Phylogenetic analysis and accessory genome diversity reveal insight into the evolutionary history of Streptococcus dysgalactiae

Abstract

Streptococcus dysgalactiae (SD) is capable of infecting both humans and animals and causing a wide range of invasive and non-invasive infections. With two subspecies, the taxonomic status of subspecies of SD remains controversial. Subspecies equisimilis (SDSE) is an important human pathogen, while subspecies dysgalactiae (SDSD) has been considered a strictly animal pathogen; however, occasional human infections by this subspecies have been reported in the last few years. Moreover, the differences between the adaptation of SDSD within humans and other animals are still unknown. In this work, we provide a phylogenomic analysis based on the single-copy core genome of 106 isolates from both the subspecies and different infected hosts (animal and human hosts). The accessory genome of this species was also analyzed for screening of genes that could be specifically involved with adaptation to different hosts. Additionally, we searched putatively adaptive traits among prophage regions to infer the importance of transduction in the adaptation of SD to different hosts. Core genome phylogenetic relationships segregate all human SDSE in a single cluster separated from animal SD isolates. The subgroup of bovine SDSD evolved from this later clade and harbors a specialized accessory genome characterized by the presence of specific virulence determinants (e.g., cspZ) and carbohydrate metabolic functions (e.g., fructose operon). Together, our results indicate a host-specific SD and the existence of an SDSD group that causes human–animal cluster infections may be due to opportunistic infections, and that the exact incidence of SDSD human infections may be underestimated due to failures in identification based on the hemolytic patterns. However, more detailed research into the isolation of human SD is needed to assess whether it is a carrier phenomenon or whether the species can be permanently integrated into the human microbiome, making it ready to cause opportunistic infections.

Phenotypic and Genotypic Characterization of Antimicrobial Resistance in Streptococci Isolated from Human and Animal Clinical Specimens

“…The tested strains isolated from animals came from cattle and were assigned to the SDSD subspecies. However, strains infecting companion animals sometimes have been identified as SDSE [ 33 ]. Our studies have shown that the resistance of this species to drugs used in human therapy applies to both subspecies.…”

Evolutionary dynamics of the accessory genomes of Staphylococcus aureus

“…Using accessory genomes in disease epidemiology proved to be effective because gene turnover (i.e., gain and loss) occurs faster than the accumulation of mutations in A. baumannii over very short microevolutionary scales ( 33 ). In Streptococcus dysgalactiae , the distinction between its two subspecies and their ability to adapt to either human or bovine host lie in a specialized accessory genome characterized by the presence of specific surface-protein virulence determinants and carbohydrate metabolic functions ( 34 ). In S. aureus from different vertebrate hosts, accessory gene pools consisting of host-specific genes promote adaptive evolution after host-switching events ( 10 ).…”

The Genetic Diversity and Antimicrobial Resistance of Pyogenic Pathogens Isolated from Porcine Lymph Nodes

“…However, the identification of S. dysgalactiae strains into subspecies was not performed because the taxonomy of S. dysgalactiae remains unclear. Recent studies indicate that S. dysgalactiae may be segregated into two distinct groups: one includes only human strains, while the other includes animal strains of swine, canine and equine origin, as well as more phylogenetically distinct bovine strains [ 37 ]. Most S. dysgalactiae isolates in this study belonged to Lancefield group C, as is consistent with previous reports [ 7 , 38 ], but some isolates belonged to group A.…”