Comparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains

Abstract

Streptococcus anginosus is a prevalent member of the human flora. While it has been found in the microbiota of "healthy" asymptomatic individuals, it has also been associated with genitourinary tract infections and bacteremia. Based upon multilocus sequence analysis, two subspecies and two genomosubspecies have been characterized for the species. We previously conducted whole-genome sequencing of 85 S. anginosus isolates from the urinary tract. Here, we present genomic analysis of this species, including isolates from the urinary tract as well as gut and fecal, vaginal, oral, respiratory, and blood and heart samples. Average nucleotide identity and core genome analysis revealed that these strains form two distinct groups. Group 1 is comprised of the S. anginosus type strain and other previously identified S. anginosus subspecies and genomosubspecies, including isolates from throughout the human body. In contrast, group 2 consists of predominantly urinary streptococci (n = 77; 85.6%). Both of these S. anginosus groups are distinct from other members of the Streptococcus anginosus group (SAG) species S. intermedius and S. constellatus. Genes conserved among all strains of one group but not in any strains in the other group were next identified. Group 1 strains included genes found in S. intermedius and S. constellatus, suggesting that they were lost within the ancestor of the group 2 strains. In contrast, genes unique to the group 2 strains were homologous to more distant streptococci, indicative of acquisition via horizontal gene transfer. These genes are ideal candidates for use as marker genes to distinguish between the two groups in the human microbiota. IMPORTANCE Whole-genome analysis of S. anginosus strains provides greater insight into the diversity of this species than from marker genes alone. Our investigation of 166 publicly available S. anginosus genomes via average nucleotide identity and core genome analysis revealed two phylogenomically distinct groups of this species, with one group almost exclusively consisting of isolates from the urinary tract. In contrast, only 8 urinary strains were identified within the other group, which contained the S. anginosus type strain, as well as all identified subspecies and genomosubspecies. While genomic analysis suggested that this urinary group of S. anginosus is genomically different from the previously characterized S. anginosus subspecies, phenotypic characterization is still needed. Given prior reports of the prevalence of S. anginosus in the urinary tract of both continent and incontinent females, future studies are needed to investigate if the symptom state of the urinary tract is associated with these two different groups.

Keywords: Streptococcus; Streptococcus anginosus; urinary tract; urobiome.

FIG 1

Phylogenetic tree of the S. anginosus core genome. The inner ring corresponds to the isolation source. The outer ring corresponds to the grouping defined here. Isolates associated with one of the S. anginosus genomosubspecies or subspecies are indicated by a colored branch as well as the dotted line connecting the branch to the isolation source and group ring. These designations were determined by referring to Babbar et al. (12).

FIG 2

ANI analysis of publicly available genome assemblies of members of S. anginosus strains and S. constellatus and S. intermedius. The bar on the right indicates the species, group, and genomosubspecies or subspecies. ANI values of >95% are shown in red hues; ANIs of <95% are shown in blue hues. The tree at the top of the heatmap indicates the ANI-based relationship of the sequences examined, colored by species or group.