Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link

Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released.

Volume 31, Supplement—May 2025
SUPPLEMENT ISSUE
Supplement

Genomic Characterization of Escherichia coli O157:H7 Associated with Multiple Sources, United States

Joseph S. WirthComments to Author , Molly M. Leeper, Peyton A. Smith, Michael Vasser, Lee S. Katz, Eshaw Vidyaprakash, Heather A. Carleton, and Jessica C. Chen
Author affiliation: Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (J.S. Wirth); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.S. Wirth, M.M. Leeper, P.A. Smith, M. Vasser, L.S. Katz, E. Vidyaprakash, H.A. Carleton, J.C. Chen)

Main Article

Table 3

Antimicrobial resistance determinants in the 729 REPEXH01 isolates in a genomic characterization of Escherichia coli O157:H7 associated with multiple sources, United States*

Antimicrobial class % Resistant isolates
Aminoglycosides† 99.6
Folate pathway inhibitors‡ 99.6
Phenicols§ 99.6
Sulfonamides¶ 99.6
Quaternary ammonium compounds# 99.6
Tetracyclines** 99.5
Cephalosporins†† 1.9
Fluoroquinolones‡‡ 0.3
Penicillins§§ 0.3

*Antimicrobial resistance determinants were determined by using ResFinder (https://cge.cbs.dtu.dk/services/ResFinder). Resistance was defined by the presence of one or more determinants. REPHEXH01, recurring strain of Shiga toxin–producing Escherichia coli O157:H7. †aadA1, aph(3”)-Ib, and aph (6)-Id. ‡dfrA1 and dfrA8.§floR. ¶sul1 and sul2. #qacE. **tet(A) and tet(B). ††blaCMY-2 and blaCTX-M-27. ‡‡qnrB19. §§blaTEM-1B.

