In vitro colonization of chicken cecum microbiota by antimicrobial resistant bacteria with and without antibiotics

The chicken gut microbiota acts as source of zoonotic human pathogens and as a reservoir of antimicrobial resistance (AMR) determinants, which may spread among commensals and pathogens within the chicken cecum. In this study, using PolyFermS in vitro chicken ceacum model, we investigated the ability of two chicken isolates, i.e., vancomycin-resistant Enterococcus faecium CCUG59168 (vanA, Tn1546-mediated, pVEF1 plasmid) and ESBL-producing Escherichia coli HV292.1 (blaCTX-M-1, ISEcp1, IncI1 plasmid), to proliferate in two distinct chicken cecum microbiota, with and without antibiotic pressure (vancomycin and cefotaxime). We further evaluated the impact of strains and antibiotics on the complex chicken gut microbiota structure and dynamic (qPCR and 16S rRNA metabarcoding), functionality (HPLC-RI) and resistome profile (shot-gun metagenomics). Our data showed that the colonization of exogenous AMR strains within an established adult chicken cecum microbiota depends on basal community composition. VAN and CTX supplementation enhanced the colonization ability of both strains, in a donor-independent way. The colonization of the cecum microbiota with the AMR indicator strains alone did not impact the microbiota composition and functionality (short-chain fatty acids), nor altered antimicrobial resistance genes (ARGs) structure. On the contrary, antibiotic supplementation profoundly impacted the ceca microbial community and the effect appeared to be antibiotic and donor dependent. Interestingly, more than 80% of the ARGs were encoded on bacterial chromosome (unbinned contigs and MAG) after 30 days of fermentation. The resistome of VAN led to an increase in proportion of multidrug, floroquinolone, and macrolide resistance ARGs, while CTX-treated reactors was enriched in ARGs conferring resistance against multidrug, peptide, glycopeptide, lincosamide drug classes. In conclusion, our study revealed for the first time that the colonization of exogenous AMR strains in chicken cecum is donor-dependent, and that antibiotic pressure favor the colonization of the AMR strains tested and significantly impact the resistome of the chicken gut.