Episodes

  • Implementing a National Action Plan to Combat AMR in Pakistan With Afreenish Amir

    Implementing a National Action Plan to Combat AMR in Pakistan With Afreenish Amir
    May 9 2025
    Episode Summary Afreenish Amir, Ph.D., Antimicrobial Resistance (AMR) Project Director at the National Institute of Health in Pakistan, highlights significant increases in extensively drug-resistant typhoid and cholera cases in Pakistan and discusses local factors driving AMR in Asia. She describes the development and implementation of a National Action Plan to combat AMR in a developing country, emphasizing the importance of rational antimicrobial use, surveillance and infection control practice. Ashley's Biggest Takeaways AMR is a global and One Health issue.Pakistan has a huge disease burden of AMR.Contributing factors include, but are not limited to, overcrowding, lack of infection control practices, poor waste management practices and over-the-counter prescription practices.Promoting the rational use of antimicrobials is imperative at all levels—from tertiary care to primary care practitioners.Typhoid and cholera are high-burden infections in Pakistan, with typhoid being a year-round issue and cholera being seasonal.A holistic approach, involving various sectors and disciplines, is necessary in order to address the global AMR threat.Amir highlights the need for better communication and collaboration to bridge gaps and build trust between different organizations. Featured Quotes: I've been working at the National Institutes of Health for the last 7 years now. So, I've been engaged in the development and the implementation of the national action plan on AMR, and that gave me the opportunity to explore the work in the field of antimicrobial resistance. Reality of AMR in Pakistan [Pakistan] is an LMIC, and we have a huge disease burden of antimicrobial resistance in the country right now. A few years back, there was a situational analysis conducted, and that has shown that there is presence of a large number of resistant pathogens within the country. And National Institutes of Health, they have started a very standardized surveillance program based upon the global antimicrobial use and surveillance system back in 2017. And [those datasets have] generated good evidence about the basic statistics of AMR within the country. So, for example, if I talk about the extensively drug-resistant typhoid, typhoid is very much prevalent in the country. Our data shows that in 2017 there were 18% MDR typhoid cases through the surveillance data. And in 2021 it was like 60%. So that has shown that how the resistance has increased a lot. A number of challenges are associated with this kind of a thing, overcrowded hospitals, poor infection prevention and control (IPC) measures. So, there is AMR within the country—there's a huge burden—and we are trying to look for the better solutions. Local Factors Driving AMR Bacteria, they do not know the borders. We have a close connection with the other Asian countries, and we have a long border connected with the 2 big countries, which are Afghanistan and India and Bangladesh and China. So, we see that it's not limited to 1 area. It's not regional. It’s also a history of travel. When the people travel from one area to the other, they carry the pathogen as a colonizer or as a carrier, and they can infect [other] people. So, it's really connected, and it's really alarming as well. You never know how the disease is transmitted, and we have the biggest example of COVID—how things have spread from 1 country to the other, and how it has resulted in a massive pandemic. AMR is similar. We have seen that it's not limited to 1 region. We are part of this global community, and we are contributing somehow to the problem. First, I'll talk about the health care infrastructure. We do have the capacities in the hospitals, but still, there's a huge population. Pakistan is a thickly populated country. It's a population of around 241 million. And with the increasing population, we see that the infrastructure has not developed this much. So now the existing hospitals are overcrowded, and this has led to poor infection control practices within the hospitals. The staff is not there. In fact, ID consultants are not available in all the hospitals. Infection control nurses are not available in all the hospitals. So, this is one of the main areas that we see, that there is a big challenge. The other thing that can contribute is the poor waste management practices. Some of the hospitals—private and public sectors—they are following the waste management guidelines—even the laboratories. But many of the hospitals are not following the guidelines. And you know that AMR is under one health. So, whatever waste comes from the hospital eventually goes to the environment, and then from there to the animal sector and to the human sector. [Another big] problem that we are seeing is the over-the-counter prescription of antimicrobials. There is no regulation available in the country right now to control the over-the-counter prescription of antibiotics. They are easily available. People are taking...
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    38 mins
  • Discovering Fossilized Microbes in Antarctic Ice Cores With Manuel Martinez Garcia

