First report of carbapenemase-producing bacteria from poultry farms in the United Arab Emirates: an emerging One Health threat

Abstract

Carbapenemase-producing bacteria represent a critical global public health threat, yet their presence and molecular characteristics in food animal production systems remain poorly understood. This study provides the first comprehensive report of carbapenemase-producing bacteria isolated from poultry farms in the United Arab Emirates, offering important One Health insights into emerging antimicrobial resistance risks at the human–animal–environment interface. A total of 77 samples were collected from broiler farmhouses and slaughterhouses belonging to two major poultry companies in Al Ain, United Arab Emirates, between June 2023 and April 2024. Isolates were screened on MacConkey agar supplemented with meropenem, and carbapenemase production was confirmed using the modified carbapenem inactivation method. Antimicrobial susceptibility testing was performed, followed by whole-genome sequencing for species identification, resistome and virulome characterization, plasmid profiling, and comparative genomic analysis. Three isolates (3.9%) were confirmed as carbapenemase producers, two of which exhibited multidrug resistance. Whole-genome sequencing identified one Klebsiella pneumoniae ST11 KL105 isolate carrying bla NDM-5 and two Metapseudomonas otitidis isolates harboring the intrinsic carbapenemase bla POM-1 . The K. pneumoniae isolate contained multiple plasmid replicons and a broad resistome. Virulence analysis revealed a complete yersiniabactin locus, enterobactin operon, ompA , and ECP-like pilus genes. Comparative genomic analysis demonstrated that the bla NDM-5 genetic environment was highly conserved and nearly identical to that of a human ST11 isolate recovered in India in 2019. The two M. otitidis isolates showed a highly syntenic chromosomal bla POM-1 locus and clustered closely with a human isolate from the United States (2016). This study documents the presence of carbapenemase-producing bacteria in poultry production systems in the UAE, including a high-risk bla NDM-5 –harboring K. pneumoniae ST11 clone. The close genomic relatedness to human clinical isolates highlights the potential for cross-sectoral dissemination and underscores the importance of integrated genomic surveillance across animal, human, and environmental reservoirs.