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Volume 29, Number 9—September 2023
Dispatch

Reoccurring Escherichia coli O157:H7 Strain Linked to Leafy Greens–Associated Outbreaks, 2016–2019

Jessica C. Chen1Comments to Author , Kane Patel1, Peyton A. Smith, Eshaw Vidyaprakash, Caroline Snyder, Kaitlin A. Tagg, Hattie E. Webb, Morgan N. Schroeder, Lee S. Katz, Lori A. Rowe2, Dakota Howard, Taylor Griswold, Rebecca L. Lindsey, and Heather A. Carleton
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton); Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)

Main Article

Figure 2

Annotated plasmids of reference genome 2019C-3201 of Escherichia coli O157:H7 containing clade-specific genomic features. A) p2019C-3201_1 annotated with prokka version 1.14.5 (yellow annotations) (11). Mapped list of Roary features (pan_genome_references.fa) onto plasmid (95% nucleotide identity; gray annotations) (14). Features highlighted had >90 sensitivity and >90 specificity to a subset of clade 1 isolates (pink annotations). The region with specific/sensitive features covers a large portion of the plasmid and predominately contains genes encoding hypothetical proteins with unknown functions and common plasmid-associated genes. Three features did not map in Geneious because they were either below 95% identity (2 features) or were identified as partial copy (1 feature). B) p2019C-3201_2 annotated with prokka v1.14.5 (yellow annotations). Mapped list of Roary features (pan_genome_references.fa) onto plasmid (100% nucleotide identity; gray annotations). Features highlighted had >90 sensitivity and >97 specificity (blue annotations) to a subset of clade 1 isolates. The region with specific/sensitive features covers a large portion of the plasmid and is associated with conjugation. Image was generated using Geneious version 2021.2 (https://www.geneious.com).

Figure 2. Annotated plasmids of reference genome 2019C-3201 of Escherichia coli O157:H7 containing clade-specific genomic features. A) p2019C-3201_1 annotated with prokka version 1.14.5 (yellow annotations) (11). Mapped list of Roary features (pan_genome_references.fa) onto plasmid (95% nucleotide identity; gray annotations) (14). Features highlighted had >90 sensitivity and >90 specificity to a subset of clade 1 isolates (pink annotations). The region with specific/sensitive features covers a large portion of the plasmid and predominately contains genes encoding hypothetical proteins with unknown functions and common plasmid-associated genes. Three features did not map in Geneious because they were either below 95% identity (2 features) or were identified as partial copy (1 feature). B) p2019C-3201_2 annotated with prokka v1.14.5 (yellow annotations). Mapped list of Roary features (pan_genome_references.fa) onto plasmid (100% nucleotide identity; gray annotations). Features highlighted had >90 sensitivity and >97 specificity (blue annotations) to a subset of clade 1 isolates. The region with specific/sensitive features covers a large portion of the plasmid and is associated with conjugation. Image was generated using Geneious version 2021.2 (https://www.geneious.com).

Main Article

References
  1. Scallan  E, Hoekstra  RM, Angulo  FJ, Tauxe  RV, Widdowson  MA, Roy  SL, et al. Foodborne illness acquired in the United States—major pathogens. Emerg Infect Dis. 2011;17:7–15. DOIPubMedGoogle Scholar
  2. Mead  PS, Griffin  PM. Escherichia coli O157:H7. Lancet. 1998;352:1207–12. DOIPubMedGoogle Scholar
  3. Bielaszewska  M, Schmidt  H, Liesegang  A, Prager  R, Rabsch  W, Tschäpe  H, et al. Cattle can be a reservoir of sorbitol-fermenting shiga toxin-producing Escherichia coli O157:H(-) strains and a source of human diseases. J Clin Microbiol. 2000;38:3470–3. DOIPubMedGoogle Scholar
  4. Heiman  KE, Mody  RK, Johnson  SD, Griffin  PM, Gould  LH. Escherichia coli O157 Outbreaks in the United States, 2003-2012. Emerg Infect Dis. 2015;21:1293–301. DOIPubMedGoogle Scholar
  5. Marshall  KE, Hexemer  A, Seelman  SL, Fatica  MK, Blessington  T, Hajmeer  M, et al. Lessons learned from a decade of investigations of Shiga toxin–producing Escherichia coli outbreaks linked to leafy greens, United States and Canada. Emerg Infect Dis. 2020;26:2319–28. DOIPubMedGoogle Scholar
  6. Tolar  B, Joseph  LA, Schroeder  MN, Stroika  S, Ribot  EM, Hise  KB, et al. An overview of PulseNet USA databases. Foodborne Pathog Dis. 2019;16:457–62. DOIPubMedGoogle Scholar
  7. Lin  Y, Yuan  J, Kolmogorov  M, Shen  MW, Chaisson  M, Pevzner  PA. Assembly of long error-prone reads using de Bruijn graphs. Proc Natl Acad Sci U S A. 2016;113:E8396–405. DOIPubMedGoogle Scholar
  8. Redondo-Salvo  S, Bartomeus-Peñalver  R, Vielva  L, Tagg  KA, Webb  HE, Fernández-López, et al. COPLA, a taxonomic classifier of plasmids. BMC Bioinfo. 2021;22:390. DOIGoogle Scholar
  9. Katz  LS, Griswold  T, Williams-Newkirk  AJ, Wagner  D, Petkau  A, Sieffert  C, et al. A comparative analysis of the Lyve-SET phylogenomics pipeline for genomic epidemiology of foodborne pathogens. Front Microbiol. 2017;8:375. DOIPubMedGoogle Scholar
  10. Bouckaert  R, Vaughan  TG, Barido-Sottani  J, Duchêne  S, Fourment  M, Gavryushkina  A, et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLOS Comput Biol. 2019;15:e1006650. DOIPubMedGoogle Scholar
  11. Seemann  T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9. DOIPubMedGoogle Scholar
  12. Cherry  JL. Recent genetic changes affecting enterohemorrhagic Escherichia coli causing recurrent outbreaks. Microbiol Spectr. 2022;10:e0050122. DOIPubMedGoogle Scholar
  13. Punshon  T, Jackson  BP, Meharg  AA, Warczack  T, Scheckel  K, Guerinot  ML. Understanding arsenic dynamics in agronomic systems to predict and prevent uptake by crop plants. Sci Total Environ. 2017;581-582:209–20. DOIPubMedGoogle Scholar
  14. Page  AJ, Cummins  CA, Hunt  M, Wong  VK, Reuter  S, Holden  MTG, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31:3691–3. DOIPubMedGoogle Scholar
  15. Brynildsrud  O, Bohlin  J, Scheffer  L, Eldholm  V. Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol. 2016;17:238. DOIPubMedGoogle Scholar

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1These first authors contributed equally to this article.

2Current affiliation: Tulane National Primate Research Center, Covington, Louisiana, USA.

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Page updated: August 20, 2023
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