VIENNA – Following last week's announcement by Cepheid and Oxford Nanopore Technologies to partner on automated nanopore sequencing workflows for infectious diseases, the firms provided more details on their upcoming plans on the sidelines at the European Society of Clinical Microbiology and Infectious Diseases global congress here this week.
Last week, the companies said they had completed a proof-of-concept study and would begin developing an end-to-end workflow that would include sample and library preparation using Cepheid's GeneXpert cartridges, sequencing with Oxford Nanopore's instruments, and informatics pipelines from both companies.
In an interview this week, Patrick Harkins, Cepheid's VP of global strategy, said that while it will be a "long road" to deploy next-generation sequencing for infectious diseases, Cepheid has looked for a way to facilitate that process.
Although companies like Delve Bio and research groups have been trying to bring clinical sequencing to the hospital laboratory setting, high equipment costs along with the longer turnaround times compared to PCR and greater expertise needed have made it difficult, he added.
Sunnyvale, California-based Cepheid has an installed base of more than 60,000 GeneXpert automated PCR instruments across the world and wanted to utilize that customer base to broaden NGS applications for infectious diseases, Harkins said.
GeneXpert cartridges, only used for PCR so far, are designed in a way they can also be harnessed for NGS sample and library preparation. Each cartridge has a set of chambers that can perform distinct reactions for a multipart workflow, he explained.
The proof-of-concept study with Oxford Nanopore, which lasted about a year and will likely remain unpublished, focused on how Cepheid's sample prep and Oxford Nanopore's sequencing could best be combined for infectious disease testing, enabling whole-genome sequencing of culture isolates. Sequencing data so far "looks great," Harkins noted.
The goal is to provide "a sample-to-answer solution workflow for folks that is just much, much easier than even existing automated approaches," he said.
The partnership is not exclusive, opening opportunities for both companies to collaborate with others. In 2023, for example, Oxford Nanopore signed a collaboration with BioMérieux on infectious disease applications.
Oxford Nanopore "has a lot of traction in the infectious disease space in research-use settings, and we think that their platform has some unique advantages in terms of turnaround time, as well as the ability to get the cost per sample to an acceptable place for customers without batching," Harkins said.
Danaher subsidiary Cepheid has "good knowledge globally of how infectious disease testing is carried out in the clinic," which was a key reason Oxford Nanopore sought to work with the firm, Thomas Bray, Oxford Nanopore's VP of business development, said in a separate interview. While nucleic acid amplification-based testing can rapidly identify pathogens, it is not able to provide information on strains or antimicrobial resistance, so there is a need for a whole-genome sequencing-based approach, he added.
Cepheid and Oxford Nanopore have no timeline for launching their research-use-only workflow, according to Harkins, but are talking to key opinion leaders about validation studies.
"Folks in the [microbiology] space and infectious disease diagnostic space are looking for new tools, they want new tools, they want to be part of next-generation sequencing," he said.
Bray said the companies hope to publish feasibility studies from key opinion leaders in the future, which will help to inform the next round of product development. The companies "want to make sure that we understand clearly how this unified workflow can be deployed," he said.
It will likely launch in an early-access rollout in the US and the UK, with plans to eventually go global, Harkins said. The firms have decided to take a "phased approach" to introducing the workflow to users, getting feedback, and refining the product before going through any regulatory process, he noted.
NGS for infectious disease testing is not the limit of the partnership, Harkins added, with cancer and human genetics as potential future use cases.
The workflow will be compatible with multiple informatics tools, including Oxford Nanopore's EPI2ME and third-party software. In addition, Cepheid recently licensed an informatics tool from an undisclosed "leading industry player" that offers comprehensive antimicrobial resistance gene profiling, SNP-based clonality for outbreak and surveillance tracing, and an artificial-intelligence antibiotic susceptibility prediction algorithm, Harkins said, which Cepheid will directly commercialize.
While he was careful to note that the nanopore sequencing workflow under development will be for research use only, there are multiple potential clinical diagnostic applications, such as comprehensive pathogen identification and AST prediction. Currently, "physicians simply do not have the tools to give them the confidence to move away from treating empirically when they have a complex infection," he said, and whole-genome sequencing of pathogens could be used to improve those problems.
The research-use-only product, meantime, could be a "new weapon" to help researchers track disease outbreaks across the world, Bray added. In the future, the companies would like their workflow to be able to start directly from blood culture samples, he noted.