Longitudinal study reveals persistence of multidrug resistant Escherichia coli and horizontal transfer of antimicrobial resistance genes in the antibiotic free poultry production pyramid

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 AMR bacteria. The aim of this study was to characterize the AMR dynamic of transmission and persistence in an experimental facility simulating the broiler production pyramid (WPC eposter 380). Multiresistant E. coli isolated from feces (n=121) of chickens from five families followed over three generations including two sibling batches, one for reproduction and one for meat production, and from each of the two breeding environment samples (n=31) were subjected to whole genome sequencing (Illumina technology). A subset of isolates (n=36) were also sequenced using Oxford Nanopore MinION technology. The 152 E. coli isolates mainly belonged to the phylogroup A (55.9 %) and to the phylogroup B1 (36.2%). A very strong association was observed between phylogroups and batches, with most phylogroup A isolates (96.5 %) coming from the reproduction batch, and most phylogroup B1 isolates (90.9 %) coming from the meat production batch. The major sequence types ST2701 (A), ST93 (A), ST162 (B1), and ST 453 (B1) were shared between families and persisted through generations, and in the environment. The detected AMR genes in E. coli isolates showed a weak diversity, with several genes (i.e. strA, aadA, sul, dfrA, tet(A), blaTEM1) being shared by diverse ST and even phylogroups. However, MinION-based analysis showed that they were carried by independent plasmids, i.e. pIncFIB and pIncHI1 in ST2701, pIncBOKZ in ST93, pIncI1 in ST453. Exchange of AMR genes between ST was nonetheless observed at the level of mobile genetic elements (Insertion Sequences, integrons, transposons). Our results indicate that the persistence of specific ST in the breeding environment contributes to the transmission of AMR to animals of the successive batches without direct vertical transmission (mother to offspring) between generations. Rearrangements observed in the genetic environment of AMR genes also indicate occasional horizontal transfers within the breeding facility