Captive ungulates as sentinels of antimicrobial resistance: genomic and phenotypic characterization of extended-spectrum β-lactamase–producing Escherichia coli at a United Arab Emirates urban zoo

Antimicrobial resistance (AMR) in captive wildlife remains poorly characterized, particularly in zoological collections within the Middle East. This study investigated the occurrence, phenotypic resistance patterns, and genomic characteristics of extended-spectrum β -lactamase (ESBL)–producing Escherichia coli in clinically healthy captive ungulates at Al Ain Zoo, one of the largest zoological institutions located in an urban area in the United Arab Emirates (UAE). Fecal samples were collected non-invasively from 101 ungulates during routine husbandry and screened for ESBL-producing E. coli . Antimicrobial susceptibility testing (AST) was performed using the VITEK 2 system, and the identified ESBL-producing and multidrug resistant E. coli isolates underwent whole-genome sequencing for resistome, virulome, plasmid, and phylogenetic analyses. ESBL-producing E. coli were detected in 35 of 101 animals, corresponding to a carriage frequency of 34.7% (95% CI: 25.4–43.9%). Phenotypically, all isolates were resistant to β -lactam antibiotics, while resistance to fluoroquinolones and tetracycline was common. In contrast, susceptibility to aminoglycosides, imipenem, and polymyxin B was fully preserved. Based on exhibiting resistance to three or more antimicrobial classes, 26 of 35 isolates (74.3%) were classified as MDR. Genomic analysis revealed that all ESBL-producing E. coli harbored the bla CTX-M-15 gene, frequently accompanied by resistance determinants to quinolones ( qnrS1 ), tetracyclines ( tet(A) ), sulfonamides, trimethoprim, and aminoglycosides. All AMR genes were located on conjugative plasmids, predominantly IncF-type backbones. The isolates exhibited a polyclonal population structure encompassing 18 multilocus sequence types and several small SNP-defined clusters, alongside a moderate virulence gene burden lacking Shiga toxin or classical extra-intestinal pathogenic markers. This study provides the first genomic baseline of ESBL-producing E. coli in zoo-housed ungulates in the UAE and Middle East region, highlighting the value of urban zoological collections as sentinel sites for integrated One Health AMR surveillance supporting animal health, conservation, and public health.