Occurrence, variability and evolutionary relations of efflux pump determinants across five pathogenic Staphylococcus species.

Multidrug efflux pumps (MDR EPs) play a major role in the emergence of antimicrobial resistance in Staphylococcus aureus. Among these, the native NorA is the most well-studied MDR EP in this species. However, efflux-mediated resistance is only scarcely characterized in other staphylococci. The aims of this study were to assess the genetic variability and phylogenetic relations of main efflux pump genes in S. aureus and four other pathogenic staphylococci, and to identify new putative MDR transporters in these species. Nucleotide sequences of norA, norB, norC, norB/C, mepA and related sequences of S. aureus, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus lugdunensis and Staphylococcus hominis were compiled and assessed for gene variability. The norA variability was further evaluated in a collection of clinical strains of S. epidermidis, S. haemolyticus and S. hominis. Phylogenetic analyses were performed to characterize the evolution of norA across the five species and to explore potential relations between norB, norC, norB/C and related sequences. Additional putative MDR transporter genes were searched in public databases and then BLAST searched against complete genomes of each species. Only S. aureus presented several norA and norB alleles. The relations between the norA genes of the five species follow the evolutionary relations of these staphylococci. Phylogenetic analysis also revealed the existence of a norB/C gene in S. aureus, which is homologous to the norB/C genes of S. epidermidis, S. haemolyticus, S. lugdunensis and S. hominis. It also indicated that S. aureus norB and norC as well as the newly assigned S. haemolyticus norB/C-like are related genes, absent in the other species. In silico analysis identified several new candidate MDR transporters in the five species. This study provides a novel, comprehensive comparative analysis of major efflux pump determinants across five clinically relevant Staphylococcus species. This analysis expanded our knowledge of the norA evolutionary pathways and provided a framework for a more consistent annotation of norB, norC and related determinants among these staphylococci. The identification of putatively new MDR transporter determinants in staphylococcal species of clinical relevance other than S. aureus provides a framework for future functional studies.