Data Sheet 2_Pangenome analysis of Clostridium perfringens and its virulence association with Carbohydrate Active Enzymes.pdf

BackgroundClostridium perfringens is an important foodborne pathogen responsible for severe economic loss in the food industry and around one million human gastrointestinal infections annually in the US. Carbohydrate Active Enzymes (CAZymes) are important to host-associated strains of C. perfringens, as they aid disease severity by degrading host tissues for nutrition. This study analyzed 126 publicly available C. perfringens genomes, clustering them into three major clades to investigate host-disease associations of CAZymes, alongside virulence and antimicrobial resistance factors.
ResultsThe pangenome analysis yielded hierarchical clustering of C. perfringens into three clades (clades 1-3), each of which was substantially (q < 0.05) enriched for functional genes. Clade 1 (n = 38) was associated with avian necrotic enteritis (NE) and was functionally enriched with the CAZyme glycosyl hydrolase (GH) 18, essential for attachment and colonization to the host intestine. Additionally, antimicrobial resistance genes fosD (n = 1), lnuD (n = 5), and Mel (n = 2) were exclusively found in clade 1, and the clostridial toxin TpeL was significantly (p = 1.33E-07) associated with clade 1. Clade 2 (n = 26) consisted primarily of canine and equine pathogens, whereas clade 3 (n = 62) was composed largely of strains from diverse hosts, including all but one nonpathogenic isolate. Across all clades, genomes encoded an average of 101.50 ± 2.45, 104.31 ± 1.59, and 96.45 ± 9.22 CAZymes, respectively. Further genomic analysis of the NE-associated C. perfringens TAMU (CPT) strain revealed the absence of the canonical netB toxin gene and the presence of unique iron acquisition transporters, suggesting the involvement of alternative virulence mechanisms in disease development.
ConclusionThis study reveals clade- and host-specific CAZyme profiles and highlights the role of GH18 in colonization, while major clostridial toxins primarily drive severe infections. These insights enhance the understanding of C. perfringens pathogenicity and aid in developing targeted interventions.

【背景】产气荚膜梭菌（Clostridium perfringens）是一种重要的食源性致病菌，可给食品工业造成严重经济损失，在美国每年引发约一百万例人类胃肠道感染。碳水化合物活性酶（Carbohydrate Active Enzymes, CAZymes）对产气荚膜梭菌的宿主关联菌株具有重要意义，其可通过降解宿主组织获取营养，从而加重疾病严重程度。本研究分析了126株公开可用的产气荚膜梭菌基因组，将其聚类为三个主要演化支，旨在探究CAZymes的宿主-疾病关联，同时一并分析毒力因子与抗菌耐药因子。
【结果】泛基因组分析将产气荚膜梭菌进行层级聚类，得到三个演化支（演化支1-3），每个演化支均显著富集功能基因（q值<0.05）。演化支1（样本量n=38）与禽坏死性肠炎（necrotic enteritis, NE）相关，其功能上显著富集糖苷水解酶18（glycosyl hydrolase 18, GH18），该酶对宿主肠道的黏附与定殖至关重要。此外，抗菌耐药基因fosD（n=1）、lnuD（n=5）与Mel（n=2）仅在演化支1中被检出，梭菌毒素TpeL也与演化支1显著相关（p=1.33×10^-7）。演化支2（n=26）主要包含犬源与马源致病菌株，而演化支3（n=62）则主要来源于多种宿主的菌株，仅包含1株非致病分离株。三个演化支的基因组平均编码CAZymes数量分别为101.50±2.45、104.31±1.59与96.45±9.22。对与坏死性肠炎相关的产气荚膜梭菌TAMU（CPT）菌株进行进一步基因组分析后发现，其缺失经典的netB毒素基因，但携带独特的铁获取转运蛋白，这表明该菌株的疾病发生可能依赖其他毒力机制。
【结论】本研究揭示了产气荚膜梭菌的演化支特异性与宿主特异性CAZymes谱特征，明确了GH18在定殖过程中的关键作用，同时证实主要梭菌毒素是重症感染的主要致病因子。这些研究结果加深了人们对产气荚膜梭菌致病机制的理解，并可为靶向干预手段的开发提供依据。