Dual transcriptional profiles during C. difficle hypervirulent ribotype 078 infected by a newly temperate bacteriophage JD032

Phage therapy is a relatively new alternative treatment of bacterial infection and has drawn attention due to an increase in multi-drug resistant pathogens, including Clostridium (Clostridiodes) difficile (CD). Here, we presented the isolation, propagation and characterization of a newly discovered 35,109 bp temperate phage JD032 from CD hypervirulent ribotype 078 (RT078) strain TW69, and investigated the dual transcriptional profiles between JD032 and CD RT078 strain TW11 at four typical stages during phage infection using RNA-seq. JD032 can effectively kill in vitro a variety of RT078 strains. RNA-seq results revealed progressive replacement of bacterial host mRNA with phage transcripts, from 4.20% in 30 min to 26.01% in 75 min, upon exposure of CD host cells to JD032 phage. Like most dsDNA bacteriophages, the expression dynamics of JD032 was typically divided into early, middle and late genes. One early gene, transcriptional regulator JD032_orf016, belongs to Xenobiotic Response Element family, indicating a close involvement in lytic-lysogeny decision. In addition, 17.7% (668/3781) differentially expressed genes (DEGs) in TW11 were identified during phage infection. The significantly enriched KEGG pathway categories of up-regulated and down-regulated DEGs are distinctly different. It is noteworthy that many anti-phage associated genes, involved in CRISPR-Cas, restriction modification and toxin-antitoxin systems, were newly characterized to be markedly affected upon phage infection, reflecting complex mechanisms of phage-host interactions. This study provided the first description of the interaction between the anaerobic bacterium and phage and identified several key genes involved in CD against phage infection, enhancing understanding of the survival mechanisms of bacterium and host.