Meet the Microbiologist

• Preventing Foodborne Pathogens With Plant-Derived Compounds with Karl Matthews

  Karl Matthews, Ph.D., Professor of Microbial Food Safety at Rutgers University, discusses ways to eliminate pathogens like Salmonella, E. coli O157:H7 and Listeria from fresh fruits and vegetables. He highlights the importance of preventative measures from farm to table, including the use of water antimicrobials, like chlorine, and photosensitizers, like curcumin. Watch this episode: https://youtu.be/6Wkef9RyUVE Ashley's Biggest Takeaways We consume billions of microorganisms in the food that we eat each day. Fresh fruits and vegetables that are not thermally processed are likely to carry a higher microbial load than cooked foods. Many of those microbes are not concerning to human health. However, when pathogens of human health concern are present, the food can become unsafe to eat. Scientists use many methods from pre-harvest through post-harvest to keep food free of human pathogens. Water antimicrobials, such as chlorine, and photodynamic inactivation using photosensitizers, such as curcumin, are 2 preventative measures that Matthews and colleagues are investigating. Curcumin is a natural chemical compound found in the turmeric plant. It is responsible for giving tumeric its yellow color. Curcumin is also a photosensitizer, meaning that it can absorb light energy and transfer it to another molecule to initiate chemical reactions that produce cytotoxic singlet oxygen. Featured Quotes When I look at [what makes fruits and vegetables safe to eat] as far as from a microbiological perspective, it's are they free of pathogens of human health concern? And so, we might think about organisms, such as Salmonella or the Shiga toxin producing E coli or Listeria. There are a number of processes and initiatives that are put into place, from the pre-harvest through post-harvest levels to try to ensure that the product is not contaminated with microorganisms of human health concern. Each day, we're consuming literally billions of microorganisms in the foods that we eat, and particularly the raw fruits and vegetables that we're eating that are not being thermally processed in any fashion by which you might reduce the microbial load. Oftentimes we think about the bacteria that might well be there. But we do know that there's viruses that could be present. There's certain type of protozoa that might be present. Many of us know of norovirus and the concerns associated with that particular pathogen. So, there's a multitude of microorganisms that might well be associated with fresh fruits and vegetables, but there's really a very limited number or types that are actually of concern from a human health standpoint. In my program, we're working on E. coli O157:H7, in particular. It's a certain serotype of E. coli, a diarrheagenic E. coli, what's also known as a Shiga toxin-producing E. coli. We work with Salmonella, and we work with Listeria monocytogenes, but there's other microorganisms, such as Campylobacter, Yersinia, Staphylococcus aureus. All of those types of pathogens can also be associated with foods—and different types of foods, at that—and be of concern to the general public—the consumer. If we look at a lot of the processing of foods that are taking place, not only here in the United States, but globally, many times, what will happen is they're utilizing some type of a water antimicrobial, and I stress that because, oftentimes, these antimicrobials are added to the water to control the microbial load in the water. So, ultimately, you're not basically putting on water and putting on a whole load of microorganisms along with it. And also, you can prevent cross contamination through that. Here in the U.S. and elsewhere, we'll often put additional chlorine into the water. So, let's say we're increasing the chlorine concentration to 20 parts per million, or 50 parts per million, or maybe in poultry processing, they're utilizing peracetic acid. These are 2 common antimicrobials that are being used. What we wanted to do is find out could we utilize some other types of methods that might well control microorganisms on the commodity itself? And that's where we started looking at photodynamic inactivation and coupling that with the use of a photosensitizer. And in this particular case, the photosensitizer we were using was curcumin. The reason for working with curcumin is that it's naturally used in foods as a food dye. It's also used as a flavoring agent, and so forth. So, it's there, and it's being used—not just in the U.S., but [also] globally. And we thought we would try to see if we utilize this compound, could we have an additive effect to it? If you apply certain wavelengths of light, you can inactivate microorganisms, but if you apply that wavelength to something like a photosensitizer type molecule (curcumin), you could generate singlet oxygen molecules. And those singlet oxygen molecules would act like little explosions on the cell membrane and basically blow it apart and, therefore, inactivate the organism. We looked at the ability of this to inactivate Listeria monocytogenes, Salmonella, as well as E. coli O157:H7, so these Shiga toxin-producing E. coli, and what we did indeed find is that it was very effective. We looked at it in comparison to peracetic acid use in the poultry industry, and we found it to be equivalent, at least to treatments that we were utilizing on poultry skin, with inactivation of the microorganisms, such as Listeria, on the poultry skin. So, it is really exciting. Links for This Episode ​​​​​​Preventing Foodborne Outbreaks Starts in the Field. Influences of photosensitizer curcumin on microbial survival and physicochemical properties of chicken during storage.

