摘要
      猪链球菌是养猪业中一个重要的经济和福利问题。泛基因组分析为发现与细菌病原体发病机制有关的基因提供了一种计算机方法。在本研究中，我们对208个猪链球菌分离株进行了全基因组分析，分为致病型、可能的机会性和共生型，以确定猪链球菌的新的候选毒力相关基因（VAG）。利用卡方检验和LASSO回归模型，确定了与猪链球菌P1/7标记SSU_RS09525、SSU_RS09155和SSU_RS03100（>95%同一性）相对应的三个辅助pan基因与致病病理类型具有显著相关性。提出的新型SSU_RS09525 + /SSU_RS09155编号 + /编号：RS03100 + 基因型鉴定了96%的致病性致病型菌株，为预测北美猪链球菌分离株的致病性提供了一种新的基因分型方案。此外，携带抗微生物耐药性基因（ARGs）和VAG的可移动遗传元件已被鉴定，但似乎在ARGs和VAG传播中没有发挥主要作用。
Abstract
Streptococcus suis is a significant economic and welfare concern in the swine industry. Pan-genome analysis provides an in-silico approach for the discovery of genes involved in pathogenesis in bacterial pathogens. In this study, we performed pan-genome analysis of 208 S. suis isolates classified into the pathogenic, possibly opportunistic, and commensal pathotypes to identify novel candidate virulence-associated genes (VAGs) of S. suis. Using chi-square tests and LASSO regression models, three accessory pan-genes corresponding to S. suis strain P1/7 markers SSU_RS09525, SSU_RS09155, and SSU_RS03100 (>95% identity) were identified as having a significant association with the pathogenic pathotype. The proposed novel SSU_RS09525 + /SSU_RS09155 + /SSU_RS03100 + genotype identified 96% of the pathogenic pathotype strains, suggesting a novel genotyping scheme for predicting the pathogenicity of S. suis isolates in North America. In addition, mobile genetic elements carrying antimicrobial resistance genes (ARGs) and VAGs were identified but did not appear to play a major role in the spread of ARGs and VAGs.

https://link.springer.com/article/10.1186/s13567-022-01039-8