Microbe Magazine Podcast

During the pandemic, the need to develop therapeutic approaches became critical and so the need to study them in a structured way to critically evaluate their effectiveness. Innovative strategies to conduct clinical trials under difficult circumstances were required. We will discuss these strategies with some people who created them! Objectives: • Understand the main challenges to conduct clinical trials in the middle of a pandemic both in the developed and developing world • Discuss strategies for patient recruitment and evaluation. • Deliberate on future strategies to study new therapies for emerging pathogens. Guests: • David Boulware, MD MPH. Professor of Medicine and Infectious Diseases, University of Minnesota. • Eduardo López-Medina, MD. Assistant Professor of Pediatrics at Universidad del Valle, and Director of Pediatric Infectious Diseases, Centro Medico Imbanaco, Cali Colombia.

Accurate antibiotic susceptibility testing, or AST, is a key tool in addressing the rise in antibiotic-resistant bacteria. But AST is one of the most complicated and rapidly changing areas in the clinical microbiology, and the resulting confusion can make it difficult for clinical laboratories to keep up with best practices. Dr. Romney Humphries joins to talk about controversies and myths about AST. This episode was recorded with a live, remote audience at the World Microbe Forum. It is brought to you by the Journal of Clinical Microbiology, available at jcm.asm.org and on twitter @JClinMicro. Visit asm.org/eic for links.

Malaria continues to be a major “killer’ in the developing world affecting the most vulnerable populations with more than 500,000 deaths per year. Emergence of resistance to antimalarial drugs is major public health issue. In this episode, we will discuss the latest information on this rapidly evolving field with one of the foremost experts in the field. • Review the main factors leading to malaria resistance • Discuss the main genetic mechanism of resistance to antimalarials. • Elaborate on future approaches for the prevention of resistance in Plasmodium spp. Guest: Professor Sir Nicholas White. Professor of Tropical Medicine at Oxford University and Mahidol University in Thailand. Visit https://asm.org/eic for links and https://journals.asm.org/journal/aac to read the AAC Journal

In addition to Staphylococcus aureus, there are a small number of other coagulase-positive staphylococci. We have become increasingly aware of these due to improvements in identification methods used in clinical laboratories. Staphylococcus argenteus is a coagulase-positive Staphylococcus that, until now, had mainly been detected in Australia, the Pacific Islands and Thailand. It was thought that the species might be geographically restricted, however a paper in the June issue of the Journal of Clinical Microbiology describes a large number of isolates collected from patients in North America. We’ll be talking to two of the authors of this paper. Guests: Dr. Julianne Kus, Dr. Audrey Schuetz

The development of β-lactam/β-lactamase inhibitors seems to be expanding rapidly and promise to be the best short-term strategy against the most recalcitrant Gram-negative pathogens. In this podcast, we will discuss the current state of the art in this field. Objectives: • Discuss how the discovery of β-lactam/β-lactam inhibitors has evolved • Review the current state-of-the-art of developing of novel β-lactam/β-lactamase inhibitors • Analyze the current and future clinical applications of these drugs against major antimicrobial-resistant pathogens. Guests: Robert Bonomo, MD. Professor and Associate Chief of Staff for Academic Affairs; Director Case-VA Center for Antimicrobial Resistance and Epidemiology, Case Western Research University, School of Medicine. Past Editor of AAC Pranita Tamma, MD. MH.S. Associate Professor of Pediatrics and Director, Pediatric Antimicrobial Stewardship Program. Johns Hopkins University. Editor of AAC. Visit https://aac.asm.org to read more

Our options for susceptibility testing have greatly increased in recent years. In addition to classical phenotypic susceptibility testing by disk diffusion and measurement of the minimum inhibitory concentration, genotypic tests are increasingly available. Genotypic tests range from tests for a single organism and one resistance gene to tests for 20 or more organisms and multiple resistance genes. But what should the clinical microbiologist do when the results of phenotypic and genotypic are in conflict? Welcome to Editors in Conversation. This episode is brought to you by the Journal of Clinical Microbiology, available at jcm.asm.org and on twitter @JClinMicro. I'm JCM Editor in Chief, Alex McAdam. This podcast is supported by the American Society for Microbiology, which publishes JCM. Guests: Dr. Patricia Simner, Dr. Jennifer Dien Bard Visit https://jcm.asm.org to read more

The incidence of fungal infections is rising in immunocompromised people, and the morbidity and mortality of these infections are high. Recent threats include multi-drug resistant Candida auris, however antifungal resistance is rising in other species as well, such as Aspergillus fumigatus. But have advances in diagnostic testing kept up with the accelerating threats of fungal infections? Guests: Dr. Esther Babady, Dr. Sean Zhang, Dr. Shawn Lockhart Visit https://jcm.asm.org to read more

