Identification of CTX-M Type ESBL E. coli from Sheep and Their Abattoir Environment Using Whole-Genome Sequencing

Abstract

Widespread dissemination of extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) in animals, retail meats, and patients has been reported worldwide except for limited information on small ruminants. Our study focused on the genotypic characterization of ESBL E. coli from healthy sheep and their abattoir environment in North Carolina, USA. A total of 113 ESBL E. coli isolates from sheep (n = 65) and their abattoir environment (n = 48) were subjected to whole-genome sequencing (WGS). Bioinformatics tools were used to analyze the WGS data. Multiple CTX-M-type beta-lactamase genes were detected, namely blaCTX-M-1, blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, blaCTX-M-32, blaCTX-M-55, and blaCTX-M-65. Other beta-lactamase genes detected included blaCMY-2, blaTEM-1A/B/C, and blaCARB-2. In addition, antimicrobial resistance (AMR) genes and/or point mutations that confer resistance to quinolones, aminoglycosides, phenicols, tetracyclines, macrolides, lincosamides, and folate-pathway antagonists were identified. The majority of the detected plasmids were shared between isolates from sheep and the abattoir environment. Sequence types were more clustered around seasonal sampling but dispersed across sample types. In conclusion, our study reported wide dissemination of ESBL E. coli in sheep and the abattoir environment and associated AMR genes, point mutations, and plasmids. This is the first comprehensive AMR and WGS report on ESBL E. coli from sheep and abattoir environments in the United States.

Molecular characteristics of global β-lactamase-producing Enterobacter cloacae by genomic analysis

“…pneumonia [26], Achromobacter xylosoxidan [27], Escherichia. coli [28], Acinetobacter pittii [29] and E. cloacae [30] in a variety of countries, however, was quite rare in our study. Which may be related Fig.…”

Implications of different waterfowl farming on cephalosporin resistance: Investigating the role of blaCTX-M-55

“…ST93, ST206, and ST1276 each appeared in 2 isolates, whereas the remaining ST types were represented by only one isolate ( Table 4 ). Based on our literature search, it was found that 9 of these ST types have been associated with bla CTX-M-55 previously (ST10, ST38, ST48, ST93, ST156, ST162, ST224, ST1011, ST2011) ( Zhang et al, 2014 ; Zurfluh et al, 2015 ; Miao et al, 2017 ; Atlaw et al, 2021 ; Chenouf et al, 2021 ; Li et al, 2021 ; Nittayasut et al, 2021 ; Shin et al, 2021 ; Truong et al, 2021 ; Chotinantakul et al, 2022 ; Dos Anjos Adur et al, 2022 ; Soncini et al, 2022 ). The remaining 18 ST types, comprising 25 E. coli strains, were found to be associated with bla CTX-M-55 for the first time, with ST6707 being detected in 6 stains.…”

Antimicrobial Use Survey and Detection of ESBL-Escherichia coli in Commercial and Medium-/Small-Scale Poultry Farms in Selected Districts of Zambia

“…While the selection of AMR is often associated with hospital antibiotic use, many animal reservoirs now exist. There are several reports of drug-resistant Enterobacteriaceae in various livestock, including poultry, sheep, cattle, and pigs [7][8][9][10]. Furthermore, despite the lack of prior antibiotic exposure in wildlife, AMR has been reported in monkey [11], green sea turtles [12], and black rhinoceros [13], probably due to exposure to antibiotic-resistant organisms at the human-animal-environment interface.…”