Enhancing detection of newborn screening conditions via data analytics

Enhancing detection of newborn screening conditions via data analytics | www.APHLblog.org

For over 50 years, newborn screening programs across the United States have implemented laboratory screening and follow-up programs to detect and report infants at high risk for rare diseases. As we look towards the future, current testing challenges will likely become more pronounced with the anticipated addition of new conditions to the Recommended Uniform Screening Panel (RUSP), increasing sophistication of testing platforms and methodologies, and greater complexity of biomarker profiles.

Building the data analytic capacity of newborn screening programs will help support the analysis and interpretation of patient data, providing tools and resources to create efficiencies in time-intensive program activities.

APHL and the Newborn Screening and Molecular Biology Branch of the Centers for Disease Control and Prevention (CDC) are exploring solutions aimed at improving the interpretation of laboratory tests by expanding data analytic capacity in the following ways:

  • Increasing state newborn screening programs’ capacity to evaluate and interpret laboratory test data by providing Newborn Screening Bioinformatics Fellows
  • Creating a Newborn Screening Data Analytic Workgroup focused on sharing and harmonizing best practices and solutions
  • Enhancing data-driven decision making in the newborn screening community by designing and developing data science resources to address newborn screening-specific data challenges

In March 2019, APHL and CDC hosted a national meeting in Atlanta, GA to broaden their efforts, engage state newborn screening programs in a collective data analytics initiative, and discuss progress toward enhanced disease detection utilizing improved data analytics resources and technologies specific to newborn screening.

The meeting provided a forum for participants to discuss the needs around biochemical and molecular screening methodologies and their related data analytics requirements, as well as the value of data to improving health outcomes.

This national dialogue will help guide CDC development of an in-house data analytics resource that will improve the interpretation of biochemical and molecular test results.

This activity was supported by Cooperative Agreement #NU60OE000103-04 funded by the Centers for Disease Control and Prevention. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of CDC or the Department of Health and Human Services.

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Are antibiotics making printers great…again?

Are antibiotics making printers great...again? | www.APHLblog.org

By Eric Ransom, APHL-CDC Antimicrobial Resistance Fellow

Let’s be honest: printers have never been that great. These frustrating devices turn what should be a simple office task into a game of chance. Is there paper? Did it jam? Can I get by without replacing the toner cartridge… again? Ugh! I personally cannot wait until this archaic technology sails off into the sunset. Goodbye frustration and hello forestation.

You can imagine my surprise when I heard a PRINTER could help fight one of the most significant public health threats of our time: antibiotic resistance. That’s right. The end of the antibiotic era looms, but hope lies with a printer!

To be fair, this is not your ordinary printer that puts ink to paper. This is a bioprinter that “prints” antibiotics! The technology ultimately helps clinicians decide which antibiotic is most likely to be effective in treating an infection. Prescribing the proper antibiotic is key to saving lives today and preserving antibiotics for tomorrow.

More specifically, the bioprinter makes antibiotic panels for broth microdilution susceptibility testing, a gold-standard method in clinical and public health microbiology. To make an antibiotic panel, the bioprinter dispenses minuscule amounts of antibiotics into a 96-well plate containing liquid that supports microbial growth. Microbiologists can then add a patient’s microbe to the plate and observe which antibiotic (or combination of antibiotics) inhibits growth. If an antibiotic inhibits growth on the plate, chances are good that it will also inhibit growth in the person. Results are shared with clinicians so they can prescribe the best antibiotic(s) to treat the infection. What makes the bioprinter unique is that it can easily make antibiotic plates with complex antibiotic combinations and new-to-market antibiotics. The latter is especially exciting given it can take years before new-to-market antibiotics are included on commercially available plates and systems found in most hospital laboratories.

In 2018, the Centers for Disease Control and Prevention announced a pilot program to implement the bioprinter technology in the Antibiotic Resistance Laboratory Network, a consortium of 56 public health laboratories that aims to rapidly detect and respond to antibiotic resistance. The pilot program already uses the bioprinter to offer expanded antibiotic susceptibility testing for hard-to-treat infections in four public health laboratories: Wisconsin State Laboratory of Hygiene, Minnesota Department of Health Public Health Laboratory, Wadsworth Center Laboratories and Tennessee State Public Health Laboratory. This susceptibility testing is free, compliant with patient testing regulations, and available for all qualifying isolates from any hospital laboratory. The testing is also performed within three working days to quickly assist clinicians with therapeutic management.

The pilot program has already begun susceptibility testing with a new drug combination (aztreonam-avibactam) against Enterobacteriaceae producing a metallo-β-lactamase (MβL). These are some of the most resistant microbes, and there are very few effective treatment options. To qualify for this particular testing, isolates must be non-susceptible to all current β-lactam antibiotics (including either ceftazidime-avibactam or meropenem-vaborbactam). Moving forward, the pilot program will expand testing to include other highly resistant microbes and new-to-market antibiotics.

So how exactly does the bioprinter pilot program work in practice? Let’s say a hospital patient has symptoms of a serious infection. Samples from the patient are tested in the hospital’s laboratory to identify the responsible microbe and to determine possible treatment options. If the microbe is found to be highly resistant and clinicians are in need of additional treatment options, the microbe is sent to one of the four public health laboratories piloting the bioprinter program. Microbiologists there can use the bioprinter to print plates for testing the newest antibiotics to see what, if any, are effective in treating the patient’s infection. Results are then returned to clinicians where the patient is being treated.

