Genomic insights into carbapenemase- and extended-spectrum β-lactamase–producing gram-negative bacteria in aquatic and terrestrial animal reservoirs in the United Arab Emirates

Abstract

Background The global spread of carbapenemase- and extended-spectrum β-lactamase (ESBL)–producing Gram-negative bacteria represents a major One Health challenge, driven by interconnected human, animal, and environmental reservoirs. However, genomic data on antimicrobial-resistant bacteria associated with aquatic and terrestrial animals in the United Arab Emirates (UAE) remain scarce, limiting assessment of their potential role in resistance dissemination. This study investigated the phenotypic and genomic characteristics of resistant Gram-negative bacteria recovered from these animal reservoirs. Methods Sixty aquarium-associated samples were collected, yielding 69 Gram-negative isolates. Antimicrobial susceptibility testing, phenotypic detection of ESBL and carbapenemase activity, molecular screening of resistance genes, and whole-genome sequencing of selected isolates were performed. Phylogenetic analyses were conducted to assess evolutionary relatedness with global strains. Results The isolates were mainly identified as Citrobacter, Pseudomonas, Acinetobacter, and Escherichia coli. Resistance to β-lactam antibiotics was widespread, with 87% of isolates confirmed as ESBL producers and 37.7% classified as multidrug resistant. Carbapenemase activity was detected in 14.5% of isolates. Genomic analyses revealed diverse ESBL, AmpC, and carbapenemase genes, including blaCTX-M-15, blaCTX-M-55, blaCMY-82, blaNDM-1, and for the first time multiple OXA-type carbapenemases (blaOXA-51, blaOXA-421, and blaOXA-848, blaOXA-1005, blaOXA-211-like, and blaOXA-396-like), frequently associated with mobile genetic elements. ESBL-producing E. coli ST602 and ST10 clustered closely with human, food, wildlife, and environmental strains from national and international sources. Conclusion Aquatic and terrestrial animals in the UAE serve as important reservoirs for clinically relevant antimicrobial resistance. These findings underscore the need for integrated One Health genomic surveillance to mitigate the transboundary spread of high-risk resistant lineages.