Smithsonian National Museum of Natural History

Superbugs, Antimicrobial Resistance, the Environment, and You

Superbugs, Antimicrobial Resistance, the Environment, and You

Aired November 9, 2022

Ashley Peery:

So hello again. My name is Ashley Peery. I'm an educator with Smithsonian National Museum of Natural History. I'm a blonde-haired woman wearing a purple shirt, and in my background you're seeing an image of my basement, which has some schematic drawings. On the screen, you are seeing an image of today's speaker, as well as some information about the program, and you're joining us today for Superbugs Antimicrobial Resistance, the Environment, and You. This is our second program in the Shared Planet, Shared Health Series. Now, this is a monthly webinar series that explores the connections between human health, animal health, and environmental health, also known as One Health. So the series is a continuation of programs connected to the exhibit outbreak epidemics in a connected world that is at the Natural History Museum. That exhibit actually just reopened in a new format. It's a bilingual English Spanish format, so if you happen to be around the DC Metro area, pop into the museum and check out the new look.

Before we get started though, whether this is your first time joining us or you've attended a webinar with us before, we're so glad that you're here and I've got a few housekeeping notes to go through. So first, this webinar does offer closed captioning. If you do need the close captioning, you can access that by clicking CC, which should be located at the bottom of your Zoom interface.

Next, as you think of questions, please put them into the Q&A box instead of the chat box. I think I accidentally said chat box earlier, but in this webinar, you're going to put your questions into the Q&A and get them in as soon as you think of them because the Q&A time flies by and we want to make sure that we can get through as many of your questions as possible. Also, in the Q&A box is where we'll be communicating with you. So as the webinar goes on, you'll get a few links from us that are connected to the content, and so keep an eye out there. All right. The flow for today's program is that we'll start with a presentation from our speaker, Dr. Amanda Beaudoin, and then after her presentation, I'll join her on screen to take your questions.

So with that, let's go ahead and introduce today's speaker. Amanda Beaudoin is the director of One Health Antibiotic Stewardship at the Minnesota Department of Health. She holds a doctor of veterinary medicine degree from Cornell, as well as a PhD in veterinary epidemiology from the University of Minnesota. Dr. Beaudoin has clinical experience in equine and small animal medicine. She's worked for the Centers for Disease Control and Prevention, providing technical assistance to foreign governments that were working to establish surveillance for antimicrobial resistance in human hospitals. Currently, Dr. Beaudoin works with partners in Minnesota and beyond to advance antimicrobial stewardship in human, animal and environmental health. So please join me in welcoming Amanda.

Amanda Beaudoin:

Great, thank you Dr. Peery. I will share my slides and just give me a heads up so I know that it's showing up full screen.

Ashley Peery:

All right, we're seeing your slides.

Amanda Beaudoin:

All right.

Ashley Peery:

Take it away.

Amanda Beaudoin:

Okay, great. Well, thank you again for the introduction and thank you to those who have joined us today. My talk today is called Superbugs Antimicrobial Resistance, the Environment, and You. By the end of this presentation and our subsequent discussion, I hope that you'll recognize antimicrobial resistance as a problem for the health of individual people in animals and to the broader health of the public. You will understand why antimicrobial resistance impacts what we refer to as the One Health continuum and appreciate what is known and unknown about the natural environment's intersection with antimicrobial resistance. And lastly, I hope that you will identify a few ways to prevent antimicrobial resistance and protect your health.

To get us started a bit of terminology, I will use the term germs collectively to refer to microorganisms, including bacteria and fungi that can cause infection in people and animals. Largely, we will be talking about bacteria. Both bacteria and fungi live in and on the bodies of living creatures and are essential inhabitants of nearly all environments in the world. These organisms are vital to health, but they can also cause infection when the natural defenses of a person or animal are overcome. Antimicrobials are medications that are used to treat infection by germs. We will focus on antibiotics, substances that can kill or slow the growth of bacteria. Antibiotics are naturally produced by bacteria for communication and self-defense. Humans use natural and synthetic antibiotics to treat bacterial infections. The impact of antibiotics cannot be overstated. Since they entered into use in the 1930s, they have saved millions of lives from infection and have facilitated the advancement of all aspects of medical practice.

Antimicrobial resistance happens when infection causing germs like bacteria and fungi become able to resist the medications designed to kill them or slow their growth. Despite all the medical advancements we have in 2022, untreatable infections can really throw a wrench into things. As we will hear, antimicrobial resistance impacts people, animals, and ecosystems, and it spreads through healthcare facilities, communities, animal populations and natural environments.

Resistant infections can be associated with high mortality rates and are a major concern for patients in inpatient healthcare settings, like hospitals and nursing homes. They can move across facilities and healthcare networks, making collaborative detection and prevention essential. And with each year, we learn more and more about the impact of resistance outside of healthcare in communities, animals, and the natural environment.

When a bacterial population is exposed to an antibiotic medication, it undergoes genetic changes as part of a response to that stress. Small genetic changes or mutations occur in individual bacteria over time, and those that can withstand the impacts of antibiotics will survive and replicate. Bacteria multiply quickly, giving resistant organisms the ability to spread throughout populations and environments. We will see the process of mutation in action through this video from Harvard Medical School in Technion Israel Institute of Technology.

