New Lab Matters: Making data fly

Cover of Fall 2019 issue of Lab Matters magazine illustrating high volume of data

In today’s technology-connected world, information moves quickly. But in the world of public health, pathogens often travel faster than the data needed to diagnose, treat and prevent illness. Reporting delays and incomplete or incompatible data delay insights into pressing public health problems. The solution? Investing in public health infrastructure and resources to rapidly deliver data to public health and clinical decision makers.

Here are a few of this issue’s highlights:

Read the full issue.

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Supporting rapid exchange of public health data is urgent, crucial and laden with challenges

By Jody DeVoll, advisor, communications, APHL 

In an era when digital communications move at blazing speeds, public health laboratories still have to resort to fax, email or phone to exchange data with some partners. Yet, this is only one of the obstacles to rapid exchange of critical public health laboratory data needed for public health surveillance, emergency response and patient care.

The volume of public health laboratory data presents an obstacle in and of itself. Infectious diseases, environmental toxins, foodborne illnesses, radiological exposure, hazardous chemicals, high consequence pathogens, antibiotic resistance: public health laboratories test them all. Add to this exponential increases in volume from the expansion of advanced molecular technologies like next-generation and whole genome sequencing, and the result is terabytes of data that public health laboratories must manage, interpret, store and share.

In addition, dozens of different, stand-alone systems make programming and maintenance of laboratory reporting systems labor-intensive and costly. For example, the US Centers for Disease Control and Prevention (CDC) maintains over 100 surveillance programs, each with its own reporting system. Dari Shirazi, APHL’s health information technology manager, explains how these many systems affect public health laboratory operations: “It’s as though you have a houseful of furniture to arrange in dozens and dozens of different houses and, periodically, you receive shipments of additional furniture that also has to be arranged.”

Of course, CDC is not public health laboratories’ only data exchange partner. Other federal partners, state and local health agencies, hospitals and others also require laboratory data, and they too want it parsed and transmitted through their proprietary systems.

With all these demands, data scientists at public health laboratories face a mountain of work, yet their numbers are few. The number of graduates in public health informatics has not kept pace with demands for workers from public and private sector institutions. As a result, graduates can choose from an array of positions, and they often choose private sector jobs which tend to be higher paying and longer-term than lower-salaried, time-limited positions at a public health laboratory.

Huge data volumes, a multitude of reporting systems and a shortage of public health data scientists make data exchange a laborious, costly and frustrating enterprise for public health laboratories. However, the implications extend beyond laboratories to the populations the data is intended to protect, in other words, us. According to Peter Kyriacopoulos, APHL’s senior policy director, “We are fast approaching the confluence of events on the management of public health data that threatens the very relevance of governmental public health. The volume of data generated by new laboratory technologies adds to the burden of over 100 inefficient data reporting systems that each have been designed to move specific information to a point at CDC, which constrains the utility of that information.

Fortunately, there are signs of change. Four national health organizations — APHL, the Healthcare Information and Management Systems Society (HIMSS), the Council of State and Territorial Epidemiologists (CSTE) and the National Association for Public Health Statistics and Information Systems (NAPHSIS)  – launched the Data: Elemental to Health campaign calling for a $1 billion investment in congressional funding over the next decade to modernize public health data/IT systems and develop a skilled workforce of data/IT specialists. Under the plan, state, local, tribal and territorial health departments would receive direct funding for these purposes through the CDC.

Over the last six months, the campaign has convened stakeholders, made the case for improved data systems to congressional and administration staff, appeared before the House Appropriations Subcommittee, hosted Hill briefings and organized a Day of Digital Action. Already there are results:

  • The House appropriations bill includes $100 million in fiscal 2020 for public health data systems and workforce modernization
  • The House LIFT America Act authorizes $100 million per year for five years to develop public health data systems and train staff
  • The Senate Saving Lives Through Better Data Act authorizes $100 million per year for five years for systems and people
  • The Senate Lower Health Care Costs Act authorizes “such sums as may be necessary” over five years to modernize data systems.

How would legislation initiated through the campaign support public health laboratories? First and foremost, it would help them to strengthen their LIMS. Shirazi explains, “A LIMS is a living, breathing thing that has to grow with lab needs. These needs change every year as the lab takes on new and novel types of testing.” Building LIMS capacity would enable laboratories to expand capability for data capacity, exchange and analytics; eliminate manual entry of test results; and provide secure, instantaneous communication of results to health partners. In addition, legislation initiated through the campaign would underwrite laboratory systems for exchange of electronic health records, National Notifiable Disease Surveillance System data, vital health records (e.g., notices of births and deaths) and other public health surveillance data.

Looking forward, the US would do well to complement the advances initiated under the Data: Elemental to Health campaign with a data transfer solution that consolidates all public health data systems into one. Kyriacopoulos notes that: “the creation of a single reporting site, that multiple data providers and users can report to and receive information from, would be a significant improvement that would allow for the efficient and comprehensive use of this data throughout the federal/state/local public health system.”

