Emergence of ESBL-Producing Escherichia coli in Shrimp Aquaculture, Kerala, India.

The present study evaluated 63 shrimp aquaculture farm sites in the Thrissur and Alappuzha districts of Kerala State, India. A total of 206 samples were analyzed, and 50 extended-spectrum β-lactamase (ESBL)-producing Escherichia coli strains were identified with antibiotic susceptibility testing (AST) profiles. All the strains were multidrug-resistant (MDR), with multiple antibiotic resistance (MAR) indices ranging from 0.32 to 0.64. PCR detection revealed a high prevalence of ESBL genes, blaCTX-M-gp-1 (86%), blaTEM (58%), blaSHV (50%), DHA (58%) and blaCMY-2 (48%). Quinolone and fluoroquinolone genes are aac(6')-Ib-cr (100%), qnrS (78%), OqxA (52%), OqxB (18%) and qnrB (8%). Non-ESBL genes included tetA+tetB (98%, 2%), sul1+sul2 (90%, 76%) and cmlA (48%). Plasmid replicon typing showed that IncFIB and IncN (96%), IncI1 (92%), IncFIC (78%) and IncFIA (56%) as predominant plasmid types. Phylogrouping revealed the presence of pathogenic lineages B2 (40%) and D (14%), whereas phylogroups E (86%) and C (82%) were more prevalent. Pulsed-field gel electrophoresis (PFGE) demonstrated high genetic heterogeneity among the strains, indicating non-clonal dissemination across farms. These findings indicate a surge in ESBL-producing E. coli exhibiting elevated resistance mechanisms, posing a significant public health threat. This underscores the urgent need for coordinated cross-sectoral interventions to mitigate AMR risks, curb the dissemination of resistance genes, and safeguard aquatic ecosystems and public health.