Building REDI-NET: A Defense Against Emerging Pathogens

In this episode of Food, Farms, and Forests Podcast, we talk to Dr. Emily McDermott, assistant professor of medical and veterinary entomology, and Dr. Cameron Osborne, a postdoctoral fellow, to discuss the REDI-NET project and how their research is contributing to building the database for the Department of Defense. 

REDI-NET, which stands for Remote Emerging Disease Intelligence Network, is a collaborative initiative involving the University of Arkansas, the University of Notre Dame, and the Department of Defense. Its main goal is to “detect, predict, and contain” potential infectious diseases that could emerge in animals and be passed on to humans.   

Dr. McDermott and Dr. Osborne explain how their work is helping develop standardized pathogen surveillance protocols to enhance the Department of Defense's readiness against emerging diseases. They discuss the project's objectives, the metagenomic approach used for disease detection, and the challenges and successes they’ve encountered along the way. 

Tune in to learn how their research is shaping the future of global pathogen surveillance and protection.

Learn more about REDI-NET.

This work is supported by the US Army Medical Research and Development Command under Contract No.W81XWH-21-C-0001, W81XWH-22-C-0093 and HT9425-23-C-0059. The views, opinions and/or findings contained in this report are those of the author(s) and should not be construed as an official Department of the Army or Navy position, policy or decision unless so designated by other documentation.

Related links:

Dale Bumpers College of Agricultural Food Life Science

Entomology and Plant Pathology Department

Arkansas Agricultural Experiment Station

U of A System Division of Agriculture

Mpala Research Centre

Protocols.io 

Transcript

 [00:00] Intro/Outro

Welcome to the Arkansas Food, Farms and Forests Podcast. The podcast bringing you the latest on food, fiber and forestry research from the Arkansas Agricultural Experiment Station, the research arm of the University of Arkansas System Division of Agriculture.

[00:18] Jenifer

Welcome to Food, Farms & Forests. I’m Jenifer Fouch. 

Today, we’re diving into REDI-NET, a project aimed at developing standardized pathogen surveillance protocols for the Department of Defense. 

REDI-NET, is short for Remote Emerging Disease Intelligence Network. It’s a collaborative effort involving the University of Arkansas, the University of Notre Dame, and the Department of Defense, focusing on enhancing readiness against emerging diseases.

REDI-NET is going to be an online database dashboard where the Department of Defense personnel can access this information. 

Joining us today are Dr. Emily McDermott, Assistant Professor of Medical and Veterinary Entomology in the Entomology and Plant Pathology Department, and Cameron Osborne, a postDr.al fellow. 

Emily and Cameron, welcome to Food Farms & Forests.

Emily

Thank you.
 
 

[00:58] Jenifer

I'm excited to learn about this. It’s a big project that your research is a part of. Emily, let's start with you. Can you tell me a little bit more about REDI-NET. What it is, and just a summary of what the project is?

[01:11] Emily
 
 Sure. So, the REDIT-NET is a collaborative research consortium. It is a collaboration between the University of Notre Dame, who is the lead on this particular project, as well as the Department of Defense, and us here at the University of Arkansas. Our goals are really to increase the emerging pathogen surveillance capabilities of the Department of Defense globally. 
 
 So, one of kind of the big challenges we see in terms of disease surveillance is that, with traditional pathogen surveillance or disease surveillance approaches, you're only looking for what you know is already there. So, you know, you might say we're interested in looking for Lyme disease or we're interested in looking for malaria. But as I think a lot of people are a lot more aware of, and the last few years, is that there's a lot of other things out there that could start causing problems at any time. 
 
 The challenge of trying to find something when you don't know what it is, is really, really difficult to approach. So, the REDI-NET essentially is taking kind of a two-pronged approach to this. So, one of our main objectives is to develop standardized research and surveillance protocols. So that all of the different labs to eventually be using the REDI-NET are using the exact same methodologies. And this means that all of the results generated across labs are going to be, you know, validated. We know everybody's doing things the exact same way. But the really kind of exciting part about REDI-NET is that rather than taking that single disease approach to it, we're using what's called a metagenomic approach. So, we are sequencing all of the genetic material in these different samples that we're collecting. And then we can use bioinformatics to basically identify where each one of those sequences came from. And so, we can see, you know, there's Lyme disease in this, or there's malaria, but there's also these viruses in here. And maybe those are viruses that we are aware of, and maybe they're brand new viruses, and so this gives us a lot more information. 
 