[She plays video.]

Video voiceover:

So what we ended up building was basically a Petri dish, except that it's two feet by four feet, and the way we set it up is that there are nine bands, and at the base of each of these bands, we put a normal Petri dish, thick agar with different amounts of antibiotic. On the outside, there's no antibiotic. Just in from that, there's barely more than E. coli can survive. Inside of that, there's 10 times as much, a hundred times and then finally, the middle band has a thousand times as much antibiotic and then across the top of it or thin agar, the bacteria can move around it. The background is black because there's ink in it and the bacteria appear as white.

First, you see they spread in the area where there's no antibiotic up until the point they can no longer survive. Then a mutant appears on the right. It's resistant to the antibiotic. It spreads until it starts to compete with other mutants around it. When these mutants set the next boundary, they too have to pause and develop new mutations to make it into 10 times as much antibiotic. And then you see the different mutants repeat this at 100 and after about 11 days, they finally make it into 1000 times as much antibiotic as the wild type can survive. And so we can see by this process of accumulating successive mutations that bacteria which are normally sensitive to an antibiotic can involve resistance to extremely high concentrations in a short period of time.

Amanda Beaudoin:

Impressive, those bacteria. Well, unfortunately, mutation as a result of antibiotic exposure isn't all there is to the story. Highly resistant bacteria can share the very genes that give them resistance qualities with other bacteria called horizontal gene transfer. This sharing of resistance instructions can occur among bacteria of the same species and among bacteria of different species. The transfer of resistance genes can happen through several different mechanisms, and often a cluster of resistance genes is transferred at the same time. This horizontal gene transfer can occur even outside of the presence of antibiotics. It happens within the bodies of people and animals and in our built in natural environments. When genes are transmissible, resistance itself can spread. Some of the most concerning types of resistance including CRE, a major superbug, have been able to spread quickly across the globe as a result of horizontal gene transfer.

An important connection to make when trying to understand the public health problem of antibiotic resistance is how treatment decisions for individual patients influence the larger population patterns that we see. On this slide, you can see two circles on the left representing patients and their microbiomes or the collection of bacteria that live in and on the patient's bodies. The microbiomes are made up of non-resistant or susceptible bacteria in blue and antibiotic resistant bacteria in pink. The patient in the top circle is treated with an antibiotic. Because antibiotics work by killing or slowing the growth of bacteria, the blue bacteria that are susceptible to the antibiotics are reduced in number, leaving the pink bacteria, which can replicate the antibiotics effort. Sorry, which can resist the antibiotics efforts to replicate. The proportion of resistant bacteria to susceptible bacteria in that patient's microbiome changes with more resistant or pink bacteria than susceptible bacteria.

On the other hand, the patient who does not receive an antibiotic maintains a higher diversity of bacteria in the microbiome. In addition to potentially impacting how the microbiome can do its job to keep that patient healthy, changes to the bacterial makeup of an individual alter the mix of bacteria that are shed out into the environment. An increase in the proportion of resistant bacteria means that more resistant bacteria will move out into the environment. Because bacteria naturally leave our bodies and enter the environment every day, antibiotic use for individual patients can influence the bacteria that others are exposed to in the world.

When antibiotics are used in healthcare facilities, the risk of other patients acquiring a resistant germ from the healthcare environment increases. For example, studies show that in nursing homes with lots of antibiotic use, all residents, not just those who have received antibiotics, are at greater risk for adverse bacterial infection outcomes when compared to residents in nursing homes with low antibiotic use. The process of selection of resistant bacteria can happen anywhere where an antibiotic is present in sufficient concentration. For example, when we treat an infection in the urinary tract, selection can occur in any part of the body that that antibiotic reaches, including the gastrointestinal tract where most of our body's bacteria reside. By targeting antibiotics as well as possible to the offending germ and body side of infection, clinicians can lower the risk of selecting for antibiotic resistance.

This phenomenon of antimicrobial resistance is not manmade. Like all living organisms on the planet, germs respond to environmental stressors through adaptation. Bacterial antibiotic resistance genes can be found in areas of the world that have been untouched by humans or pharmaceutical drugs. The image shown here is from a 2011 paper in the Journal Nature by D'Costa et al. The research team conducted targeted metogenomic analyses of ancient DNA from 30,000 year old permafrost sediments. A highly diverse collection of genes, including resistance to several antibiotics was found. Some of the antibiotic resistance genes resembled those that we see clinically today. These results and others show that antibiotic resistance is a natural occurrence that existed long before antibiotics were deployed for clinical use.

Although it is a natural phenomenon, humans can impact the resistance trajectory. The natural process of resistance is amplified when germs are exposed to antimicrobials and when resistant germs and resistance genes spread. Shortly after the introduction of antibiotics in the 1930s, clinical resistance was seen and by the 1950s, some treatments had become a real challenge. Over the next decades, new antibiotics were discovered and developed, allowing us to switch treatments when needed and continue to accelerate all aspects of medicine.

