Detection of the antibiotic resistance gene content of normal microbiota Bacteroides, Parabacteroides and Phocaeicola isolates from European countries

Abstract Background The Bacteroides fragilis group (BFG) species are the most significant anaerobic pathogens and they are also the most antibiotic resistant anaerobic species. Therefore, surveying their antimicrobial resistance levels and investigating their antibiotic resistance mechanisms is recommended. Since their infections are endogenous and they are important constituents of the intestinal microbiota, the properties of the intestinal strains are also important to follow. The aim of this study was to investigate the main antibiotic gene content of normal microbiota isolates and compare them with the gene carriage of strains isolated from infections. Results We detected 14 antibiotic resistance determinants of 184 intestinal BFG strains that were isolated in 5 European countries (Belgium, Germany, Hungary, Slovenia and Turkey) and compared these with values obtained earlier for European clinical strains. Differences were found for antibiotic resistance genes that are considered to be mobile, with higher degrees for cfxA , erm (F) and tet (Q) and with lower degrees for msrSA , erm (B) and erm (G). In addition, a different gene prevalence was found depending on the taxonomical groups, e.g. B. fragilis and NBFB. Some strains with both the cepA and cfiA β-lactamase genes were also detected which is thought to be exceptional since up till now, the B. fragilis genetic divisions were defined by the mutual exclusion of these two genes. Conclusions In our study we found that the prevalence of some antibiotic resistance genes detected in the clinical and intestinal BFG strains differ, which we accounted for the differential composition of the Bacteroides microbiota and/or the MGE mobilities at the luminal vs. mucosal sites of the intestine.