Global Transcriptional Response of Clostridium difficile Carrying the φCD38-2 Prophage

Clostridium difficile is one of the most dangerous pathogens in hospital settings. Most strains of C. difficile carry one or more prophages, and some of them, like phi CD38-2 and phi CD119, can influence the expression of toxin genes. However, little is known about the global host response in the presence of a given prophage. In order to fill this knowledge gap, we used high-throughput RNA sequencing (RNA-seq) to conduct a genome-wide transcriptomic analysis of the epidemic C. difficile strain R20291 carrying the phi CD38-2 prophage. A total of 39 bacterial genes were differentially expressed in the R20291 lysogen, 26 of them being downregulated. Several of the regulated genes encode transcriptional regulators and phosphotransferase system (PTS) subunits involved in glucose, fructose, and glucitol/sorbitol uptake and metabolism. phi CD38-2 also upregulated the expression of a group of regulatory genes located in phi-027, a resident prophage common to most ribotype 027 isolates. The most differentially expressed gene was that encoding the conserved phase-variable cell wall protein CwpV, which was upregulated similar to 20-fold in the lysogen. Quantitative PCR and immunofluorescence showed that the increased cwpV expression results from a greater proportion of cells actively transcribing the gene. Indeed, similar to 95% of lysogenic cells express cwpV, as opposed to only similar to 5% of wild-type cells. Furthermore, the higher proportion of cells expressing cwpV results from a higher frequency of recombination of the genetic switch controlling phase variation, which we confirmed to be dependent on the host-encoded recombinase RecV. In summary, phi CD38-2 interferes with phase variation of the surface protein CwpV and the expression of metabolic genes.