Extended-spectrum beta-lactamase (ESBL)-producing E. coli in livestock and free-roaming wildlife: a combined phenotyping whole-genome sequencing One Health approach

Abstract

Antimicrobial resistance (AMR) in Enterobacterales, particularly extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec), poses a significant public health concern. Widespread antimicrobial use exerts selection pressure, driving the persistence and spread of resistant bacteria in diverse environments. While ESBL-Ec is well-documented in clinical and agricultural settings, its presence in reservoirs remains poorly understood. This study assessed the prevalence, AMR profiles, and genetic diversity of ESBL-Ec in Swiss dairy cattle and wildlife. Between 2021 and 2023, 775 samples were analysed, including rectal swab samples from dairy cows (n=475), and fecal or cloacal swab samples and wildlife (n=300). ESBL-Ec was detected in 0.6% of dairy cattle and 3.7% of wildlife. Whole-genome sequencing of 54 ESBL-Ec isolates identified 28 sequence types with no overlap between livestock and wildlife, suggesting distinct evolutionary trajectories. Phenotypic testing revealed resistance beyond beta-lactams, notably against aminoglycosides, tetracyclines, and sulfonamides, whereas all isolates remained susceptible to tigecycline and meropenem. Multidrug resistance was prevalent (89%), with blaCTX-TEM1 (in dairy cattle), blaCTX-M55 and blaTEM-176 (in red foxes) widely distributed across Switzerland. Clonal plasmids (IncFIB, IncX1) were detected across hosts and some individuals harbored multiple ESBL-Ec strains. Despite their low prevalence, spatial clustering indicated local persistence in both livestock and wildlife, highlighting potential transmission. The observed presence of clinically relevant ESBL-Ec in wildlife highlights the need for a One Health approach to tackle the dangers of AMR. Our findings contribute to AMR surveillance by providing baseline data on ESBL-Ec reservoirs and informing the design of strategies to mitigate its environmental spread.