Genomic Characterization of Antibiotic Resistant Isolated From Domestic Chickens in Pakistan.

Poultry husbandry is important for the economic health of Pakistan, but the Pakistani poultry industry is negatively impacted by infections from . We performed Illumina whole genome sequencing on 92 isolates obtained from the livers of deceased chickens originating in five Pakistani geographical regions. Our analysis indicates that the isolates are predominantly from the B1 and A clade and harbor a diverse number of antibiotic resistance and virulence genes, with no linkage between phylogeny and antibiotic resistance gene presence but some association between phylogeny and virulence gene and SNP presence for the B1 and E phylogroups. The colistin resistance gene and the quinolone resistance gene were both found in 13/92 isolates. Alarmingly, 82/92 of the strains characterized in this study are multidrug resistant with 100% (92/92) resistance to lincomycin, 81.5% (75/92) to streptomycin, 79.3% (73/92) to ampicillin and 66.3% (61/92) to ciprofloxacin. These results provide a high-resolution analysis of poultry-associated isolates in an area with a high endemic burden of antibiotic resistance. Surveillance of antibiotic resistance in poultry associated isolates is an important pillar of the One Health concept to integrate analysis of potential pathogens in human, animal, and environmental niches.