Table_1_Populational genomic insights of Paraclostridium bifermentans as an emerging human pathogen.XLSX

Paraclostridium bifermentans (P.b) is an emerging human pathogen that is phylogenomically close to Paeniclostridium sordellii (P.s), while their populational genomic features and virulence capacity remain understudied. Here, we performed comparative genomic analyses of P.b and compared their pan-genomic features and virulence coding profiles to those of P.s. Our results revealed that P.b has a more plastic pangenome, a larger genome size, and a higher GC content than P.s. Interestingly, the P.b and P.s share similar core-genomic functions, but P.b encodes more functions in nutrient metabolism and energy conversion and fewer functions in host defense in their accessory-genomes. The P.b may initiate extracellular infection processes similar to those of P.s and Clostridium perfringens by encoding three toxin homologs (i.e., microbial collagenase, thiol-activated cytolysin, phospholipase C, which are involved in extracellular matrices degradation and membrane damaging) in their core-genomes. However, P.b is less toxic than the P.s by encoding fewer secretion toxins in the core-genome and fewer lethal toxins in the accessory-genome. Notably, P.b carries more toxins genes in their accessory-genomes, particularly those of plasmid origin. Moreover, three within-species and highly conserved plasmid groups, encoding virulence, gene acquisition, and adaptation, were carried by 25–33% of P.b strains and clustered by isolation source rather than geography. This study characterized the pan-genomic virulence features of P.b for the first time, and revealed that P. bifermentans is an emerging pathogen that can threaten human health in many aspects, emphasizing the importance of phenotypic and genomic characterizations of in situ clinical isolates.

双发酵副梭菌（Paraclostridium bifermentans，简称P.b）是一种新兴人类致病菌，其系统基因组学特征与索氏梭菌（Paeniclostridium sordellii，简称P.s）亲缘关系密切，但二者的群体基因组特征与毒力能力仍有待深入研究。
本研究针对P.b开展了比较基因组学分析，并将其泛基因组（pan-genome）特征与毒力编码谱与P.s进行了对比。研究结果显示，相较于P.s，P.b拥有更为可塑性的泛基因组、更大的基因组尺寸以及更高的GC含量。
值得关注的是，P.b与P.s的核心基因组（core-genome）功能相似，但P.b的附属基因组（accessory-genome）中，营养代谢与能量转换相关功能的编码量更多，而宿主防御相关功能的编码量更少。P.b可通过在核心基因组中编码三类毒素同源物——即微生物胶原酶、巯基活化溶细胞素、磷脂酶C（这些毒素参与细胞外基质降解与细胞膜损伤），启动与P.s及产气荚膜梭菌（Clostridium perfringens）相似的细胞外感染过程。然而，由于P.b核心基因组中编码的分泌型毒素更少，且附属基因组中编码的致死毒素也更少，其毒力弱于P.s。
尤为值得注意的是，P.b在附属基因组中携带更多毒素基因，尤其是质粒来源的毒素基因。此外，25%~33%的P.b菌株携带有三类物种内高度保守的质粒群，这些质粒群编码毒力、基因获取与适应性相关功能，且其聚类依据分离来源而非地理区域。
本研究首次系统表征了P.b的泛基因组毒力特征，揭示了双发酵副梭菌是一种可多维度威胁人类健康的新兴致病菌，强调了原位临床分离株的表型与基因组学表征的重要性。