Isolation and whole-genome characterization of multidrug-resistant Acinetobacter baumannii from Indian retail meat: unveiling high-risk clones and zoonotic transmission threats via comparative genomics.

Abstract

Acinetobacter baumannii is a multidrug-resistant (MDR) pathogen increasingly detected in livestock and food products, raising concerns about zoonotic transmission. This study characterized A. baumannii isolates from retail meat sources in India, assessing their genomic diversity, antimicrobial resistance (AMR), virulence factors (VFs), and mobile genetic elements (MGEs). Nine A. baumannii isolates from chicken, buffalo, pork, mutton, and prawn were identified via CHROMagar™, biochemical tests, BD Phoenix™ M50, and rpoB PCR. Antibiotic susceptibility was determined using MIC assays. Whole-genome sequencing (WGS) was performed, followed by phylogenetic, resistome, virulome, and mobilome analyses with global animal, avian and meat isolates. All nine isolates exhibited resistance to β-lactams (amoxicillin-clavulanic acid, ampicillin, aztreonam, cefazolin, cefoxitin) but remained susceptible to tetracycline, amikacin, ciprofloxacin, and carbapenems. Genomic analysis revealed 3.67-3.9 Mbp genomes with 27-49 contigs, harboring 17-22 AMR genes per isolate. Global phylogenetic analysis identified two major clades with host- and country-specific clustering (e.g., ST-1512-OCL2-KL9 in Indian retail chicken, ST-25-OCL6-KL14 in French companion animals). Core VFs included biofilm formation (ompA, csuA-E, pgaA-D), iron acquisition (basA-J, bauA-F), and LPS biosynthesis genes. Plasmid prediction identified 242 plasmids (55 conjugative, 32 mobilizable), with 112 carrying AMR genes (AAC, APH, sul2, tet(B)). MGEs (IS, Tn, ICE) were linked to bla, bla, and aminoglycoside resistance genes. Capsular (KL) and lipooligosaccharide (OCL) loci showed geographic and host-specific distributions (e.g., KL14-OCL6 in France, KL19-OCL1 in UK livestock). Retail meat serves as a reservoir for MDR A. baumannii, with genomic features mirroring clinical strains. The presence of high-risk clones (IC-2, IC-5), carbapenem resistance genes (bla, bla), and mobilizable AMR plasmids underscores the risk of zoonotic transmission. A One Health approach integrating WGS-based surveillance is critical to mitigate the spread of AMR A. baumannii through food chains.