Campylobacter prophage diversity reveals pervasive recombination between prophages from different Campylobacter species

Abstract

ABSTRACT Prophages, bacteriophages integrated into bacterial genomes, play a critical role in the genetic diversity and evolution of bacterial species. In this study, we investigated the prophage population harbored in Campylobacter species. A total of 446 high-quality and complete genomes of Campylobacter isolated from different sources revealed 431 prophages. We analyzed the phylogenomic relationships between 490 phages and prophages, unveiling a wide diversity of undescribed prophages. Bacteriophage pangenomes revealed shared genetic repertoires among different phage genera. In addition, we found recombination events between prophages from different phage genera, mainly in prophages infecting Campylobacter jejuni and Campylobacter coli , showing distinct evolutionary histories in specific regions of the prophage genomes. Specifically, these regions showed variations in gene content, enrichment in structural genes and others in hypothetical proteins, genes involved in transcription, DNA-associated factors, and genes associated with lysis. Finally, Campylobacter prophages alter the host genetic repertoire by carrying virulence factors and antibiotic-resistance genes. IMPORTANCE Prophages play an important role in shaping the genetic diversity and evolution of their hosts. Acquisition or loss of prophages can lead to genomic variations, including changes in the bacterial phenotype promoted by recombination events, genetic repertoire exchanges and dissemination of virulence factors, and antibiotic resistance. By studying prophages in Campylobacter species, scientists can gain insights into the evolutionary patterns, pathogenicity mechanisms, epidemiology, and population dynamics of these species. This has implications for public health, antibiotic resistance surveillance, and the development of targeted therapeutic approaches.