However, we now find ourselves in a situation where resistant infections could compromise modern medicine. In a 2019 report that I encourage you to read, CDC has outlined urgent, serious and concerning resistance threats. In that report, they estimate that nearly three million people in the US have resistant infection each year and 35,000 people die as a result. Medical scenarios that are complicated by the problem of resistance include sepsis, chronic conditions like diabetes, surgery, organ transplants, and cancer therapy. But resistance is not only found in the superbugs associated with healthcare. Some community-acquired bacteria are highly resistant, including Neisseria gonorrhoeae, which causes gonorrhea, a sexually transmitted disease. Gonorrhea has developed resistance to all but one group of antibiotic drugs and half of all infections are resistant to at least one antibiotic. The bacteria spreads easily and tests to detect resistance are not available at the time of treatment, making this a growing threat to health in the community.

In 2020, the U.S. saw significant increases in resistant infections. Because of the COVID-19 pandemic, patients were sicker and had longer hospital stays. There were stresses to healthcare and diagnostic testing capacity. Some patients delayed care in the first years of the pandemic and healthcare and public health organizations experienced reporting delays. This means that although we know that some aspects of resistance have increased, the impact of the COVID-19 pandemic on the problem of resistance is still being measured. But there are several things that can be done to combat antibiotic resistance. And before the pandemic, there were several years where we showed improvement in the rates of resistance. First, when we prevent infections, we decrease antimicrobial use and the potential for transmission of resistant germs from infected individuals. Prevention helps to both stem the emergence and transmission of resistance. Second, the best way to understand the burden of resistant germs or infections caused by them is to conduct surveillance or to track them over time.

Surveillance also allows us to assess whether interventions to curb resistance are working. In addition to tracking the germs themselves, tracking antibiotic prescriptions is needed to estimate the selective pressure we are placing on germs. Prescribers like data too. Giving healthcare providers reports on how they prescribe antibiotics, including on how their prescribing might be inappropriate or unnecessary, has been associated with approved prescribing behaviors. This type of tracking and reporting is a core part of the antimicrobial stewardship concept. Antimicrobial stewardship is a coordinated approach taken in clinical settings to ensure that the right antimicrobials are available, selected and used only when needed. Stewardship, in turn, is supported by practices to ensure that an infection is promptly diagnosed so that the right treatment can be selected to target the infection causing germ. Inevitably, germs will develop resistance to new antimicrobials. We need to ensure that new drugs are being developed and that alternatives to antimicrobials are explored. We'll talk a little bit more about that later.

All of these actions are critical, but if we are to succeed, they all must be conducted in every sector where antimicrobials are used, this includes both human and animal health and across the globe. We must also make efforts to prevent antimicrobial drugs, resistant germs and their genes from ending up in the natural environment. This attention to the connection between human, animal and environmental health is referred to as One Health. Antimicrobial resistance is a One Health challenge. One Health is the idea that the health of people is connected to the health of animals and to the environment. Resistant infections affect animals including pets, wildlife, and livestock, including those that are used for food. Just like people, animals can help spread the problem of resistance. Resistant germs can spread across settings in communities, the food supply, healthcare facilities, and around the world. This movement of resistant germs and resistance genes increases the burden of infections in both people and animals.

The resistant germs that have been identified that pose the greatest threat to human health have also been identified in animals, including pets, and in the natural environment. They can cause challenging infections and can be transmitted within veterinary hospitals. With fewer treatment options available for those patients, some clinical infections might be untreatable even in our household pets. People and animals can share resistant germs and a major threat to compromise human patients in healthcare settings. The CRE superbug has also been identified in dogs and cats around the world. The evidence that this germ can be shared between people and pets within households and in the veterinary settings can make prevention and detection as important in animals as it is in people. Although some of the specifics look a little bit different from healthcare, the approaches of infection prevention and antimicrobial stewardship work in veterinary settings. Collaboration and sharing of evidence-based approaches among veterinarians, public health and healthcare professionals goes a long way.

People and animals, antibiotics, resistance germs, and resistance genes, just like everything that happens in our daily life, the natural environment catches it all. In this depiction from Berkner et al., antibiotics are shown as tiny red dots. As you can hopefully see, there are myriad pathways for antibiotics used in humans, animals, and crops to enter the natural environment. Processes like pharmaceutical and ethanol production also contribute to antibiotic containing wastewater. Once in the environment, antibiotics impose the selective pressures previously discussed on germs in the natural ecosystem. Resistant germs shed from people and animals into the environment by groundwater, wastewater, runoff from field applied manure and human bio solids and aquaculture.

By now, I think you're sufficiently convinced that resistant germs and their genes can be anywhere and everywhere. Resistome is a term that we use to describe the collection of resistance traits present in a microbial community. When thinking about the resistome, community is loosely described. Your body is a community and your microbiome or the microorganisms that make you, well, you has its own resistome. When we take antibiotics or use probiotics or even eat yogurt, we have the potential to shift our microbiome. When we're exposed to new environments, including when we travel to other countries and eat new foods, we can take on new bacterial passengers, either for a short time or for an extended duration. Built environments also encompass unique resistance. For example, in a healthcare facility, resistance genes are present in the germs carried by patients, but they are also hiding out in the built environment.

Resistant germs in their genes exist on some surfaces, and bacteria, especially love sink drains. The replication of bacteria and the horizontal transfer of genes can happen on these inanimate surfaces. Resistant germs can move from patients to patients or from the patient environment onto patients. They can be transferred from the hands of healthcare workers or by medical equipment or contaminated surfaces. Infection prevention experts work with public health to identify the cause of resistant outbreaks in hospitals and nursing homes, sometimes outbreaks that impact multiple people.

