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CDC Building NGS Quality Management Tools as Public Health Labs Increase Use of Sequencing


NEW YORK – With public health laboratories increasingly adopting next-generation sequencing, the US Centers for Disease Control and Prevention and the Association of Public Health Laboratories are building quality management tools to help labs standardize and optimize these workflows.

Funded by the CDC's Office of Advanced Molecular Detection, the Next Generation Sequencing Quality Initiative is developing a quality management system based on guidelines from the Clinical and Laboratory Standards Institute (CLSI) that will support labs "as they develop and implement NGS-based tests," said Colette Fitzgerald, deputy director for science in the division of laboratory systems at CDC.

CLSI is a Wayne, Pennsylvania-based non-profit that develops laboratory standards.

The project launched in 2019 and is slated to run for three years, Fitzgerald said, adding that the initiative has begun producing and posting quality management documents to its website with the first focused on personnel, equipment, and process management.

The move to develop quality management guidelines reflects the rise in recent years of NGS within public health laboratories, a space that had previously lagged behind other settings such as academic labs in terms of adoption.

"Five year ago, there weren't that many public health labs that even had a sequencer," said Christin Hanigan, senior specialist, advanced molecular detection, with the APHL. "Very quickly over the course of three or four years, all 50 states have at least one sequencer and many of them have multiple sequencers."

With that expansion, there were initial challenges with "getting the infrastructure and the sequencer and getting the bioinformatics capabilities," she said. "And now the next phase for people who are implementing this technology for testing is really having comprehensive quality management tools, because this type of testing is very different than some of the conventional and more classic microbiology testing that has been done to date."

Foodborne testing has led the way in terms of adoption of NGS by public health labs, Hanigan said, adding that within the last year the space has completed a shift from gel electrophoresis to whole-genome sequencing for surveilling major foodborne pathogens including listeria, salmonella, and Escherichia coli.

"One of the major focuses of the project is to make this transition easier for laboratories," said Rebecca Hutchins, a scientific consultant at Booz Allen Hamilton who is working with CDC and APHL on the initiative. "There are always going to be early adopters who face issues and come up with solutions, and we want to be able to capture those solutions and share them broadly so that the next wave of adopters who are looking to maybe retire their [electrophoresis], or whatever their prior methods were, have an easier and smoother pathway."

Hutchins noted that in addition to expanding their use of NGS, public health labs are also more frequently implementing it as a frontline technique.

"Sequencing used to be the last thing a laboratory would do in their workflow in order to gain additional detail," she said. "We're seeing in multiple cases now that it is becoming the first part of the lab's workflow, because it provides such a rich dataset that it can inform downstream workflows. I think we're in a period of transition where more and more laboratories are using it as the first step when a sample comes in."

This move of NGS into a more frequent frontline role heightened the need for a set of quality standards given that results from such testing will inform any testing downstream of it, Hutchins said. "That does highlight to some extent the need for the highest quality [procedures] so that all of the information flowing downstream has integrity."

Hanigan said that while many public health labs already have NGS quality management programs within their labs, the CDC initiative aims to help speed the process.

"I think the power of this project is that in some cases [public health labs] are stretched really thin and a lot of them may not be expanding their use of the technology because they don't have the infrastructure to really have a broad quality management system," she said. "I think the goal is to have these tools so that they can get up to speed even faster."

Hanigan said that currently a significant portion, though not a majority, of the country's public health labs use NGS only for surveillance of foodborne pathogens and need support to expand beyond that space. The "vast majority" of labs, she said, have at this point expanded their use of NGS beyond foodborne pathogen surveillance and into other areas like monitoring of vaccine-preventable diseases. Many of these labs have well-established wet lab processes but may need help with quality management in areas like bioinformatics, which many such labs have outsourced but are now looking to bring in house, Hanigan said.

"And then we have a few states that are very far ahead and are helping in this project and providing a lot of the tools that they have developed and being a resource that we can take and expand to be more broadly applicable," she said.

The initiative will post quality management tools to its website on a rolling basis as they are finalized Hutchins said.

"It's a fairly dynamic technology and environment, and so our thinking is that we will have to keep up with it over time and so [posting on] a rolling basis is better," she said, noting that in its meetings with different labs the project working group came to realize that it will need to continue to evolve its guidelines to keep up with the pace of technological change in the space.

"It became apparent that as new sequencing technologies are being released people are adopting them," she said. "So we quickly developed additional guidances and documentation to include those newer technologies, and I think that the vision moving forward is that it will be beneficial to keep up with the technology and provide new resources as things change."