Unravelling the Resistome of Carbapenem-Resistant E. coli from Bovine Mastitis via Whole-Genome Sequencing.

CREC with multiple resistance genes detected in bovine mastitis demands urgent AMR surveillance and One Health intervention.

This study investigated carbapenem-resistant Escherichia coli (CREC) isolated from bovine mastitis cases in Gujarat, India, combining phenotypic antimicrobial susceptibility testing with whole-genome sequencing (WGS). Of 790 mastitic milk samples, 130 confirmed E. coli isolates were identified, of which 33 (25.38%) demonstrated imipenem resistance. Nine isolates exhibited multidrug-resistant (MDR), extensively drug-resistant (XDR), or pan-drug-resistant (PDR) phenotypes. WGS of four representative isolates revealed genome sizes of 4.7–5.4 Mb and GC content of 50.4–50.8%. Multiple resistance determinants were identified, including carbapenemase genes (blaNDM, blaOXA-48, blaTEM, blaCMY, blaCTX-M), aminoglycoside-modifying enzymes, macrolide resistance genes, and efflux pump systems. Mobile genetic elements including integrases, transposases, and CRISPR-Cas systems were detected, indicating significant genomic plasticity and potential for horizontal gene transfer. Phenotypic resistance was high across key antimicrobials, notably colistin (79.23% including intermediate strains) and ampicillin (56.15%). Phylogenetic analysis suggested clonal dissemination within the bovine population, with genomic similarities to high-risk human clinical clones. These findings raise serious public health concerns regarding zoonotic transmission of CREC from dairy cattle to humans. The authors emphasize the need for robust antimicrobial resistance (AMR) surveillance programs, antibiotic stewardship in veterinary and agricultural settings, and a One Health framework to mitigate the risk of livestock-associated CREC spreading to human populations.

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