Molecular characterization of antimicrobial resistance in Escherichia coli from dairy farm environment

The present study was carried out to study the prevalence and genetic mechanisms of antimicrobial resistance in E. coli strains from dairy farms. A total of 60 E. coli strains were initially isolated from 192 dairy farm samples using a selective antibiotic approach and confirmed as E. coli by PCR. Among these, 48 E. coli isolates predominantly from fecal samples were further studied. These isolates were majorly classified in phylogroup A (43.75 %) and B1 (16.66 %) and showed predominant resistance against ampicillin (60.41 %) followed by piperacillin (56.25 %), tetracycline (54.16 %), and other β-lactams such as cefotaxime (47.91 %) and cefuroxime (43.75 %). A significant portion (22.9 %) of the E. coli isolates were multidrug-resistant (MDR) and 50 % were ESBL-positive. Multiple antibiotic resistance (MAR) index ≥0.4 was exhibited by three isolates. Genotypic analysis identified resistance genes associated with β-lactams (bla_CTX-M-1, 64.58 %; bla_TEM, 35.41 %; bla_CTX-M-9, 4.16 %), tetracycline (tetA,37.58 %; tetB, 47.91 %), trimethoprim (dfrA17, 16.66 %), aminoglycosides [aac(6′)-Ib-cr, 2.08 %] and fluoroquinolones [qnrB, 25 %; qnrS, 16.66 %; gyrB (S492N), 45.83 %; gyrA (S83L), 45.83 %; gyrA(S87L), 39.58 %; parC (S80I), 14.58 %]. E. coli isolates also showed a high frequency of mobile genetic elements (MGEs) such as IS26 (56.25 %), IncFIB plasmids (52.08 %), and Tn3 transposons (56.25 %). Class 1 integrons harbouring 200 and 800 bp gene cassettes were also detected in 5 E. coli isolates (10.4 %). Overall, this study highlights the high prevalence of diverse AMR genes in cattle-derived E. coli and their strong association with various MGEs. These findings emphasize the need for continuous genomic surveillance to mitigate resistance spread, particularly within and from dairy environments.