Recombination drives genetic diversification of Streptococcus dysgalactiae subspecies equisimilis in a region of streptococcal endemicity

Abstract

Infection of the skin or throat by Streptococcus dysgalactiae subspecies equisimilis (SDSE) may result in a number of human diseases. To understand mechanisms that give rise to new genetic variants in this species, we used multi-locus sequence typing (MLST) to characterise relationships in the SDSE population from India, a country where streptococcal disease is endemic. The study revealed Indian SDSE isolates have sequence types (STs) predominantly different to those reported from other regions of the world. Emm-ST combinations in India are also largely unique. Split decomposition analysis, the presence of emm-types in unrelated clonal complexes, and analysis of phylogenetic trees based on concatenated sequences all reveal an extensive history of recombination within the population. The ratio of recombination to mutation (r/m) events (11:1) and per site r/m ratio (41:1) in this population is twice as high as reported for SDSE from non-endemic regions. Recombination involving the emm-gene is also more frequent than recombination involving housekeeping genes, consistent with diversification of M proteins offering selective advantages to the pathogen. Our data demonstrate that genetic recombination in endemic regions is more frequent than non-endemic regions, and gives rise to novel local SDSE variants, some of which may have increased fitness or pathogenic potential.

Figure 1. Population structure of Indian SDSE isolates.

The 52 STs clustered into seven SLV-defined CCs. STs part of the same SLV defined CC are joined by black lines. When grouped at the less stringent DLV level seven CCs are defined (light shaded circles).

Figure 2. Minimum evolutionary tree of concatenated SDSE MLST loci.

The tree was constructed using concatenated sequences of 52 SDSE STs. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. Only bootstrap values greater than 80% are shown. Clonal complexes at both the SLV and DLV level, and singletons (s), as determined using eBURST, are also depicted.

Figure 3. Split decomposition analysis of Indian STs.

Shaded circles indicate DLV defined CCs. Solid lines enclose SLV defined CCs. STs associated with stC36, stg245 and stg480 are also indicated.

Figure 4. Phylogenetic relationship of SDSE based on emm nucleotide sequence.

The tree was constructed using the ME algorithm. Bootstrap values in which associated taxa are clustered in greater than 60% of cases are shown next to branches. CC_slvs and CC_dlvs associated with emm-types are also shown.