In Mother Nature, host the mother of all resistomes, water, soil, and atmospheric environments host germs in their unique and varied resistance profiles. Naturally occurring resistance informed by the antibiotics and other chemicals that germs have used for millennia to converse and to compete is accompanied by resistance elements that have spilled over from human driven activities. We should consider the concept of the resistome in the bigger picture. Though patient transfers, international travel and interaction from person to person are important, we must also consider our interactions with the outdoors. Resistance genes move around, they're replicated and shared across regions, countries, and the world.

Let's take some time to focus on antimicrobial resistance in the natural environment. In addition to the myriad naturally occurring and constantly changing elements in the natural resistome, antibiotics, resistance genes and germs are added through human activity. When a person or animal is treated with an antibiotic, most of the drug is broken down by the body. The altered antibiotic, referred to as metabolites, and some of the original intact antibiotic leaves the body through urine or feces. These residues end up in wastewater, ground water and storm water and are spread as fertilizer onto agricultural fields in the form of animal manure and human bio solids. You now have an appreciation that people and animals shed resistant germs and genes from their bodies. These elements enter the environment through the same routes. Wastewater is known to alter the biodiversity of ecosystems by depositing chemicals, including antibiotics, microorganisms, and micro pollutants.

And we also know that stress imposed by pollution can increase selection of resistant bacteria and natural ecosystems through adaptation and sharing of resistance genes. Pollution can also give resistance a physical leg up. If you needed just one more reason to stress about the impact of plastics on the planet and health, well, here it is. Microplastics found in aquatic environments provide billions of little islands where bacteria can gather and share their resistance genes. Essentially, these unnatural microplastics provide a tremendous increase in the surface area available for bacteria to gather, form biofilms, which are like protective shields and replicate and share genetic material easily.

Studying the natural environment resistome and quantifying its role in the public health problem of resistance is challenging to say the least. At every turn, from the methodology development to interpretation of data, unknowns exist. First, how do we meaningfully measure the presence of antibiotics? How do we meaningfully measure resistant bacteria and resistance genes in nature? Say we decide to measure antibiotics. Do we measure it a single time point or overtime? And in what season, during summer when the water is easy to collect and people are recreating in it daily or during cold and flu season when most antibiotics are used, but the water is frozen over? Which antibiotics do we look for? Detection of different drugs can change over space and time and can be related to whether they persist on organic material or break down under sensitivity to UV light. There is also no standardized way to define and measure resistant bacteria in genes.

You now know that resistance is an ancient, natural process. I'm sure you can imagine how difficult it is to determine what the baseline of normal is of resistance in the ecosystems. It is helpful to quantify any resistant bacteria and resistance genes if we know what we're really looking for. These are just a few of the challenges that face researchers working in this space. But despite these challenges, much has been learned about antibiotic contamination, the resistome and the of humans in natural spaces. Minnesota scientists, for example, have determined that lake sediment maintains an antibiotic record that collected over decades, aligns with the history of individual antibiotic drugs entry onto the market for clinical use. This work and other water sampling underscores the role of wastewater effluence and urban areas as the primary factors that are associated with entry of antibiotic compounds into water. Lesser inputs have been described from agricultural runoff, but urban intercepts are the most important.

Antimicrobial resistance, however we choose to define it, is found at the highest levels insights that are influenced by human activity. But we do see clinically relevant resistance in pristine locations, including in designated wilderness water bodies right here in Minnesota and in remote glaciers. Some studies of glaciated terrain have described a resistance gradient increasing with the level of exposure to human activity. Research to understand the implications of resistance in ecosystems is increasing. Chemicals, microorganisms, micro pollutants released into the environment through wastewater and other contamination alter the biodiversity of microbial ecosystems and cause stress on bacterial populations.

Despite the increasing availability of quantitative data measuring the presence of these things, there is little evidence showing a connection between transmission of resistance directly from the environment to people. Outside of acquisition of resistant germs through food, most research in this area has looked at water. In one study, surfers were determined to be at risk for exposure to in carriage of clinically important resistant germs in the coastal waters of England and Wales. The risk was influenced by the amount of time that they spent in the water, the amount of water consumed, and the concentration of resistant bacteria that was present. Researchers in this space are advocating for a systematic review and some basic science to help fill the knowledge gaps regarding this important area.

Even without understanding all of the implications of resistance in antibiotic contamination of the environment, the connected nature of resistance means that we can all make a difference. All users of antibiotics contribute to resistance, so we must make improvements in how we use them in all sectors. Because development of resistance is complex and interactions between people, animals, and the earth are occurring constantly, it's impossible to really directly link cause and effect. That means there's room for improvement everywhere. Exposure to resistant germs or their genes is not limited only to the sector from which they emerge. Luckily, the methods of resistance prevention are similar regardless of setting and effective tools and approaches like antibiotic stewardship can be shared across human and animal sectors.

