Making Sequencing More Practical for Infectious Disease Research

Genomic sequencing has transformed how researchers study infectious diseases — from tracking emerging pathogens to understanding antimicrobial resistance.^1,2 But despite its potential, sequencing remains difficult to integrate into everyday research workflows. For many laboratories, the challenge isn’t access to sequencing technology itself, but the complexity of the end-to-end workflow and the expertise required to deploy it effectively.³

The real barrier: workflow complexity

Sequencing workflows often involve multiple manual steps, specialized expertise, and disconnected tools that span sample preparation, library preparation, sequencing, and data interpretation.³ These demands can stretch timelines, introduce variability, and limit the pool of users who can realistically adopt sequencing.

As a result, genomic sequencing is frequently confined to highly specialized labs, leaving many researchers without a practical path to apply genomic approaches to the infectious disease questions they are trying to answer.^3,4

Why integration matters

Addressing this challenge requires more than incremental improvements to individual technologies. It calls for a more integrated way of thinking about the entire workflow — from the moment a sample enters the lab to the point where genomic data can be meaningfully interpreted.

Patrick Harkins, Vice President of Global Strategy at Cepheid, explains that this workflow‑level view is essential:

“The broad field of sequencing has advanced rapidly, but much of that progress has happened in the silos of separate workflow steps: sample preparation, library preparation, sequencing, and analysis each making independent advances,” says Harkins.

This perspective underpins Cepheid’s expanded collaboration with Oxford Nanopore Technologies. Rather than treating each stage of the sequencing process as a separate challenge, the work is focused on aligning technologies around how laboratories operate in practice.

“This collaboration is about taking a step back to a user-centric view, and designing an end-to-end workflow that not only offers advanced technology at each step but also provides a seamless user experience across the steps, which is intended to allow more labs to have scaled utilization of Next-generation Sequencing.”

Combining complementary strengths

Cepheid and Oxford Nanopore bring distinct, complementary capabilities to this effort.

Cepheid’s GeneXpert® system is widely recognized for helping simplify complex laboratory processes through automation and ease of use. In this collaboration, GeneXpert technology is being leveraged to help reduce the hands-on complexity associated with sample and library preparation, a common bottleneck in sequencing workflows.

Cepheid’s cartridge‑based approach is intended to help address these bottlenecks with a simplified ‘sample‑in, library‑out’ workflow. In keeping with Cepheid’s legacy of advancing ease of use for ‘wet lab’ activities, Cepheid is also developing a turnkey informatics solution for the back end of the workflow, which will provide species identification, resistance profiling, and genomic antibiotic susceptibility prediction.

Oxford Nanopore contributes its nanopore-based sequencing platform, designed to generate rich genomic data in a flexible and timely manner across various research applications. The nanopore technology reads DNA or RNA directly using a biological–electronic interface, enabling analysis of short to ultra-long genomic fragment lengths. The platform is available in formats that scale from distributed and benchtop to high‑throughput instruments, making it suited to diverse research settings.

From a design standpoint, usability and adoption are key considerations. As Ritu Kamal, Sr. Director of Product Innovation Management at Cepheid, notes:

“From the beginning, the focus has been on usability — understanding where complexity shows up in research lab environments and designing workflows that reduce unnecessary steps,” says Kamal. “Making sequencing more practical isn’t about adding more technology; it’s about helping researchers move from sample to insight with less friction.”

Learning from early experience

The collaboration builds on insights gained during an initial phase of research use, where early users provided feedback on what works and what creates challenges in research laboratory environments. Those learnings are informing the next phase of development, with an emphasis on practicality, consistency, and broader accessibility for infectious disease research.

In its current phase, the collaboration is focused on research applications in areas such as bloodstream infections and antimicrobial resistance, building on experience with bacterial pathogen analysis.

For additional details on the current scope of research, see the phase 2 partnership announcement.

Current work is being advanced for research use only, reflecting a deliberate and responsible approach to innovation. The focus is on learning and iteration, guided by close engagement with the research community.

Looking ahead

As infectious disease threats continue to evolve, the need for genomic tools that are not only powerful but also practical will only grow. By bringing together complementary technologies and a shared focus on workflow integration, Cepheid and Oxford Nanopore are working toward a future where genomic sequencing can be more readily applied across a wide range of research settings.

Over the longer term, the collaboration reflects a shared ambition to ultimately support the development of an end-to-end in vitro diagnostic solution for complex infectious diseases.

The aim is straightforward: reduce complexity, support adoption, and help make genomic insights more accessible.