Bacteriophage infection drives loss of β-lactam resistance in methicillin-resistant Staphylococcus aureus

Abstract Bacteriophage (phage) therapy is a promising means to combat drug-resistant bacterial pathogens. Infection by phage can select for mutations in bacterial populations that confer resistance against phage infection. However, resistance against phage can yield evolutionary trade-offs of biomedical relevance. Here we report the discovery that infection by certain staphylococcal phages sensitizes different strains of methicillin-resistant Staphylococcus aureus (MRSA) to β-lactams, a class of antibiotics against which MRSA is typically resistant. MRSA cells that survive infection by these phages display significant reductions in minimal inhibitory concentration against different β-lactams compared to uninfected bacteria. Transcriptomic profiling reveals that these evolved MRSA strains possess highly modulated transcriptional profiles, where numerous genes involved in S. aureus virulence were downregulated. Phage-treated MRSA exhibited attenuated virulence phenotypes in the form of reduced hemolysis and clumping. Despite sharing similar phenotypes, whole-sequencing analysis revealed that the different MRSA strains evolved unique genetic profiles during infection. These results suggest complex evolutionary trajectories in MRSA during phage predation and open up new possibilities to reduce drug resistance and virulence in MRSA infections. Competing Interest Statement MT, AJHV, and CYM filed a provisional patent for the work presented in this paper through the Wisconsin Alumni Research Foundation (P240267US01) Footnotes Expanded author list; supplemental files updated; Figure 2 revised to include data on USA300 clinical strains; Added section, figure, and supplemental table (Figure 4, Table S5) on RNA-seq of evolved MRSA strains; added section, figure, and supplemental table (Figure 6, Table S6) on co-treatments of MRSA with phage and beta-lactam; updated sections to include additional data on a wider array of S. aureus strains, phages, and antibiotics.