 2, EHEC-0024-2013 (2014).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 70.

    Fuller, C. A., Pellino, C. A., Flagler, M. J., Strasser, J. E. & Weiss, A. A. Shiga toxin subtypes display dramatic differences in potency. Infect. Immun. 79, 1329–1337 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 71.

    Tesh, V. L. et al. Comparison of the relative toxicities of Shiga-like toxins type I and type II for mice. Infect. Immun. 61, 3392–3402 (1993).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 72.

    Tarr, G. A. M. et al. Contribution and interaction of Shiga toxin genes to Escherichia coli O157:H7 virulence. Toxins (Basel) 11, 607 (2019).

    CAS 
    Article 

    Google Scholar 

  • 73.

    Chui, 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. 53, 986–990 (2015).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 74.

    Goma, M. K. E., Indraswari, A., Haryanto, A. & Widiasih, D. A. Detection of Escherichia coli O157:H7 and Shiga toxin 2a gene in pork, pig feces, and clean water at Jagalan slaughterhouse in Surakarta, Central Java Province, Indonesia. Vet. World 12, 1584–1590 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 75.

    Baranzoni, G. M. et al. Characterization of Shiga toxin subtypes and virulence genes in porcine Shiga toxin-producing Escherichia coli. Front Microbiol. 7, 574 (2016).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 76.

    Mohlatlole, R. P. et al. Virulence profiles of enterotoxigenic, Shiga toxin and enteroaggregative Escherichia coli in South African pigs. Trop. Anim. Health Prod. 45, 1399–1405 (2013).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 77.

    Blanco, M. et al. Serotypes, virulence genes, and intimin types of Shiga toxin (verotoxin)-producing Escherichia coli isolates from cattle in Spain and identification of a new intimin variant gene (eae-xi). J. Clin. Microbiol. 42, 645–651 (2004).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 78.

    Kobayashi, N. et al. Virulence gene profiles and population genetic analysis for exploration of pathogenic serogroups of Shiga toxin-producing Escherichia coli. J. Clin. Microbiol. 51, 4022–4028 (2013).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 79.

    Meng, J., Zhao, S. & Doyle, M. P. Virulence genes of Shiga toxin-producing Escherichia coli isolated from food, animals and humans. Int J. Food Microbiol 45, 229–235 (1998).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 80.

    Mora, A. et al. Phage types, virulence genes and PFGE profiles of Shiga toxin-producing Escherichia coli O157:H7 isolated from raw beef, soft cheese and vegetables in Lima (Peru). Int J. Food Microbiol. 114, 204–210 (2007).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 81.

    Sallam, K. I., Mohammed, M. A., Ahdy, A. M. & Tamura, T. Prevalence, genetic characterization and virulence genes of sorbitol-fermenting Escherichia coli O157:H- and E. coli O157:H7 isolated from retail beef. Int J. Food Microbiol 165, 295–301 (2013).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 82.

    Solomakos, N. et al. Occurrence, virulence genes and antibiotic resistance of Escherichia coli O157 isolated from raw bovine, caprine and ovine milk in Greece. Food Microbiol. 26, 865–871 (2009).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 83.

    Tóth, I. et al. Virulence genes and molecular typing of different groups of Escherichia coli O157 strains in cattle. Appl. Environ. Microbiol. 75, 6282 (2009).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 84.

    Rao, S. et al. Antimicrobial drug use and antimicrobial resistance in enteric bacteria among cattle from Alberta feedlots. Foodborne Pathog. Dis. 7, 449–457 (2010).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 85.

    Benedict, K. M. et al. Antimicrobial resistance in Escherichia coli recovered from feedlot fattle and associations with antimicrobial use. PLoS ONE 10, e0143995 (2015).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 86.

    Stanford, K., Johnson, R. P., Alexander, T. W., McAllister, T. A. & Reuter, T. Influence of season and feedlot location on prevalence and virulence factors of seven serogroups of Escherichia coli in feces of western-Canadian slaughter cattle. PLoS ONE 11, e0159866 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 87.