Implementation of the bioprinter in the AR Lab Network has the potential to be truly impactful. First, clinicians are given a resource to find new, effective treatment options for their patients’ most resistant infections. Second, compiled data from this pilot program can be used to improve antibiotic prescribing, capture national antibiotic efficacy, help establish antibiotic breakpoints and even inform infection control and prevention practices.

The bioprinter pilot program is a remarkable step forward in the fight against antibiotic resistance. It is important to realize though that this crisis still requires comprehensive long-term intervention including discovery of new antibiotics, development of new diagnostics, and an unequivocal commitment to antibiotic stewardship in healthcare and beyond. In the short term, though, a printer might just be exactly what the doctor ordered.

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Lab Culture Ep. 17: Exploring bioinformatics: From fellow to full time in Virginia

Lab Culture Ep. 17: Exploring bioinformatics: From fellow to full time in Virginia | www.APHLblog.org

Kevin Libuit went from the APHL-CDC Bioinformatics Fellowship to a contractor to working full-time as a bioinformatician at the Virginia state lab (VA Division of Consolidated Laboratory Services (DCLS)). First he talks about when he discovered bioinformatics as a field and how the fellowship propelled his career. Then Kevin takes the mic and interviews Dr. Denise Toney, director of Virginia DCLS, about the value and growing need for bioinformaticians in public health labs.

 

 

Kevin G. Libuit, M.S.
Bioinformatics Lead Scientist, Division of Consolidated Laboratory Services (DCLS), Virginia Department of General Services

Denise Toney, PhD
Director, Division of Consolidated Laboratory Services (DCLS), Virginia Department of General Services

Links:

APHL-CDC Fellowships

APHL-CDC Bioinformatics Fellowships

Virginia Division of Consolidated Laboratory Services (DCLS)

APHL Off the Bench (new Facebook group!)

 

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How my fellowship and an interest in oysters took me to France

How my fellowship and an interest in oysters took me to France | www.APHLblog.org

By Chelsea Carman

When I applied to APHL’s Infectious Diseases Laboratory Fellowship in 2017, I had no idea I’d find myself spending three weeks in Nantes, France, with a leading expert in norovirus detection in oysters. While I love to travel, and France had been on my list of places to explore, I never anticipated that I would have this opportunity during my fellowship or that the opportunity would be made possible through the network of researchers connected through it.

I began my year-long fellowship at the Massachusetts Department of Public Health State Laboratory last summer. Less than a year before, the state faced a norovirus outbreak linked to consumption of raw oysters from Wellfleet, MA. Oysters are filter feeders, so whatever is in their surrounding environment will filter through their body and possibly bioaccumulate, (i.e., accumulate in the oyster rather than being excreted). When people eat the oysters raw, they can be exposed to a potentially infectious dose of the virus.

The state public health lab did not have a protocol to test oysters for norovirus, so I was tasked with this project. I was invited to visit the Shellfish Purification Plant in Newburyport, MA, which is the oldest depuration facility in the world and the largest in the US. I thought this hour and a half trip to the tip of Plum Island on the north shore of Massachusetts would be the furthest I would travel during this fellowship, and was happy to enjoy this fascinating field trip.

As part of my research, I began contacting experts in similar fields. Upon connecting with an international expert in norovirus detection in oysters, I was invited to visit and train at IFREMER, a French research and national reference lab. I was thrilled to accept!

A few months later I was in Nantes, France, a beautiful and green city on the Loire River, approximately 30 miles inland from the western Atlantic coast. There I spent three weeks learning the ISO method for detection of norovirus in oysters along with another visiting researcher from Morocco. I also learned about other research projects at the lab, and its responsibilities as a national reference lab.

On my second day there, the public transportation workers went on strike, so I joined some of the lab scientists and walked to work through the morning mist on a forest trail. I happened to mention that it was my birthday that day, and soon one of the students had organized a group dinner to celebrate. I gained a strong sense of inclusiveness from the group and had a truly memorable experience. It was wonderful to be able to ask as many questions as I wanted about their work (sometimes with the aid of Google translate because my French was quite limited), which was enormously helpful for my own project.

From my time training in the IFREMER lab, I learned the nuances of dissecting out the digestive tissue of an oyster, as well as two different homogenization and ribonucleic acid (RNA) extraction techniques. It was an opportunity to work with people that routinely work with both oysters and norovirus. While I could have read and interpreted the protocols from Massachusetts, it was extremely helpful to observe the intricate steps and ask the experts questions to fully understand the protocol. I’m now back in Massachusetts and have implemented much of what I learned into my project.

Once I returned and shared my experience with friends and family, they had one question for me: Do I still eat oysters? I did eat oysters but then I started finding live pea crabs inside them. Pea crabs are a parasite in the oyster and I felt they represented a large physical manifestation of all the other potential parasites, bacteria or viruses that can reside in oysters. That was enough to make me avoid them, at least for a while. I might begin eating them again after I complete this project; I’m still young and have a relatively good immune system to protect me from whatever might be lurking in an oyster!

 

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