 

Photo credit: James Marvin Phelps

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New Lab Matters: A game-changer in the fight against antibiotic resistance

New Lab Matters (cover): A game-changer in the fight against antibiotic resistance

Given the global rise of drug-resistant pathogens over the past few decades, some physicians and scientists warn of a possible antibiotic apocalypse—a scary, post-antibiotic era. But a $160 million CDC effort now aims to keep antibiotic resistance rare. And as our feature article shows, the “game-changing” keystone of this effort is the Antibiotic Resistance Laboratory Network.

Here are just a few of this issue’s highlights:

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Self-directed regional networks: Connecting neighbors strengthens labs

The Pacific Rim Consortium met in person for the first time at the Hawaii Public Health Laboratory in March, 2019.

(Photo: The Pacific Rim Consortium met in person for the first time at the Hawaii Public Health Laboratory in March, 2019.)

How can a public health laboratory with limited resources sustain and expand its capabilities? One strategy is to leverage the resources and expertise of its neighbors.

With support from the US Centers for Disease Control and Prevention (CDC), APHL is assisting with development of self-directed regional laboratory networks (SDRN) to facilitate collaboration and resource management among neighboring public health and environmental laboratories. SDRNs operate independently, establishing their own governance and strategic priorities based on their unique needs. Soon these networks will be linked through a Coordination Council, which will bring together representatives from each of the SDRNs for joint planning and resource development.

A growing community of networks

Today, 48 states and one territory, Guam, are members of an SDRN. The original SDRN was founded over forty years ago when laboratory directors in New England came together in the mid-1970s to share common concerns around newborn screening legislation then pending in multiple states. This group evolved to become the New England Public Health Laboratory Directors Group (NEPHLD), and then became NEEPHLD when it expanded its constituency to include laboratories responsible for environmental testing.

However, the regional model did not pick up momentum until a review by APHL and CDC demonstrated its value in the early 2000s. This provided the impetus to form the Northern Plains Consortium in 2006, the Southeast Consortium in 2015, the Mid-Atlantic Consortium in 2017, and the Midwest, Pacific Rim, Four Corners and Central Plains networks in 2018 and 2019.

Members “have our back”

SDRN member laboratories report many benefits from participation. Members share technical expertise, technologies and capacity, and they forge relationships with colleagues at other laboratories, making it easier to collaborate when emergencies arise or a testing system goes down. Emily Travanty, PhD, scientific director of the Laboratory Services Division at the Colorado Department of Public Health and Environment reports: “Our fellow consortium members have our back when we need them. For example, the Utah Public Health Laboratory did TB testing for us when our laboratory was in the midst of renovations. Because of them, we were able to still meet our test turn-around times and keep our customers happy.”

Members also collaborate on fundraising, informatics systems, training and leadership development, as well as recruitment and retention. According to Denise Toney, PhD, director of the Virginia Division of Consolidated Laboratory Services:

“The Mid-Atlantic Consortium provides a venue to share ideas, resources and expertise across our region so we don’t have to reinvent the wheel. One project we worked on collectively was a compensation study, funded by CDC and APHL. Our members are using this data to educate their own state leaders about the salary levels needed to recruit and retain top-notch scientific staff in our region.”

SDRNs show strong prospects for the future, with planning in progress within and across networks. With sustainability a perennial challenge for state and local laboratories, that’s good news for public health.

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New Lab Matters: The promise and challenge of newborn screening in 2019

New Lab Matters cover depicts a newborn baby

Newborn screening is a public health success story, ongoing for 56 years. On the one hand, new treatment and laboratory testing options open up the possibility of expanded screening panels. On the other hand, testing laboratories and follow-up providers are generally under-resourced and straining to keep pace with growing workloads. But as our feature article shows, scientists are working diligently to improve the accuracy and precision of existing tests and to bring on new disorders, even as they continue the high-stakes work of screening tens of thousands of infants a year.

Here are just a few of this issue’s highlights:

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New Lab Matters: The ABCs of PFAS

New Lab Matters: The ABCs of PFAS | www.APHLblog.org

First discovered in the 1930s, per- and polyfluoroalkyl substances (PFAS) now pervade almost every aspect of modern life. In fact, PFAS compounds are found in everything from dental floss to cookware. But human exposure to PFAS comes at a cost, and as old compounds are removed from production, new compounds take their place. So how does a public health laboratory handle this challenge with limited resources? As our feature article shows, by establishing new public-private partnerships.

Here are just a few of this issue’s highlights:

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New Lab Matters: Time to welcome the next generation of public health laboratory scientists

New Lab Matters: Time to welcome the next generation of public health laboratory scientists | www.APHLblog.org

The Bureau of Labor Statistics estimates that 12,000 new laboratory professionals are needed each year to meet consumer demand. At the same time, while automation has eliminated some less-skilled laboratory jobs, the growing sophistication of public health laboratory analyses has generated demand for scientists with highly specialized training. As our feature article shows, laboratories are recruiting new talent for the “hidden profession” by taking a hard look into what they really want, and how they want to work.

