Bacteriophages play major roles in the biology of their bacterial hosts, driving bacterial pathogenicity, genome evolution and population dynamics. Additionally phages are being explored as alternatives to antibiotics for problematic infections, due to their ability to specifically lyse bacterial cells. Clostridium difficile infection (CDI) is a major healthcare problem associated with exposure to antibiotics. Part of the difficulty in combating CDI is the constant emergence of novel genotypes (ribotypes) in clinics. Outside the hospital environment, C. difficile has been isolated from food, animals and the natural environment. These reservoirs can contain clinically relevant strains, as well as those less associated with CDI. Key to understanding the pathogenic success of this species is understanding the evolution of virulence across strains.
To determine the impacts of phage infection upon C. difficile biology, firstly phages and bacterial strains were isolated and characterised from environmental sources. One of the isolated phages, phiCDHM1, surprisingly encodes homologs of the bacterial agr quorum sensing (QS) system. This form of bacterial communication is often associated with control of virulence factors, e.g. sporulation, toxin production and biofilm formation. C. difficile strains have different agr loci, and the phage- carried cassette is an additional loci that may be transferred via HGT. Infection with this phage induces a global gene expression response, including virulence associated genes. Secondly, in silico detection of 281 phages from sequenced C. difficile genomes showed that ~70% of strains carry phages. Previously known C. difficile phages can modulate toxin production via the carriage of transcriptional regulators. The analysis of the 281 phages revealed multiple novel phage types and their host-strain ecology (from toxigenic to non-disease associated strains). Interestingly, many of those carry genes that are predicted to alter toxin production. These findings show that it is of critical importance to investigate further the roles of phages in this major human pathogen.