Persistence of multidrug resistant Escherichia coli in poultry

International audienceAntimicrobial resistance (AMR) has decreased in French broiler production for the last 10 years, linked to lower antibiotics use. Nonetheless, animal gut and the breeding environment are still considered as reservoirs of resistant zoonotic bacteria. The aim of this study was to characterize the dynamic of AMR transmission and persistence in an experimental facility simulating a broiler production system with no antibiotic exposition.Chickens from five families were followed over three generations and two breeding environments (meat production and lineage reproduction), and commensal E. coli strains were isolated from feces at different weeks of age, as well as from building surfaces before flock entry. Among the ca. 600 non-redundant isolates collected, a subset of 128 multidrug resistant isolates (at least 4 antibiotic classes) were subjected to sequencing with lllumina and/or Oxford Nanopore technologies. The vast majority of isolates (91%) belonged to six unrelated sequence types from phylogroups A (ST206, ST2701, ST93) and B1 (ST162, ST1611 and ST453), none being reported as major causes of human or animal infection. These ST were shared between chicken families, generations and sample type (feces or surfaces), but segregated by breeding environment: isolates of phylogroup A were associated with reproductive animals while isolates of phylogroup B1 were associated with production animals. The AMR gene repertoire of sequenced isolates showed a weak diversity, with several genes (i.e. tet(A), blaTEM-1, sul2, dfrA1, aadA1) being shared by most ST. However, they were carried by independent plasmids, i.e. pIncF and pIncHI1 in ST2701 isolates, pIncZ in ST93 isolates, or pIncI1 in ST453 isolates. Our results indicate that the transmission of AMR in animals of successive generations is mainly driven by the persistence of specific clones in the breeding environment, rather than direct vertical transmission (from mother to offspring) or horizontal transmission of resistance plasmids