School of Biological Sciences, University of California San Diego, San Diego, California, USA.
Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA.
mSphere. 2023 Apr 20;8(2):e0068722. doi: 10.1128/msphere.00687-22. Epub 2023 Feb 7.
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 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 type strain and other previously identified subspecies and genomosubspecies, including isolates from throughout the human body. In contrast, group 2 consists of predominantly urinary streptococci ( = 77; 85.6%). Both of these 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 , 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. Whole-genome analysis of strains provides greater insight into the diversity of this species than from marker genes alone. Our investigation of 166 publicly available 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 type strain, as well as all identified subspecies and genomosubspecies. While genomic analysis suggested that this urinary group of is genomically different from the previously characterized subspecies, phenotypic characterization is still needed. Given prior reports of the prevalence of 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.
咽峡炎链球菌是人类菌群中的常见成员。虽然它已在“健康”无症状个体的微生物群中被发现，但它也与尿路感染和菌血症有关。根据多位点序列分析，该物种已被确定为两个亚种和两个基因组亚种。我们之前对 85 例来自尿路的分离株进行了全基因组测序。在这里，我们对该物种进行了基因组分析，包括来自尿路以及肠道和粪便、阴道、口腔、呼吸道以及血液和心脏样本的分离株。平均核苷酸同一性和核心基因组分析表明，这些菌株形成两个不同的组。第 1 组由模式株和其他先前鉴定的亚种和基因组亚种组成，包括来自人体各处的分离株。相比之下，第 2 组主要由尿链球菌组成（=77；85.6%）。这两个组都与咽峡炎链球菌组（SAG）的其他成员中间链球菌和星座链球菌不同。接下来鉴定了一组中所有菌株都保守但另一组中任何菌株都没有的基因。第 1 组菌株包含在中间链球菌和 中发现的基因，表明它们在第 2 组菌株的祖先中丢失了。相比之下，第 2 组菌株特有的基因与更远的链球菌同源，表明它们是通过水平基因转移获得的。这些基因是区分人类微生物群中这两个组的理想候选标记基因。对 株的全基因组分析比仅使用标记基因提供了对该物种多样性的更深入了解。通过平均核苷酸同一性和核心基因组分析对 166 个公开可用的 基因组进行的调查显示，该物种存在两个系统发育上不同的组，其中一组几乎完全由来自尿路的分离株组成。相比之下，另一个组中只鉴定到 8 个尿株，其中包含模式株以及所有鉴定出的亚种和基因组亚种。虽然基因组分析表明该尿路组与先前表征的 亚种在基因组上不同，但仍需要进行表型特征分析。鉴于先前有报道称 在有和无尿失禁的女性的尿路中普遍存在，未来的研究需要调查尿路的症状状态是否与这两个不同的组有关。