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• Early Microbial Life with Michael Lynch and Vaughn Cooper

  Michael Lynch, Ph.D., Director of the Center for Mechanisms of Evolution at Arizona State University and Vaughn Cooper, Ph.D., professor of Microbiology and Molecular Genetics at the University of Pittsburgh, School of Medicine, examine the origins and trajectory of early microbial life (EML) and discuss the collaborative report between the American Academy of Microbiology and the Gordon and Betty Moore Foundation, which explores the journey of life on Earth, from non-living chemical compounds to early unicellular life, to the vast diversity of organisms we see today. This episode is brought to you by the American Academy of Microbiology, a think tank at American Society for Microbiology and the Gordon and Betty Moore Foundation, which has been dedicated to advancing scientific discovery for the past 25 years. Links for This Episode: Project Report Early Microbial Life: Our Past, Present and Future. Article: The Great Oxidation Event: How Cyanobacteria Changed Life. MTM Podcast: From Hydrothermal Vents to Cold Seeps: How Bacteria Sustain Ocean Life With Nicole Dubilier. Take the MTM listener survey! 

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• How FMTs, Coprophagia and the Milk Microbiome Inform Wildlife Conservation With Sally Bornbusch

  Sally Bornbusch, Ph.D., is an NSF postdoctoral fellow in biology conducting microbial ecology research in animal care and conservation at the Smithsonian National Zoo & Conservation Biology Institute. She discusses how FMTs are being used to mitigate health concerns in wild animals in captivity, shares key findings about the milk microbiome from the Smithsonian milk repository, the largest collection of exotic animal milks in the world, and explains the science behind eating poo (Coprophagia).  Links for This Episode Why Do Animals Eat Poop? (And Why It Might Be a Good Thing). Faeces as food: a framework for adaptive nutritional coprophagy in vertebrates. Even Monkeys Should Eat Their Vegetables. Take the MTM listener survey! 

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• Agnostic Diagnostics and the Future of ASM Health With Dev Mittar

  Dev Mittar, Ph.D., Scientific Director of the ASM Health Scientific Unit discusses the use of metagenomic next generation sequencing to develop agnostic diagnostic technology, giving scientists and clinicians alike, a tool to diagnose any infectious disease with one single test. He also discusses how the ASM Health Unit is empowering scientists and leveraging microbial science innovations to address critical global health challenges and improve lives worldwide. Ashley's Biggest Takeaways The Division of Research, Innovation and Ventures is a small entrepreneurial arm of BARDA that takes on early-stage projects with high potential of turning into medical countermeasures. Prior to his role as Scientific Director for ASM Health, Mittar worked as a health scientist and program officer at DRIVe, where he focused on advancing high-impact science. He is particularly passionate about his work to develop agnostic diagnostics—a single test that uses metagenomic next generation sequencing to identify any pathogen from 1 clinical sample. Mittar discusses applications for this technology in surveillance (pandemic preparedness), variant detection, AMR and clinical settings (diagnosing complicated infections where etiology is not clearly defined). He also shares how a recent bout with illness emphasized the value and potential of this technology to save money, time, pain and suffering of the patient. Agnostic diagnostics can also help prevent the overuse/misuse of antibiotics, which are key factors in the spread of antimicrobial resistance. Furthermore, when this technology is coupled with the use of metatranscriptomics, it can provide information about the patient’s immune profile that can be helpful in developing personalized treatment strategies, as opposed to a one-size-fits-all approach. ASM is organizing around 3 scientific units, ASM Health, ASM Mechanism Discovery and ASM Applied and Environmental Microbiology. These units will empower researchers and scientists to use science make a difference in the world and provide a forum for them to come together to shape the future of the field. Links for This Episode Learn More About ASM’s Scientific Units. Join the Conversation on ASM Connect, our online community platform. Browse Volunteer Opportunities. Become an ASM Member. Register for ASM Microbe 2025.

