The Role of Genomics in Advancing and Standardising Bacteriophage Therapy

Bacteriophage therapy, which employs bacterial viruses to selectively eliminate pathogenic bacteria, has re-emerged as a promising strategy in the face of increasing antimicrobial resistance. However, its widespread clinical implementation is constrained by concerns regarding safety, standardisation, and predictable efficacy. In this review, we examine the key role of genomics in transforming phage therapy from an empirical practice into a standardised and personalised modality of contemporary medicine. We describe how whole-genome sequencing (WGS) provides a basis for safety assessment by enabling systematic screening to exclude virulence factors, antibiotic resistance genes, and markers of lysogeny. WGS also facilitates the prediction of therapeutic efficacy and supports more rational phage selection by identifying receptor-binding proteins and characterising bacterial defence systems. In clinical settings, WGS data are increasingly used to monitor the evolution of bacterial populations and to adapt phage cocktails during treatment, thereby supporting personalised, adaptive phage therapy. Looking ahead, further progress is likely to come from integrating synthetic biology and artificial intelligence to engineer phage-based therapeutics with programmable specificity and predictable properties. Together, these developments are shaping a new paradigm of phage therapy as a scientifically grounded, standardised and controlled strategy to treat infections caused by antibiotic-resistant bacteria.