Evolution of the Staphylococcus argenteus ST2250 Clone in Northeastern Thailand Is Linked with the Acquisition of Livestock-Associated Staphylococcal Genes

Abstract

Staphylococcus argenteus is a newly named species previously described as a divergent lineage of Staphylococcus aureus that has recently been shown to have a global distribution. Despite growing evidence of the clinical importance of this species, knowledge about its population epidemiology and genomic architecture is limited. We used whole-genome sequencing to evaluate and compare S. aureus (n = 251) and S. argenteus (n = 68) isolates from adults with staphylococcal sepsis at several hospitals in northeastern Thailand between 2006 and 2013. The majority (82%) of the S. argenteus isolates were of multilocus sequence type 2250 (ST2250). S. aureus was more diverse, although 43% of the isolates belonged to ST121. Bayesian analysis suggested an S. argenteus ST2250 substitution rate of 4.66 (95% confidence interval [CI], 3.12 to 6.38) mutations per genome per year, which was comparable to the S. aureus ST121 substitution rate of 4.07 (95% CI, 2.61 to 5.55). S. argenteus ST2250 emerged in Thailand an estimated 15 years ago, which contrasts with the S. aureus ST1, ST88, and ST121 clades that emerged around 100 to 150 years ago. Comparison of S. argenteus ST2250 genomes from Thailand and a global collection indicated a single introduction into Thailand, followed by transmission to local and more distant countries in Southeast Asia and further afield. S. argenteus and S. aureus shared around half of their core gene repertoire, indicating a high level of divergence and providing strong support for their classification as separate species. Several gene clusters were present in ST2250 isolates but absent from the other S. argenteus and S. aureus study isolates. These included multiple exotoxins and antibiotic resistance genes that have been linked previously with livestock-associated S. aureus, consistent with a livestock reservoir for S. argenteus These genes appeared to be associated with plasmids and mobile genetic elements and may have contributed to the biological success of ST2250.IMPORTANCE In this study, we used whole-genome sequencing to understand the genome evolution and population structure of a systematic collection of ST2250 S. argenteus isolates. A newly identified ancestral species of S. aureus, S. argenteus has become increasingly known as a clinically important species that has been reported recently across various countries. Our results indicate that S. argenteus has spread at a relatively rapid pace over the past 2 decades across northeastern Thailand and acquired multiple exotoxin and antibiotic resistance genes that have been linked previously with livestock-associated S. aureus Our findings highlight the clinical importance and potential pathogenicity of S. argenteus as a recently emerging pathogen.

Keywords: Staphylococcus argenteus; Staphylococcus aureus; antibiotic resistance; genomic epidemiology.

FIG 1

(A) Phylogenetic tree constructed from SNPs in the S. aureus (red) and S. argenteus (blue) core genome alignment. Outer ring: STs of clusters containing 10 or more isolates. Inner ring: BAPS clustering represented by three bands to depict three parameter values, i.e., 20, 40, and 60, of the estimated number of clusters. (B) Bayesian analysis to define the age of the MRCA of S. argenteus ST2250 and the five predominant S. aureus STs (ST88, ST1, ST97, ST6, and ST121). Error bars denote 95% CIs (see Materials and Methods for details). (C) Distribution of rates of spread of ST2250, ST121, and ST6, which had a temporal signal. Each box shows the interquartile range, and the whiskers indicate the boundary of 1.5 times the interquartile range. The white marker denotes the median value. The colored area is the probability density of the data at different values.

FIG 2

(A) Bayesian phylogenetic tree of S. argenteus ST2250 including isolates from Thailand and elsewhere. Node values are node ages in years. Bars on the nodes show 95% CIs. The arrow shows the node in which the tet(L) gene was acquired. (B) Phylogenetic tree of the data presented in panel A with ancestral states of nodes inferred from maximum-likelihood analysis. Pie charts show the marginal probability of each status (country of origin) for each node.

FIG 3

(A) Phylogenetic tree based on SNPs in the core genome of S. aureus and S. argenteus and the presence or absence of accessory genes across the genomes. Heatmap colors denote the frequency of each accessory gene across the collection. (B) Comparative pangenome analysis of S. aureus and S. argenteus. The values on each side of the table show the percentages of isolates of that species harboring the gene, and the values within the table are the numbers of genes shared by those isolates. (C) The relative frequency of known antibiotic resistance genes in the S. argenteus and S. aureus populations. (D) Alignment of genomic components of plasmids P1-tetL-cad-bla and P2-cad-bla, and known plasmid p18813-P04.