Ciprofloxacin resistant Escherichia coli: characterisation of phylogeny, virulence and antimicrobial resistance of isolates from extra intestinal infections of humans and chickens in selected geographical locations of Sri Lanka

Introduction: Ciprofloxacin resistant Escherichia coli strains are widely distributed. The phylogenetic backgrounds, antimicrobial resistance profiles, and virulence genes present in ciprofloxacin-resistant E. coli strains isolated from chickens and humans were evaluated in the study to identify their connection.
Method: A total of 92 non-duplicate E. coli isolates collected between July 2020 to July 2021 from humans with urinary infections (n=57) and chickens with colibacillosis (n=35) were included in the study. Antimicrobial resistance of the isolates was determined using the disk diffusion method following EUCAST guidelines. Phylogroup, plasmid-mediated quinolone resistance genes, and virulent genes were identified using PCR.
Results: Results revealed a high occurrence of ciprofloxacin resistance, with 65% of E coli isolates from urinary tract infections (UTI) in humans and 100% of chicken E. coli isolates showing resistance. Human strains showed significant co-resistance to third- and fourth-generation cephalosporins (p<0.001), whereas chicken isolates were co-resistant to amoxicillin-clavulanate (p<0.001) and trimethoprim-sulfamethoxazole (p<0.001). Ciprofloxacin resistant human isolates (24%) showed co-resistance to carbapenems. Phylogenetic analysis indicated ciprofloxacin resistant chicken and human E. coli isolates belonged to different lineages. Human E. coli strains were predominantly in phylogroup B2 of which 58% were O25b-ST131. Chicken isolates were distributed across multiple phylogroups. A significant proportion of ciprofloxacin resistant chicken E. coli harbored the qnrS gene while human isolates harboured the qnrB gene. Variations in the rates of occurrence of virulence genes, cvaC, iutA, traT, papC, and hlyA among humans and chickens E. coli isolates were also observed.
Conclusion: There were discernible differences in co-resistant profiles, plasmid-mediated qnr genes, and virulent genes between E. coli strains derived from humans and chickens.