Prevalence and whole-genome sequence-based analysis of shiga toxin-producing escherichia coli isolates from the recto- anal junction of slaughter-age irish sheep

Siobhán C. McCarthy*, Guerrino Macori, Gina Duggan, Catherine M. Burgess, Séamus Fanning, Geraldine Duffy

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)


Shiga toxin-producing Escherichia coli (STEC) organisms are a diverse group of pathogenic bacteria capable of causing serious human illness, and serogroups O157 and O26 are frequently implicated in human disease. Ruminant hosts are the primary STEC reservoir, and small ruminants are important contributors to STEC transmission. This study investigated the prevalence, serotypes, and shedding dynamics of STEC, including the supershedding of serogroups O157 and O26, in Irish sheep. Recto-anal mucosal swab samples (n = 840) were collected over 24 months from two ovine slaughtering facilities. Samples were plated on selective agars and were quantitatively and qualitatively assessed via real-time PCR (RT-PCR) for Shiga toxin prevalence and serogroup. A subset of STEC isolates (n = 199) were selected for whole-genome sequencing and analyzed in silico. In total, 704/840 (83.8%) swab samples were Shiga toxin positive following RT-PCR screening, and 363/704 (51.6%) animals were subsequently culture positive for STEC. Five animals were shedding STEC O157, and three of these were identified as supershedders. No STEC O26 was isolated. Post hoc statistical analysis showed that younger animals are more likely to harbor STEC and that STEC carriage is most prevalent during the summer months. Following sequencing, 178/199 genomes were confirmed as STEC. Thirty-five different serotypes were identified, 15 of which were not yet reported for sheep. Serotype O91:H14 was the most frequently reported. Eight Shiga toxin gene variants were reported, two stx1 and six stx2, and three novel Shiga-toxin subunit combinations were observed. Variant stx1c was the most prevalent, while many strains also harbored stx2b.

Original languageEnglish
Article numbere01384-21
JournalApplied and Environmental Microbiology
Issue number24
Early online date13 Oct 2021
Publication statusPublished - 24 Nov 2021
Externally publishedYes

Bibliographical note

Funding Information:
This project was funded by the Food Institutional Research Measure, administered by the Department of Agriculture, Food and the Marine, Ireland (grant number 15/F/629). We thank Paula Reid for assisting with the statistical analysis of the data.

Publisher Copyright:
© 2021 American Society for Microbiology.


  • Non-O157 STEC
  • Sheep
  • Shiga toxin-producing Escherichia coli
  • Supershedding
  • Wholegenome sequencing

ASJC Scopus subject areas

  • Biotechnology
  • Food Science
  • Ecology
  • Applied Microbiology and Biotechnology


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