About that one-year decline in life expectancy

The Centers for Disease Control and Prevention released a report that said life expectancy decreased by a full year in 2020. While the calculation is correct, the interpretation and message from that number is more challenging. For STAT, Peter B. Bach provides context to the measurement:

Don’t blame the method. It’s a standard one that over time has been a highly useful way of understanding how our efforts in public health have succeeded or fallen short. Because it is a projection, it can (and should) serve as an early warning of how people in our society will do in the future if we do nothing different from today.

But in this case, the CDC should assume, as do we all, that Covid-19 will cause an increase in mortality for only a brief period relative to the span of a normal lifetime. If you assume the Covid-19 risk of 2020 carries forward unabated, you will overstate the life expectancy declines it causes. […]

Bach wonders if the CDC should have released the report at all, if most people were just going to misunderstand it. That seems like the wrong direction though. Life expectancy is a useful metric, and if you know there are a lot of chances for miscommunication, you try your best to explain the numbers with the audience in mind.

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Multiple Causes of Death

There's a 6 percent figure from the CDC that could be easily misinterpreted. Here's what it means. Read More

The importance of sustained federal funding for public health

Erik Riesdorf of Wisconsin prepares specimens for testing in the laboratory

By Stephanie Barahona, associate specialist, Public Health Preparedness and Response, APHL and Sam Abrams, specialist, Public Health Preparedness and Response, APHL

As hospitals across the country work to manage a constant influx of COVID-19 patients, their partners in public health are addressing critical community and statewide testing needs. While both the healthcare and public health systems are responding to the pandemic, their approach is different: healthcare systems focus on providing individual patient care while public health supports an entire population’s health. In this response, and like many before, the role of the public health laboratory in detecting and responding to threats has never been more critical. But public health laboratories are often only funded when there is a crisis such as Ebola, Zika, vaping and now COVID-19. This approach to federally fund laboratories while in emergency mode leaves the nation vulnerable.

Preparedness funding 101

Although public health laboratories receive funding support from their state and local governments, the federal government provides the majority of their preparedness and response funding. Via the Epidemiology and Laboratory Capacity for Prevention and Control of Emerging Infectious Diseases Cooperative Agreement (ELC) and the Public Health Emergency Preparedness Cooperative Agreement (PHEP), the US Centers for Disease Control and Prevention (CDC) is the primary funder of state, local and territorial public health laboratories. For 25 years, the ELC has been a source of significant financial support that enables public health laboratories to conduct surveillance and respond to vector-borne diseases, food and waterborne diseases and other emerging threats such as pandemic influenza and COVID-19. In Fiscal Year 19 (FY19), which represents August 1, 2019, to July 31, 2020, total ELC funding was approximately $231 million, of which 43% went to public health laboratories to support testing and surveillance needs.

On an annual basis, approximately 90% of funding for public health preparedness and response efforts come from PHEP. Following the anthrax attacks of 2001, total PHEP funding to public health agencies peaked in 2003 at $970 million (unadjusted)—a year in which public health laboratories received $167.7 million for biological and chemical preparedness. Over the years, this funding has decreased considerably. In FY 2019 (July 1, 2019, to June 30, 2020), PHEP funding totaled $620 million. This was similar to 2018 when the jurisdictions received $620 million, of which public health laboratories received $81.5 million (Figure 1).

Figure 1: PHEP Funding to Public Health Laboratories, 1999-2018 (in millions $)

Funding has continued to lag for ELC and PHEP, creating challenges for laboratories to remain adequately prepared. ELC-recipient public health laboratories remain underfunded by 70% in personnel support while laboratory equipment and supplies, which are critical for detecting infectious diseases, face a shortage of 60%. Over 39% of ELC funding requests for health information systems went unfunded in FY19, resulting in $29 million less than health departments needed to sustain syndromic surveillance, electronic laboratory reporting and other systems necessary to track patient cases and limit the disease burden. Cuts to PHEP funding impacted preparedness activities as well. Up to half of state public health laboratories faced cuts over the past few years, resulting in the inability to expand capabilities for new assays and tests and hiring necessary staff.

Staying ahead of emerging threats

Funding shortages are most evident during a public health crisis. The federal government has largely responded to public health emergencies through just-in-time supplemental funding. The 2014 Ebola virus epidemic exposed significant gaps in US operational readiness to respond to a threat of its kind. Congress responded with millions of dollars, of which $110 million went to state, local and territorial health departments via the ELC. Approximately $21 million of these funds were provided to public health laboratories over a three-year period (extended in most cases to four years) to enhance biosafety and biosecurity, infection control and other urgent gaps. By enhancing outreach efforts, public health laboratories were able to engage clinical laboratorians and provide guidance on risk assessments, appropriate use of personal protective equipment, decontamination and other biosafety issues.

When the funding ended in 2018, many public health laboratories were forced to reduce biosafety staff and diminish outreach efforts. This presented challenges to recruiting and maintaining qualified staff as many worried about a subsequent loss of funds. The emergence of Zika proved similar to Ebola, with CDC issuing $97 million in supplemental funding via the ELC.  