 This, and all of this data, then is funneled into the REDI-NET dashboard. And so, this is an online portal that all of our Department of Defense users will eventually have access to. The data is thrown into this; then we have automated pipelines where we're able to identify what these pathogens are. And then it's providing the users with output in terms of we've detected this particular pathogen in your sample. Then those users can take the steps of protecting personnel or, you know, applying pesticides or whatever needs to be done for that. And so that's the ultimate goal of REDI-NET is to have this near real-time data in the decision pipeline.

[04:33] Jenifer

And how did you initially get involved with this project?

[04:36] Emily

We are involved now as what we're calling a gold laboratory. So, the REDI-NET is split into a tiered laboratory approach. So, we have gold, silver and bronze labs. Originally, the project started with three gold laboratories: Notre Dame lab, the Walter Reed Bio Systematics Unit, and the Naval Medical Research Center. We were brought on as a fourth gold lab in this third phase of the project to leverage our expertise in veterinary entomology, zoonotic disease, and animal health.

[05:17] Jenifer

So, third phase. You said earlier this is the third year of the project. That's when we were introduced as that gold and that gold tier. And so, the project has been going on for a while, and now it's in the third year.

[05:30] Emily

Yes. That's correct. And so, the first two phases of the project really focused on developing the standardized collection protocols for a number of different environmental sample types as well as developing that online infrastructure for the data portal. And there's a lot of work that's gone into that on the Notre Dame side of things. 
 
 In this third phase of the project, our objectives were really to go from kind of environmental sampling to what we're calling active vertebrate sampling. So, a lot of these emerging diseases, have their origins in animals. Bird flu is in the news a lot in dairy cattle. And so, you know, we talk about things like SARS coming from bats and wild animals, but domestic animals like livestock can also play a really huge role in that. And so, we have been developing active vertebrate sampling SOPs (standard operation procedures) focused on livestock as an area where we could see a lot of what we would call spillover between animals and people for emerging vector-borne diseases.

[06:41] Jenifer

So, a lot of the research that you are doing here is going to be a part of the final results of REDI-NET.

[06:48] Emily

Yes. The way that we are kind of set up as a consortium is that these first three phases are primarily research-based. So, testing these different SOPs, finding out what works, what can be applied broadly. 
 
 We have side research projects that we've done in terms of pathogen discovery and comparison of some of these different sample types and what they can tell us. And then what we are moving towards is an operational phase of the REDI-NET. 

So, in phase four of the project, we're starting a rollout to these, what we call, global combatant commands of the U.S. military, so that our actual DoD (Department of Defense) stakeholders will be able to use the tools that we have developed for actual surveillance for warfighter protection.

[07:45] Jenifer

And part of that research and part of that work behind the scenes for REDI-NET was a recent trip that Cameron, you took to Kenya. Can you talk to us a little bit about that trip, the objective of the trip, and what was it like? What did you get accomplished there?

[07:59] Cameron

Yeah. So, as you heard Dr. McDermott discuss, we're developing these standard operating procedures to be used by people all around the world. One of the most important things we need to do is to make sure these SOPs match the capabilities of each of these commands or areas. 
 
 So, we have one of these silver labs located in Kenya at the Mpala Research Centre, in Laikipia County, up on this plateau, just at the base of Mount Kenya. I had the opportunity to travel there and meet with the team, discuss how they can best collect samples that we're interested in and including filth flies to look for any sort of bacteria or pathogens that might be on these flies transmitted to people. They're working with ticks. So, I got to get a feel for the type of cattle they're working with and to help enhance the protocols that we're developing here to make sure that we're accounting for all the different types of collections strategies. 
 
 I'm working with primarily non-entomologists at these locations. So, I was able to go in and kind of discuss the different types of flies they might be discovering in their samples to help build an ID guide for them so that they can determine which flies they're collecting and what would be most important to look for pathogens on.

[09:11] Jenifer

Was this the first time you went down to Kenya specifically for this purpose, with this research?

[09:18] Cameron

Yeah. So, this is my first time traveling out of the country for such a big project. I was supposed to travel during my Ph.D. Unfortunately, that was right during Covid, so I was unable to travel. And this presented a really amazing opportunity to go not only overseas but to a really beautiful area in Kenya. 

Obviously, it’s very different than what we're seeing here in Arkansas. But what's really interesting is we're still seeing the same kind of flies that I discussed, similar species. And also, the type of environment is something we also are worried about here, the spillover and human interactions between wild animals, domesticated livestock, and humans. So, two very different spots. But a similar thing that we're worried about.

