Comparative genomic analysis of Acinetobacter baumannii isolates from seafood markets and healthcare environments: a case study from Kerala, India

Background Acinetobacter baumannii is renowned for causing difficult-to-treat infections and for its rapid acquisition of MDR. While traditionally viewed as a nosocomial pathogen, increasing evidence suggests that it persists in diverse environmental reservoirs. However, much of the global and most Indian surveillance have predominantly focused on hospital outbreaks, leaving its ecological diversity underexplored. Methods This study investigated A. baumannii isolates from seafood markets in Cochin, Kerala, India, to assess their clinical potential. Four isolates (AB02, AB05, AB07, AB08) were sequenced and compared against 479 publicly available Indian genomes from clinical, animal and environmental origins. Results Despite their small number, the isolates showed remarkable genomic diversity and clinically relevant features. They possessed distinct STs (ST1422, ST479 and ST2276; as per pasture MLST scheme) and remained distant from clinical isolates in core genome phylogeny. Resistome analysis revealed a limited repertoire, primarily intrinsic blaOXA-51 family and blaADC variants. Notably, isolate AB05 harboured blaOXA-72 on a plasmid, its first report in India. Virulome analysis identified conserved chromosomal determinants (ompA, bap, csu pili, siderophore systems, T6SS*) across isolates, with AB05 uniquely harbouring the hypervirulence-associated HemO cluster. Conclusions Taken together, the resistome-virulome patterns and phylogenetic context of these isolates challenge the conventional view of clinically relevant environmental A. baumannii as mere reflections of hospital contamination. Instead, they point towards the existence of naturally persisting, environmentally adapted lineages that have harboured and/or acquired clinically relevant traits. Within this framework, we hypothesize that seafood market environments may act as dynamic interfaces where diverse A. baumannii lineages circulate prior to or alongside clinical emergence, warranting further investigation through One Health genomic surveillance.