Before we get into what everyone can do in their daily lives to combat antibiotic resistance, here is a glimpse at some scientific innovations and inspiring approaches because bacteria will always grow to adapt to any antibiotic developed, identification of antibiotic alternatives is critical. One such approach called bacteria phage or just phage therapy targets specific infection causing bacteria. The use of phages, which are natural viruses that can target and kill bacteria is still new, but there have been wonderful stories of success. You can read one of those stories on the Minnesota Department of Health website following the stories link provided by the webinar hosts.

And although it's not new technology, vaccination will continue to be an important part of the solution to resistance. Vaccination reduces the number of infections, which in turn decreases antibiotic use in transmission of germs. Pneumococcal conjugate vaccines are a great example of the impact that vaccines can have on resistance. These vaccines protect against infection by streptococcus pneumonia. After global uptake of the pneumococcal vaccine, rates of childhood death and incidents of resistant strains decreased considerably. Vaccination works for animals too. Widespread vaccination in the US against one type of salmonella in poultry is likely what has contributed to falling rates of infection in people.

New ways to more quickly detect resistance in individuals and populations have also emerged. Rapid diagnostic testing can identify the germ or germs causing an infection or identify the resistance genes of concern directly from a patient's biological sample. With experience gained from wastewater detection of SARS-CoV-2, the virus that causes COVID-19, CDC is exploring how innovative solutions and wastewater surveillance can be used to improve detection and response for resistance. Although selection of genetic traits has long been a part of animal husbandry, over time scientific advancements have allowed breeders to incorporate traits that are associated with reduced disease susceptibility, while maintaining those characteristics that are associated with good production value.

In more novel work, scientists have shown that targeted gene editing can increase animal resistance to major germs. When fewer animals get sick, fewer antibiotics are used. This technology has been used to breed pigs that are resistant to dangerous viruses like PRRS. Gene editing faces challenges in acceptance by consumers and regulators, so mainstream use of this technology is a long way off in the United States, but the does hold promise. On the other end of the science spectrum are prairie strips, a natural innovation to reduce environmental release of antibiotics and resistance from agricultural fields. Prairie strips incorporate diverse native plant species that offer resiliency and stability to agricultural lands. Research is being conducted at Iowa State University to investigate whether their placement within and at the edge of manure covered fields can help combat the transport of antibiotic resistant contaminants downstream.

And lastly, what can we all do every day to increase awareness and combat resistance? Here is a bit of a hit list. Talk to your healthcare provider about your risk for resistant infections, especially if you have chronic conditions or immune compromised or receive healthcare frequently. Talk to your provider about your own risks and how you can lessen them. Be aware that antibiotics should only be used when needed. This includes for children, adults, and pets. In the US, about 30% of all antibiotics for outpatients are unnecessary or inappropriately prescribed and about 50% of those antibiotics prescribed for upper respiratory tract infections are not even needed. Just having an open mind that antibiotics are not always needed and can sometimes do more harm than good is important. US antibiotic awareness week is coming up during November 18th through 24th. Keep an eye out for messages from CDC, your local health department and healthcare organizations. Take part by amplifying messages you see on social media and elsewhere.

Stay healthy and stay home when sick. Decrease the need for antibiotics by avoiding infections. We all should be very good at this now. Wash your hands properly and keep your vaccinations up-to-date. Make sure to wash your hands after caring for animals and prepare your food safely. And for goodness sakes, don't share an ice cream cone with your dog or snuggle with baby chicks. Take care when traveling abroad and tell your healthcare provider if you receive healthcare in another country. When traveling, try to consume safe food and drinks. Raw foods can be contaminated with germs, including those resistant to antimicrobials. Some resistant germs associated with healthcare, including the CRE superbug and candida auris, a dangerous fungus, are more common outside of the US. International healthcare remains a major risk factor for acquiring these germs.

Dispose of unwanted medications in a designated takeback site. Proper disposal keeps antibiotics and other pharmaceuticals out of the natural environment. Drop boxes for leftover medications can be found in law enforcement offices and increasingly in pharmacies, including some locations of large pharmacy chains. If we work together in health sectors, industry and in the community, we can make progress in the fight against antibiotic resistance. Thank you and I look forward to our discussion.

Ashley Peery:

Wow, thanks, Amanda. I'm applauding you for such a rich talk. The audience has a lot of questions, so if it's okay with you, we'll go ahead and dig in. Our first question is from Grace. So Grace asks beyond avoiding household antimicrobials and antibiotics, do you see connections between zoonotic diseases and increased resistance via healthy exposures to the soil and outdoors?

Amanda Beaudoin:

So if I understand correctly, you're curious about just zoonotic disease and how we engage in the outdoors and might encounter those organisms. We certainly here in Minnesota, and I think in other neighboring states, have seen increases in infections like blastomycosis, which is a fungal infection that we get from the soil. And what we've seen during COVID-19 is that a lot more people are interested in getting out and about and maybe more people and their dogs are coming into contact with some of these organisms.

Another thing I can think of when it comes to zoonotic disease is how we're encountering vectors like ticks and mosquitoes. The more we move around out in the environment, the more we're going to acquire these vectors and put ourselves at risk. And essentially, we know that there are ways to prevent vector-borne disease if we are wearing the appropriate clothing and using repellents as directed. So yes, encountering the environment is positive in so many ways, but sometimes does put us at risk for some zoonotic pathogens.