[10:01] Jenifer

Yeah, that's always very interesting how research from here can be applied elsewhere in the world. And that might be something that people might wonder, well, why? How is there a connection? Can you talk a little bit more about those similarities, and how do you, as a scientist, take “here's what we know about the specific climate or animals and how it applies somewhere else in the world.”

[10:21] Cameron

Yeah. I mean, it's a small world at the end of the day. Really, we're trying to train up these individuals about how best to assess the threats to their environment and to make the strategies that we're developing as applicable as possible, as broadly applicable as possible.

[10:38] Jenifer

So, when it comes to REDI-NET and having partner sites, how is that beneficial to the end goal of REDI-NET?

[10:44] Cameron

I think one of the most important things that I learned about from this trip was how these silver labs who are doing the day-to-day sampling, are actually carrying out the procedures that we're developing here at the University of Arkansas. And that was important for me to be able to help develop those and refine those for the most broadly applicable situations as possible. And ultimately, as these get rolled out to new global combatant commands around the world, we hope to get that feedback and start to continue or continue to refine and make these SOPs the best they can be.

[11:18] Jenifer

Speaking of refining the SOPs, what has been some of the unique challenges or some of the things or some of the unique successes that you both have found last year that you have been involved with this project?

[11:31] Emily

I would say one of the challenges that we've been facing and working on is the inclusion of new sample types and trying to use the existing sample processing SOPs that were developed in the first two phases of REDI-NET, so that we don't have to start from scratch, right? 
 
 The goal of this is to make things as easy for our end users as possible, so we don't want to have to say, well, if you're using ticks, then you use this sample processing. But if you're using flies then it's a whole completely different other thing that you have to use. If we have users who are collecting both types of arthropod samples, we want them to essentially be able to do the same thing with them. 
 
 But obviously flies and ticks are different. And when we start thinking about considerations in terms of both the, you know, physical nature of a tick versus a more soft-bodied fly, we have to think about how we're grinding these samples up could be a little bit different. But also the way that ticks versus flies transmit pathogens is different as well. 
 
 So, when we're talking about ticks, they're biting us. They're biting cows or whatever else is in the environment. And those pathogens are going to be on the inside of them. Filth flies on the other hand - this is a really general term that we use for flies, species that develop in filth, and obviously there's pathogens in filth. But rather than those flies being infected with those pathogens in the same way that a tick would be, we're talking about things like bacteria and viruses on the outside of the ticks. 

So, Cameron has been working a lot on, “well, does it matter if we grind up these flies, or can we just sort of shake them up in a solution and get the stuff off of them?” And that eliminates a lot of problems with the downstream processing where the kind of bits of fly or tick or whatever kind of mess up some of the additional steps that you have to do. And so, you have to get rid of them. If we can just wash them off and get what we need, then that eliminates a whole step and it makes things a lot easier. So, that's one of the things that we've been looking at. 
 
 Like I mentioned, we're also doing fecal collections for animals. And so we've looked at different types of animal feces in terms of extraction. And when we think about mammal feces versus bird feces, birds have a very different excretory system than mammals do. And so the chemical composition of, you know, chicken poop is very different than that of cat poop. And so, we've been looking at, you know, how do you sample these things? Both, like in the field. But also, do the kits that we use work for, you know, chicken poop as well as they do for, for cow poop? And so evaluating some different kits and making sure that those standardized protocols are going to be acceptable for multiple different kinds of a particular sample type.

[14:44] Jenifer

Very good. And what about you? Do you have anything to add, Cameron?

[14:47] Cameron

Yeah. So, we discussed the fly-washing experiments which has been a little project of ours. And it works really well here at the University of Arkansas. We've got a colony of flies we can pull from. We got really good results. I took these same methods to Kenya and didn't get anything off of the flies. So, this presented a unique challenge and something important for us to know how this is going to function in the real world. And so, trying to develop strategies to optimize and overcome some of those hurdles that we're seeing in these real world collections.

[15:17] Jenifer

So, we're in the middle of phase three right now with some of these unique challenges and the SOPs and finalizing all of that. What is next? When does phase three end? You mentioned, Emily, phase four - what is that timeline like? What is next for REDI-NET?

[15:34] Emily

Phase three of the project will go through the end of this August. And then we'll begin phase four. So, phase four is kind of straddling this research aspect with moving into the operational aspect. And so, this first part of phase four will again be another year.
 
  So, we're going to be doing a lot of reaching out to stakeholders as we start to roll out to those GCC’S (global combatant commands) and getting their feedback. 
 
 And then, we'll be taking feedback from those stakeholders and evaluating it in the lab and seeing if there are things that we need to tweak. If they have suggestions for, like Cameron said, you know, we can develop this here on a farm in Arkansas, but it might not work out in Kenya. And so, when we get the type of feedback from stakeholders, we can tweak things in the lab, we can test and validate it. 
 
