Development and evaluation of a sensitive approach for detection and recovery of third-generation cephalosporin- and carbapenem-resistant Enterobacterales from ready-to-eat frozen stone fruit.

Antimicrobial resistance (AMR) is a global public health threat, but the role of foods in its dissemination is poorly understood. We examined the incidence of foodborne bacteria carrying AMR genes considered high-priority research targets by the World Health Organization. Frozen, ready-to-eat, avocado, coconut, mango, and peach (n = 161) were tested for bacteria encoding extended-spectrum β-lactamases (ESBLs) and carbapenemases. Over 600 presumptive-positive isolates were recovered and analyzed with a pooled sequencing (Pool-seq) strategy. Coconut samples exhibited the highest bacterial loads and prevalence/diversity of AMR genes. Isolates harbouring the β-lactamase genes bla_ctx-m, bla_tem, and bla_shv, identified in 14 coconut and 2 mango samples, were further characterized by whole-genome sequencing and antimicrobial susceptibility testing. The most common gene was bla_ctx-m-15, detected in 20 unique strains. Two carbapenemase-producing strains were isolated from coconut: Enterobacter roggenkampii encoding bla_ndm-1 and Escherichia coli encoding bla_ndm-5. Subsequent quantitative PCR (qPCR) analysis of enrichments for bla_ctx-m/bla_ndm indicated a potentially higher prevalence of these genes than observed by colony screening. This study presents a practical method for recovering ESBL- and carbapenemase-producing bacteria from foods. Mapping their distribution in food products is crucial to assessing the role of foods in the global spread of AMR and developing effective public health interventions.