Genomic and translational characterisation of Autographviridae phage SAKp26.2 for catheter-associated biofilm clearance in drug-resistant Klebsiella pneumoniae

AMR has become a multi-million death crisis primarily driven by carbapenem-resistant Gram-negative infections, and it is projected to worsen sharply by 2050, especially in South Asia, unless major interventions are implemented. One of the major contributors to this burden is Klebsiella pneumonia. The WHO has categorised carbapenem-resistant Klebsiella pneumoniae as a critical priority pathogen, and the current prevalence of carbapenem-resistant hypervirulent K. pneumoniae has raised concerns about potential future pandemics. The bacteria can mediate the transfer of resistance from environmental to clinical strains. Moreover, biofilm-associated infections caused by multidrug-resistant K. pneumoniae exacerbate healthcare challenges, particularly in hospital-acquired infections associated with medical devices such as catheters and implants. Amid escalating antibiotic failures, bacteriophages have re-emerged from the pre-antibiotic era as a new-age therapeutic alternative to combat drug-resistant bacterial infections. We report SAKp26.2, a novel Autographviridae phage isolated from hospital sewage, which acts as a potent antibacterial and antibiofilm agent against several clinical, drug-resistant K. pneumoniae strains. Combination treatment of SAKp26.2 with antibiotics resulted in a significant delay in the emergence of treatment resistance compared to monotherapy, supporting its potential as a phage-antibiotic synergistic therapeutic. The phage has a genome size of 41,282 bp and lacks any virulence or antibiotic resistance genes. SAKp26.2 is a strong depolymerase-producing phage and is equipped with other critical lysis-associated enzymes. A rapid elimination of biomass and bacteria residing in biofilms was achieved, resulting in a 99% reduction within 4 hours. Additionally, our study illustrates an association between efficiency of plating and kill-kinetics performance, reflecting how phage replication efficiency within a host population may influence the epidemiological spread of infection. Notably, the phage also showed significant biofilm clearance from urinary tract catheters, indicating potential biomedical applications. Overall, this study integrates fundamental phage biology with a clinically relevant scenario, bridging the gap between bench and bedside.