Assessment of antibiotic resistance genes and integrons in commensal Escherichia coli from the Indian urban waste water: Implications and significance for public health

Abstract

Antibiotics like β-lactams, quinolones/fluoroquinolones, aminoglycosides and tetracycline constitute the major mainstay of treatment against most infectious diseases including Escherichia coli. Indiscriminate use of antibiotics for human and animal well-being has generated an enormous evolutionary pressure on bacteria especially E.coli, which has a highly plastic/evolving genome. Though, antibiotic resistance (AR) has been extensively studied in pathogenic E.coli, commensal strains have been studied less owing to lesser clinical significance. However, commensal strains pose a serious threat as reservoirs and transmitters of resistance genes to other bacteria. Therefore, the present study was undertaken to investigate the prevalence of resistance genes and integrons in commensal E.coli isolated from river Yamuna, Delhi, India, which receives plentiful urban waste water. Eighty three well-characterized E.coli strains of phylogroups A and B1 isolated from river Yamuna were investigated. Antimicrobial susceptibilities and minimal inhibitory concentrations (MICs) for β-lactams, aminoglycosides, tetracycline and quinolone/fluoroquinolone were determined by disk diffusion and Etest, according to Clinical and Laboratory Standards Institute (CLSI) guidelines. Production of Extended spectrum β-lactamases (ESBL) and AmpC was investigated. Prevalence of antibiotic-resistance genes for β-lactams (blaTEM,blaSHV, blaCTX-M, blaOXA, blaCMY-42), aminoglycosides (rmtA, rmtB, rmtC, armA, str, aacC2), tetracycline (tetA, tetR, tetM, tetW), and plasmid-mediated quinolone resistance, PMQR (qnrA, qnrB, qnrC, qnrD, qnrS, qep, aac) were assessed. Integrons and gene-cassette arrays were characterized. Commensal E.coli strains showed a higher resistance to ampicillin (95%), less to cefazolin (45%) and still lesser to tetracycline (15%). About 19% of these strains showed multidrug resistant (three or more classes of antibiotics), of which 15% also produced ESBLs. None of the strains produced AmpC β-lactamases. About 6% of the strains were concurrently fluoroquinolone-resistant and ESBL producers. The blaTEM was present in most strains (95%), followed by blaCTX-M (15%). Aminoglycoside-resistance genes viz. str and armA were detected in 6% and 8% strains, respectively; tetracycline-resistance genes viz. tetA and tetR in 3% and 6% strains, respectively; and PMQR gene viz. qnrS in 15% of the strains. Class I integron was detected in 64% of the isolates, of which 7 strains had 3 different variable region gene-cassette arrays. dfrA and aadA gene families were widespread among the gene-cassettes identified.