    Discovering Fossilized Microbes in Antarctic Ice Cores With Manuel Martinez Garcia
    Mar 14 2025
    Manuel Martinez Garcia, Ph.D., a professor of microbiology in the Physiology, Genetics and Microbiology Department at the University of Alicante in Spain, paints a picture of what microbial life looked like thousands of years ago by analyzing microbial genomic signatures within ice cores collected from the Antarctic ice shelves in the 1990s. Links for the Episode New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves – mSphere paper. Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles – Nature communications article. Manuel Martinez Garcia’s Lab website. How stable is the West Antarctic Ice Shelf? – Press Release from Alfred Wegener Institute.Take the MTM listener survey! Watch this episode: https://youtu.be/CHCMO74_gIY Ashley’s Biggest Takeaways There is a unique habitat beneath Antarctic ice shelves, where microbes live without light and rely on unusual energy sources. Ice cores from these Antarctic ice shelves can preserve fossilized genomic records of microbial life from long ago. Comparing past and present samples can help us understand how microbial life is responding to environmental stressors, like temperature changes and acidification, over time.It can also provide key insights to changes in biodiversity. Featured Quotes: Motivation for the Research Ice shelves are like massive floating ice that are in Antarctica, mainly. They can be as big as, for example, France, the country. So, they are super big—they are enormous. And they can be as thick as, let's say, 1000 meters. So, this is a massive [piece of] ice that we have in our planet. And beneath that massive ice, we can have a very peculiar and a special habitat in which microbes live without light. They have to manage, to thrive and reproduce, without using a standard energy like we have on the surface of the sea or in the forest, where we have light that is driving and providing the energy for the ecosystem. But in this case, these ecosystems are totally different. [The ice shelves] are deep and interconnected. Basically, there are different oceanic currents, for example, there is one Circumpolar Current that surrounds Antarctica, and there are also other currents that basically go from the bottom to the surface, moving, you know, all the water masses. The interesting part of this story is that every single second in our lives, this sea that is beneath the platform, the ice shelf, is frozen over and over, and then we have different layers of antiquity that preserve the microbes that are living in the ocean. So, for example, let's say, 1000 years ago, the sea water was frozen, and then we can find a layer beneath the Antarctica ice shelf, where these microbes are preserved and frozen. Basically, it's like a record—a library of microbes, fossil records of microbes—from the past ocean, from 1000 years ago until present, more or less. And then we can go to these records, to these layers of frozen sea water, and pick these samples to somehow recover the genetic material of the microbes that were preserved and frozen 1000 years ago or 500 years ago, in the way that we can somehow reconstruct or build the genetic story of the microbes from the past, for example, pre-industrial revolution to present. We need to think that microbes sustain the rest of the food web. So, they sustain of the rest of life in the ocean. They provide carbon for the rest of organisms, the fishes, whales [and other] big animals that we have in our oceans. And if the microbes are responding in a way that is not satisfactory, or in the way that we think can maintain the food web, this is kind of scary. And this is what we are trying to do: we are trying to go back to the past and see how the microbes are changing [genetically]. Sample Collection We didn't collect the samples. [They were collected] back in the 90s, so, 40 years ago, by a German group led by the Alfred Wegener Institute, which is probably one of the most famous polar institutes in the world. They, basically, led an expedition, I think it was in 92, and they decided to go to this ice shelf in Antarctica, in the Filchner–Ronne Ice Shelf to collect these ice cores. And then the surprise was when they were progressing in the drilling, they realized that on the top part of the ice core was fresh water, meteoric snow that was compacted forming the ice. But they realized that below that part, there was a sea water that was frozen. And then they thought that these samples were very interesting, because they somehow store material from the past, and they shipped these samples to Alfred Werner Institute in Bremerhaven in Germany. And half of the samples were stored for 40 years until I decided to contact the Institute and to propose this research. And I basically contacted the director of the Institute, and also the group of Frank Wilhelm, to propose the idea. And basically...
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    49 mins
  • Revenge of the Microbes With Brenda Wilson and Brian Ho

