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

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, isolated from environmental water, 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% G + C 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 (TSP19) 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, suggests possible therapeutic and biotechnological potential of VIPKPNMC05. 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.