Occurrence and associated characteristics of a mutated ant(6')-Ia gene among Enterococcus faecium strains expressing phenotypic susceptibility to high levels of streptomycin

Enterococcal high-level resistance to streptomycin (HLR-S) (MIC [≥] 2000 {micro}g/ml), conferred by production of a variety of aminoglycoside modifying enzymes (AMES), has been reported worldwide and a nucleotidyltransferase (ANT) enzyme encoded by the ant(6)-Ia gene is frequently associated with this phenotype. However, during a study conducted by our group on whole genome sequencing (WGS) analyses of Enterococcus faecium isolates, we observed that 32 E. faecium strains identified as susceptible to high-levels of streptomycin by the disk diffusion method had the of ant(6)-Ia gene annotated in their genomes. Antimicrobial susceptibility to streptomycin was reassessed by phenotypic testing and the presence of the ant(6)-Ia gene was confirmed by PCR in all the isolates. Alignment of the ant(6)-Ia gene with a reference sequence revealed a deletion of the first 48 nucleotides and four nonsynonymous mutations, leading to the substitution of a Glutamine to Methionine and an Aspartic Acid to Asparagine in the amino acid sequence. The protein structure was modelled by using the Phyre2 platform and the results indicated alterations in the N-terminus region leading to changes in the predicted binding site. Also, by searching the NCBI database we identified the genomes of 71 strains carrying the mutated gene. MLST analysis revealed that most strains carrying the mutated gene, including those described in this study belonged to hospital-adapted lineages, suggesting the occurrence of clonal dissemination of a subset of mutated isolates. HIGHLIGHTSO_LIThe presence of a mutated ant(6)-Ia gene was identified among Enterococcus faecium isolates expressing phenotypic susceptibility to high levels of streptomycin. C_LIO_LINonsynonymous mutations and inactivating changes in the ant(6)-Ia gene led to incongruities between phenotypes and genotypes. C_LIO_LIAlterations in the amino acid sequence had impacts on protein structure, with changes in the N-terminus region and the binding site. C_LI