Extended-Spectrum Beta-Lactamase (ESBL)-Producing E. coli in Livestock and Free-Roaming Wildlife: A Combined...

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 animal 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 analyzed, including rectal swab samples from dairy cows (n = 475) and fecal or cloacal swab samples from wildlife (n = 300). ESBL-Ec was detected in 3/475 (0.6%, 95% confidence interval [CI] 0.2%-1.8%) of dairy cattle and 15/300 (5%, 95% CI 3.1%-8.1%) wildlife samples, with higher prevalence in birds (6/99, 6.1%, 95% CI 2.8%-12.6%) than mammals (9/200, 4.5%, 95% CI 2.4%-8.3%). Whole-genome sequencing (WGS) of 54 ESBL-Ec isolates identified 28 sequence types (STs) 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 (MDR) was prevalent (89%), with bla_TEM-1 (in dairy cattle), bla_CTX-M55 and bla_TEM-176 (in red foxes) widely distributed across Switzerland. Clonal plasmids (IncFIB, IncX1) were detected in both wildlife and dairy cattle, and some animals harbored multiple ESBL-Ec strains. Despite the low prevalence of plasmids, 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 animal reservoirs and informing the design of strategies to mitigate its environmental spread.