Science Friday - How Election Science Can Support Democracy | The Genetic Roots Of Antibiotic Resistance

Episode Date: March 12, 2024

How Election Science Can Support DemocracyThis week, the election season shifted into full gear with the Super Tuesday slate of primaries. But as the ballot options become more cemented, it’s not just pollsters and campaign operatives who are preparing for the elections—scientists are too.The Union of Concerned Scientists has established what it calls an election science task force, looking at everything from ballot design to disinformation to voting security. Dr. Jennifer Jones, program director for the Center for Science and Democracy at the Union of Concerned Scientists, joins Ira to describe the goals of the effort in the weeks and months ahead.The Genetic Roots Of Antibiotic ResistanceAntibiotic resistance—when pathogens no longer respond to the conventional antibiotic medications—is a serious medical problem. According to the CDC, over 2.8 million antibiotic-resistant infections occur in the U.S. each year, causing some 35,000 deaths. It’s in part due to overprescription of antibiotics in medicine, and the widespread use of antibiotics in animal agriculture. But the problem isn’t entirely of humans’ making. The roots of antibiotic resistance go back millions of years.A recent study in the Proceedings of the National Academy of Sciences collected hundreds of soil and poop samples from around the world, to try to trace back the genetics of how resistance arose in Enterococcus, a genus of bacteria that live in the guts of pretty much every land animal. In the course of their analysis, the researchers identified 18 entirely new species in the genus Enterococcus, with over 1,000 genes that had never been seen before.Dr. Michael Gilmore, the Chief Scientific Officer at Mass Eye and Ear, joins Ira to talk about the study and what the team hopes to learn about the causes of antibiotic resistance.Transcripts for each segment will be available the week after the show airs on sciencefriday.com. Subscribe to this podcast. Plus, to stay updated on all things science, sign up for Science Friday's newsletters.

How much do we know about the world's bacteria? We're somewhere around 1% with respect to interococcus. It boggles the mind, really, what's left in that 99% that hasn't been even ever seen before. It's Tuesday, March 12th, but of course, it's Science Friday. I'm SciFry producer Charles Bergquist. Researchers are collecting soil and poop samples from around the world and searching them for new species of enterococcus bacteria. They hope the work will help them,

better understand how antibiotic resistance came to be, and how it moved from the soil into people. Coming up, we'll talk about that project, but first, if you haven't noticed, we're in an election cycle again. Can science help monitor the upcoming elections? Here's Ira Flato. It's not just pollsters and campaign operatives who are preparing for the elections. Scientists are two. The Union of Concerned Scientists has an election science task force at operation, looking at everything from ballot design to disinformation to voting security. Joining me now to talk about that is Dr. Jennifer Jones, the program director for the Center for Science and Democracy at the Union of Concerned Scientists.

Welcome to Science Friday. Thanks for having me. Tell us about the project. In a nutshell, what is, what's your aim here? Well, I refer to stuff. We want folks to know that science really matters for our democracy, that all of us should be able to show up and participate in our democracy and that our vote should count. It should matter. And so we really want to use science, data and evidence to help create that free, fair, and transparent election

system that we need. So we're doing that by looking at a number of different issues from fair maps to ballot design and the role that data transparency can play in making. sure that everyone's vote counts and matters. When you say data transparency, how transparent and accessible is the data behind an election? Will officials learn from past problems here? Well, data is not transparent, and that is a huge issue, right? So what we mean when we talk about data, this is the sort of thing where we're tracking how many voters actually showed up. where there errors with voters and their votes? If I showed up and I made a mistake on my ballot, which is easy to do because ballots can be very poorly designed and confusing, did anybody contact me?

Did I get a chance to fix that error? So some of the data that we want to look at is looking at those participation rates, looking at those ballot rejection rates, those error rates. What can we learn from that? And then what we ultimately want to do is be able to call out the best practices and make recommendations for the future. Ira, let me also just note that part of the issue here is that there's no standardized protocol within states and across states. So that's a real issue. Are there new risks that we're seeing this election or are we mainly dealing with the same lists of threats that we have had in previous elections? There are absolutely threats that have existed since, you know, really voting and elections have happened in this country. You know, disinformation that is used against voters, especially communities of color, falling out fake data and then using that in the future to further restrict the voting rights of people of color continues to be a major issue.

