Data_Sheet_2_New Insights on Streptococcus dysgalactiae subsp. dysgalactiae Isolates.PDF

Streptococcus dysgalactiae subsp. dysgalactiae (SDSD) has been considered a strict animal pathogen. Nevertheless, the recent reports of human infections suggest a niche expansion for this subspecies, which may be a consequence of the virulence gene acquisition that increases its pathogenicity. Previous studies reported the presence of virulence genes of Streptococcus pyogenes phages among bovine SDSD (collected in 2002–2003); however, the identity of these mobile genetic elements remains to be clarified. Thus, this study aimed to characterize the SDSD isolates collected in 2011–2013 and compare them with SDSD isolates collected in 2002–2003 and pyogenic streptococcus genomes available at the National Center for Biotechnology Information (NCBI) database, including human SDSD and S. dysgalactiae subsp. equisimilis (SDSE) strains to track temporal shifts on bovine SDSD genotypes. The very close genetic relationships between humans SDSD and SDSE were evident from the analysis of housekeeping genes, while bovine SDSD isolates seem more divergent. The results showed that all bovine SDSD harbor Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas IIA system. The widespread presence of this system among bovine SDSD isolates, high conservation of repeat sequences, and the polymorphism observed in spacer can be considered indicators of the system activity. Overall, comparative analysis shows that bovine SDSD isolates carry speK, speC, speL, speM, spd1, and sdn virulence genes of S. pyogenes prophages. Our data suggest that these genes are maintained over time and seem to be exclusively a property of bovine SDSD strains. Although the bovine SDSD genomes characterized in the present study were not sequenced, the data set, including the high homology of superantigens (SAgs) genes between bovine SDSD and S. pyogenes strains, may indicate that events of horizontal genetic transfer occurred before habitat separation. All bovine SDSD isolates were negative for genes of operon encoding streptolysin S, except for sagA gene, while the presence of this operon was detected in all SDSE and human SDSD strains. The data set of this study suggests that the separation between the subspecies “dysgalactiae” and “equisimilis” should be reconsidered. However, a study including the most comprehensive collection of strains from different environments would be required for definitive conclusions regarding the two taxa.

停乳链球菌停乳亚种（Streptococcus dysgalactiae subsp. dysgalactiae，SDSD）曾被认为是严格的动物病原体。然而，近期关于人类感染的报道表明该亚种的宿主生态位发生了拓展，这可能源于其获得了增强致病性的毒力基因。既往研究曾在2002至2003年采集的牛源SDSD中，检测到化脓性链球菌（Streptococcus pyogenes）噬菌体携带的毒力基因，但这类可移动遗传元件的具体身份仍有待阐明。为此，本研究旨在对2011至2013年采集的SDSD分离株进行分型鉴定，并将其与2002至2003年采集的SDSD分离株，以及美国国家生物技术信息中心（National Center for Biotechnology Information，NCBI）数据库中公开的化脓性链球菌基因组（包括人类SDSD与停乳链球菌似马亚种（S. dysgalactiae subsp. equisimilis，SDSE）菌株）进行比较，以追踪牛源SDSD基因型的时间演变特征。管家基因（housekeeping gene）分析结果显示，人类SDSD与SDSE之间存在极为紧密的遗传亲缘关系，而牛源SDSD分离株则表现出更高的遗传分化度。研究结果显示，所有牛源SDSD均携带有成簇规律间隔短回文重复序列（Clustered Regularly Interspaced Short Palindromic Repeats，CRISPR）/Cas IIA系统。该系统在牛源SDSD分离株中的广泛分布、重复序列的高度保守性，以及间隔区（spacer）中观察到的多态性，均可作为该系统具有活性的指示标志。综合来看，比较基因组分析显示，牛源SDSD分离株携带来源于化脓性链球菌前噬菌体的speK、speC、speL、speM、spd1与sdn毒力基因。本研究数据表明，这些毒力基因随时间推移得以保留，且似乎仅为牛源SDSD菌株所特有。尽管本研究中完成分型的牛源SDSD基因组尚未进行全序列测定，但本数据集（包括牛源SDSD与化脓性链球菌菌株的超抗原（superantigens，SAgs）基因具有高度同源性）提示，水平基因转移事件发生在宿主生态位分化之前。除sagA基因外，所有牛源SDSD分离株的链球菌溶血素S（streptolysin S）编码操纵子基因均呈阴性；而所有SDSE与人类SDSD菌株中均检测到了该操纵子的存在。本研究数据集提示，应当重新审视停乳链球菌两个亚种——"dysgalactiae"与"equisimilis"之间的分类界定。不过，若要针对这两个分类群得出确定性结论，还需开展纳入来自不同环境的菌株的大规模研究。