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Consortium Hopes to Drive Adoption of Next-Gen Sequencing for Infectious Disease Diagnostics


NEW YORK – A consortium of clinicians and researchers wants to help implement next-generation sequencing in infectious disease diagnostics.

Dubbed the Consortium for Clinical Metagenomics in Infections Diseases (CCMID), the initiative is working to determine best practices for NGS-based infectious disease diagnostics and develop guidelines to help drive the technology’s use in routine clinical care.

"CCMID was mainly created to help drive the field forward as a whole," said David Gaston, a clinical microbiologist at Vanderbilt University Medical Center and a cofounder of the consortium. "We would love to see clinical metagenomics become routine practice within clinical microbiology."

Established in late 2022, CCMID is a collaborative effort among microbiologists, researchers, clinicians, and industry partners. The consortium now has more than 50 members, Gaston said, including representatives from the US Centers for Disease Control and Prevention, the Department of Health and Human Services, as well as technology vendors such as Illumina and Oxford Nanopore Technologies.

"What we have done is taking a fairly broad-based approach to the membership," said Steve Miller, chief medical officer at Delve Bio and another cofounder of CCMID. "There is a lot to do, and by having a broad membership, we can break [the tasks] out into manageable projects."

Before joining Delve Bio, a San Francisco-based startup that is commercializing an NGS-based neuro-infectious pathogen assay originally developed by Charles Chiu’s lab at the University of California, San Francisco, Miller served as the director of UCSF’s clinical microbiology lab.

According to Gaston, one of the big barriers to the wide implementation of NGS for clinical microbiology is that the right use cases where the technology is most useful are still not clearly defined. To address that, a major task for the consortium is to draw up guidelines based on the existing scientific evidence and collective expertise of its members to help define the appropriate use cases of NGS in clinical microbiology.

As part of the effort, the team is also deploying a national survey to analyze existing sequencing-based assays at reference labs as well as the perceived need for the broader field.

Another hurdle for NGS-based infectious disease diagnostics, Gaston said, is the lack of sufficient standards to help benchmark and evaluate the performance of the tests.

"When you have a test that is potentially more sensitive, has a broader detection range, and can detect more organisms, how do you show that those are in fact true detections? That has been a challenge in the field because oftentimes, if other tests methods are negative, it comes down to a subjective clinical adjudication," Miller said.

Gaston noted that CCMID is working to establish standardized measures to help evaluate the quality and performance of different sequencing-based assays.

Additionally, CCMID is hoping to facilitate methods development. Instead of focusing on certain sequencing modalities, the consortium is open to "​​a very broad and diverse set of technologies," including both short-read and long-read platforms, he noted.

Eventually, CCMID aims to initiate multi-center clinical studies to demonstrate the utility of NGS in infectious disease diagnostics.

Toward that goal, it is in the process of forming an organizational structure that can receive external funding from government agencies, industry partners, and philanthropy, Gaston said, in order tofinancestudies while maintaining scientific independence.

Currently, CCMID members meet virtually every month and are divided into smaller working groups to tackle different projects, Gaston said. As the team continues to achieve its milestones, it also plans to present its results in studies and at conferences, he added.

While researchers continue to integrate NGS into infectious disease diagnostics, commercial efforts to bring sequencing-based assays to market have also been underway. BioMérieux and Oxford Nanopore Technologies, for instance, have been working together to develop nanopore sequencing-based tests for infectious diseases.

Though NGS-based testing is picking up steam, Gaston said, he still believes some of the traditional microbiology techniques will stick around. "The tried-and-true technologies will continue to have a place," he noted. "On the whole, I don’t think that [NGS] will replace those methods, but I do think it will enhance them."

The best way forward is "to be able to appreciate all of the technologies that are available and utilize them together as much as possible," he said.

Given the nature of infectious diseases, the CCMID researchers are also cognizant of the need and the challenges associated with implementing NGS-based workflows at all types of hospitals, not just the few with many resources. 

"Cancer centers have consolidated [patients], and people travel to go see their specialists," Miller said. "You can't do that with infectious disease. When you get sick, you go to the nearest hospital."

Gaston noted that the ultimate goal for CCMID is to make NGS-based diagnostics accessible to as many infectious disease patients as possible to improve their healthcare. "​​The whole underlying principle is patient care," he said. "We think that these technologies can benefit patients, and we really want to figure out how to be able to do that."