Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens

作者：Yuqing Feng, Xuezheng Fan, Liangquan Zhu, Xinyue Yang, Yan Liu, Shiguang Gao, Xiaolu Jin, Dan Liu, Jiabo Ding, Yuming Guo, Yongfei Hu · 发表于：Microbial Genomics · 年份：2020 · DOI：10.1099/mgen.0.000441 · 被引用次数：52 · 研究领域：Clostridium difficile and Clostridium perfringens research、Streptococcal Infections and Treatments、Bacterial Identification and Susceptibility Testing

Clostridium perfringens is associated with a variety of diseases in both humans and animals. Recent advances in genomic sequencing make it timely to re-visit this important pathogen. Although the genome sequence of C. perfringens was first determined in 2002, large-scale comparative genomics with isolates of different origins is still lacking. In this study, we used whole-genome sequencing of 45 C . perfringens isolates with isolation time spanning an 80‐year period and performed comparative analysis of 173 genomes from worldwide strains. We also conducted phylogenetic lineage analysis and introduced an openness index (OI) to evaluate the openness of bacterial genomes. We classified all these genomes into five lineages and hypothesized that the origin of C. perfringens dates back to ~80 000 years ago. We showed that the pangenome of the 173 C . perfringens strains contained a total of 26 954 genes, while the core genome comprised 1020 genes, accounting for about a third of the genome of each isolate. We demonstrated that C. perfringens had the highest OI compared with 51 other bacterial species. Intact prophage sequences were found in nearly 70.0 % of C. perfringens genomes, while CRISPR sequences were found only in ~40.0 %. Plasmids were prevalent in C. perfringens isolates, and half of the virulence genes and antibiotic resistance genes (ARGs) identified in all the isolates could be found in plasmids. ARG-sharing network analysis showed that C. perfringens shared its 11 ARG...