NextGen Sequencing, Listeria, and Cool Tools
Every year about this time the Association for Public Health Laboratories (APHL) hold their annual conference. APHL is a non-profit organization of public health laboratories that work together to promote the effective use of public health laboratory testing in support of public health initiatives at the local, state, national and international levels. This year, the 2016 APHL Annual Meeting and Tenth Government Environmental Laboratory Conference was held June 6-9th in Albuquerque, New Mexico. I had the chance to catch up with one of my colleagues, Mary Kate Yost-Daljev from J Michael Consulting (JMC) about it when she returned.
Mary Kate told me that from a big picture perspective, one of the things that struck her as novel was the buzz around next-generation sequencing (NGS) and the big data of sequencing. NGS is a protocol in which DNA strands can be sequenced in a parallel, high throughput method using non-Sanger based methods resulting in faster throughput of larger DNA sections. Basically, it allows you to sequence entire genomes or large portions of genomes in the time it used to take to sequence individual genes. It’s become so important in public health that one of the preconference workshops was entirely dedicated to it. Then during the conference itself, there were multiple sessions on how to analyze NGS data, how to get it from one place to another, how to store it, and what to do with the information that is a result of it. Part of the reason discussion of NGS was so pervasive is that it is applicable to basically every public health initiative, from newborn screening, to infectious disease, to chronic disease. She went on to say that the NGS is causing some interesting conversations in the public health arena because the data being gathered is huge, both in that it takes up a lot of space and what it could mean to healthcare can be very complex. Everyone is excited about the potential impact of the data but it seems like there isn’t yet consensus on how to collect, store, analyze and use the data to its best effect, and what hardware, software and human resources are needed to support it. However, this is definitely part of the future of public health so it’s good that APHL members are taking the time to consider and discuss it at length.
We then discussed specific sessions and one that stood out to her was on food borne illness, testing food, and food surveillance. The presentation started with a review of a program started by the FDA a few years ago giving grant money to states labs to allow them to set up food surveillance programs. In South Carolina, this program lead to the discovery of Listeria monocytogenes in Blue bell ice cream (Readers might remember this story as it was in the news nationwide.) In fact, using pulsed-field gel electrophoresis (PFGE) and the Pulse Net surveillance system, the lab was able to link the particular strain of Listeria from the ice cream to past cases in humans. Frequently, sporadic cases of food borne illness are never linked to a food source, but in this case South Carolina linked the strain back to cases that had happened in the past suggesting that the ice cream had been contaminated for a long time. This example from South Carolina highlights the power of food surveillance and the Pulse Net program in identifying and linking human cases to sources of infection. The presentation was especially interesting because although the story was a public health success, illustrating the best in how public health can work, the presenter also talked about the negative economic impact of the program. Because of the outbreak, Bluebell had to close 3 plants, which at this time there are no plans to reopen. So although the story is a great success in that it prevented thousands of people from being exposed to Listeria, approximately 1500 people lost their jobs causing a significant economic impact. For more on this session, take a look here: http://www.aphl.org/conferences/proceedings/Documents/2016_Annual_Meeting/48Davis.pdf
And of course Mary Kate and I couldn’t talk about the APHL meeting without giving a shout out to all the cool things APHL is doing. One area that APHL has been really putting time and effort into is the tools that they produce to help public health labs. One was a tool for calculating your return on investment that can be useful for communities that struggle with funding for public health and also as an outreach mechanism to show the community the impact of the public health lab. More on that here: http://www.aphl.org/conferences/proceedings/Documents/2016_Annual_Meeting/06Kurimski-Waddell-Bean.pdf
The self-assessment tool is a personal favorite of the JMC and Yahara team, since we partnered with APHL to develop the software used for this online tool. This tool that allows labs to gather data about their laboratory standards, operations, output and capabilities through an extensive online assessment program. Assessments at the national level allow labs to compare themselves to others in the nation as well as track their individual progress over time. http://www.aphl.org/conferences/proceedings/Documents/2016_Annual_Meeting/61Andrews.pdf
Finally, another tool that is rolling out this summer is a Public Health Laboratory System Database. By having a one stop shop for the capabilities and capacity of all public health laboratories, APHL can rapidly assess the nation’s readiness to respond to new and emerging threats. The software can also provide a snapshot of the public health laboratory infrastructure to ensure funding and support are sufficient to cover the needs of the member laboratories. http://www.aphl.org/conferences/proceedings/Documents/2016_Annual_Meeting/60Kim.pdf
Still curious about the conference? One great thing about APHL, they want to share the knowledge, so for a full run down of the conference presentations and abstracts, check out their website. http://www.aphl.org/conferences/proceedings/Pages/default.aspx
Abbey Vangeloff has a background in life sciences and software. She works as a Project Manager, Business Analyst, and Marketing Manager at Yahara software.