Genome characterization and receptor-binding protein identification of Klebsiella phage vB_VIPKPNMC05, a member of a novel viral family Pituviridae

Abstract Klebsiella pneumoniae is an opportunistic pathogen and a leading cause of antimicrobial-resistant infections in the Philippines. Here, we report the genome sequence of Klebsiella phage vB_VIPKPNMC05, which targets a multidrug-resistant (MDR) K. pneumoniae strain with capsule type K8. VIPKPNMC05 has a siphovirus morphology and exhibits a broad lytic activity against several strains of K. pneumoniae, K. quasipneumoniae, Pseudomonas aeruginosa, and Escherichia coli. The linear double-stranded DNA genome (34,476 bp; 51.0% GC content) encodes 58 protein-coding sequences (CDS), 37 of which are involved in phage morphogenesis, DNA replication, transcription regulation, and host lysis. Notably, a receptor-binding protein (RBP) with a putative depolymerase (Dpo) was identified. Structural prediction using AlphaFold 3 showed that the tailspike protein (TSP) forms a homotrimer structure with a conserved C-terminal pectin lyase domain. The TSP module is conserved among Enterobacteriaceae-infecting phages and may have been acquired through horizontal gene transfer. Whole-genome comparisons revealed 52-54% similarity to known phages, suggesting that VIPKPNMC05 represents a distinct lineage. Based on taxonomic analysis, we propose that VIPKPNMC05 belongs to a novel phage family, Pituviridae. The absence of virulence, toxin, and antimicrobial resistance genes, along with its broad host range and lytic lifestyle, supports the potential of VIPKPNMC05 as a promising candidate for phage therapy and other biotechnology applications. To our knowledge, this is the first report of a newly discovered phage family from the Philippines, underscoring the importance of local phage bioprospecting for therapeutic applications.