Characterization of antibiotic-resistance phenotypic and genotypic traits in new human isolates of Akkermansia muciniphila

Akkermansia muciniphila is a commensal bacterium commonly found in healthy gut microbiota. This microorganism is widely considered as a next-generation beneficial bacterium, candidate to improve metabolic disorders. Recently the EFSA's Panel on Nutrition, Novel food, and Food Allergens has declared that pasteurized A. muciniphila DSM 22959 (also MucT, ATCC BAA-835) can be considered safe as a novel food, opening the door to its commercialization as a food supplement. Information on antimicrobial resistance (AMR) for bacteria deliberately introduced into the food chain is of paramount importance. However, there is little information regarding the AMR patterns of A. muciniphila and reference cut-off values to distinguish strains with acquired resistance from susceptible strains. In this study, we combined a genomic approach with the evaluation of the antibiotic susceptibility profile in five human A. muciniphila isolates. Genomic mining for AMR genes and MICs determinations revealed that only one strain harboring tetW gene showed reduced sensitivity to tetracycline, whereas all A. muciniphila strains showed low sensitivity to ciprofloxacin and aminoglycosides. All strains harbor the gene adeF, which code for a subunit of the resistance-nodulation-cell division (RND) efflux pump system, potentially involved in the resistance to ciprofloxacin. Conversely, only two strains showed a possible genetic determinant for resistance to aminoglycosides, indicating that poor sensitivity to this class of antibiotics could be due to a more general intrinsic mechanism. To clarify the role of the efflux pump in ciprofloxacin reduced susceptibility, we determined MIC in presence of the protonophore CCCP, and the efflux pump inhibitors PAßN. Our results revealed that the susceptibility towards ciprofloxacin was not affected by alteration of the electrochemical proton gradient or by the inhibition of efflux pumps.