Molecular Epidemiology of Multi-Drug Resistant E. coli Isolated from Poultry Birds in Six Agroclimatic Zones of West Bengal, India: A Cross-Sectional Study

This study depicts the antimicrobial resistance (AMR) pattern of E. coli (n: 503) isolated from cloacal swabs collected from chicks and duck in the six agroclimatic (hill, tarai, red & laterite, old alluvial, new alluvial and coastal saline) zones of West Bengal, India. Resistance to ampicillin (47.1%), ceftriaxone (27.0%), aztreonam (25.2%), tetracycline (20.0%), enrofloxacin (19.6%), and nalidixic acid (18.8%) was quite frequent, however, majority of the isolates were sensitive to amoxicillin-clavulanic acid (97%), chloramphenicol (97.5%) and imipenem (> 98%). In general, duck isolates demonstrated a higher level of antibiotic resistance while resistance was negligible for the isolates from the red & laterite zones. This study identified considerable number of extended-spectrum (n: 120) and A mpC type β-lactamase producers (n: 95). Phylotype A (285) was the most abundant followed by B1 (40) and C (87), while the other groups consisted of 91 isolates—B2 (25), D (31). F (34), and clade-1 (1). Logistic regression analysis demonstrated that the isolates of duck origin (OR: 4.44 (95% CI 2.5, 7.8), p < 0.001) and those belonging to virulent phylotypes (OR: 1.79 (95% CI 1.16, 2.75), P < 0.001) were more likely to be an ESBL producer. Likewise, the isolates from old alluvial zone were significantly and more frequently associated with ESBL production (OR: 2.04 (95% CI 1.04, 4.02), p < 0.001), ceftazidime (OR: 2.06 (95% CI 1.06, 4.04), p < 0.001) and quinolone [NAL: (OR: 2.42 (95% CI 1.23, 4.73), p < 0.01); ENR: (OR: 3.72 (95% CI 1.30, 6.72), p < 0.001)] resistance. The current study provided a first-ever thorough examination of the factors influencing antimicrobial resistance in poultry and the potential influence of variables such as agroclimatic zones, bird types [(broiler (chicken), layer (chicken), duck (mainly as layer)], and phylotypes on resistance pattern. Our findings highlight that there might be other factors contributing to AMR, in addition to the usage of antibiotics, in a particular sector. Therefore, a comprehensive approach through enhanced biosecurity and identification of loopholes that permit resistant elements to expand is needed, to tackle AMR in poultry sector.