    Revenge of the Microbes With Brenda Wilson and Brian Ho
    Jan 16 2025
    Episode Summary Mother-Son duo, Brenda Wilson, Ph.D., professor of microbiology and the Associate Director of Undergraduate Education in the School of Molecular and Cellular Biology at the University of Illinois at Urbana Champaign and Brian Ho, Ph.D., researcher and lecturer at the Institute of structural and molecular biology, a joint institute between the Department of structural and molecular biology at the University College of London and the Department of Biological Sciences at Birkbeck University of London discuss the inspiration and motivation for their recent book, Revenge of the Microbes: How Bacterial Resistance is Undermining the Antibiotic Miracle, 2nd Edition, emphasizing the global nature of AMR and providing a unique perspective on what is needed to solve it. Ashley’s Biggest Takeaways: Dynamics surrounding the AMR crisis are complex and require an understanding of many different perspectives, including those of the farmers, health care professionals, pharmaceutical companies and individuals, in order to foster true and lasting global collaboration on the issue.Point-of-care diagnostics are critical to improving treatment decisions and reducing hospital costs.Better communication and education are needed in order to rebuild trust in scientists and institutions.Continuous research is necessary, as AMR will continue to evolve.Citizens are a key piece of the puzzle when it comes to pushing for change and supporting solutions to AMR. Featured Quotes: Wilson: “I'll start with actually my Ph.D., which is talking about bacterial antibiotic biosynthesis. And so, I did some work in that arena, but since then, I've actually been working on bacterial protein toxins. These are very potent eukaryotic modulators that when bacteria get into the host, they release these proteins that are very large, that are able to interact with very specific cells. They actually get inside the cells—into the cytosol—and then they affect various signaling pathways in the host that can go anywhere from killing the cell to modulating some of the processes that the cell undertakes, even differentiating them and causing cancer. So, one of my main focuses in my lab has always been to understand the structure and function of these toxins, to understand how they affect the eukaryotic cell system. And then now that we know a lot about them, we're actually moving more into the direction of trying to basically use them as biologics. We have some platforms that we call bacterial toxin inspired drug delivery, where we're using the mechanisms of how they work and their exquisite specificities to be able to actually use them for therapeutic applications.” Ho: “I got my start doing molecular genetics, actually, with John Mekalanos at Harvard, and I was kind of at the ground floor of the seminal work looking at the Type VI secretion system. And so, I got a front row seat to the kind of discovery and a lot of the initial understanding of the system. And I've kind of taken that work and expanded beyond it to look at kind of the ways different bacteria interact with each other within microbial communities. So my current work is looking at both DNA conjugation as well as the type six antagonism, and how the bacterial interactions kind of work together to build a larger population dynamics and interface with like the hosts that kind of house a your microbial communities.” Antimicrobial Resistance Wilson: “In 2005 [when the first edition of Revenge of the Microbes was written], there was very little activity or understanding about antibiotic resistance and how important it was. Outside of the field, doctors were encountering it. But oftentimes what was happening is they just said, ‘Oh, well, we'll just find another drug, you know.’ And pharmaceutical companies, they were recognizing that there was a problem, and they would go off trying to hunt for new ones. And then right around the late 90s, there was a big impetus, because they thought, ‘Oh, we, we have a miracle here, because we now do complete genomes. We can get out the comparative genomics and all the high throughput things, all the animations,’ and that this would lead to many more new discoveries. And I think the pharmaceutical companies were very disappointed, and they started backing out of what they deemed a huge commitment. Two decades later, people already were starting to get aware, at least in the field, and even the industry and the physicians. People were getting aware, but I think that they were stumbling, because of their silos, in trying to get interactions with each other. And I think part of it was that they felt that, ‘Oh, we can try to solve it ourselves.’ And in reality, this is a problem that that is concerning everyone, and everyone is contributing to it. Everyone has to find a solution to help, and we need to have more synergy. There have to be more interactions, and we have to do this at a much more global scale. And so that ...
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    52 mins
  • Binning Singletons With Joseph James

    Binning Singletons With Joseph James
    Jan 6 2025

    Joseph James, biologist at the U.S. Environmental Protection Agency, discusses his career trajectory and the creation of Binning Singletons, a unique mentorship program built on peer-to-peer networking at scientific meetings and conferences and was first implemented in 2019 at ASM Microbe.