bad ballot design. Again, where it's so easy to make a mistake and have your vote not counted. And then, you know, let's also talk about the role of gerrymandering, creating voter districts that intentionally seek to dilute the votes of some groups of people, again, especially communities of color. So these are longstanding and well-known tactics that keep us from having a democracy. And then, you know, we can also talk about some of our concerns. with artificial intelligence and disinformation and deep fakes this year that are going to be a real problem. These deep fakes are real now, right? They are. And a real concern is that at the federal level, we do not have any meaningful policy and legislation that's been enacted this year to protect the voters

from deep fakes to even stop candidates or supporter groups from using deep fakes and other forms of disinformation. I think it's also important to call that out. You know, in past elections, we have seen the use of disinformation, you know, purposely misleading people about issues, about polling places. So this is not new. It's existed, especially with the rise of social media in recent years, but the concerns around artificial intelligence means that you could have bad actors, whether it is an international group, whether it is a domestic group, purposely seeking to keep people away from the ballots, misleading people on issues, to again sway elections that are not free and fair and truly representative. We have at the Union of Concerned Scientists, what we call the disinformation

playbook, that people can check out and educate themselves about what to look for. And I think that's a starting place. All right. That's a good way to end our conversation with useful information, Dr. Jones. Thank you for taking time to be with us today. It was a pleasure. Dr. Jennifer Jones is the program director for the Center for Science and Democracy at the Union of Concern Scientists. Antibiotic resistance is a serious medical problem. That's when pathogens no longer respond to the conventional medications. It's in part due to over-prescription of antibiotics in medicine and the widespread use of antibiotics. in animal agriculture.

But here's something new. Turns out the roots of antibiotic resistance go way back before humans were around, millions of years, to the soil. A recent study in the proceedings of the National Academy of Sciences collected hundreds of soil and poop samples from around the world

to try to trace back the genetics of how resistance arose and interococcus bacteria. That's a group of bacteria that live in the guts of pretty much every land animal. Joining me now is Dr. Michael Gilmore. He's the chief scientific officer at Mass Eye and Ear and Professor at Harvard Med School.

Welcome to Science Friday. Thanks so much, Ira. Pleasure to be here. Tell us about this bacteria and why study it? Yeah, so Interococcus is especially interesting. In the time that we've used antibiotics on humans, antibiotics-resistant bacteria have emerged to cause problems, and two of those bacteria are members of the Interococcus family. That's out of thousands of possible bacteria. So it caught

our attention that Interoccus arose, and it arose twice. So that said there's something special about this. So now it's among the leading causes of antibiotic-resistant infection. So you're trying to map out the genetics of many of these species. They see how they fit together, right? How do you go about doing that? Exactly. You know, genomics is the new lens to understand and view the world through, and that's showing us so much that we didn't understand before. You know, when you look at it through the microscope of bacteria, they'll look tiny and kind of round, and it's hard to distinguish one from the other. But when you look at the genomes, you can see every detail of the organism's biology. We can't completely understand it yet,

but all the information is there. So we compare the genomes, and we ask, how far apart are they? It's sort of like 23 and me on bacteria. So you collect them from around the world? Some of the more exotic ones come from where? We teamed up with some elite adventures, a group called Adventures in Scientists for Conservation, and their adventures go to places where humans have never been.

And this included glaciers in Greenland, mountains and Nepal, a lot of different places. So they're out there collecting poop samples that they send back to you in a mailer, so to speak? Yes. You know, it's, we get all kinds of samples. We get dead insects. We get poop samples. Sometimes we get a piece of intestine or something like that.

They're appropriately labeled as, you know, biological specimens and put in the mail, but sometimes they get pretty stinky by the time they arrive. I can imagine there's some grad students opening it, not you, right? Yeah, that's right. We need extreme adventures for that. You know, I'm struck by the fact that these bacteria are in all sorts of animals, from people to penguins, to insects, even some aquatic species. Just how similar are all of them?

You know, the human use of antibiotics on people and on animals has really changed the genomes of these bacteria. And that's one of the things we learned from this study. And, you know, when we look at the bacteria that come from human antibiotic-resistant infections, those intro-coxye have genomes that are as much as 25% larger than the strains that are in the wild. And that's because they've collected all kinds of things in the effort to survive in the face of a lot of antibiotic use. some of the things they collected are useful, some not, as far as we can tell. But that's one of the profound differences between hospital strains and strains from the wild.

Also, in the hospital, we mainly see two species. In the wild, our collection has shown that there are probably thousands of species. We just added 18 new species, bringing the total to about 80, but we would project based on our rate of hit of new species, there are tens of thousands of species out there that we don't know about. And what do you make use of? What does this tell you? Well, a lot of things. So our interest is mainly trying to understand how antibiotic resistance emerged in Interococcus. And Interroccus got an early start when animals first crawled on land, 425 or 425. 50 million years ago, one of the things that distinguishes innerocococcus is they're kind of like

the cockroach of bacteria. They survived very harsh conditions. So when the first invertebrates crawled onto land and pooped in sand, a proto innerocococcus was in their gut. And it was probably one of the ones that survived the best on the sand and then reentered another animal when it crawled on shore and was passed that way. So the ability to survive a very harsh exposure is the hallmark of innerococcus. And turns out we work very, very hard to decontaminate hospital beds after patient use and things

like that. But one of the challenges is innerococcus. It's super difficult to kill. So that, I think, is core to its biology as well as the reason it emerged as a problem in hospitals. Now, in your research, you call out two species as being covered. kind of unusual. And I'm talking about dragonflies and chickens. Wow. Yeah. Why? Yeah. So one of the ways we get interocococci in our guts is from the food we eat. Chickens eat a lot of different things.