Response to COVID-19 is no different. Congress is appropriating billions of dollars and public health agencies now face a surge of funds at the height of a pandemic:

  • At the beginning of the response, CDC redirected funds from its internal activities to state, local and territorial health departments via the Crisis Response Cooperative Agreement.
  • An initial $10 million was distributed to select jurisdictions through the ELC.
  • On March 5, the president signed the Coronavirus Preparedness and Response Supplemental Appropriations Act, 2020 (PL 116-123). This act provided funding to prevent, prepare for and respond to COVID-19. By March 16, CDC via the Public Health Crisis Response Cooperative Agreement awarded $569.8 million to 65 jurisdictions. On April 6, another $160 million was awarded to 34 jurisdictions. This included 27 jurisdictions with high COVID-19 case counts or evidence of rapidly accelerating case counts and seven US territories and freely associated states with unique COVID-19 response challenges.
  • In addition, the Coronavirus Aid, Relief and Economic Security (CARES) Act, provided billions in supplemental funding, with a total of $631 million awarded via the ELC to state, local and territorial health agencies to increase testing capability and capacity, improve surveillance and additional efforts necessary for the US to successfully combat COVID-19.

Finding long-term solutions

While these additional funding sources are a welcome relief to underfunded public health systems, they do not provide a long-term solution for combating new threats.  With each response, public health is behind—they have no ability to be ready to respond to novel and large-scale threats. This lag limits the ability for public health laboratories to quickly ramp up testing capacity needed to stay ahead.

Consistent and sustainable federal funding for public health laboratories is key to stay ahead of threats. Such funding provides:

  • A warm base where laboratories are poised to quickly and safely respond, which encompasses highly trained laboratory scientists, biosafety professionals and other support personnel; high-throughput equipment and electronic data messaging tools; and communication systems and agreements in place with other laboratories such as commercial laboratories.
  • The opportunity for scientists to validate and verify equipment and assays, ensuring timely, accurate results and sustained confidence in quality laboratory testing.
  • Reagents and other laboratory supplies, including personal protective equipment, so that laboratorians can appropriately and safely perform testing and provide ample capacity within their jurisdictions.
  • A national laboratory system comprised of private and public laboratories working side by side to protect the public’s health.

The post The importance of sustained federal funding for public health appeared first on APHL Lab Blog.

Failed CDC data pipeline

The New York Times reports on how the CDC struggled and failed on many levels. On the data front, where it was so important in the beginnings to gauge what was about to happen, the CDC failed to get accurate data to the people who needed to make decisions quickly:

The C.D.C. could not produce accurate counts of how many people were being tested, compile complete demographic information on confirmed cases or even keep timely tallies of deaths. Backups on at least some of these systems are made on recordable DVDs, a technology that was state-of-the-art in the late 1990s.

The result is an agency that had blind spots at just the wrong moment, limited in its ability to gather and process information about the pathogen or share it with those who needed it most: front-line medical workers, government health officials and policymakers.

Painful.

Also, a little too familiar.

In 2014, I wrote a guide on how to make government data sites better. I used the CDC data offerings as my running example.

I criticized how hard it was to get data in a usable format, how the extraction tools were a chore to use, the lack of context to go with the data, and the challenge of just finding the data on a sprawling website.

The kicker at the end:

There’s plenty more stuff to update, especially once you start to work with the details, but this should be a good place to start. It’s a lot easier to point out what you can do to improve government data sharing than it is to actually do it of course. There are so many people, policies, and oh yes, politics, that it can be hard to change.

Maybe give it a try anyway.

Seek out the people who care.

Maybe start with an area you are already strong, improve on it, and branch from there. In the case of CDC, a start with WONDER or Data.CDC might be where it’s at. Or maybe start by unifying the topic pages and all those spreadsheets.

As an outsider looking in, I can’t say for sure the best place to start. I don’t know all the administrative baggage that comes with updating these sites. I would just hate to come back to this five years from now and see that nothing changed or worsened because of age.

Nothing changed. And it worsened with age.

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Bad denominator

With coronavirus testing, many governments have used the percentage of tests that came back positive over time to gauge progress and decide whether or not it’s time to reopen. To calculate percentage, they divide confirmed cases by total tests. The denominator — total tests — often comes from the CDC, which apparently hasn’t done a good job calculating that denominator, because not all tests are the same.

Alexis C. Madrigal and Robinson Meyer for The Atlantic:

Mixing the two tests makes it much harder to understand the meaning of positive tests, and it clouds important information about the U.S. response to the pandemic, Jha said. “The viral testing is to understand how many people are getting infected, while antibody testing is like looking in the rearview mirror. The two tests are totally different signals,” he told us. By combining the two types of results, the CDC has made them both “uninterpretable,” he said.

Oh.

