Genetic diversity of pre-CTXφ phages in Vibrio cholerae

pre-CTXφ phage is the precursor of phage CTXφ. Unlike CTXφ, pre-CTXφ does not include the cholera toxin coding genes, ctxAB, which are the most important virulence genes in Vibrio cholerae toxigenic strains. However, pre-CTXφ carries zot and ace genes. After pre-CTXφ integrates into non-toxigenic strains, the zot and ace genes can cause cholera-like diarrhea in humans and lead to potential public health risks. In this study, we collected 1649 publicly available draft genomes and 43 complete genomes of V. cholerae, and performed a comprehensive analysis of the genetic diversity of pre-CTXφ in V. cholerae genomes based on comparative genomics and population genetics. The results revealed that the copy numbers of pre-CTXφ vary among different phylogenetic lineages. Especially in L3b.4 lineage, the copy numbers of pre-CTXφ in strains showed an increasing trend over isolation years. We also found that co-integration of pre-CTXφ and CTXφ exists in strains from L2, L4, L7 and L3b lineages. Meanwhile, the phylogenetic tree of pre-CTXφ/CTXφ gene family showed that pre-CTXφ was located at the ancestral position. These findings enrich our knowledge about the integration and evolution of the pre-CTXφ phages in V. cholerae genomes, helping for the detection and infection control of Vibrio cholerae carrying pre-CTXφ.