    Links for the Episode Binning Singletons and Peer-to-Peer Networking
    • Learn more about Binning Singletons.
    • Contact Joe James: Joe@binningsingleton.com
    • Follow Binning Singletons on Bluesky.
    • Binning Singletons: Mentoring through Networking at ASM Microbe 2019—mSphere article.
    • Binning Singletons: Tackling Conference Networking When You Don’t Know Anyone—Guest post on Addgene Blog.
    • Mastering a Mentoring Relationship as the Mentee—asm.org article that James says has really helped him explain Binning Singletons as a coaching form of mentorship.
    • Mapping a Mentoring Roadmap and Developing a Supportive Network for Strategic Career Advancement—article on developing networks of mentors, another area Binning Singletons tries to address.
    • #FEMSmicroBlog: Networking at Online Conferences (for Early Career Scientists).
    • Take the MTM listener survey!
    James’ Research
    • Dietary lead modulates the mouse intestinal microbiome: Subacute exposure to lead acetate and lead contaminated soil.
    • In situ differences in nitrogen cycling related to presence of submerged aquatic vegetation in a Gulf of Mexico estuary.
    • Quantifying stream periphyton assemblage responses to nutrient amendments with a molecular approach.
    • Analysis of Bacterial Communities in Seagrass Bed Sediments by Double-Gradient Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA Genes.
    • Use of composite data sets for source-tracking enterococci in the water column and shoreline interstitial waters on Pensacola Beach, Florida.
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    56 mins
  • Biorisk Assessment and Management With Saeed Khan

    Biorisk Assessment and Management With Saeed Khan
    Nov 11 2024
    Saeed Khan, Ph.D., Head of the Department of Molecular Pathology at Dow diagnostic research and reference laboratory and President of the Pakistan Biological Safety Association discusses the importance and challenges of biosafety/biosecurity practices on both a local and global scale. He highlights key steps for biorisk assessment and management and stresses the importance of training, timing and technology. Ashley's Biggest Takeaways Adequate biosafety and biosecurity protocols depend on a thorough understanding of modern challenges, and scientists must be willing and able to respond to new technological threats appropriately.In the microbiology lab, the threat goes beyond the physical pathogen. Implications of genomics and cyber security must be built into biorisk management techniques, including data storage and waste management practices.Risk assessments involve evaluation of both inherent and residual risk.Inherent risk is linked to the pathogen.Residual risk varies according to the lab, equipment, employee, environment, etc.As a result, biosafety and biosecurity risks are constantly changing, and assessments must be repeated strategically and often.Khan recommended repeating a risk assessment whenever a key variable in the equation changes, i.e., new equipment, new employee, new pathogen. He also recommended (at minimum) conducting routine risk assessments every 6 months, or twice a year. Featured Quotes: “We need to have basic biosafety and biosecurity to stay away from these bugs and the modern challenges, like cyber biosecurity and genomics. These are the new areas, which are potential threats for the future, and where we need to train our researchers and students.” “Starting from simple hand washing or hand hygiene, the basic things we use are gloves, goggles and PPE to protect the workers, the staff and the patient from getting infected from the environment, laboratory or hospitals. These are the basic things, and it's very crucial, because if one is not using gloves in the lab or not wearing the lab coat, he or she may get infected from the sample, and the patient can get infected from the physician and doctors or nurse if they are not following the basic biosafety rules. These [things] are routinely important. Every day we should practice this.” “But there are [also] new challenges. Particularly in the microbiology lab, we [used to] think that once we killed the bacteria, then it's fine. But nowadays, it's not the way we should think about it. Though you kill the bacteria practically, it still has a sequence, [which] we call the genome, and if you have that information with you, you theoretically have the potential to recreate that pathogen… that can be used or maybe misused as well.” “[Working with] scripts of pathogens, like smallpox or the polioviruses, we call this synthetic biology. Different scientists are doing it for the right purposes, like for production of vaccines, to find new therapeutics, to understand the pathology of the diseases. But on [the other hand]—we call it dual use research of concern (DURC)—the same can be misused as well. That's why it's very important to be aware of the bugs that we are working with, and the potential of that pathogen or microbe, to the extent that can be useful or otherwise.” “So, we should be aware of the new concern of the technology, synthetic biology and DURC. These are new concepts—cyber, biosecurity and information security [are all] very much important these days. You cannot be relaxed being in the microbiology lab. Once we have identified a pathogen, declared a result to the patient and the physician, and it's been treated, we [still] need to be worried about waste management—that we discard that waste properly and we have proper inventory control of our culture. It should be safe in the locker or on in the freezers and properly locked, so we should not be losing any single tube of the culture, otherwise it may be misused.” Risk Assessment “The best word that you have used is risk assessment. So, it should gage the severity of the issue. We should not over exaggerate the risk, and we should not undermine the risk. Once the risk assessment been made, we can proceed.” “Right from the beginning of touching a patient or a sample of the patient until the end of discarding the sample, that is called biorisk management. It's a complete science that we need to be aware of—not in bits and pieces. Rather a comprehensive approach should be adopted, and each and every person in the organization should be involved. Otherwise, we may think [we are] doing something good, but someone else may spoil the whole thing, and it will be counterproductive at the end.” “We should involve each and every person working with us and the lab, and we should empower them. They should feel ownership that they are working with us, and they are [as] responsible as we are. So, this the whole process needs to be properly ...
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    50 mins
  • From Hydrothermal Vents to Cold Seeps: How Bacteria Sustain Ocean Life With Nicole Dubilier

