Table_1_Comparative Genome Analysis and Spore Heat Resistance Assay Reveal a New Component to Population Structure and Genome Epidemiology Within Clostridium perfringens Enterotoxin-Carrying Isolates.XLSX

Clostridium perfringens causes a variety of human and animal enteric diseases including food poisoning, antibiotic-associated diarrhea, and necrotic enteritis. Yet, the reservoirs of enteropathogenic enterotoxin-producing strains remain unknown. We conducted a genomic comparison of 290 strains and a heat resistance phenotyping of 30 C. perfringens strains to elucidate the population structure and ecology of this pathogen. C. perfringens genomes shared a conserved genetic backbone with more than half of the genes of an average genome conserved in >95% of strains. The cpe-carrying isolates were found to share genetic context: the cpe-carrying plasmids had different distribution patterns within the genetic lineages and the estimated pan genome of cpe-carrying isolates had a larger core genome and a smaller accessory genome compared to that of 290 strains. We characterize cpe-negative strains related to chromosomal cpe-carrying strains elucidating the origin of these strains and disclose two distinct groups of chromosomal cpe-carrying strains with different virulence characteristics, spore heat resistance properties, and, presumably, ecological niche. Finally, an antibiotic-associated diarrhea isolate carrying two copies of the enterotoxin cpe gene and the associated genetic lineage with the potential for the emergence of similar strains are outlined. With C. perfringens as an example, implications of input genome quality for pan genome analysis are discussed. Our study furthers the understanding of genome epidemiology and population structure of enteropathogenic C. perfringens and brings new insight into this important pathogen and its reservoirs.

产气荚膜梭菌（Clostridium perfringens）可引发多种人类与动物肠道疾病，涵盖食物中毒、抗生素相关性腹泻以及坏死性肠炎。然而，产肠毒素肠致病性菌株的自然储存宿主仍未明确。本研究对290株产气荚膜梭菌开展基因组比较分析，并对其中30株进行耐热表型鉴定，以阐明该病原菌的种群结构与生态特征。产气荚膜梭菌基因组具备保守的遗传骨架：单株平均基因组中超过半数的基因，在95%以上的菌株中均保持保守。研究发现，携带肠毒素cpe（Clostridium perfringens enterotoxin, cpe）基因的分离株共享特定遗传背景：携带cpe基因的质粒在不同遗传谱系中呈现差异化分布模式；且相较于全部290株菌株，携带cpe基因分离株的泛基因组拥有更大的核心基因组与更小的附属基因组。本研究对与染色体携带cpe菌株相关的cpe阴性菌株进行系统表征，阐明其起源；同时揭示了两类截然不同的染色体携带cpe菌株，二者在毒力特征、孢子耐热特性以及推测的生态位上均存在显著差异。最后，本研究还对一株携带两份肠毒素cpe基因的抗生素相关性腹泻分离株，以及具备产生同类菌株潜力的相关遗传谱系进行了详细梳理。本研究以产气荚膜梭菌为模型，探讨了输入基因组质量对泛基因组分析的潜在影响。本研究深化了学界对肠致病性产气荚膜梭菌的基因组流行病学与种群结构的认知，为这一重要病原菌及其自然储存宿主的研究提供了全新视角。