Ashley Peery:

Thanks for that. So the next question comes from Margaret. In Ed Yong's book, We Contain Multitudes, in case you've read it, the author spoke of very few bacteria as being bad. Most bacteria are actually good. And when we use antibiotics, the bad bacteria can take over. How can we increase the good bacteria?

Amanda Beaudoin:

Ooh, that's a wonderful question. I agree. Most of the bacteria are good because when you think about how we have billions of them, and I think when we are considering how can we keep ourselves healthy and our bacterial populations inside of us healthy, we can continue to eat as well as we can, engage with the outdoors because that actually increases our microbiomes diversity. And then there are things that people are more commonly talking about. Now, there's the concept of prebiotics and the concept of probiotics. In prebiotics, that's the idea we're consuming something that we might not use all of, but the bacteria in our bodies are able to access. And so vegetables, fibrous foods like beans and other legumes, those can be excellent prebiotics that are natural, and we might not absorb all of that fiber, for example, but the bacteria really love it. So keeping a healthy diet in that way.

And then on the other side is this concept of probiotics. So probiotics are actually new organisms that we might be adding into our body. And when we do that in a way like eating yogurt or drinking kombucha or eating kimchi, that does have a nice effect on increasing our diversity and keeping everything nice and healthy. Now, I think people also have questions about where you take prebiotics and probiotics as supplements. And really when a supplement works for one individual, that's a supplement that works for one individual, which has their own unique microbiome. And so there's still questions out there about these supplements that you could buy that are prebiotics or probiotic. Will it work for me? And who knows? It might, it might not, but what you really should do is if you're interested in the supplement side of these, talk to your healthcare provider and see if they think that those are appropriate for you to take. Otherwise, there are ways for us to support our microbiome naturally through the foods we eat.

Ashley Peery:

Awesome. So that's actually a really good segue to the next question, which again is for Margaret. Margaret, you are knocking them out of the park with the questions. She asks, how much bacteria is found in plants? Is it possible that antibiotic resistant bacteria from farm runoff would be incorporated into the raw food that we eat? So food, but on the flip side, is there a chance that there are some AMR bacteria in raw foods?

Amanda Beaudoin:

Yeah, so when we think about foodborne bacteria and things that you've heard about, a salmonella outbreak, an E. coli outbreak, there are two ways to think about that. Those foods could have bacteria on them. And a lot of the ways that that happens is we're growing these foods in our soils, in our soils that are out there just in nature, but also that we contribute to the fertilization of the soil with natural fertilizers. We also know that out there in the world, all of our vegetables aren't being grown in a dome. So there's wildlife that moves through where our food is produced. So there are multiple ways that our food can get contaminated on the outside with bacteria, which is why it's always important for us to be preparing our food safely, which means washing it and cooking it when we need to.

And then the question about bacteria on the inside, there are some particular food items, and I can think of beans sprouts and things like spinach where they are very water-based. And what they are able to do is pull bacteria from the environment, from the soil up when they're pulling their water in, and they can sometimes end up with bacteria that are inside the vegetable. And so this is why we have a public health infrastructure to identify outbreaks. This is also why most public health professionals don't recommend that be eating sprouts. I don't eat sprouts. The risk of sprouts carrying bacteria is high enough that they're not on my menu. But when we do find that there is contamination of a food product that is broad, our public health system and our ways of tracking these foodborne illnesses hopefully will allow us to detect that and then talk to folks and find out what they ate and trace that back, maybe even all the way to the farm.

Ashley Peery:

Wow, I had no idea about bean sprouts and lettuce carrying bacteria potentially on the inside. So let's switch gears. The next question it's evolution and it comes from Rudolph. Rudolph asks, Does E. coli demonstrate the process for mutation better than other bacteria? From your video, for example, E. coli was evolving to resist insane amounts of antibiotic.

Amanda Beaudoin:

I feel as though I can answer Rudolph's question at a very superficial level by saying, rather than comparatively, by saying that E. coli is very good at sharing its resistance determinants and sharing resistance genes that are of considerable concern to human health. And it's very good at doing that in people and in settings of highest risk, like in healthcare. I'm not a microbiologist, so I can't really say that E. coli is top of the heap, but I'm able to say that it is quite good at sharing its resistance determinants with others.

Ashley Peery:

Okay. That sounds like maybe that's a topic we're still exploring.

Amanda Beaudoin:

I think the microbiologists know the answer to that.

Ashley Peery:

Okay. Our next question comes from Grace. You alluded in your talk that sometimes antibiotics are prescribed and they're not needed. But Grace asks, how would you suggest pushing doctors to do culture and sensitivity if one has an infection needing treatment to determine if those antibiotics are even necessary?

Amanda Beaudoin:

Yeah, that's a good question, so that's a great question. I think the shortest answer is open up the conversation because oftentimes, healthcare providers are having a one-way conversation. You come in, you're ill, your desire is to feel better and the provider is there needing to figure it out. And I think that the first step is really just to open up that conversation and maybe say something like, "I'm aware that antibiotics aren't always needed, especially for some common conditions like upper respiratory tract infections, and so is it needed in this situation?" And I think that's the first step because it's really difficult to say a blanket statement of what might be needed, but opening up that conversation so that the provider can talk to you about what's happening in your individual situation is pretty important.

