AUTHOR=Rafique Muhammad , Potter Robert F. , Ferreiro Aura , Wallace Meghan A. , Rahim Abdul , Ali Malik Akbar , Siddique Naila , Abbas Muhammad Athar , D’Souza Alaric W. , Burnham Carey-Ann D. , Ali Naeem , Dantas Gautam TITLE=Genomic Characterization of Antibiotic Resistant Escherichia coli Isolated From Domestic Chickens in Pakistan JOURNAL=Frontiers in Microbiology VOLUME=10 YEAR=2020 URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.03052 DOI=10.3389/fmicb.2019.03052 ISSN=1664-302X ABSTRACT=

Poultry husbandry is important for the economic health of Pakistan, but the Pakistani poultry industry is negatively impacted by infections from Escherichia coli. We performed Illumina whole genome sequencing on 92 E. coli 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 mcr-1 and the quinolone resistance gene qnrS1 were both found in 13/92 isolates. Alarmingly, 82/92 of the E. coli 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 E. coli isolates in an area with a high endemic burden of antibiotic resistance. Surveillance of antibiotic resistance in poultry associated E. coli isolates is an important pillar of the One Health concept to integrate analysis of potential pathogens in human, animal, and environmental niches.