    From Hydrothermal Vents to Cold Seeps: How Bacteria Sustain Ocean Life With Nicole Dubilier
    Sep 27 2024

    Nicole Dubilier, Ph.D., Director and head of the Symbiosis Department at the Max Planck Institute for Marine Microbiology, has led numerous reserach cruises and expeditions around the world studying the symbiotic relationships of bacteria and marine invertebrates. She discusses how the use of various methods, including deep-sea in situ tools, molecular, 'omic' and imaging analyses, have illuminated remarkable geographic, species and habitat diversity amongst symbionts and emphasizes the importance of discovery-driven research over hypothesis-driven methods.

    Watch this episode: https://www.youtube.com/watch?v=OC9vqE1visc

    Ashley's Biggest Takeaways:
    • In 1878, German surgeon, botanist and microbiologist, Heinrich Anton de Bary, first described symbiosis as the living together of two or more different organisms in close physical intimacy for a longer period of time.
    • These relationships can be beneficial, detrimental or commensal, depending on the organisms involved.
    • Microbial symbiosis research holds great potential to contribute to sustainable energy production and environmental health.
    Links for This Episode:
    • Learn more about one of Dubilier's research vessels and see videos from the expidition.
    • Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels.
    • Chemosynthetic symbioses: Primer.
    • Take the MTM listener survey!
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    31 mins
  • When Proteins Become Infectious: Understanding Prion Disease With Neil Mabbott

    When Proteins Become Infectious: Understanding Prion Disease With Neil Mabbott
    Aug 23 2024

    From Bovine Spongiform Encephalopathy (BSE) to Creutzfeldt-Jakob disease (CJD), Neil Mabbott, Ph.D., has worked for nearly 2 decades on understanding the mechanisms by which prion proteins become infectious and cause neurological disease in humans and animals. He discusses the remarkable properties of prions and addresses complexities surrounding symptoms, transmission and diagnosis of prion disease.
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    56 mins
  • Trillion Dollar Microbes Make the Bioeconomy Go Round With Tim Donohue

    Trillion Dollar Microbes Make the Bioeconomy Go Round With Tim Donohue
    May 28 2024
    Episode Summary Timothy Donohue, Ph.D.—ASM Past President, University of Wisconsin Foundation Fetzer Professor of Bacteriologyand Director of the Great Lakes Bioenergy Research Center (GLBRC) calls genomics a game-changer when it comes the potential of microbes to create renewable resources and products that can sustain the environment, economy and supply chain around the world. He also shares some exciting new advances in the field and discusses ways his research team is using microorganisms as nanofactories to degrade lignocellulose and make a smorgasbord of products with high economic value.

    Take the MTM listener survey! Ashley's Biggest Takeaways:
    • The bioeconomy can be broadly defined as the use of renewable resources, including microorganisms, to produce valuable goods, products and services.
    • Microbes have the potential to create products that cannot be made by existing synthetic chemistry routes.
    • Using raw, renewable resources to create a circular bioeconomy is beneficial to the environmental footprint, economic footprint and supply chain security around the globe.
    Links for This Episode:
    • The theme of our Spring 2024 Issue of Microcosm, our flagship member magazine is Microbes and the Bioeconomy: Greasing the Gears of Sustainability, launches this week and features an article based on this MTM conversation. If you are an ASM Member, check back on Wed., June 30 for the newly published content! Not a member? Consider renewing or signing up today, and begin exploring endless potential to boulster your career and network with professionals, like Donohue, in your field.
    • Get Bioeconomy Policy Updates.
    • Heading to ASM Microbe 2024? Check out this curated itinerary of sessions on the bioeconomy, including those discussing the use of algae for bioproduction and synthetic biology for natural product discovery.
    • Learn more about the Great Lakes Bioenergy Research Center.
    • MTM listener survey!
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    49 mins