METHODS: Escherichia coli was isolated from 453 collected samples, including 210 cloacal swabs and 243 environmental samples. The antimicrobial susceptibility profile of the E. coli isolates was assessed for sixteen antibiotics using the disc diffusion method. The E. coli isolates were evaluated for phenotypic ESBL production using modified double disc synergy. After extraction of genomic DNA, ESBL resistance genes, phylogenetic group, and virulence genes were detected by PCR using appropriate primers. ESBL genes were further confirmed by sequencing. The molecular typing of E. coli strains was determined by Multilocus Sequence Typing (MLST).

RESULTS: A total of 93.8% (425/453) E. coli were isolated from the collected samples. Out of 334 E. coli isolates screened, 14.7% (49/334) were phenotypically ESBL producers. All the ESBL-EC were resistant to tetracycline, ciprofloxacin, and ampicillin. Thus, 100% of the ESBL-EC were multidrug resistant. Of the ESBL-EC 81.6% were positive for at least one ESBL encoding gene. The most prevalent ESBL gene detected was blaTEM (77.6%; 38/49) followed by blaCTX-M (32.7%; 16/49) and blaSHV (18.4%; 9/49). The majority of ESBL-EC belonged to phylogenic groups A followed by B1 accounting for 44.9% and 12.2%, respectively. The most frequently identified sequence types were ST10 (n = 3) and ST206 (n = 3). The most detected virulence genes in the E. coli isolates were astA (33.3%; 22/66) followed by iss (15.2%; 10/66).