 And then eventually we'll move away from kind of a research focus of this to providing support to hopefully completely operational REDI-NET program, where our military stakeholders are conducting surveillance, they're pushing their data through these pipelines, and then we're there on the other end helping interpret those results because it does get very, very complicated when you're thinking about the, you know, millions and millions of copies of DNA from lots of different things in a particular sample. Being able to kind of parse out what that all means, both in terms of what it is, but from a, you know, a biological standpoint, what's relevant and what might not be.

[17:21] Jenifer

What is it like for you guys as scientists to be a part of a project like this to build something from scratch, collaborating with other researchers as well. And then here in a couple of years to see the final product?

[17:37] Emily

It's been really exciting. This is the first time for me working together with a group of this size. We actually just got back a few weeks ago from our annual consortium meeting in Washington, D.C. So, every year, the entire REDI-NET team comes together and discusses where we are in the project, what's needed to move forward, challenges that we've been facing. And it's really great to be able to sit down together and talk these things through. It's very, I think, productive to, to have these conversations in person. And also to meet, you know, people from all over the world who are working on the same project. So, I think it's been, really exciting thing to be part of.

[18:26] Jenifer

What about for you, Cameron, very early on in your career, having the opportunity to work on something like this?

[18:32] Cameron

Yeah, I finished my Ph.D. in August and joined the lab here at the University of Arkansas in November. My Ph.D. was on a very specific problem, a very tiny sliver of a field. And it was interesting. But really joining this project, I'm able to take a step back and see the big picture of how we can develop tools that are going to help so many people. And that's been so rewarding to actually be a part of.

[18:55] Jenifer

Yeah, a big group like you mentioned, Emily. Who were the collaborators or who are the collaborators on REDI-NET?

[19:01] Emily

So, the lead PI (project investigator) on the project is Dr. Nicole Achee at the University of Notre Dame. The other Notre Dame co-PI is Dr. John Grieco. At Walter Reed Biosystematics Unit), Dr. Yvonne Linton is our co-PI. And at NMRC (Naval Medical Research Center), it’s Dr. Le Jiang.

[19:19] Jenifer

And how is this project being funded?

[19:24] Emily

This project is being funded through the Department of Defense.

[19:27] Jenifer

Is there anything else about the project, about this journey that we didn't discuss that you guys would like to talk about?

[19:34] Emily

Well, you know, we've talked a lot about how this has a real military focus. But the idea is that the techniques and things that we're developing through REDI-NET are going to have a much broader impact. So, one of the things that I think is really, really cool about this, you know, is when we talk about military projects and things like this, there's a lot of data security associated with it. And so, everything is kind of protected. But the SOPs that we've developed are actually publicly available. So, in this last phase of the project, we've publicly posted all of the REDI-NET sampling, processing surveillance SOPs on Protocols.io. And so, they are available for open access to anyone in the world to use. 
 
 And so, our hope is that you know, while the data generated from REDI-NET may need to remain more controlled, the tools that we're developing are available much more broadly.

[20:41] Jenifer

How can people find that?

[20:43] Emily

So Protocols.io is a website where people can post different protocols for lots of different things. If you search REDI-NET on Protocols.io, you should be able to find all of those different SOPs.

[20:59] Jenifer

Very good. Thank you. Cameron, anything else you'd like to add?

[21:03] Cameron

Yeah, one of the other great parts of being or one of the other great things about this project is being able to work with so many people around the world. Emily mentioned that we had our consortium meeting just a few weeks ago, and being able to put faces to all the names I've been seeing for the past few months was really exciting. And discussing new projects that might be arising from this kind of work with partners around the world.

[21:25] Jenifer

Thank you guys so much for your time and for educating us on REDI-NET. This is all very exciting and we would love an update here in a few months, maybe next year I'll see how things are going.
 
 

[21:36] Emily

Absolutely. As soon as we get phase four awarded, we'll be sure to let you know.

[21:42] Jenifer

And thank you all so much.

[21:43] Cameron

Thank you. 

[21:46] Jenifer

That was Dr. Emily McDermott and Dr. Cameron Osborne talking to us about REDI-NET. Thanks for listening. I'm Jenifer Fouch. Don't forget to subscribe.

[21:56] Intro/Outro

The Arkansas Food, Farms and Forests podcast is produced by the Arkansas Agricultural Experiment Station, the research arm of the University of Arkansas System Division of Agriculture. Visit aaes.uada.edu for more information.