Ashley Peery:

Awesome. Good thing to keep in mind. Our next question, we're going to switch gears a little bit. This question is related to surveillance, and it's from Borchuea. I hope I'm pronouncing your name correctly, and apologies if I'm not. But Borchuea asks, how are surveillance of genes conferring AMR infection in animals and in people integrated? So getting us out of the silos, which is a great question. And are antibiotic stewardship policies consistent across jurisdictions? In the US, which governance bodies are involved in managing AMR risk?

Amanda Beaudoin:

Okay. Wow, that's like a-

Ashley Peery:

Big question, but a great one.

Amanda Beaudoin:

Cornucopia of questions, but yes, they're good ones. So starting at the beginning, how do we even do surveillance for resistant organisms? And I'll start by talking about for people. We do have some systems that we don't have in place for animals. And one of the most important things that we have in place in the United States is called the Antimicrobial Resistance Lab Network, or ARLN, which is a system that CDC has set up to really make sure that we're identifying some of these really urgent threats. And so what happens is someone might be ill, they have a specimen taken, urine, feces, blood, whatever that might be, it goes to the lab and the lab finds that they have one of these highly concerning organisms. The information about that is then sent to public health, which then tracks a certain number of these organisms, reports them to CDC, so we have some information on that at the national level. So that's an example of how that might work for people.

And then we have a system called NARMS, the National Antimicrobial Resistance Monitoring System, and that's called integrated surveillance. And so the NARMS program takes information that CDC is collecting in people and USDA and FDA are collecting in animals and there's even now some environment and some seafood sampling and they combine that into an integrated surveillance report so that we can track resistance over time. And then when it comes to some of the things I talked about today where the superbug of CRE, for example, is coming up in our pets and we've seen some transmission in households. We've seen outbreaks in veterinary hospitals. We don't actually have an established surveillance system for some of the highly concerning bacteria to human health, but trying to find them in our pets.

And so that's something that a lot of conversation is happening right now, different states with CDC and with veterinary laboratories is that we really need to be looking for this because animals that live in our homes with us are in close proximity to us. They might be receiving similar antibiotics because they're treated a lot like our kids and our family members. And so we are just learning how we can do surveillance for those bad bugs. What we do here in Minnesota is the Minnesota Department of Health works closely with the University of Minnesota where our veterinary diagnostic lab is for this state. And when they find something that meets a surveillance criteria that they think that they need to pass on to public health for additional testing, they do that. So we're working on growing systems like that.

And then the question about antimicrobial stewardship, so it's super important. It's the way that we're going to of remove a lot of the selective pressure. In human healthcare hospitals and nursing homes have requirements from the Centers for Medicaid and Medicare services. So as of the plethora of requirements they have to that federal agency, part of that is having an antimicrobial stewardship program within individual facilities that can look a little bit different, but they are required if they're getting CMS reimbursement to have certain criteria baked into their approach. The Joint commission, which accredits a lot of hospitals in the United States, they also have standards. So that's really what happens in healthcare. On the animal side of things, we are working on that. We have a growing awareness in clinical veterinary practice, let's say, on the companion animal side that antibiotic stewardship programs are important. So there are a few publications that are out now about how you might implement that in your clinic.

My friends over at University of Minnesota and I have developed a handbook for stewardship in small animal practice. And so there's work growing on that. A lot of what works in healthcare is probably going to work to change prescribing behaviors and companion animal clinic based medicine. And then because VetMed is so diverse, just want to mention agriculture. In animal agriculture, antibiotic stewardship is really built into a lot of the ways that the use of pharmaceuticals is regulated for our food producing animals. So from this time that FDA is looking to approve a drug, they're approving it for a specific condition, for a specific duration, for a specific life stage of that animal and it goes on the drug label. And then part of stewardship is having the veterinarian, having that practitioner follow what's on the label. That's really important. And then all of the other aspects of making sure that we're having appropriate diagnosis and in preventing disease transmission on all of that. It was a long question, so a long answer.

Ashley Peery:

Thank thanks for that detailed answer. Your answer and your presentation have pointed out how multifaceted the problem is and so the solution has to be multifaceted as well. So to keep burning through the questions, Paul asks, what contributed to the increase in resistance during the pandemic?

Amanda Beaudoin:

Well, first, let's say we know what works and what works is infection prevention, antimicrobial stewardship, having the ability to get rapid answers from the laboratory about what the infection is, and having people when they're sick come in and seek healthcare. And that's especially important for some of the community-based infections. If you have as STD or even if you have a foodborne illness, whatever it might be, you're going to go in to have that managed to maybe be treated and that can help prevent infection. So all of those pieces and then very importantly, the amount of staff that we had available, and not just number of staff, but capacity in our healthcare facilities was really strained. So we know what works and that's doing all those things. And we just really, because the pandemic was overwhelming, we lost progress on whether it was diagnostics, getting people in for the appropriate treatment and on the antibiotic use front, some antibiotic stewardship programs and justifiably so, the people who run those programs were doing other things, maybe they weren't able to do as much prospective audit with feedback to their providers, whatever that might be.