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Face mask respirator and its usefulness with different beard styles

The Centers for Disease Control and Prevention made this graphic to show what beard styles work and do not work with a respirator. If there is hair in the way, the seal breaks. The CDC made it a couple of years ago for No-shave November, hence the playful tone, but with coronavirus concerns, it’s once again made relevant.

It reminds me of the trustworthiness of beards.

Also, wash your fingers.

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Lab Culture Ep. 21: 2019 Year in Review

Collage of photos depicting APHL's 2019 year in review

Are we already at the end of 2019?! While to many of us it felt like the year flew by, APHL staff, members and partners accomplished a LOT in an effort to protect the public’s health. In this episode, Scott Becker, APHL’s executive director, reviews some of the highlights of the year along with Gynene Sullivan, APHL’s manager of communications, who is finalizing our Annual Report.

Follow APHL on TwitterFacebook and Instagram so you don’t miss anything!

Links:

APHL: Lung Injury Response Associated with Vaping

CDC: Outbreak of Lung Injury Associated with the Use of E-Cigarette, or Vaping, Products

APHL work on opioids

Data: Elemental to Health advocacy campaign

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

APHL AIMS Platform

Lab Matters (Fall 2019): Making Data Fly

NewSTEPs Data Repository

APHL Newborn Screening Systems Quality Improvement Projects Award Recipients Announced

APHL Public Health Laboratory Fellowships

APHL Emerging Leader Program

Lab Culture Ep. 9: What is the APHL Emerging Leader Program?

CDC: US Measles Cases and Outbreaks in 2019

“Launching Whole Genome Sequencing in the Public Health Realm” Lab Matters (Fall 2013)

Accreditation for Human and Animal Food Labs

APHL Conferences

Lab Culture Extra: Progress in Sierra Leone

APHL Global Health Program: Countries we serve

Global Laboratory Leadership Programme (GLLP)

Laboratory Response Network (LRN)

Lab Culture Ep. 20: 20 Years of the Laboratory Response Network

“Two Decades of Preparedness Excellence: The Laboratory Response Network” Lab Matters (Fall 2019)

The LRN’s job is to prepare, detect and respond. But what exactly does that mean?

Strengthening Lab Biosafety & Biosecurity

“Ensuring Readiness for Rabies in Puerto Rico” Lab Matters (Spring 2019)

“Public Health System Recovery in Full Swing: Hurricane Response in Puerto Rico and the US Virgin Islands” Lab Matters (Spring 2019)

In Puerto Rico, a new molecular bacteriology lab allows better control of foodborne outbreaks

APHL Publications

“US officials identify ‘strong culprit’ in vaping illnesses” Associated Press (video interview)

The post Lab Culture Ep. 21: 2019 Year in Review appeared first on APHL Lab Blog.

CDC findings mark a breakthrough in investigation of lung injury associated with vaping

Man vaping

Statement from Scott J. Becker, executive director, Association of Public Health Laboratories

Silver Spring, MD, November 8, 2019 — “Test results announced today by the Centers for Disease Control and Prevention mark a breakthrough in the ongoing investigation of lung injury associated with e-cigarette use or vaping.

“Laboratory scientists testing samples of lung fluid from 29 patients found vitamin E acetate present in all samples. These results provide direct evidence of this toxin at the primary site of injury within the lungs. They also complement tests conducted by the Food and Drug Administration and state public health laboratories that identified vitamin E acetate in e-cigarette or vaping products.

“While this is a big step in helping us understand what may be causing these injuries, these findings do not rule out the potential for other compounds or ingredients as contributing factors. There may be more than one cause of the outbreak.

“APHL applauds state public health laboratories, CDC, FDA and partners including the Council of State and Territorial Epidemiologists for their extraordinary collaboration and tireless and innovative work.

“This has been a complex investigation, and the work continues. But good science takes time, and public health laboratory work is critical to helping solve this important health challenge and stopping the outbreak.”

# # #

More APHL’s support of the EVALI response

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CDC findings mark a breakthrough in investigation of lung injury associated with vaping

Man vaping

Statement from Scott J. Becker, executive director, Association of Public Health Laboratories

Silver Spring, MD, November 8, 2019 — “Test results announced today by the Centers for Disease Control and Prevention mark a breakthrough in the ongoing investigation of lung injury associated with e-cigarette use or vaping.

“Laboratory scientists testing samples of lung fluid from 29 patients found vitamin E acetate present in all samples. These results provide direct evidence of this toxin at the primary site of injury within the lungs. They also complement tests conducted by the Food and Drug Administration and state public health laboratories that identified vitamin E acetate in e-cigarette or vaping products.

“While this is a big step in helping us understand what may be causing these injuries, these findings do not rule out the potential for other compounds or ingredients as contributing factors. There may be more than one cause of the outbreak.

“APHL applauds state public health laboratories, CDC, FDA and partners including the Council of State and Territorial Epidemiologists for their extraordinary collaboration and tireless and innovative work.

“This has been a complex investigation, and the work continues. But good science takes time, and public health laboratory work is critical to helping solve this important health challenge and stopping the outbreak.”

# # #

More APHL’s support of the EVALI response

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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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