Overlapping population structures of nasal isolates of Staphylococcus aureus from healthy Dutch and American individuals

Abstract

To understand Staphylococcus aureus nasal carriage and its relationship with subsequent disease, insight into the natural (nonclinical) bacterial population structure is essential. This study investigated whether the distributions of S. aureus genotypes that cause colonization differ by geographic locales. High-throughput amplified fragment length polymorphism (AFLP) analysis was performed on nasal isolates of S. aureus from healthy American (n = 391) and Dutch (n = 829) volunteers. In total, 164,970 binary outcomes, covering 135 different markers per isolate, were scored. Methicillin resistance was defined for all strains; pulsed-field gel electrophoresis typing was performed for the American isolates. The overall population structures of the American and Dutch S. aureus isolates were comparable. The same four major AFLP clusters (I to IV) and subclusters were identified for both collections. However, the Dutch methicillin-susceptible S. aureus (MSSA) isolates were overrepresented in AFLP cluster III (P = 0.0016). Furthermore, the majority of the American methicillin-resistant S. aureus isolates (90.5%) were located in AFLP cluster I (P < 0.0001). This result identifies differences in the local prevalence of certain S. aureus genotypes. AFLP clusters II and III, which represent multilocus sequence typing clonal complexes 30 and 45, respectively, account for 46.4% of all MSSA isolates in the study, suggesting that these two lineages have evolved as extremely successful pandemic colonizers of humans. In conclusion, the overall population structures of American and Dutch nasal carriage isolates of S. aureus are surprisingly similar, despite subtle geographic differences in the prevalence of certain S. aureus genotypes.

FIG. 1.

Two-dimensional hierarchical clustering of the 1,222 S. aureus strains. The green/red figure represents 164,970 binary outcomes generated by high-throughput AFLP with 135 marker fragments per strain. Marker absence corresponds with green, and marker presence corresponds with red (gray represents ambiguous positions [i.e., weak bands] that are scored as marker absence in the mathematical analyses). The dendrogram on the y axis represents the phylogenetic clustering of the 1,222 strains. The dendrogram on the x axis shows the clustering of the 135 AFLP markers, many of which segregate in specific groups. The colored, striped bars on the right represent the distribution of the U.S. strains (blue) and the reference strains Mu50 and N-315 (light green). The Dutch carriage strains (n = 829) are not pointed out separately. In conjunction with PCA, four major branches (I, II, III, and IV) were identified; these are represented by the black and white bar on the right of the figure. AFLP cluster IVa has been annotated separately (between AFLP cluster I and II), because these S. aureus strains were assigned (arbitrarily) to cluster IV, based on PCA (Fig. 2 to 4).

FIG. 2.

PCA of the AFLP data for all 1,222 S. aureus isolates. The different cubes (plotted in three-dimensional space), colored according to the source, represent every strain in the study. Each axis represents the score calculated for that strain on each PC. The four circles indicate the different phylogenetic AFLP clusters. The two reference strains (N315 and Mu50) are not visible, as they are hidden by other strains.

FIG. 3.

Distribution of the American MSSA (n = 307) and the American MRSA (n = 84) isolates. PCA analysis of the AFLP data for all strains (n = 1,222), showing only the 391 American S. aureus isolates with the distribution of the MSSA versus the MRSA strains.

FIG. 4.

Distribution of PFGE types of the 391 American S. aureus isolates over the four AFLP clusters. PCA of the AFLP data of all strains (n = 1,222), showing only the 391 American S. aureus isolates (which includes the American isolates that did not fit within the established USA PFGE lineages [“unique”]). The cubes are colored according to the PFGE type.