Genome-based characterization of a novel prophage of Vibrio parahaemolyticus, VPS05ph1, a novel member of Peduoviridae.

Vibrio parahaemolyticus is a globally important bacterium related to climate warming and health threat to human and marine animals. Yet, there is limited knowledge about its polylysogeny harboring multiple prophages and the genetic information. In this study, two prophages (VPS05ph1 and VPS05ph2) were identified in a V. parahaemolyticus isolate through genomic and transcriptional analyses. Both prophages were determined as HP1-like phages, located in a novel phylogenetic lineage of Peduoviridae. They shared a moderate genome-wide sequence similarity with each other and high synteny with the closest relatives, but showed low identities to the repressor counterparts of the representative phages within the family. In addition, no bacterial virulence genes, antibiotic resistance genes and known phage-encoded lytic proteins were identified on both prophage genomes. Moreover, the V. parahaemolyticus isolate was induced with mitomycin, which caused aberrant cellular morphology and nonviability of bacterial cells and excision of prophage VPS05ph1, accompanied by the respective inhibition and promotion of transcriptions of the cI-like and cox-like regulator genes for phage decision making. Results in this study provide the genetic context of polylysogeny in the V. parahaemolyticus isolate, support the diversity and prevalence of HP1-like phages in vibrios, and promote to explore interactions between the HP1-like prophage and its vibrio host.

Characterization of the Prophage Repertoire of African Salmonella Typhimurium ST313 Reveals High Levels of Spontaneous Induction of Novel Phage BTP1.

In the past 30 years, Salmonella bloodstream infections have become a significant health problem in sub-Saharan Africa and are responsible for the deaths of an estimated 390,000 people each year. The disease is predominantly caused by a recently described sequence type of Salmonella Typhimurium: ST313, which has a distinctive set of prophage sequences. We have thoroughly characterized the ST313-associated prophages both genetically and experimentally. ST313 representative strain D23580 contains five full-length prophages: BTP1, Gifsy-2D23580, ST64BD23580, Gifsy-1D23580, and BTP5. We show that common S. Typhimurium prophages Gifsy-2, Gifsy-1, and ST64B are inactivated in ST313 by mutations. Prophage BTP1 was found to be a functional novel phage, and the first isolate of the proposed new species "Salmonella virus BTP1", belonging to the P22virus genus. Surprisingly, ∼109 BTP1 virus particles per ml were detected in the supernatant of non-induced, stationary-phase cultures of strain D23580, representing the highest spontaneously induced phage titer so far reported for a bacterial prophage. High spontaneous induction is shown to be an intrinsic property of prophage BTP1, and indicates the phage-mediated lysis of around 0.2% of the lysogenic population. The fact that BTP1 is highly conserved in ST313 poses interesting questions about the potential fitness costs and benefits of novel prophages in epidemic S. Typhimurium ST313.

Polylysogeny magnifies competitiveness of a bacterial pathogen in vivo.

The rise of next generation sequencing is revealing a hidden diversity of temperate phages within the microbial community. While a handful of these phages have been well characterized, for the vast majority, the role of phage carriage, and especially multiple phage carriage, is poorly understood. The Liverpool epidemic strain of Pseudomonas aeruginosa is an aggressive pathogen in cystic fibrosis lung infections that has recently been found to contain several unique prophages within its genome. Here, we experimentally investigate the role of two of these phages in vivo, using an insect model of infection. We find that while no benefit is conferred by phage carriage in single bacterial infections, phages confer a large fitness advantage during mixed infections by mediating bacteria-bacteria competition. Differences between the two phages appeared to be associated with the rate at which the competitor acquired the phage, and therefore resistance. However, the advantage was greatest in the polylysogen, carrying both phages. These findings suggest that the LES phages may play an important role in host invasions and more generally show that the carriage of multiple phages may itself be beneficial by hindering the spread of resistance in rival bacterial populations.