Isolation and genomic characterization of a novel Pseudomonas jumbo phage ΦBRkr

ABSTRACT Jumbo phages generally have large viral genomes packaged in large virions and exhibit a broad host spectrum. However, the detailed variation in host spectrum among jumbo phages, particularly in the context of bacterial phage defense systems, is not fully understood yet. In the present study, we isolated a novel Pseudomonas virus, ΦBRkr, from sewage water in Japan. Transmission electron microscopic analysis and whole-genome sequencing revealed that ΦBRkr is a jumbo phage with a total DNA length of 306,291 bp, and suggested a novel Pawinskivirus -like phage. Furthermore, ΦBRkr showed broader infectivity against 100 genetically diverse Pseudomonas aeruginosa clinical isolates (62.0% of host spectrum) compared with Phikzvirus ΦNK1 (40.0% of host spectrum). By examining the correlation between phage infectivity and the presence of predicted phage defense systems across these 100 strains in an exploratory screening, we found that among the 50 predicted defense systems evaluated, the Jumbo phage killer (Juk) AB system emerged as the potential candidate showing a distinct differential restriction between the two phages. While ΦNK1 completely failed to infect any strains harboring the predicted JukAB, ΦBRkr may evade this defense mechanism in some strains. Genomic comparisons revealed that, unlike ΦKZ and ΦNK1, ΦBRkr lacks a homolog of the KZ241 gene, which is known to trigger the JukAB system. It has been suggested that this absence likely confers a stealth advantage to ΦBRkr during P. aeruginosa infection. These results contribute to a deeper understanding of the diversity of Pseudomonas jumbo phages and provide insights into their advantageous properties for future applications. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogen causing severe multidrug-resistant infections, making phage therapy a promising alternative treatment. Jumbo phages are attractive candidates because they typically infect a wide range of bacterial strains. However, bacteria constantly deploy diverse defense systems to block viral infections, which can limit therapeutic efficacy. In this study, we isolated a novel jumbo phage, ΦBRkr, which exhibits a broad intra-species host range, infecting 62.0% of 100 diverse clinical P. aeruginosa isolates tested. Our results suggest that its ability to effectively evade the predicted Jumbo phage killer (Juk) defense system, a robust barrier restricting other well-known jumbo phages, contributed to its broader host range. Viral genomic evidence implies this phage employs a natural stealth strategy by lacking the specific protein targeted by the putative Juk system. Uncovering how certain phages naturally bypass robust bacterial immunities provides critical insights for selecting and developing highly effective phages for future applications.