Comparative genomic analysis of a multidrug-resistant ExPEC strain IITR156 isolated from the confluence of three Indian rivers

Abstract

Extra intestinal pathogenic Escherichia coli (ExPEC) with the potential to cause a wide range of infections in extra-intestinal sites is emerging threat to human health. Earlier studies have explored genomic characteristics of ExPEC isolates of human, avian, and porcine origin but genomic studies of environmental ExPEC isolates are very scarce. The environmental isolate, Escherichia coli IITR156 isolated in this study from the Triveni Sangam water sample showed resistance to antibiotics belonging to different classes including penicillin, beta-lactam combination agent, macrolide, cephalosporin, fluoroquinolone and aminoglycoside. Strain IITR156 was found to be harbouring plentitude of antibiotic resistant genes (ARGs) such as blaOXA-1, blaTEM-1, blaCTX-M-15, aac(3)-IIc and aac(6′)-Ib-cr, virulence genes including chuA, chuS, ybtA, ybtE, ybtP, epcA, and epcB, heavy metal resistant genes (HMRGs) such as arsRBC, cusB, cusF, cutA, tehA, nikABC, rcnA, rcnB, zraP, zitB, and zupT . Many of the ARGs and virulence genes were carried by mobile genetic elements such as genomic islands, transposons and plasmids indicating horizontal acquisition of genes. Comparative genomic analysis revealed that the strain IITR156 is closely related to other E. coli with ST 8881 isolated from human clinical samples. The presence of clinically relevant ARGs and virulence genes in an environmental isolate and its close relatedness to clinical isolates raise concerns and warrant immediate public attention.