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Oxford Nanopore Technologies, the company delivering a new generation of nanopore-based molecular sensing technology for real-time genomic analysis, and Cepheid, a Danaher company and a leader in molecular diagnostics for infectious diseases, have announced an expansion of their partnership to develop a workflow for rapid bacterial and fungal pathogen identification. Following a successful phase one collaboration announced at the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Global 2025, the companies are advancing to the next phase of development, building on a promising beta solution already in use by researchers.

Phase Two Collaboration

In this next phase, the updated workflow will enable pathogen identification, antimicrobial resistance profiling, and genomic antibiotic susceptibility testing predictions for bloodstream infection and sepsis research. These analyses will be performed using both culture isolates and positive blood cultures. This phase will include additional user-friendly product design elements and expanded access through a co-commercialised research use only (RUO) launch.

“Phase two reflects our shared commitment to making advanced infectious disease research more practical and widely achievable”, said Vitor Rocha, President of Cepheid. “By leveraging the scale and simplicity of Cepheid’s GeneXpert® platform together with Oxford Nanopore’s sequencing technology, we are increasing access to critical infectious disease information.”

“We are very encouraged by the success and early feedback from the first phase solution and are excited to broaden the workflow’s transformative possibilities to additional research labs,” said Francis Van Parys, CEO of Oxford Nanopore Technologies. “We have ambitions of a future where Oxford Nanopore sequencing can enable insights when and where they are needed for complex infections.”

Experience from Phase One Research Use

The initial workflow, designed to profile bacterial and fungal pathogens from culture isolates for sepsis and bloodstream infection research, has shown promise. Multiple infectious disease researchers already have early beta access, and by Q3-2026, the workflow will be available through an early access program to several leading physician-scientists.

“Rapid genomic testing for infectious diseases has the potential to improve patient care by enabling prompt, accurate prediction of antibiotic resistance, while also strengthening public health surveillance of emerging strains,” said Dr. Rahul Batra, Deputy Director of the Centre for Clinical Infection & Diagnostics Research (CIDR) at Guy’s and St Thomas’ NHS Foundation Trust. “We're excited to collaborate with Cepheid and Oxford Nanopore to explore faster and more streamlined approaches that could make genomic insight available where it is needed most.”

Cepheid and Oxford Nanopore share a long-term ambition to deliver an end-to-end in vitro diagnostic (IVD) solution for complex infectious diseases, with the goal of enabling more accurate and timely clinical decisions. They will be present at ESCMID Global this week, showcasing research-stage progress and engaging with the scientific community. Visit them at booths C50 (Cepheid, as part of the Danaher Group) and C70 (Oxford Nanopore Technologies).

For Research Use Only. Not for use in diagnostic procedures.