Identification of aminoglycoside phosphotransferases of clinical bacterial isolates in the microbiota of russians

Abstract

Antibiotic resistance is one of the biggest threats to modern medicine. Response to antimicrobial treatment is seriously disrupted by aminoglycoside phosphotransferases (Aph) - enzymes produced by bacteria. The aph genes were annotated in many bacterial species, including commensals of the gut microbiota that can transfer these genes to clinically important strains. For this study we prepared a catalog of 21 aph genes. The in silico analysis of 11 intestinal microbiomes of healthy Russians revealed the presence of 3 cataloged aph genes in 7 microbiota samples, namely aph(3'')-Ib, aph(3')-IIIa and aph(2'')-Ia. The most frequent was the aph(3')-IIIa gene detected in 6 metagenomes. Of note, this gene was first discovered in Enterococcus faecalis, but in this study we observed it in sequences typical for commensal Ruminococcus obeum and opportunistic Enterococcus faecium, Roseburia hominis, Streptococcus pyogenes and Staphylococcus epidermidis. Similarly, aph(2'')-Ia originally present in E. faecalis was detected in a sequence typical for Clostridium difficile. Our findings are consistent with the reports on the strong association between the geographical origin of the individual and frequency of aph genes. We suggest that clinical examination should include antibiotic sensitivity tests run not only on the causative agent, but also on the gut microbiota, for a better treatment outcome.