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bioRxiv · 10.1101/2025.10.05.680490

Bacteriophage density influences the rate of resistance evolution

Phan, T.·Shrestha, A.·Schow, J. X.·Peters, T. L.·Miller, C. R.·Van Leuven, J. T.
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Abstract

The antagonistic relationship between bacteria and bacteriophages (phages) drives genetic changes that result in phage resistance. Phage resistance mutations arise in natural microbial communities and during the treatment of diseases with phages (phage therapy), making it important to understand the dynamics of resistance acquisition. It is well-established that when bacteria are challenged with phages in dense liquid cultures, bacterial populations quickly become dominated by phage-resistant variants. However, these conditions--well-mixed liquid cultures with high phage concentrations--are not necessarily common in microbial ecosystems. We developed a simplified mathematical model of phage resistance evolution to explore how phage and host concentration impact the dynamics of resistance evolution. The model was parameterized with microbial growth data from two pathogens and their phages: Pseudomonas aeruginosa and Paenibacillus larvae. Our analyses revealed two fundamental discoveries about resistance evolution. First, phage resistance evolution is predictably governed by a core set of parameters that exhibited high resolution across all bacterial strains: intrinsic growth rate of susceptible bacteria, resistance acquisition rate, fitness cost of resistance, and phage adsorption rate. Second, competitive interactions and fitness costs are the primary drivers of resistance patterns rather than intrinsic mutation rates. We observed three distinct growth patterns--delayed growth, two phase growth, and complete suppression--corresponding to specific parameter regimes as initial phage concentration increased. Two phase growth patterns emerged when competitive dynamics remained balanced, enabling coexistence of susceptible and resistant populations. Complete suppression patterns occurred when low proliferation thresholds combined with extreme competitive asymmetries created unsustainable conditions for resistant bacteria. These findings demonstrate that phage resistance evolution is fundamentally an ecological process where competitive context determines outcomes independently of mutation capacity, with important implications for phage therapy design.

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Phan, T., Shrestha, A., Schow, J. X., Peters, T. L., Miller, C. R., Van Leuven, J. T.. 2025-10-05. Bacteriophage density influences the rate of resistance evolution. https://doi.org/10.1101/2025.10.05.680490

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