Prévalence, facteurs de risque et mécanismes de dissémination des gènes de résistance aux antibiotiques, l’espèce équine et l’espèce porcine ont été étudiées en insistant particulièrement sur les antibiotiques de haute importance en médecine humaine dans chaque filière (céphalosporines de 3e génération et fluoroquinolones respectivement).

Antimicrobial resistance has become an essential issue in the last decades because of the extensive use of antimicrobials in numerous sectors. In order to follow the OneHealth approach, it is critical to have a precise picture of each situation, to adjust recommendations and prevent resistance gene dissemination as well as plasmid and clone spread. Our objectives were adapted to the animal populations under study. Therefore, our results were compatible with each sector. In the equine sector, we quantified phenotypic resistance and identified β-lactamase (ESBL/AmpC) genes present in the intestinal microbiome of healthy horses and we identified risk factors associated with their carriage both in France and in Quebec. Then, in France we characterized ESBL/AmpC gene spread mechanisms. We demonstrated that commensal E. coli originating from the feces of healthy horses were mostly non-susceptible to ampicillin, amoxicillin/clavulanic acid and streptomycin. The presence of multidrug resistant E. coli and of E. coli carrying ESBL/AmpC genes was found in around 45% and 8% of horses respectively. The most frequently detected gene was blaCTX-M-1, although blaCTX-M-2 and blaCTX-M-14 were also identified in France. The AmpC gene blaCMY-2 was identified in both localities. Medical treatment, staff number, activity, and participation in an equestrian event within the last three months were identified as risk factors for MDR or ESBL/AmpC E. coli. In France, commensal E. coli from healthy horses most commonly possessed the IncHI1-ST9 plasmid. This plasmid carries blaCTX-M-1/2 genes and the fos operon. For the swine sector in Quebec, our objectives were to gather data provided by the Animal pathogenic and zoonotic E. coli (APZEC) database between 2008 and 2017, to assess the presence of a spatio-temporal cluster for enrofloxacin non-susceptible ETEC:F4 and to characterize these isolates and the mobile genetic elements they carry. Enrofloxacin is an antibiotic classified as highly important in human medicine and as such needs to come under higher scrutiny. For this sector, we demonstrated that more than 90% of enterotoxigenic E. coli (ETEC) isolates from diseased swine submitted to the EcL between 2008 and 2016, were multidrug resistant. The main virotype in 2014 was LT:STb:F4. It was subsequently replaced by the LT:STb:STa:F4 virotype. A spatio-temporal cluster of LT:STb:STa:F4 isolates non-susceptible to enrofloxacin was detected between 04/2015 and 09/2016 in the centre of the Monteregie region. These isolates constituted an ETEC:F4 high risk enrofloxacin non-susceptible clone, which has been spreading in North America since 2013. Isolates belonging to this clone are ST100, O149H10, phylogroup A, and fimH gene negative. These isolates are multidrug resistant and associated with a higher pathogenicity and virulence than isolates detected before 2000. They all carry the incFII replicon.  Resistance and mechanisms of dissemination are different according to the animal species being studied. This is likely due to different patterns of antimicrobial use in each industry and possible interactions with different protagonists in contact with the animals. It is essential to understand the situation for each animal species in order to adapt recommendations for efficiently limiting the spread of resistance genes, plasmids and clones.

Keyphrases: Céphalosporinases, Cheval, ETEC, Antimicrobial resistance, Cephalosporinase, ESBL, Fluoroquinolones non-susceptibility, Equine, Swine, Short-chain fructo-oligosaccharides, ETEC, High-risk clone.