Phages and their ecological strategies to advance phage therapy

The rise of antimicrobial resistance is a major global threat, driving the need for alternative approaches such as using bacteriophages (bacterial viruses). Bacteriophages are naturally occurring, diverse, and abundant, and have a plethora of unique strategies for hijacking bacterial transcription. However, our understanding of the traits beneficial to effective phage takeover is limited. Here, I aim to address this by applying an ecological framework (Grime’s CSR triangle) to phages using transcriptional profiling as a proxy for ecological strategy. I combined these data with phenotypic and genomic data to improve our understanding of what functional traits contribute to effective phage takeover. I focus on a successful urinary tract phage cocktail targeting Escherichia coli and Shigella sonnei, both major healthcare-associated pathogens. I first screened a large collection of clinical bloodstream isolates to assess sensitivity and distinguish ecological specialists from generalists. I then extensively characterised the phenotypic characters that define the lifecycles and stability of urinary tract phages, identifying key parameters that I could correlate with transcriptomic data and performance in urinary tract-like environments. I present the first transcriptionally profiled Phapecoctaivrus phage, which revealed that most genes were expressed mid-infection. I also profiled three Tequatrovirus phages and showed that they have a more generalist approach, with similar amounts of genes maximally expressed throughout their infection cycle. The core genes observed revealed strong temporal conservation, with 92% being expressed in the same phase. The transcriptomic response of the infected bacterial cells revealed metabolic shifts and prophage gene induction during infection. These data highlight takeover strategies and challenges for therapeutic application. Together, these results support the idea of a transcription-based ecological framework that links phage traits and bacterial response to therapeutic performance. This ecological framework provides a foundation for selecting ecologically informed cocktails, advancing optimal phage trait selection, and contributing to the broader development of phage therapy against antimicrobial resistance.