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

  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 the antibiotics without a prescription from the doctors, and the pharmacist is giving the patients any kind of medicine. And either it is effective/not effective, it's a falsified, low-quality antibiotic for how long in duration antibiotic should be taken. So, there are multiple of things or reasons that we see behind this issue of AMR. Rational Use of Antimicrobials It is a complex process how we manage this thing, but what we are closely looking at in the country right now is that we promote the rational use of antimicrobials at all levels—not only at the tertiary care levels, but also at the general practitioner level. They are the first point of contact for the patients, with the doctors, with the clinicians. So, at this point, I think the empirical treatment needs to be defined, and they need to understand the importance of this, their local antibiograms, what are the local trends? What are the patterns? And they need to prescribe according to those patterns. And very recently, the AWaRE classification of WHO, that is a big, big support in identifying the rational use of antimicrobials—Access, Watch and Reserve list—that should be propagated and that should be understood by all the general practitioners. And again, I must say that it's all connected with the regulations. There should be close monitoring of all the antibiotic prescriptions, and that can help to control the issue of AMR. National Action Plan on AMR So, when I joined NIH, the National Election plan had already been developed. It was back in 2017, and we have a good senior hierarchy who has been working on it very closely for a long period of time. So, the Global Action Plan on AMR, that has been our guiding document for the development of the national action plan on AMR, and we are following the 5 strategic objectives proposed in the global action plan. The five areas included: The promotion of advocacy and awareness in the community and health care professionals. To generate evidence through the data, through the surveillance systems. Generation of support toward infection prevention and control services IPC. Promoting the use of antimicrobials both in the human sector and the animal sector, but under the concept of stewardship, antimicrobial consumption and utilization. Invest in the research and vaccine and development. So, these are some of the guiding principles for us to develop the National Action Plan, and it has already been developed. And it's a very comprehensive approach, I must say. And our institute has started working on it, basically towards recreating awareness and advocacy. And we have been successful in creating advocacy and awareness at a mass level. Surveillance We have a network of Sentinel surveillance laboratories engaged with us, and they are sharing the data with NIH on a regular basis, and this is helping NIH to understand the basic trends on AMR and what is happening. And eventually we plan to go towards this case-based surveillance as well, but this is definitely going to take some time because to make people understand the importance of surveillance, this is the first thing. And very recently, the Institute and country has started working towards the hospital acquired infection surveillance as well. So, this is a much-needed approach, because the lab and the hospital go hand in hand, like whatever is happening in the lab, they eventually reach the patients who are in the hospitals. Wastewater surveillance is the key. You are very right. Our institute has done some of the work toward typhoid and cholera wastewater surveillance, and we were trying to identify the sources where we are getting these kinds of pathogens. These are all enteric pathogens. They are the key source for the infection. And for the wastewater surveillance mechanism, we can say that we have to engage multiple stakeholders in this development process. It's not only the laboratory people at NIH, but we need to have a good epidemiologist. We need to have all the water agencies, like the public health engineering departments, the PCRWR, the environmental protection agencies who are working with all these wastewater sites. So, we need to connect with them to make a good platform and to make this program in a more robust fashion. Pathogens and Disease Burdon For cholera and typhoid within Pakistan, I must say these are the high burden infections or diseases that we are seeing. For typhoid, the burden is quite high. We have seen a transition from the multidrug-resistant pathogens to the extensively drug-resistant pathogens, which now we are left with only azithromycin and the carbapenems. So, the burden is high. And when we talk about cholera, it is present in the country, but many of the times it is seasonal. It comes in during the time of the small zone rains and during the time of floods. So, every year, during this time, there are certain outbreaks that we have seen in different areas of the country. So, both diseases are there, but typhoid is like all year long—we see number of cases coming up—and for cholera, it's mainly seasonal. Capacity Building and ASM's Global Public Health Programs Capacity building is a key to everything, I must say, [whether] you talk about the training or development of materials. I've been engaged with ASM for quite some time. I worked to develop a [One Health] poster in the local language to create awareness about zoonotic diseases. So, we have targeted the 6 zoonotic diseases, including the anthrax, including the Crimean-Congo hemorrhagic fever and influenza. And we have generated a very user-friendly kind of layout in the local language, trying to teach people about the source of transmission. What are the routes of transmission, if we talk about the CCHF? And then how this can be prevented. So, this was one approach. And then I was engaged with the development of the Learnamr.com. This is online platform with 15 different e-modules within it, and we have covered different aspects—talking about the basic bacteriology toward the advanced, standardized methods, and we have talked about the national and global strategies [to combat] AMR, One Health aspects of AMR, vaccines. So, it's a huge platform, and I'm really thankful to ASM for supporting the program for development. And it's an online module. I have seen that there are around more than 500 subscribers to this program right now, and people are learning, and they are giving good feedback to the program as well. We keep on improving ourselves, but the good thing is that people are learning, and they are able to understand the basic concepts on AMR. Links for This Episode: Experts Discuss One Health in Pakistan: Biosafety Education Inside and Outside the Lab.  Explore ASM’s Global Public Health Programs.  Download poster about zoonotic disease in English or Urdu.  Progress on the national action plan of Pakistan on antimicrobial resistance (AMR): A narrative review and the implications.  Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000 Salmonella Typhi genomes.  Wastewater based environmental surveillance of toxigenic Vibrio cholerae in Pakistan.  Point Prevalence Survey of Antimicrobial Use in Selected Tertiary Care Hospitals of Pakistan Using WHO Methodology: Results and Inferences.  Overcoming the challenges of antimicrobial resistance in developing countries.  Take the MTM listener survey! 

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