Genotypic characterization of multidrug resistant Escherichia coli isolates reveals co-existence of ESBL- and carbapenemase- encoding genes linked to ISCR1.

Antimicrobial resistance in food-producing animals has not yet judiciously been reported from Pakistan. Here, we report on the isolation rate of poultry-associated multidrug resistant extended spectrum β-lactamase (ESBL) -producing Escherichia coli in Peshawar, Pakistan. A total of 200 samples, 50 from retail-poultry meat, 50 from sick birds, 50 from the boiler farm-environment, and 50 from human beings working on or exposed to poultry were analyzed for isolation of ESBL -producing E. coli, ESBL -encoding genes and antimicrobial susceptibility. A total of 81 E. coli isolates [(50.0% Phylogroup-A, 33.3% D and 16.7% phylogroup B2)], were recovered, 36 (44.4%) of them were found to be ESBL -producers. PCR revealed that blaCTXM was the most prevalent (14/36 = 38.9%) ESBL -encoding gene followed by blaSHV2 (9/36 = 25%). Strikingly, co-occurrence of multiple ESBL - and/or carbapenemase-encoding genes in a single isolate was observed, and combination of blaCTXM + blaSHV2 was the most predominant (19.4%) followed by blaCTXM + blaNDM1 + blaOXA-48 (11.1%) and blaCTXM + blaOXA-48 (8.8%). All these ESBL producers were found to be multidrug resistant (MDR) and were carrying either integron 1 (48.5%) or 2 (51.5%). Finally, 14 of the 36 isolates were also found positive for variable region and insertion sequence common region 1, which was found linked to ESBL/carbapenemase encoding genes in 5/14 isolates suggesting its role in dissemination.