In addition to managing the daily work of testing and monitoring public health threats, APHL and its member laboratories continue to drive advances in laboratory science and informatics that benefit broader public health systems in and beyond the laboratory.

Many of these efforts are leveraging federal support, such as the Data Modernization Initiative (DMI), to build connections and tools that enable efficient sharing of knowledge and information.

Building off APHL’s established expertise in connecting public health laboratories with a broader national and global public health ecosystem, these efforts are facilitating the flow of data and specialized expertise between jurisdictions and even around the world.

Data Modernization Through ETOR

Public health outcomes rely on rapid, accurate data exchange. For laboratories, electronic test orders and results (ETOR) can streamline testing and reporting and allow more efficient planning and resource allocation. For submitters, ETOR ensures that accurate, actionable data gets into the hands of those who need it quickly.

With support under DMI and in coordination with CDC’s Public Health Data Strategy, APHL’s informatics team has been able to leverage an extensive base of knowledge, input from member laboratories and the AIMS platform to develop an accessible ETOR intermediary solution. “ETOR has and will continue to be one of the key technology drivers to support our public health laboratories,” said Michelle Meigs, MBA, director of informatics.

“ETOR has and will continue to be one of the key technology drivers to support our public health laboratories.”

 

– Michelle Meigs, MBA, Director, Informatics, APHL.

Led by APHL’s Deputy Informatics Director Dari Shirazi, the team has developed a way to centralize many ETOR functionalities, to meet laboratories’ needs in an adaptable and sustainable manner. The centralized platform eliminates the need for laboratories to build and maintain individual connections to hospitals. And as a shared resource, it provides tremendous economies of scale, said informatics specialist Rachel Shepherd.

The system can greatly reduce the need for manual data entry, a bottleneck that becomes especially problematic during surges or pandemics, said Shirazi. Add in the multiple steps and time needed for results to reach hospitals, and the process can take days. ETOR can accomplish the same task in about 15 minutes, with less opportunity for human error by eliminating double data entry.

In addition, the AIMS ETOR intermediary provides the flexibility to receive data in whatever input format a clinical partner uses and deliver it in whatever format the laboratory needs, and vice versa. “This reduces the burden on both sides as much as possible,” Shirazi said.

After working with three laboratories for the past year to prove technical feasibility, the ETOR solution is getting ready to launch for newborn screening.

With the technical framework in place, the team is looking toward opportunities for future implementations that include a broader range of testing and other clinical and laboratory partners.

“Public health uses data to make policy changes and target better solutions. To make informed decisions, you need systems in which you can ask the right questions and get the best data,” Shirazi said.

“Long term, this is going to be beneficial not only for public health laboratories, but for public health in general—better information leads to a stronger, more resilient ecosystem.”

Advances in Bioinformatics

Other testing requires a different kind of informatics support. The expanded use of next-generation sequencing and other data-intensive testing, for example, has increased the need for bioinformatics capabilities. 

“Since COVID, laboratories have been able to expand their sequencing capacity,” said Christin Hanigan, PhD, APHL’s manager of advanced molecular detection. “Now even more laboratories are exploring other uses, from wastewater surveillance to antimicrobial resistance, healthcare-associated infections, Legionella, influenza—all sorts of things.”

The number of bioinformaticians in the public health laboratory workforce has grown tremendously in that time as well, Hanigan said. Having a bioinformatician right in the lab can enable new approaches in laboratory science. For example, Kelsey Florek, PhD, MPH, a data scientist at the Wisconsin State Laboratory of Hygiene, wanted to help laboratorians conduct some bioinformatics analyses themselves, while preserving a level of access control to ensure that those analyses were meeting all needed parameters. In collaboration with Amazon Web Services and the company DEPT, Florek helped develop Easy Genomics, a solution that enables laboratory professionals to run analytic workflows without specific coding or informatics expertise.

In-house expertise also allows laboratories to be more involved in developing pipelines and analysis protocols. For example, MycoSNP, a portable workflow developed by CDC for performing whole-genome sequencing analysis of fungal organisms such as Candida auris, was refined through a collaborative effort between CDC and a work group with state public health bioinformaticians.

“I think diversity in skillsets and backgrounds can help enhance the functionality of a product,” Hanigan said. “And the involvement of people who see the unique needs of public health laboratories has been really key.”

One ongoing challenge is sharing such resources between laboratories. The rapid growth of the field has revealed the importance of building an environment that can facilitate the flow of information between groups while maintaining the quality of tools.

The CDC’s Office of Advanced Molecular Detection (OAMD) received funds to develop an AMD platform to start addressing those needs. With OAMD, APHL is administering five communities of practice to assess priority uses and needs such as data quality and security.

“OAMD really wanted to make sure that the AMD platform is informed by and meets the needs of the public health laboratories,” Hanigan said. In 2023, the communities of practice engaged more than 200 participants in more than 60 meetings.

The rise of bioinformatics in public health is also driving the relatively new field of genomic epidemiology. “These experts serve as liaisons to make sure the right information gets to the right people,” Hanigan said. “Working with epidemiologists more closely, they can translate bioinformatics results to help the data be used to guide informed public health action.”

Connecting Across the Globe

APHL’s Laboratory Twinning Initiative helps build connections on a broader scale. In 2022, the Wyoming and OregonPublic Health Laboratories were paired with the Oman Ministry of Health to develop expertise in sequencing techniques and bioinformatics technologies.

Scientists from Oman visited both states’ public health laboratories and learned a mix of bench science and bioinformatics. “Those individuals got to learn how to program, how to develop pipelines, how to use the different software tools for sequencing and analytics, and then how to take the raw data that they developed within the laboratory and transform that into a bioinformatics output,” said Wyoming Laboratory Director Joseph Reed, PhD. “The hands-on experience allowed those scientists to not only develop and learn the techniques, but then practice them to take back to their own laboratories.”

The groups have continued to collaborate through regular virtual meetings. In February 2023, staff from Oregon and Wyoming went to Oman to extend the partnership and receive reciprocal training. The US laboratorians provided guidance on general laboratory quality practices and operations and, in turn, learned about the Omani laboratory’s sample preparation and workflows. “We’ve really gained a better foundation in global public health through our conversations with them,” Reed said.

The partnership “has allowed us to expand the testing that we’re doing, to tackle problems in ways that we would not have imagined tackling them before,” he said. “And then on the flip side, we’ve provided those services to Oman to help them overcome some of their issues.”

They’re now looking to start building more back-end bioinformatics for epidemiology and surveillance, with a goal of implementing prevention techniques in communities.

The experience has shifted the way the Wyoming laboratory staff approaches some of their workflows and helped them streamline analytic processes with an eye toward making them easily shareable with different groups of scientists.

“We’ve seen it solidifying our scientists’ knowledge foundation and improving their ability to teach science to others with different experiences or backgrounds,” Reed said. “Through this, we’ve developed a good training program that we use not only with our international partners, but also domestic partners,” such as epidemiologists, university students and other regional collaborators.

Successful twinning requires time, energy and dedicated staff and leadership who are committed to meeting the expectations of the partnership—and it’s a worthwhile investment, Reed said.

“For our staff, the exposure to individuals from another country has broadened their horizons and developed some great friendships,” he said. “This has been a special experience that opened all of our eyes to different communities and cultures.”

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