And then we also saw, because the disease of COVID-19 was such a mystery at the beginning, we did see increases in antibiotic use for patients coming into hospitals with pneumonia. So a variety of different reasons that we have seen things get a little bit out of control. And so as I said, I think briefly, we have been tracking this in United States for years, certainly since the 2013 first threat report that CDC put out. And over the time from that threat report to the 2019 threat report, if you look at the 2019 threat report, it's all about the progress that we made and we had made tremendous progress. So I think now that we are coming back to a place where we can really focus on this issue, we should be able to get things under control again.

Ashley Peery:

All right. This next question is from Emma and she says there was talk about antibiotic use. Oh, hang on. Sorry. I lost my place. Let's see. So, okay, Judy asks, I'm so sorry, is it preferable in terms of level of resistance to take a short-term, a high dose antibiotic, something you might take one to two days, but it's high dose, or a long-term, 10 days lower dose antibiotic?

Amanda Beaudoin:

Well, unfortunately, that's not really a question that can be answered in the global sense. There are certain situations, certain types of infections that need to be treated quickly in over a short period of time, and there are other infections that need treatment over a longer period of time. The best recommendation is that whatever it is that we are being treated for, that we essentially make sure that we're communicating with our provider and understanding what that treatment should look like. And if our provider says, "Take these antibiotics for three days or for five days," verifying that, okay, I should take these for the duration or should I stop when I'm feeling better or what? Making sure to understand what the provider is recommending for you because the provider understands the specific infection that you have.

And then at the higher level of this question, there is ongoing progress in healthcare and certainly also in veterinary medicine because we have less information in that sector. There's ongoing progress to figure out what are the most appropriate durations for certain infections? What is the shortest amount of time that we can treat for that's going to get to the desired outcome? Because if we treat for a short amount of time and it doesn't resolve the infection, then we're left with bacteria that have already been exposed to an antibiotic. We could have a recurrent infection. We could have recurrent infection that is then resistant. So we're learning more about how do we really find that right duration because for common conditions, if we can get to the shortest appropriate duration, the number of antibiotics saved across the whole population would be tremendous.

Ashley Peery:

Yeah, absolutely. So this is actually our last question. We're getting towards the end of our webinar. And this one is, it's a different kind of question I'll say. It's from Scott. He's asking about the ancient resistance genes that were found in various animals. He said, "Do you know if these genes were expressed in typical immune related tissues? And if not, do you know where they were located genomically?"

Amanda Beaudoin:

So the resistance genes that I referred to that were found in permafrost, I'm not sure that they were associated. I admit that it's been a little while since I've read the paper in detail, but I don't think that they were associated necessarily with tissues as opposed to soil, like permafrost samples from that core. So I don't know the answer to that question, but there are several papers now that are out there. I think if you did a quick web search, you could find them and find that amount of detail on where resistance genes that look similar to what we see clinically have been found either ages ago or in parts of the world where remote caves where no people have ever tread.

Ashley Peery:

Just a good reminder that we have so much more to learn. And that is a great place for us to end because it's all the time that we have. So thank you to our audience for so many insightful questions. And thank you to you, Amanda. That was a wonderful presentation and you had a lot of insight to share during the Q&A session. I'm so glad you could join us today. So thanks to all here, including those that help make today's program possible. So that includes our donors, our volunteers, all of our partners who help us reach, educate, and empower millions of people around the world today and every day. I also need to thank our behind the scenes team. So thank you for the things that you guys do so that these webinars they happen and they go off without a hitch.

And with that, I want to invite everybody here today to join our next Shared Planet, Shared Health webinar, which is going to be coming up on December 14th. That webinar is going to feature a Smithsonian scientist, Paul Marinari. Paul is going to share decades of work put into recovering the critically endangered black-footed ferret. Believe it or not, plague is one of the obstacles that is hindering black-footed ferret reintroductions. So tune in to learn a lot more about that from Paul. You're going to see a link to register for that program in the Q&A. You're also going to see a link to our survey in the Q&A box. Please take a moment to respond. We do read all of your feedback and you help make us better when we do our next webinar. So thanks again and I'll see you next time. Take care.

Archived Webinar

This Zoom webinar aired November 9, 2022, as part of the "Shared Planet, Shared Health" series.


Since the discovery of penicillin in 1928, antibiotics and other compounds that stop microbial growth have revolutionized medicine and agriculture, but microbes continue to evade and resist these medicines through adaptation.

In this video, epidemiologist Amanda Beaudoin, Director of One Health Antibiotic Stewardship at Minnesota Department of Health, discusses the conditions that drive antimicrobial resistance (AMR), how AMR genes accumulate in the environment, and what you can do to reduce the spread of "superbugs" that threaten humans, livestock, and pets.

Moderator: Ashley Peery, educator for the Outbreak: Epidemics in a Connected World exhibition at the Smithsonian’s National Museum of Natural History

Webinar Series: Shared Planet, Shared Health

Our virtual "Shared Planet, Shared Health" programs spotlight leading research on the interconnection between humans, nonhuman animals, plants, and their shared environment. These programs feature a presentation by an expert followed by an audience Q&A session moderated by Ashley Peery, educator for the Outbreak: Epidemics in a Connected World exhibition at the Smithsonian’s National Museum of Natural History.

Resource Type
Videos and Webcasts
Life Science
Outbreak: Epidemics in a Connected World