This preprint reports that trimethoprim and exposure to acidic conditions each strongly suppress bacteriophage production and reduce Shiga toxin output in Shiga toxin–producing Escherichia coli (STEC). The suppression observed was approximately a 100‑fold reduction in phage production. Importantly, these effects persisted even when STEC were co‑exposed to antibiotics known to increase phage activity by damaging bacterial DNA. The suppression operates independently of canonical bacterial SOS responses, and trimethoprim’s effect partially depends on the bacterial glutamate‑dependent acid stress response. In mechanistic assays, trimethoprim allowed early events in phage induction but blocked phage genomic replication. When tested in a clinical STEC isolate, trimethoprim similarly reduced toxin production despite the presence of DNA‑damaging antibiotics. The authors propose these findings as a lead toward new treatment options that might avoid antibiotic‑induced increases in toxin production. This work is presented as a preprint and has not undergone peer review.
Shiga toxin–producing Escherichia coli are pathogenic largely because they carry genes for lethal Shiga toxins on temperate bacteriophages that infect these bacteria. When phages are induced, phage replication and lytic cycles can increase expression and release of toxin, which is associated with severe clinical complications, particularly in children and immunocompromised patients. For this reason, the use of antibiotics in STEC infections is generally contraindicated: certain antibiotics that damage bacterial DNA can trigger phage induction and thereby amplify toxin production, limiting therapeutic options to supportive care and fluid resuscitation in clinical practice.
The authors describe two stimuli—acid exposure and trimethoprim—that each reduce phage production by roughly 100‑fold. This suppression holds even under conditions where DNA‑damaging antibiotics, which normally increase phage activity, are present. The authors characterized the stimuli further to determine dependencies on known bacterial stress pathways and to define the stage of the phage life cycle affected. Specific experimental methods, quantitative details beyond the ~100‑fold suppression, and the identities and concentrations of the DNA‑damaging antibiotics used were not reported in the source summary and therefore are not available here.
According to the authors, the suppressive effect of trimethoprim on phage activity does not depend on the canonical bacterial SOS response that is well established to mediate phage induction after DNA damage. Instead, trimethoprim’s action partially relies on the bacterial glutamate‑dependent acid stress response. Mechanistically, trimethoprim permits the earliest steps of phage induction to occur but blocks genomic replication of the phage, preventing full production of phage particles. The preprint does not provide additional experimental parameters or molecular details in the summary; those specifics would require consultation of the full manuscript.
The authors tested whether the observations generalized to a clinical STEC strain and found that trimethoprim potently suppressed Shiga toxin production in that isolate. This suppression occurred even when the clinical strain was exposed to antibiotics that usually increase phage activity. Exact strain identifiers, experimental conditions, and toxin quantification methods are not detailed in the abstract summary and were not reported in the source text provided.
These results suggest a potential strategy to mitigate the major clinical risk of antibiotic treatment in STEC infections—namely, antibiotic‑triggered phage induction and toxin release—by using agents that block phage genomic replication such as trimethoprim or by exploiting acid‑related pathways. The authors present this as a lead toward a new therapeutic option that could allow intervention without provoking lethal increases in Shiga toxin. However, important limitations are that the report is a preprint and has not been peer reviewed, and the abstract does not include clinical trial data, safety assessments, or in vivo efficacy. Additional data, including dose ranges, pharmacokinetics, effects in animal models or patients, and the potential impact on antibiotic resistance or bacterial clearance, were not reported in the source summary.
The study lists funding support from the Natural Sciences and Engineering Research Council and the Farncombe Family Chair in Phage Biology. The authors declared no competing interests. This manuscript is posted on bioRxiv as a preprint with DOI https://doi.org/10.64898/2026.09.17.752489 and has not been certified by peer review.
In the experiments summarized in this preprint, trimethoprim and acid exposure each strongly suppressed phage production and reduced Shiga toxin output in STEC, including in the context of DNA‑damaging antibiotics that normally enhance phage activity. The suppression appears independent of the canonical SOS response and involves blocking phage genomic replication, with a partial requirement for the glutamate‑dependent acid stress response in the case of trimethoprim. These findings identify a potential avenue for therapeutic development to treat STEC infections without inducing toxin amplification, but peer review and further in vivo and clinical studies are needed to evaluate safety, efficacy, and practical application. Some experimental details and quantitative parameters beyond those summarized were not reported in the abstract and would require consulting the full manuscript.