Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae

Abstract

Streptococcusdysgalactiae (SD) is an emerging pathogen in human and veterinary medicine, and is associated with several host species, disease phenotypes and virulence mechanisms. SD has traditionally been divided into the subspecies dysgalactiae (SDSD) and subsp.equisimilis (SDSE), but recent molecular studies have indicated that the phylogenetic relationships are more complex. Moreover, the genetic basis for the niche versatility of SD has not been extensively investigated. To expand the knowledge about virulence factors, phylogenetic relationships and host-adaptation strategies of SD, we analyzed 78 SDSD genomes from cows and sheep, and 78 SDSE genomes from other host species. Sixty SDSD and 40 SDSE genomes were newly sequenced in this study. Phylogenetic analysis supported SDSD as a distinct taxonomic entity, presenting a mean value of the average nucleotide identity of 99%. Bovine and ovine associated SDSD isolates clustered separately on pangenome analysis, but no single gene or genetic region was uniquely associated with host species. In contrast, SDSE isolates were more heterogenous and could be delineated in accordance with host. Although phylogenetic clustering suggestive of cross species transmission was observed, we predominantly detected a host restricted distribution of the SD-lineages. Furthermore, lineage specific virulence factors were detected, several of them located in proximity to hotspots for integration of mobile genetic elements. Our study indicates that SD has evolved to adapt to several different host species and infers a potential role of horizontal genetic transfer in niche specialization.

Streptococcus dysgalactiae ssp. dysgalactiae in Norwegian bovine dairy herds: Risk factors, sources, and genomic diversity

“…Furthermore, a modest number of ST were identified among the 89 sequenced SDSD isolates from 27 geographically spread farms, and one ST (ST453) was identified in 15 different herds. In a previous study, we sequenced SDSD from different species and found that SDSD delineated according to host species (Porcellato et al, 2021). By documenting that a few SDSD genotypes are more prevalent and can be found in geographically spread bovine dairy herds, our study supports the existence of bovine-adapted SDSD.…”

“…The isolates had been collected by freezing the first SDSD isolates obtained from clinical mastitis (n = 5) and subclinical mastitis (n = 5) every month between April and November 2019. Of the 90 sequenced isolates, 20 have been described previously (Porcellato et al, 2021). All genomes are available at DDBJ/ENA/Gen-Bank under the BioProject PRJEB42928.…”

“…For multilocus sequence type (MLST) assignment, the draft genome was used as input in the MLST 2.0 (cge .cbs .dtu .dk/ services/ MLST) using the MLST scheme of Streptococcus dysgalactiae ssp. equisimilis (McMillan et al, 2010;Porcellato et al, 2021). To test whether any sequence type (ST) was associated with specific sampling sites (milk, body sites, environment), the frequency of each ST in each site was compared against that of other ST (as one group) using Fisher's exact test.…”

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

“…This gene shares greater than 70% identity between bovine SDSD and Streptococcus equi. Among the bovine SDSD genomes, the mga gene and an open reading frame (ORF) previously identified as homologous to S. pyogenes M proteins ( Porcellato et al, 2021 ) were observed upstream of the cspZ gene. The mga gene of bovine SDSD shares approximately 70% identity with S. pyogenes , but the ORF is around 40% identical to the S. pyogenes sequence.…”

“…The subspecies SDSE, initially regarded as human commensal bacteria ( Suzuki et al, 2011 ), is now recognized to be an important human pathogen, causing several infections, including bacteremia, cellulitis, endocarditis, peritonitis, septicemia, pneumonia, pharyngitis, and toxic shock syndrome, similar to those caused by S. pyogenes ( Brandt and Spellerberg, 2009 ; Bruun et al, 2013 ; Hagiya et al, 2013 ; Fuursted et al, 2016 ). Additionally, β-hemolytic isolates from animal hosts have been frequently identified as SDSE ( Acke et al, 2015 ; Pinho et al, 2016 ; Oh et al, 2018 , 2020 ; Porcellato et al, 2021 ).…”