Genomic analysis of ST117, 155, 1011, 167, 744, and 17391 in poultry-associated multidrug resistant Escherichia coli isolates from India

Multidrug-resistant Escherichia coli originating from poultry farms pose a significant One Health threat because of their emergence and spread connecting agricultural farms and the environment causing infections in humans. In this study, 38 isolates were collected, all of which exhibited resistance to penicillin, cephalosporins, fluoroquinolones and tetracycline, with an average Multiple Antibiotic Resistance (MAR) Index of 0.55. Among these 38 isolates, 7 isolates having ≥ 0.6 MAR index were subjected to whole genome sequencing - KEED-2 (ST117), KEED-3 (ST155), MTBW-1 (ST1011), MTBW-2 (ST167), PUND-1 (ST117), PUND-3 (ST17391) and VELW-1 (ST744). The analysis revealed the presence of antimicrobial-resistance genes such as tetracycline (tet(A)), quinolone (QnrS1) and aminoglycosides (aph(4)-Ia, aac(3)-IVa, aac(3)-IId, aph(3’’)-Ib, aph(3’)-Ia, aph(6)-Id). Notably, the CTX-M gene was present in KEED-2 (ST117), and the TEM-1B gene was present in MTBW-1 (ST1011) and VELW-1 (ST744). In this study, pandemic clones ST167, ST744 and ST17391 were identified, which has not been reported so far in poultry environments in India to the best of our knowledge, highlighting the need for continued surveillance and effective control measures, emphasising significance for the One Health framework.