    Mercer, R. G. et al. Genetic determinants of heat resistance in Escherichia coli. Front Microbiol. 6, 932 (2015).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 88.

    Stanford, K. et al. Monitoring Escherichia coli O157:H7 in inoculated and naturally colonized feedlot cattle and their environment. J. Food Prot. 68, 26–33 (2005).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 89.

    Munns, K. D. et al. Comparative genomic analysis of Escherichia coli O157:H7 isolated from super-shedder and low-shedder cattle. PLoS ONE 11, e0151673 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 90.

    Bach, S. J. et al. Electrolyzed oxidizing anode water as a sanitizer for use in abattoirs. J. Food Prot. 69, 1616–1622 (2006).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 91.

    Stanford, K., Gibb, D. & McAllister, T. A. Evaluation of a shelf-stable direct-fed microbial for control of Escherichia coli O157 in commercial feedlot cattle. Can. J. Anim. Sci. 93, 535–542 (2013).

    Article 

    Google Scholar 

  • 92.

    Stanford, K., Hannon, S., Booker, C. W. & Jim, G. K. Variable efficacy of a vaccine and direct-fed microbial for controlling Escherichia coli O157:H7 in feces and on hides of feedlot cattle. Foodborne Pathog. Dis. 11, 379–387 (2014).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 93.

    Berenger, B. M. et al. The utility of multiple molecular methods including whole genome sequencing as tools to differentiate Escherichia coli O157:H7 outbreaks. Euro Surveill. 20, 30073 (2015).

  • 94.

    Stephens, T. P., McAllister, T. A. & Stanford, K. Perineal swabs reveal effect of super shedders on the transmission of Escherichia coli O157:H7 in commercial feedlots. J. Anim. Sci. 87, 4151–4160 (2009).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 95.

    Zhang, P. et al. Genome sequences of 104 Escherichia coli O157:H7 isolates from pigs, cattle, and pork production environments in Alberta, Canada. Microbiol. Resour. Announc. 10, (2021).

  • 96.

    Riordan, J. T., Viswanath, S. B., Manning, S. D. & Whittam, T. S. Genetic differentiation of Escherichia coli O157:H7 clades associated with human disease by real-time PCR. J. Clin. Microbiol. 46, 2070–2073 (2008).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 97.

    Croucher, N. J. et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 43, e15–e15 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 98.

    Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinforma. (Oxf., Engl.) 30, 1312–1313 (2014).

    CAS 
    Article 

    Google Scholar 

  • 99.

    Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic acids Res. 47, W256–W259 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 100.

    Yu, G. Using ggtree to visualize data on tree-like structures. Curr. Protoc. Bioinform. 69, e96 (2020).

    Article 

    Google Scholar 

  • 101.

    Silva, M. et al. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Micro. Genom. 4, e000166 (2018).

    Google Scholar 

  • 102.

    Zhou, Z. et al. GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res. 28, 1395–1404 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 103.

    Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics (Oxf., Engl.) 30, 2068–2069 (2014).

    CAS 
    Article 

    Google Scholar 

  • 104.

    Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics (Oxf., Engl.) 31, 3691–3693 (2015).

    CAS 
    Article 

    Google Scholar 

  • 105.

    Zhang, P., Gänzle, M. & Yang, X. Complementary antibacterial effects of bacteriocins and organic acids as revealed by comparative analysis of Carnobacterium spp. from meat. Appl. Environ. Microbiol. 85, e01227-19 (2019).

  • 106.

    Zheng, J., Zhao, X., Lin, X. B. & Ganzle, M. Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations. Sci. Rep. 5, 18234 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 107.

    Schliep, K., Potts, A. J., Morrison, D. A. & Grimm, G. W. Intertwining phylogenetic trees and networks. Methods Ecol. Evol. 8, 1212–1220 (2017).

    Article 

    Google Scholar 

  • 108.

    Joensen, K. G. et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J. Clin. Microbiol. 52, 1501–1510 (2014).

  • 109.

    Bortolaia, V. et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J. Antimicrob. Chemother. 75, 3491–3500 (2020).


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