They're scratch feeders naturally. So they scratch the dirt and eat insects. And the guts of those insects have interococcus. And those insects have lived in the soil where antibiotic producers naturally occur. And so we strongly suspect all of the antibiotic resistances we see in hospital patients now originated in the soil ecosystem. And we think chickens, especially those fed antibiotics to promote their weight gain, collect innerococytes in their gut, and again, especially antibiotic resistant ones. And once they're in chickens, then the chickens get processed and pass to humans. So we think it's because of the variety of things chickens eat and that they come from the soil where there's tremendous diversity. Dragonflies are also carnivores.

And for the same reason, they eat a lot of different types of insects. And we found a ton of interococcus diversity in insects. So we're not just talking about antibiotics in the sense of a pill or a liquid you get at the drugstore. You're talking about stuff that's found naturally in nature. Exactly. So antibiotics are about. a billion years old and the first organism that produced an antibiotic also had to be resistant to it. So resistances generally can be traced back to the original antibiotic producers. But once that producer started producing it in the soil, when the producing organism died and spilled out its DNA, neighboring microbes collected some of that DNA and picked up some of the resistances

and the resistances got spread outward that way. So antibiotic production and antibiotic resistance is ancient, but it had always been confined to the soil ecosystem. It was only, you know, since the 1930s that it was brought into contact with humans in a substantial way. Have you found from your hundreds of soil and poop samples, anything new there, anything that surprised you, new species or whatever? Yes. So what surprised us is that we found 18 new species that had never been seen. before. Wow. And that included over a thousand new genes that also had never been seen before. And also in some species that we did know about, we found some new toxins in collaboration with some of our

associates here at Harvard Met School. We found a new type of Botox. And we found another core forming toxin that has a very interesting novel mechanism. Huh. Do you need any fresh samples? I mean, can I listen to Sengist stuff? We do. So, you know, Now, this paper showed us where the unexplored diversity is, and it's in insects and their invertebrate relatives. We really want to systematically explore that now. You know, whereas we're up to about 80 species now, we think we can easily double that by examining maybe 5,000 or 10,000 invertebrate samples.

And we now have the high throughput genomics to do that. You know, I go through a lot of natural history museums and you see samples of all kinds of stuff there in jars or pinned to paper. Could they be sources that you could look into? Yeah, that's, you know, that really is a great idea and they certainly can be. The problem that we run into is we like to recover the live bacteria when we can so that when we find something interesting in its genome, we can culture the bacteria and explore its properties. From preserved specimens, if they're preserved in alcohol or something like that, the bacteria generally are dead.

But we can work with the DNA. But we prefer just a dead insect. And again, since innerococytes are so persistent, the innerococcus and a dead insect can survive in the male for weeks. You know, whenever we talk about sampling and finding new stuff, I'm always struck by the amount of stuff that's still out there? I mean, how much of what you have found do you think represents the total of what's out there

that we don't know about? That is the astounding thing. So our collection rate told us that we're somewhere around 1%, knowing about 1% of what's out there with respect to Interococcus. And innerococcus is one of the more common organisms. And so it boggles the mind, really, what's left in that 99% that hasn't been, ever seen before. Do you ever think about searching for phages, you know, the viruses that attack

bacteria? Absolutely. That's a very hot idea. So that's something that we've done. Many of these do have phages. Some phages are sleeping in the genomes of many of these strains. And those phages can certainly be employed for the new kinds of therapies that are being explored right now. Okay. So what do you want to look for next? What's on your agenda? Well, one of the things that we'd like to do is we know that antibiotic resistance genes originate in the soil, and we know that they end up in the hospital. We would like to put together the chain of custody in between those so that we know exactly what practices are promoting the upwelling of antibiotic resistance from the soil ecosystem so that we can effectively stop it. You know, we don't want to just have a blanket moratorium on use of antibiotics, then the companies go out of business. We want to strategically deploy antibiotics in a way that doesn't promote bringing in new resistances from the soil ecosystem.

And so we need to know how it moves. And so that's why we're out exploring nature and trying to connect the dots. Well, Dr. Gilmore, thank you for connecting the dots for us. A real pleasure, Ira. I enjoyed it, and I'm a big fan. Thank you, Dr. Michael Gilmore. He's the chief scientific officer at mass eye and ear and a professor at Harvard Med School. That's it for today.

Tomorrow, you might still feel a little sleepy on account of that time change last weekend. But we'll hear about a medical condition that causes extreme sleepiness, like being able to sleep for 30 hours straight sleepy. I'm SciFri producer Charles Bergquist. Thanks for listening. We'll see you soon.