Hard to jump: host shifts appear unlikely in a T4-like phage evolved in the lab

Yu Ning¹Enrique González-Tortuero²Jeroen Wagemans³Flor I. Arias-Sánchez^1*

• ¹Charité University Medicine Berlin, Berlin, Germany
• ²University of Salford, Salford, North West England, United Kingdom
• ³KU Leuven Kulak, Kortrijk, West Flanders, Belgium

Abstract Bacteriophage therapy is a promising alternative to antibiotics, but concerns remain about host shifts, where therapeutic phages might evolve to infect and harm beneficial commensal bacteria. Understanding the frequency of host shifts and their evolutionary constraints is critical for ensuring phage therapy safety. Using Escherichia coli-infecting phage BW-1, we conducted experimental evolution with non-permissive (unable to infect) and semi-permissive (low infectivity) bacterial strains under controlled conditions favoring adaptation. We found that host shifts are rare events, with no significant virulence increases observed in non-permissive hosts. However, adaptation to semi-permissive hosts did occur and was associated with trade-offs, where increased virulence on one host reduced infectivity on others. Whole-genome sequencing identified a single convergent regulatory SNP in all phages adapted to a semi-permissive host, highlighting constrained evolutionary pathways during adaptation. These results suggest that the high specificity of phages limits host shifts but that any adaptation may come with trade-offs affecting broader host infectivity. Our findings provide important insights into the evolutionary dynamics of phages, suggesting that phage therapeutics are unlikely to negatively affect intestinal microbiota.