Antimicrobial resistance of commensal and extended-spectrum ß-lactamase/AmpC-producing Escherichia coli in organic meat chicken farms

We examined the antimicrobial resistance of commensal Escherichia coli and occurrence of extended-spectrum beta-lactamase (ESBL)-/AmpC-producing E. coli in organic meat chicken flocks of three different fattening types using a longitudinal study design. Fourteen German small scale meat chicken farms fattening either slow-growing broiler, dual-purpose cockerels or male layer hybrids were sampled between 2023 and 2025. Throughout the fattening period, four consecutive flocks per farm were sampled five times each. Three isolates per sampling time point were picked from MacConkey agar (MCA). Additionally, MCA + 1mg/L cefotaxime (MCA+CTX) was used to selectively screen for ESBL-/AmpC-producing E. coli. In total, 696 commensal E. coli from MCA and 51 ESBL-/AmpC-producing E. coli from MCA+CTX were isolated. Antimicrobial resistance was determined using broth microdilution and minimum inhibitory concentrations were evaluated using epidemiological cut-off values. Throughout the fattening period, most commensal E. coli were susceptible in slow-growing broilers (63.0-80.0%), male layer hybrids (76.9-97.6%) and dual-purpose cockerels (69.0-89.6%). Resistance to ampicillin (11.1%; 77/696), ciprofloxacin (9.9%; 69/696), tetracycline (9.5%; 66/696), and nalidixic acid (8.3%; 58/696) was overall most prevalent in resistant commensal isolates regardless of sampling time point and fattening type. Whole genome sequencing revealed a diverse population among resistant commensal E. coli, with most resistant strains belonging to ST10 or ST155. Clonal dissemination of resistant strains was shown both within flocks or between subsequent flocks of a farm and between different farms. The providing hatchery was shown to have an influence (p < 0.001) on the recovery of resistant isolates. Only 27.5% of all flocks were positive for ESBL-/AmpC-producing E. coli for at least one sampling time point, with none of the flocks being positive throughout the whole fattening period and a high diversity of sequence types. bla_CTX-M-1 (29.2%, 7/24) was the most prevalent ESBL gene identified. This study is the first to describe antimicrobial resistance in different organic meat chicken fattening types in Germany in a longitudinal approach.