Population genetic structure of the Staphylococcus intermedius group: insights into agr diversification and the emergence of methicillin-resistant strains

Abstract

The population genetic structure of the animal pathogen Staphylococcus intermedius is poorly understood. We carried out a multilocus sequence phylogenetic analysis of isolates from broad host and geographic origins to investigate inter- and intraspecies diversity. We found that isolates phenotypically identified as S. intermedius are differentiated into three closely related species, S. intermedius, Staphylococcus pseudintermedius, and Staphylococcus delphini. S. pseudintermedius, not S. intermedius, is the common cause of canine pyoderma and occasionally causes zoonotic infections of humans. Over 60 extant STs were identified among the S. pseudintermedius isolates examined, including several that were distributed on different continents. As the agr quorum-sensing system of staphylococci is thought to have evolved along lines of speciation within the genus, we examined the allelic variation of agrD, which encodes the autoinducing peptide (AIP). Four AIP variants were encoded by S. pseudintermedius isolates, and identical AIP variants were shared among the three species, suggesting that a common quorum-sensing capacity has been conserved in spite of species differentiation in largely distinct ecological niches. A lack of clonal association of agr alleles suggests that assortive recombination may have contributed to the distribution of agr diversity. Finally, we discovered that the recent emergence of methicillin-resistant strains was due to multiple acquisitions of the mecA gene by different S. pseudintermedius clones found on different continents. Taken together, these data have resolved the population genetic structure of the S. intermedius group, resulting in new insights into its ancient and recent evolution.

FIG. 1.

Phylogenetic tree constructed by the neighbor-joining method with 1,000 bootstrap replicates of concatenated 16S rRNA gene, tuf, cpn60, and pta sequences. (A) Radiating tree indicating the three major phylotypes, with species type strains indicated by triangles. (B) Branch style tree indicating the host and geographic origins of all isolates. Methicillin-resistant, mecA-positive isolates (dots); human isolates (squares); previously identified S. pseudintermedius isolates (diamonds); and species-type isolates (triangles) are indicated, along with the agr type in roman numerals in parentheses. Bootstrap values over 50% are indicated.

FIG. 2.

Schematic diagram of the clonal relatedness of S. pseudintermedius STs predicted by eBURST analysis. Each ST is represented by a black dot, the size of which is proportional to the number of isolates of that ST. Blue and yellow dots denote the predicted group founder and subgroup founders, respectively. Single-locus variants are linked by lines. STs that include MRSP strains are indicated by red circles. STs that are not linked by branches to other STs do not share at least four identical alleles with any other ST.