Influence of recombination and niche separation on the population genetic structure of the pathogen Streptococcus pyogenes

Abstract

The throat and skin of the human host are the principal reservoirs for the bacterial pathogen Streptococcus pyogenes. The emm locus encodes structurally heterogeneous surface fibrils that play numerous roles in virulence, depending on the strain. Isolates harboring the emm pattern A-C marker exhibit a strong tendency to cause throat infection, whereas emm pattern D strains are usually recovered from impetigo lesions; as a group, emm pattern E organisms fail to display obvious tissue tropisms. The peak incidence for streptococcal pharyngitis and impetigo varies with season and locale, leading to wide spatial and temporal distances between throat and skin strains. To assess any impact of niche separation on genetic variation, the extent of recombinational exchange between emm pattern A-C, D, and E subpopulations was evaluated. Analysis of nucleotide sequence data for internal portions of seven housekeeping loci from 212 isolates provides evidence of extensive recombination between strains belonging to different emm pattern subpopulations. Furthermore, no fixed nucleotide differences were found between emm pattern A-C and D strains. Thus, despite some niche separation created by distinct epidemiological trends and innate tissue tropisms there is little evidence for neutral gene divergence between throat and skin strains. Maintenance of a relationship between emm pattern and tissue tropism in the face of underlying recombination suggests that tissue tropism is associated with emm or a closely linked gene.

FIG. 1.

Cluster analysis of strains of defined emm pattern. The dendrogram was constructed using UPGMA and shows all unique emm type-ST combinations (n = 104). Labels at branch tips indicate emm type, followed by emm pattern group (A-C [ABC], D, or E); for cases where there is more than one ST associated with a given emm type, the string ends with a numerical assignment. In all instances, isolates of a given emm type share the same emm pattern grouping. Large asterisks denote nodes at linkage distances of ≤0.6, with descendants represented by six or more distinct clones (i.e., STs) and/or emm types. From the top of the dendrogram, the clusters are comprised of the following numbers of distinct emm types, STs, and emm patterns: cluster 1, six emm types and six STs (five of pattern A-C, one of pattern D); cluster 2, eight emm types and seven STs (six of pattern D, one of pattern E); cluster 3, seven emm types and nine STs (three of pattern A-C, six of pattern D); cluster 4, six emm types and six STs (one of pattern A-C, one of pattern D, four of pattern E).

FIG. 2.

Cluster analysis of strains of defined tissue site of isolation. The dendrogram shows all unique emm type-ST combinations (n = 61) of isolates known to be recovered from either the URT or impetigo lesions. Labels at branch tips indicate emm type, followed by emm pattern group (A-C [ABC], D, or E); for cases where there is more than one ST associated with a given emm type, the string ends with a numerical assignment. In all instances, isolates of a given emm type share the same emm pattern grouping. Large asterisks denote nodes at linkage distances of ≤0.6, with descendants represented by six or more distinct clones (i.e., STs) and/or emm types. The number of URT (○) and impetigo (▴) isolates for each emm type-ST combination is indicated to the left of the branch tip labels.

FIG. 3.

ML trees of concatenated housekeeping alleles. Unrooted, radial gene trees generated by the ML method, using the concatenated sequences of the seven housekeeping alleles for each strain (nucleotide sequence length = 3,134 bp), are shown. (A) Taxa for throat (n = 20) and impetigo (n = 22) isolates were selected at a linkage distance of 0.3; the most appropriate model for evolution was used (TrN + G + I). (B) Taxa for emm pattern A-C (n = 17) and D (n = 19) strains were selected at a linkage distance of 0.3; the most appropriate model for evolution was used (HKY85 + G + I). To determine the significance of the observed groupings, bootstrap analysis with 1,000 replicates was performed, using trees reconstructed by the neighbor-joining method to avoid excessive computational time while incorporating the same ML substitution parameters. Bootstrap values of >50% are indicated. The scale bars indicate the number of nucleotide substitutions per site. In panel A, strains for which there were descendants isolated from both tissue sites based on the dendrogram in Fig. 2 are indicated (∗); branch labels indicate throat (T) or skin (S) sources of each isolate.

FIG. 4.

ML analysis of gene tree congruence. The ML trees of each housekeeping locus are compared with the ML trees from the other six housekeeping loci. The differences in log likelihood scores (Δ−ln L) are shown between housekeeping loci (squares) and 200 trees of random topology (diamonds). The lower 99th percentile of the likelihood differences between the ML tree for each locus and the 200 random tree topologies is indicated (vertical line).

FIG. 5.

Split decomposition analysis of housekeeping alleles. Splits graphs are shown for all known alleles of yqiL (A) and mutS (B) found in S. pyogenes. Representation by isolates of the three emm pattern groupings is indicated for each allele. For yqiL, nucleotide differences between the four alleles occupying the corners of the central network are indicated. Pair-wise distances between sequences were estimated using the HKY85 model of evolution incorporating ML optimized parameters. Nearly identical graphs were obtained using uncorrected Hamming distances. The scale bars indicate the number of nucleotide substitutions per site. A fit parameter of 100 indicates that all conflicts in phylogenetic signals are depicted in the graph. Splits graphs for the other five housekeeping loci are available from the authors upon request.

FIG. 5.

Split decomposition analysis of housekeeping alleles. Splits graphs are shown for all known alleles of yqiL (A) and mutS (B) found in S. pyogenes. Representation by isolates of the three emm pattern groupings is indicated for each allele. For yqiL, nucleotide differences between the four alleles occupying the corners of the central network are indicated. Pair-wise distances between sequences were estimated using the HKY85 model of evolution incorporating ML optimized parameters. Nearly identical graphs were obtained using uncorrected Hamming distances. The scale bars indicate the number of nucleotide substitutions per site. A fit parameter of 100 indicates that all conflicts in phylogenetic signals are depicted in the graph. Splits graphs for the other five housekeeping loci are available from the authors upon request.