SNIPR Biome posts positive early data for CRISPR-armed phages against E. coli infection

Edited by Robert McTiernan··3 min read

Denmark-based SNIPR Biome announced publication of final Phase I results for SNIPR001, a CRISPR–Cas-armed bacteriophage cocktail designed to selectively kill Escherichia coli in the gut, including antibiotic-resistant strains. The peer-reviewed data, appearing in The Lancet Microbe, represent the first randomized, placebo-controlled trial of a CRISPR-based antimicrobial in humans — a milestone for a therapeutic modality that has until now remained confined to preclinical work and compassionate use.

Trial specifics

The Phase I study (NCT05277350) was a randomized, double-blind, placebo-controlled, dose-escalation trial conducted in healthy volunteers. Participants received oral SNIPR001 twice daily for seven days across three dose levels. The primary endpoint was safety and tolerability; secondary assessments included biodistribution, pharmacodynamics, and gut microbiome composition.

No serious adverse events were reported in any SNIPR001 dose group, and the incidence of adverse events did not differ from placebo. Functional SNIPR001 was recovered from stool in dose-proportional concentrations, with no meaningful detection in plasma or urine, confirming restriction to the gastrointestinal tract. Gut microbiota composition remained stable relative to placebo throughout and after dosing. The largest observed reduction in E. coli levels was 78% versus placebo at day 14 in the highest-dose group, though the study was not powered for this endpoint and the difference did not reach statistical significance.

The company is now advancing SNIPR001 into a Phase Ib trial (NCT06937867), a randomized, double-blind, placebo-controlled study in patients with hematological cancer undergoing hematopoietic stem-cell transplantation (HSCT), conducted across eight US centers with a target enrollment of 24 patients. Recruitment is more than 50% complete. CEO Christian Grøndahl stated the study is “an important next step toward evaluating SNIPR001’s potential to reduce the risk of E. coli bloodstream infections in vulnerable patients undergoing stem-cell transplantation”.

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Research context

SNIPR001 uses engineered bacteriophages that bind E. coli surface receptors and deliver a CRISPR–Cas payload targeting essential bacterial genes and antibiotic resistance determinants. The resulting double-strand DNA breaks are lethal to the bacterium. Because phage tropism is species-specific, the broader commensal microbiota is spared — a property confirmed by the Phase I microbiome data and supported by preclinical mouse studies showing selective E. coli reduction.

HSCT patients face high rates of bloodstream infection from gut-derived E. coli, and rising antibiotic resistance limits conventional prophylaxis. SNIPR001 is intended as a precision decolonization strategy that avoids the collateral microbiome damage of broad-spectrum antibiotics.

No other CRISPR-armed phage therapy has reached clinical testing, making direct comparisons difficult. However, several programs target E. coli infections through alternative modalities:

  • France-based Phaxiam Therapeutics is developing conventional (non-CRISPR) E. coli phage cocktails in Phase I for urinary tract infections and in a separate Phase I/II burn wound study.
  • The ECOO1A consortium is recruiting for a Phase I/II vaccine trial targeting invasive E. coli disease.
  • US-based Alopexx has completed Phase I work on F598, a monoclonal antibody against the PNAG polysaccharide, and AV0328, a conjugate vaccine, both with broad-spectrum anti-infective intent that includes E. coli.
  • Sanofi’s ExPEC vaccine candidate failed its late-stage efficacy endpoint in early 2025, narrowing the vaccine landscape.