Phage anti-defense genes targeting NAD+ metabolism and DNA replication are associated with a broad host range against Klebsiella pneumoniae.

Phage therapy for drug-resistant Klebsiella pneumoniae (K. pneumoniae) is limited by narrow host ranges. We isolated a broad-host-range phage, vB_KP_P4, that lyses 109 diverse K. pneumoniae strains, including multidrug-resistant (MDR) and carbapenem-resistant isolates. We suggest that its broad lytic spectrum is likely linked to its capacity to overcome host intracellular defenses. We provide genetic and comparative genomic insights indicating that three phage-encoded genes, deoxycytidylate deaminase (comEB), nicotinamide-nucleotide adenylyltransferase (nadM), and a DNA polymerase clamp loader (rfcS), are correlated with the ability of vB_KP_P4 to infect diverse K. pneumoniae. Deletion of these genes collapsed the host spectrum from 109 strains to fewer than 10, significantly compromising antibacterial efficacy. The wild-type phage substantially improves survival in a mouse bacteremia model. Our study identifies candidate genetic factors associated with the broad host range phenotype, specifically targeting host immunity, and provides a new strategy for engineering therapeutic phages.