产气荚膜梭菌前噬菌体的分布特点及遗传进化分析

Distribution and genetic evolution of prophages carried by Clostridium perfringens

摘要:

【目的】分析和研究产气荚膜梭菌中前噬菌体的分布情况、基因组特点及遗传进化关系。【方法】利用PHASTER (phage search tool enhanced release)软件预测产气荚膜梭菌携带的前噬菌体，基于ANI (average nucleotide identity)值对前噬菌体进行分群，利用CARD (comprehensive antibiotic research database)、ResFinder 4.1、VFDB (virulence factors database)和BacMet (antibacterial biocide&metal resistance genes database)分析前噬菌体携带的耐药基因、毒力基因、抗菌剂/金属离子抗性基因，利用CRISPRCasFinder分析产气荚膜梭菌的CRISPR-Cas系统，利用MEGA 7.0进行前噬菌体的遗传进化关系分析。【结果】产气荚膜梭菌平均携带前噬菌体2.67条，其长度呈双峰分布，平均占基因组2.23%；前噬菌体不携带耐药基因，但携带了α毒素、唾液酶和溶血素等毒力基因以及重金属代谢基因；前噬菌体聚为3个类群，Group 1前噬菌体多为完整的前噬菌体且仅存在于A型产气荚膜梭菌；含完整的CRISPR-Cas系统的产气荚膜梭菌携带的前噬菌体相对较少，但CRISPR-Cas系统与前噬菌体的数量呈弱负相关；前噬菌体与产气荚膜梭菌噬菌体的遗传进化距离较远，仅有结构蛋白和部分酶类基因的同源性较高。【结论】产气荚膜梭菌普遍携带前噬菌体，但其CRISPR-Cas系统对前噬菌体的数量影响较小，前噬菌体携带的毒力基因和重金属代谢基因增强了产气荚膜梭菌致病性和对环境的适应性，但其功能和对产气荚膜梭菌遗传进化的影响仍需深入研究。

Abstract:

[Objective] To analyze the distribution, genomic characteristics, and genetic evolution of the prophages found in Clostridium perfringens. [Methods] Phage search tool enhanced release (PHASTER) was used to predict the prophages carried by C.perfringens. The prophages were classified into groups based on ANI value. Comprehensive antibiotic research database (CARD), ResFinder 4.1, virulence factors database (VFDB), and BacMet (antibacterial biocide & metal resistance genes database) were first employed to predict various genes related to antibiotic resistance, virulence, antibacterial biocide and metal resistance that can be encoded by the prophages, respectively. CRISPRCasFinder was then applied to predict the CRISPR-Cas system in C.perfringens, and MEGA 7.0 to analyze the genetic evolution of the prophages. [Results] Each C.perfringens genome was found to carry an average of 2.67 prophages and the size of prophage showed a bimodal distribution, accounting for 2.23% of C.perfringens genome on average. The prophages were not found to carry antibiotic resistance genes, but possessed genes of virulence factors such as alpha toxin, sialidase, and hemolysin, and genes related to the metal ion metabolism. The prophages clustered into 3 groups, and most of the prophages in Group 1 were intact and only existed in C.perfringens type A. C.perfringens with a complete CRISPR-Cas system carried a few prophages, but the number of spacers in CRISPR-Cas system was in negative correlation with the number of the prophages. The prophages showed far genetic distance from C.perfringens phages, and only structural proteins and some enzyme genes have been found to display high homology. [Conclusion] C.perfringens carries prophages, but its CRISPR-Cas system has little influence on the number of prophages. The virulence genes and metal resistance genes carried by the prophages can effectively enhance both the pathogenicity and adaptability of C.perfringens. However, their potential functions and impact on the genetic evolution of C.perfringens need to be further analyzed.