Here are just a few of this issue’s highlights:

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5 most unexpected and unique partnerships forged through the Zika response

Top 5 most unexpected and unique partnerships forged through the Zika response | www.APHLblog.org

By Kelly Wroblewski, director, infectious disease, APHL

While the US public health system has been through a number of infectious disease responses in the last decade, the Zika response was unique in both its duration and complexity. For more than 20 months (January 22, 2016 – September 29, 2017), CDC’s Emergency Operations Center was activated to respond to the US’s largest Zika virus outbreak. State and local public health departments began their responses as early as November 2015 and continue to respond today. Through the uncertainty, public health built relationships with new partners and found opportunities for unique collaborations with old partners.

APHL explores the journey in detail in our new book, A Complex Virus, A Coordinated Response: Public Health Laboratories Battle Zika. For APHL and public health laboratories, five unique and unexpected partnerships forged during the Zika response proved critical to progress on this journey. Learn about them below:

1. Vector Control

Vector control is, of course, a time-honored, if underappreciated, public health partner; after all, CDC was established in the 1940s in response to malaria. The Zika response reinvigorated those relationships as public health laboratories and vector control programs worked together on the best methods and approaches for vector surveillance (i.e., testing vectors to see if the pathogen is present) and insecticide resistance testing (testing insects to determine which sprays will be most effective). Once local transmission occurred in Florida and Texas, vector control relied on public health laboratory test results to focus mosquito control efforts on the areas where transmission was most likely to occur.

2. Maternal and Child Health and OB/GYNs

While public health laboratories may connect with maternal and child health departments for other types of testing like newborn screening, it is unusual for these groups of public health professionals to work together in response to an emerging infectious disease. Many OB/GYNs treating patients concerned about their risk of Zika infection and exposure were used to working with clinical and commercial laboratories for prenatal testing, but had never ordered a test at a public health lab. Public health labs across the country worked with their maternal and child health counterparts to ensure they had the most up-to -date information on accessing testing, knew how to correctly complete test request forms and could interpret test results to pass along to appropriate healthcare providers.

3. Commercial Laboratories

At public health laboratories, Zika testing represented a massive increase in workload. Beyond demand from patients worried about their exposure, there were multiple new tests to validate, different tests required for different patient populations and often a single specimen from which multiple laboratories needed to conduct multiple tests. In April 2016, commercial laboratories began performing Zika testing, thus distributing some of the specimen volume, taking some of the load off public health labs and offering OB/GYNs access to testing from laboratories with whom they had established relationships.

4. The Zika Coalition (So. Many. Partners.)

This group, led by the March of Dimes, was comprised of more than 70 member organizations committed to the health and wellbeing of US children and families. It was established in response to Congress’ delay in approving the Obama Administration’s emergency request for funding to respond to the Zika crisis in the US. The request was made in in February of 2016 and was not approved by Congress until that September. The Zika Coalition visited congressional offices, wrote letters and testified before the Senate Appropriations Committee advocating for and applying pressure to ensure public health got the funding necessary to respond.

5. CDC, FDA and CMS – Tri-agency Taskforce for Emergency Diagnostics

Although partnerships with the Centers for Disease Control and Prevention (CDC), the Food and Drug Administration (FDA) and the Centers for Medicare and Medicaid Services (CMS) are neither unique nor unexpected during an infectious disease emergency response, the Zika response did change their nature with the establishment of the Tri-agency Taskforce for Emergency Diagnostics. Throughout the 20 month response, as we learned more about how the Zika virus behaved, APHL worked with these agencies to ensure that laboratories had access to the best possible tests through the emergency use authorization (EUA) process (FDA’s role), guidance on how to use those tests (CDC’s role) and assurance that the tests were being implemented in compliance with quality testing standards (CMS’s role). This taskforce remains intact for future responses.

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What a Day! Day 3 of the APHL Annual Meeting

What a Day! Day 3 of the APHL Annual Meeting | www.APHLblog.org

Day 3 of the APHL Annual Meeting was a big one! We had several captivating sessions including this year’s Katherine Kelley Distinguished Lecturer, Maryn McKenna, renowned journalist and author. Listen to today’s episode to hear a few attendees share what they took away from the day.

You can listen to our show via the player embedded below or on iTunes, Stitcher or wherever you get your podcasts. Please be sure to subscribe to Lab Culture so you never miss an episode.

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Hello, Pasadena! Day 1 of the APHL Annual Meeting

Hello, Pasadena! Day 1 of the APHL Annual Meeting | www.APHLblog.org

We are in sunny Pasadena, California for the 2018 APHL Annual Meeting! Here is a little look at what we did on the first day. Stay tuned for updates every day through June 5.

You can listen to our show via the player embedded below or on iTunes, Stitcher or wherever you get your podcasts. Please be sure to subscribe to Lab Culture so you never miss an episode.

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