Genotypic and Phenotypic Characterization of Antimicrobial Resistant Escherichia coli Isolated from Quail Meat

Abstract

Antimicrobial resistance (AMR) poses a significant global health threat. The increasing prevalence of multidrug-resistant (MDR) Escherichia coli (E. coli) in commercial poultry presents a serious public health concern because of acquiring antimicrobial-resistant bacteria through food chain. The following study evaluated the prevalence, antibiotic resistance patterns, and resistant genes of MDR E. coli in quail sold at live bird markets (LBMs) in Chattogram, Bangladesh. A cross-sectional study was conducted, with poultry samples (40 quails) collected from 10 prominent LBMs. These samples underwent microbiological analysis (pre-enriched in Buffered Peptone Water and then cultured on selective media) and antimicrobial susceptibility testing against 18 antibiotics. The overall prevalence of MDR E. coli was 66% in quails. The highest resistance rates were observed against tetracycline (100%), ampicillin (97.06% in quails), and ciprofloxacin (94.12% in quails). Sensitivity to third-generation cephalosporins, such as cefotaxime and ceftazidime, was moderate, with 61.76% and 58.82% of quail isolates being susceptible, respectively. The Multiple Antibiotic Resistance Index (MARI) values ranged from 0.27 to 1.0, reflecting significant variation in antibiotic exposure across different LBMs. Genetic analysis revealed essential resistance genes, including blaTEM, blaSHV, tetA, tetB, sul1, and sul2, confer resistance to β-lactams, tetracyclines, and sulfonamides. After NGS, the genotypic analysis revealed a substantial resistome among E. coli strains carrying a total of 38 AMR genes. High-prevalence determinants included tet(A) (88.89%), dfrA14 (44.44%), mph(A) (33.33%), sul2 (66.67%), sul3 (55.56%), and blaTEM-1B (100%). The detection of 41 virulence-associated genes revealed extensive genetic diversity among the isolates. Plasmid analysis revealed 23 distinct replicon types among the nine isolates, with the highest 44.44% being most prevalent. This study underscores the urgent need for stricter regulation of antibiotic use in poultry farming. Improving hygiene standards in LBMs is crucial.