Antimicrobial resistance profiles and whole-genome sequence analysis of extended-spectrum β-lactamase (ESBL) production in commensal Escherichia coli from poultry in Türkiye

This study examines phenotypic antimicrobial resistance (AMR) and its genetic background in Escherichia coli isolated from poultry flocks in Türkiye, with a particular focus on extended spectrum β-lactamase (ESBL)-producing strains. A total of 918 E. coli isolates obtained from ceacal samples of chickens (n = 745) and turkeys (n = 173) were subjected to antimicrobial susceptibility testing using the agar disk diffusion method. Overall, high resistance rates were observed to tylosin (99.6%), ampicillin (90.8%), and oxytetracycline (84.0%), while resistance to third-generation cephalosporins (cefotaxime/ceftazidime) was detected in 11.4% of the isolates. Notably, AMR profiles varied significantly between poultry companies, indicating heterogeneous antimicrobial selection pressures within the production sector. ESBL-producing E. coli isolates exhibited high levels of multidrug-resistance, particularly to sulfamethoxazole (91.4%) and chloramphenicol (90.5%). Whole-genome sequencing (WGS) of ESBL-producing E. coli isolates (n = 87) identified several ESBL-encoding genes, with blaCTX-M-55 being the most prevalent (51.7%). Plasmid analysis demonstrated frequent associations of blaCTX-M-15 with IncFIB replicon, while blaCMY-2 was mainly linked to IncHI2A and IncI1-I plasmid types. In silico typing identified 44 distinct serotypes and 35 sequence types (STs), with O23:H4 and ST1011 being the most detected, highlighting the broad population structure of poultry associated E. coli. Virulence-associated genes were widely distributed among ESBL-producing isolates and predominantly related to adhesion, iron acquisition, stress response, and secretion systems. To the best of our knowledge, this study provides the first comprehensive WGS-based analysis of AMR in commensal E. coli from poultry in Türkiye, revealing significant public health concerns and the need for enhanced monitoring strategies.