Importance of chick origin in introducing multidrug-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae into an organic broiler farm

Multidrug-resistant (MDR) and extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae occur in organic broiler production despite limited antimicrobial use. Their origin is not fully understood. This study characterized the genetic background and transmission dynamics of antimicrobial-resistant Escherichia coli and Klebsiella pneumoniae from one German organic broiler farm throughout the fattening period. Four consecutive flocks were sampled five times each, from day-old chicks until slaughter age. Three isolates per bacterium were tested per sample using broth microdilution. In flocks 1–3 supplied by one hatchery, 37.8 % (17/45) of E. coli from non-selective medium showed MDR phenotypes from day-old chicks onwards, but no ESBL-producers were detected. Instead, MDR and ESBL-producing K. pneumoniae were isolated from selective medium in 73.3 % (11/15) of samples. Whole genome sequencing revealed clonal MDR and ESBL-producing K. pneumoniae harboring a conjugative IncFII/IncFIB resistance plasmid and belonging to ST307, an emerging high-risk clone in human medicine. MDR E. coli were genetically diverse, with distinct clusters of clonal MDR ST162 and ST57 E. coli. In flock 4, supplied by a different hatchery, no MDR or ESBL-producing E. coli and K. pneumoniae were detected. 66.7 % of E. coli and 100 % of K. pneumoniae were fully susceptible. These results demonstrate the impact of external sources, particularly chick origin, on introducing of resistant bacteria into organic broiler farms. Further research is needed to assess the prevalence and the genetic background of MDR and ESBL-producing Enterobacteriaceae in organic breeder flocks and hatcheries to identify potential transmission events and improve prevention strategies.