Trimethoprim suppress phage activity and reduces toxin production in a clinical STEC strain, even in the presence of DNA-damaging antibiotics

Shiga toxin-producing Escherichia coli (STEC) are virulent due to their production of lethal toxins, which are genetically encoded by viruses that exclusively infect these bacteria, called phages. After infection, children and immunocompromised patients are particularly at risk of developing life-threatening complications. Antibiotics are contraindicated here, because they increase phage activity, and this leads to increased toxin production. This limits treatments to fluid resuscitation and supportive care. Here, we describe how acid exposure and trimethoprim both potently suppress phage production ~100-fold, even in the presence of antibiotics that increase phage activity. We characterized these stimuli further, and found that they suppress phages independently of canonical bacterial SOS responses that are well-established to be involved in phage activity. Trimethoprim partially relies on the glutamate-dependent bacterial acid stress response to have this suppressive effect. It allows the earliest steps of phage induction to happen, but completely blocks their genomic replication. We translated these findings to a clinical STEC isolate and found that trimethoprim potently suppressed toxin production, again, even in the presence of antibiotics that increase phage activity. These findings form a key lead in finding a new option to treat these infections, without risking potentially lethal complications.