Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: killers and drivers of resistance evolution

Abstract

Bacteriophage (phage) are bacterial predators that can also spread antimicrobial resistance (AMR) genes between bacteria by generalised transduction. Phage are often present alongside antibiotics in the environment, yet evidence of their joint killing effect on bacteria is conflicted, and the dynamics of transduction in such systems are unknown. Here, we combine in vitro data and mathematical modelling to identify conditions where phage and antibiotics act in synergy to remove bacteria or drive AMR evolution. We adapt a published model of phage-bacteria dynamics, including transduction, to add the pharmacodynamics of erythromycin and tetracycline, parameterised from new in vitro data. We simulate a system where two strains of Staphylococcus aureus are present at stationary phase, each carrying either an erythromycin or tetracycline resistance gene, and where multidrug-resistant bacteria can be generated by transduction only. We determine rates of bacterial clearance and multidrug-resistant bacteria appearance, when either or both antibiotics and phage are present at varying timings and concentrations. Although phage and antibiotics act in synergy to kill bacteria, by reducing bacterial growth antibiotics reduce phage production. A low concentration of phage introduced shortly after antibiotics fails to replicate and exert a strong killing pressure on bacteria, instead generating multidrug-resistant bacteria by transduction which are then selected for by the antibiotics. Multidrug-resistant bacteria numbers were highest when antibiotics and phage were introduced simultaneously. The interaction between phage and antibiotics leads to a trade-off between a slower clearing rate of bacteria (if antibiotics are added before phage), and a higher risk of multidrug-resistance evolution (if phage are added before antibiotics), exacerbated by low concentrations of phage or antibiotics. Our results form hypotheses to guide future experimental and clinical work on the impact of phage on AMR evolution, notably for studies of phage therapy which should investigate varying timings and concentrations of phage and antibiotics. AUTHOR SUMMARYBacteriophage ("phage") are viruses that can infect and kill bacteria, but also natural drivers of antimicrobial resistance (AMR) evolution by transduction, when they carry non-phage DNA between bacteria, including AMR genes. Phage are often present alongside antibiotics in the environment and in humans, yet the joint dynamics of phage, antibiotics, and bacteria are unclear. Using laboratory work and mathematical modelling, we show for the first time that depending on timing and concentration, phage and antibiotics can either work together to kill bacteria faster, or phage can generate multidrug-resistant bacteria by transduction which are then selected for by antibiotics. This may be particularly important in the context of phage therapy, where phage are used to treat bacterial infections, often alongside antibiotics. Our conclusions highlight the urgent need for clinical and laboratory work to quantify the currently unknown contribution of phage to AMR evolution in humans. Otherwise, we may be missing opportunities to reduce the global public health burden of AMR.