Phenotypic and genotypic antimicrobial resistance of : an observational study in France.

Background: Large-scale studies are needed to clarify antimicrobial resistance in the foodborne pathogen () and the effectiveness of listeriosis treatment options. Here we examined the antimicrobial resistance patterns in over time and assessed genotype-phenotype concordances.

Methods: We analyzed 5339 isolates (2908 clinical and 2431 food isolates) collected in France and overseas territories, between 2012 and 2019. Whole genome sequencing was performed for all isolates and antimicrobial resistance profiles inferred from draft assemblies. Antimicrobial susceptibility towards 22 antimicrobials was determined for all clinical isolates, and in food isolates with acquired resistance genes.

Findings: All tested isolates were resistant to at least 3 different classes of antimicrobials, consistent with intrinsic traits. Acquired antimicrobial resistance in was rare (2.23% isolates) and more prevalent in food (mainly lineage II) compared to clinical isolates (mainly lineage I) (3.74% vs 0.98%,  < 0.0001), and in isolates with disinfectants or stress resistance traits (e.g. 20.20% vs 7.20%,  < 0.0001), suggesting co-selection of resistance in food-production environments. Acquired antimicrobial resistance could be predicted from genomes with high accuracy (>99%), except for ciprofloxacin. Acquired antimicrobial phenotypes were towards tetracyclines (mostly due to ), trimethoprim (), lincosamides (), macrolides (, ) and phenicols ().

Interpretation: The reference treatment for listeriosis (aminopenicillins/aminoglycosides) remains effective, with no acquired resistance observed. Continuous surveillance of antimicrobial resistance in clinical and food isolates is crucial to detect the emergence of novel resistance.

Funding: Institut Pasteur, INSERM, Santé Publique France, Investissement d'Avenir program Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR-10-LABX-62-IBEID).