Main Article

References
  1. 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;11:603–9. DOIPubMedGoogle Scholar
  2. Dewey-Mattia  D, Manikonda  K, Hall  AJ, Wise  ME, Crowe  SJ. Surveillance for foodborne disease outbreaks—United States, 2009–2015. MMWR Surveill Summ. 2018;67:1–11. DOIPubMedGoogle Scholar
  3. Bottichio  L, Keaton  A, Thomas  D, Fulton  T, Tiffany  A, Frick  A, et al. Shiga toxin–producing Escherichia coli infections associated with romaine lettuce—United States, 2018. Clin Infect Dis. 2020;71:e323–30. DOIPubMedGoogle Scholar
  4. 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
  5. Scallan  E, Hoekstra  RM, Angulo  FJ, Tauxe  RV, Widdowson  M-A, Roy  SL, et al. Foodborne illness acquired in the United States—major pathogens. Emerg Infect Dis. 2011;17:7–15. DOIPubMedGoogle Scholar
  6. Mead  PS, Griffin  PM. Escherichia coli O157:H7. Lancet. 1998;352:1207–12. DOIPubMedGoogle Scholar
  7. Interagency Food Safety Analytics Collaboration. Foodborne illness source attribution estimates for 2020 for Salmonella, Escherichia coli O157, and Listeria monocytogenes using multi-year outbreak surveillance data, United States. US Department of Health and Human Services, Centers for Disease Control and Prevention, Food and Drug Administration, US Department of Agriculture Food Safety and Inspection Service, editors. Atlanta and Washington; The Departments; 2020.
  8. Chen  JC, Patel  K, Smith  PA, Vidyaprakash  E, Snyder  C, Tagg  KA, et al. Reocurring Escherichia coli O157:H7 strain linked to leafy greens–associated outbreaks, 2016–2019. Emerg Infect Dis. 2023;29:1895–9. DOIPubMedGoogle Scholar
  9. 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
  10. Seemann  T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9. DOIPubMedGoogle Scholar
  11. 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
  12. Brynildsrud  O, Bohlin  J, Scheffer  L, Eldholm  V. Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol. 2016;17:1. DOIGoogle Scholar
  13. Tobe  T, Beatson  SA, Taniguchi  H, Abe  H, Bailey  CM, Fivian  A, et al. An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. P Proc Natl Acad Sci U S A. 2006;103:14941–6.
  14. Sandu  P, Crepin  VF, Drechsler  H, McAinsh  AD, Frankel  G, Berger  CN. The enterohemorrhagic Escherichia coli effector EspW triggers actin remodeling in a Rac1-dependent manner. Infect Immun. 2017;85:e00244–17. DOIPubMedGoogle Scholar
  15. 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
  16. Croucher  NJ, Page  AJ, Connor  TR, Delaney  AJ, Keane  JA, Bentley  SD, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 2015;43:e15. DOIPubMedGoogle Scholar
  17. Bouckaert  R, Heled  J, Kühnert  D, Vaughan  T, Wu  C-H, Xie  D, et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLOS Comput Biol. 2014;10:e1003537. DOIPubMedGoogle Scholar
  18. Bouckaert  RR, Drummond  AJ. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC Evol Biol. 2017;17:42. DOIPubMedGoogle Scholar
  19. Zhou  Y, Liang  Y, Lynch  KH, Dennis  JJ, Wishart  DS. PHAST: a fast phage search tool. Nucleic Acids Res. 2011;39):W347-52.
  20. Arndt  D, Grant  JR, Marcu  A, Sajed  T, Pon  A, Liang  Y, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44(W1):W16-21. DOIPubMedGoogle Scholar
  21. Swaminathan  B, Barrett  TJ, Hunter  SB, Tauxe  RV; CDC PulseNet Task Force. PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg Infect Dis. 2001;7:382–9. DOIPubMedGoogle Scholar
  22. Letunic  I, Bork  P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49(W1):W293–6. DOIPubMedGoogle Scholar
  23. Manning  SD, Motiwala  AS, Springman  AC, Qi  W, Lacher  DW, Ouellette  LM, et al. Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc Natl Acad Sci U S A. 2008;105:4868–73. DOIPubMedGoogle Scholar
  24. Iyoda  S, Manning  SD, Seto  K, Kimata  K, Isobe  J, Etoh  Y, et al. Phylogenetic clades 6 and 8 of enterohemorrhagic Escherichia coli O157:H7 with particular stx subtypes are more frequently found in isolates from hemolytic uremic syndrome patients than from asymptomatic carriers. Open Forum Infect Dis. 2014;1:ofu061. DOIPubMedGoogle Scholar
  25. Centers for Disease Control and Prevention. Persistent strain of E. coli O157:H7 (REPEXH01) linked to multiple sources [cited 2024 Mar 7]. https://www.cdc.gov/ecoli/php/data-research/repexh01-e-coli-o157h7.html
  26. Kang  Y, Jelenska  J, Cecchini  NM, Li  Y, Lee  MW, Kovar  DR, et al. HopW1 from Pseudomonas syringae disrupts the actin cytoskeleton to promote virulence in Arabidopsis. PLoS Pathog. 2014;10:e1004232. DOIPubMedGoogle Scholar
  27. Xicohtencatl-Cortes  J, Sánchez Chacón  E, Saldaña  Z, Freer  E, Girón  JA. Interaction of Escherichia coli O157:H7 with leafy green produce. J Food Prot. 2009;72:1531–7. DOIPubMedGoogle Scholar
  28. Saldaña  Z, Sánchez  E, Xicohtencatl-Cortes  J, Puente  JL, Girón  JA. Surface structures involved in plant stomata and leaf colonization by shiga-toxigenic Escherichia coli o157:h7. Front Microbiol. 2011;2:119. DOIPubMedGoogle Scholar
  29. Orsi  RH, Bowen  BM, Wiedmann  M. Homopolymeric tracts represent a general regulatory mechanism in prokaryotes. BMC Genomics. 2010;11:102. DOIPubMedGoogle Scholar
  30. Byrne  L, Adams  N, Jenkins  C. Association between Shiga toxin-producing Escherichia coli O157:H7 stx gene subtype and disease severity, England, 2009–2019. Emerg Infect Dis. 2020;26:2394–400. DOIPubMedGoogle Scholar
  31. Redondo-Salvo  S, Fernández-López  R, Ruiz  R, Vielva  L, de Toro  M, Rocha  EPC, et al. Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids. Nat Commun. 2020;11:3602. DOIPubMedGoogle Scholar

Main Article

Page created: March 19, 2025
Page updated: May 06, 2025
Page reviewed: May 06, 2025
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external