Multidrug resistance and genomic features of Escherichia coli from Sonali chicken meat: a whole-genome sequencing study in Bangladesh

Background: Antimicrobial resistance in Escherichia coli poses a significant public health threat, particularly in low- and middle-income countries where antibiotic use in poultry production is often unregulated. Sonali chickens are widely consumed in Bangladesh but remain underrepresented in antimicrobial resistance surveillance. This study aimed to investigate the prevalence, phenotypic resistance patterns, and genomic characteristics of multidrug-resistant E. coli isolated from Sonali chicken meat sold in live bird markets. Methods: A cross-sectional study was conducted using 50 Sonali chicken meat samples collected from live bird markets in Chattogram between September and December 2022. Isolation and identification of E. coli were performed using standard microbiological and biochemical methods. Antimicrobial susceptibility testing was conducted using the disk diffusion method following Clinical and Laboratory Standards Institute guidelines. Multidrug resistance patterns and Multiple Antibiotic Resistance Index were calculated. Whole-genome sequencing of 26 selected isolates was performed using the Illumina platform. Resistance genes, virulence factors, and plasmid replicons were identified using ResFinder, VirulenceFinder, and PlasmidFinder databases. Descriptive statistics and clustering analyses were applied. Results: A total of 74% (37/50) of samples yielded multidrug-resistant E. coli . High resistance was observed against tetracyclines, fluoroquinolones, sulfonamides, and β-lactams. Multiple Antibiotic Resistance Index values ranged from 0.18 to 1.00, indicating substantial antibiotic pressure. Genomic analysis identified 29 antimicrobial resistance genes, with frequent detection of tet(A) , tet(M) , tet(X4) , sul2 , dfrA variants, and blaTEM-1B . The detection of tet(X4) highlights the emergence of resistance to last-resort antimicrobials. A total of 39 virulence genes were identified, mainly associated with adhesion, stress response, and iron acquisition. 23 plasmid replicon types were detected, with p0111, IncFIB(K), and IncX1 commonly associated with resistance genes. Phylogenetic analysis revealed a genetically diverse population with evidence of horizontal gene transfer. Conclusions: Sonali chicken meat sold in live bird markets represents a significant reservoir of multidrug-resistant E. coli carrying clinically important resistance and virulence determinants. These findings underscore the urgent need for strengthened antimicrobial stewardship, improved hygiene practices, and integrated genomic surveillance within a One Health framework in Bangladesh. Trial registration: Not applicable.