Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus

Abstract

Background: Staphylococcus argenteus and S. schweitzeri, were recently proposed as novel species within S. aureus complex (SAC). S. argenteus has been reported in many countries and can threaten human health. S. schweitzeri has not been associated with human infections, but has been isolated from non-human primates. Questions regarding the evolution of pathogenicity of these two species will remain elusive until an exploratory evolutionary framework is established.

Results: We present genomic comparison analysis among members of SAC based on a pan-genome definition, which included 15 S. argenteus genomes (five newly sequenced), six S. schweitzeri genomes and 30 divergent S. aureus genomes. The three species had divergent core genomes and rare interspecific recombination was observed among the core genes. However, some subtypes of staphylococcal cassette chromosome mec (SCCmec) elements and prophages were present in different species. Of 111 tested virulence genes of S. aureus, 85 and 86 homologous genes were found in S. argenteus and S. schweitzeri, respectively. There was no difference in virulence gene content among the three species, but the sequence of most core virulence genes was divergent. Analysis of the agr locus and the genes in the capsular polysaccharides biosynthetic operon revealed that they both diverged before the speciation of SAC members. Furthermore, the widespread geographic distribution of S. argenteus, sequence type 2250, showed ambiguous biogeographical structure among geographically isolated populations, demonstrating an international spread of this pathogen.

Conclusions: S. argenteus has spread among several countries, and invasive infections and persistent carriage may be not limited to currently reported regions. S. argenteus probably had undergone a recent host adaption and can cause human infections with a similar pathogenic potential.

Keywords: Agr; Biogeographical structure; Capsular polysaccharides; Comparative genomics; Staphylococcus argenteus; Staphylococcus aureus; Staphylococcus schweitzeri; Virulence gene.

Fig. 1

Phylogenetic relationship, genome information, and relevant typing information of SAC species. A maximum likelihood phylogenetic tree of SAC was constructed based on concatenated deduced amino acid sequences of 1375 single copy core genes of the 51 strains used in this study. Bootstrap values (expressed as percentages of 1000 replications) greater than 70% are shown at the branch points and the asterisk (*) indicates a bootstrap value of 100. The color-coded clades denote different species: red, S. aureus; green, S. argenteus; blue, S. schweitzeri. S. simiae was used as an outgroup (not shown). S. argenteus strains, SJTU F20124 (GenBank accession number: LWAN00000000), F20419 (LWAO00000000), F21164 (LWAP00000000), F21224 (LWAQ00000000), and F21285 (LWAR00000000) were sequenced as part of this study. For Sequence type, CRISPR, SCCmec, agr type, Serotype, and Prophage data: -, not detected/absent; +, detected/present; NA, data not available in the MLST database; and #, the type is close but divergent from the indicated subtype

Fig. 2

Pairwise bANI of SAC species. Pairwise bANI of S. simiae, S. aureus, S. argenteus and S. schweitzeri were determined based on the 1375 common single copy genes. For comparison of S. simiae to S. aureus, S. argenteus and S. schweitzeri, the mean bANI values were 84.63 ± 5.18% (median 84.14%), 84.89 ± 5.25% (84.26%), and 84.85 ± 5.19% (84.17%), respectively. Among the members of the SAC 1596 common genes were used determine the bANI. Interspecific mean bANI values were as follows: S. aureus, 98.76 ± 1.92% (median 99.23%); S. argenteus, 99.6 ± 0.85% (99.79%); and S. schweitzeri, 98.87 ± 1.74% (99.38%). The intraspecific mean bANI values were as follows: S. aureus vs. S. argenteus, 89.79 ± 4.63% (median 89.39%); S. aureus vs. S. schweitzeri, 90.92 ± 4.77% (90.64%); and S. argenteus vs. S. schweitzeri, 94.08 ± 3.69% (94.81%). The group interval was 0.1%

Fig. 3

Population structure of Staphylococcus aureus complex. a The population memberships of the inspected species for a priori defined number of clusters K = 2–4 inferred by the Structure software. Each individual is represented by a thin vertical line divided into K colored segments that represent the individual’s estimated membership fractions in K clusters. Populations are labeled below the figure. b The detection of the true number of clusters inferred by the Structure software and set ΔK = mean(|L"(K)|)/ sd(L(K)) as a function of K. ΔK attains its highest value when K = 2

Fig. 4

Comparisons of the predicted AgrD amino acid sequences from SAC species and agr types. Strains of the same agr type for each species have a same common sequence and are represented by a single sequence in this figure. Known autoinducing peptide (AIP) molecule sequences are marked in red rectangles. Potential novel AIP molecule sequences are marked in green rectangles

Fig. 5

Principal Component Analysis of SAC virulence genes. a PCA based on the presence (1) and absence (0) of 106 virulence genes; b PCA based on the mean distance of one strain against the rest 50 strains among 30 core virulence genes. Five genes, sed, see, sej, selr and etb, were excluded from the gene because they were not present in any strain. Species are marked using different colored dots: S. aureus (red), S. argenteus (green) and S. schweitzeri (blue). The cluster of dots representing S. argenteus ST2250 strains is indicated by the arrow. The genes that provide the best strain differentiation are shown in the biplot

Fig. 6

Maximum likelihood phylogenies of nine S. argenteus ST2250 genomes. Phylogenies were inferred from (a) the concatenated SNP-containing genes of core genome and (b) a presence/absence of gene content matrix. Numbers near each node correspond to bootstrap values in percentage of 1000 replications and the asterisk (*) indicates a bootstrap value of 100%. Geographical origins of the strains are marked on the branches: US, United States; AU, Australia; CN, China