Distribution and genetic evolution of prophages carried by Clostridium perfringens

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.