During the pandemic researchers who focus on the microbiology of built environments suddenly found themselves at the center of attention. Understanding how SARS-CoV-2 may be spreading indoors became incredibly important to ensure we can operate indoors in a safe manner. We now know that SARS-CoV-2 transmits through the air in droplets and as particles, and this information has helped us to provide comprehensive advice on how people should manage the indoor environment. Last year my guests published a review in mSystems: 2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission. This is published with co-authors David A. Coil, Mark Fretz, and Jonathan A. Eisen. This paper was the most downloaded article for mSystems in 2020, and was in the top ten most downloaded articles across all ASM journals. This is maybe not surprising based on the topic covered. Guests: Leslie Dietz, Patrick Horve, Kevin Van Den Wymelenberg Links mentionoed: Microbes and social equity working

Developing non-traditional antibiotics promises novel strategies to combat multidrug-resistant organisms but would they work? Are they feasible to develop? Topics discussed: 
 • The notion of non-traditional antibiotics as potential therapeutics against MDR organisms 
 • Increasing our understanding on the clinical efficacy of non-traditional antibiotics 
 • Regulatory pathways for approval of such compounds
 Guest: Dr. John Rex, Chief Medical Officer, F2G Ltd. | Editor-in-Chief, AMR.solutions Visit https://aac.asm.org to browse issues and/or submit a manuscript.

Fermentation is a wonderful thing! Thanks to new technologies and cheaper sequencing we are now able to dig deep into the microbial friends that supply fermentation for so many wonderful foods and drinks. Topics discussed: Why cheese? Other fermented foods that can help shed light on microbial dynamics. Employing metabolomics to explore fermented food mSystems papers that focuses on fermented foods What are the gaps in understanding and what kind of technologies could help to further understanding? Pushing the frontiers of the field. Consequences of a better understanding of fermented food microbiology. Links mentioned: https://msystems.asm.org/content/5/6/e00522-20 https://msystems.asm.org/content/5/2/e00901-19 https://msystems.asm.org/content/1/5/e00052-16 https://msystems.asm.org/content/5/1/e00501-19 https://msystems.asm.org/content/4/6/e00680-19 Visit https://msystems.asm.org to read more.

Blood cultures for bacteria and yeast are among the most clinically important and high-volume tests performed by clinical microbiology labs. Because these cultures are so important to clinical care, we want to make sure that blood cultures are performed as quickly and accurately as possible, and that they are ordered, collected and utilized appropriately. We are going talk about two recent papers. The first is about diagnostic stewardship for improving utilization of blood cultures and the second is about reporting blood culture results more quickly. Guests: Maria Valeria Fabre, M.D., Eric Ransom, Ph.D. Some of the questions we’ll discuss include: • What steps can be taken to reduce the number of inappropriate blood cultures ordered in non-neutropenic adult patients? • Can the final results of blood cultures be reported earlier than the canonical 5 days? Links A Diagnostic Stewardship Intervention To Improve Blood Culture Use among Adult Nonneutropenic Inpatients: the DISTRIBUTE Study at https://jcm.asm.org/

What influential research outside of COVID-19 was published in AAC in 2020? Objectives: • Discuss pathways of young scientists in antimicrobial resistance • Highlight important papers in AAC in 2020 that were not related to COVID-19 • Stimulate discussion in important topics related to antimicrobial agents I want to welcome my co-host Dr. Maria Fernanda Mojica who is the host of the ASM Journal Club focused on Antimicrobial Agents and Resistance. Dr. Mojica is a Postdoctoral Scholar at Case Western Reserve University. Joining us to discuss their experiences and top paper of AAC in 2020 are: • Dr. Ayesha Khan: Postdoctoral Fellow, University of Texas Health Science Center, Houston, TX • Dr. Alina Iovleva: Clinical Instructor and Burroughs Wellcome Fund Scholar, University of Pittsburgh and UPMC, Pittsburgh, PA

Susceptibility testing for staphylococci other than S. aureus, or SOSA, has become increasingly complicated, as more laboratories use MALDI-TOF to routinely identify these bacteria to the species level. In particular, accurate identification of methicillin resistance has become more complex as the different species are distinguished by the accuracy of different susceptibility testing methods and breakpoints for interpreting MICs and zone sizes.  Some of the questions we’ll discuss include: What is the gold standard for detecting methicillin resistance in SOSA? How will the recommended breakpoints for detection of methicillin-resistant SOSA change? Why should we call these bacteria SOSA instead of coagulase-negative staphylococci? Guests: Dr. Romney Humphries, Dr. Lars Westblade Links mentioned: Evaluation of Surrogate Tests for the Presence of mecA-Mediated Methicillin Resistance in Staphylococcus capitis, Staphylococcus haemolyticus, Staphylococcus hominis, and Staphylococcus warneri The End of Coagulase-

What is Synthetic Microbiology and why is systems biology central to the development of this exciting scientific discipline? Topics discussed: What is synthetic microbiology? How systems biology and synthetic biology interact What studies should mSystems publish in the field of synthetic microbiology? Guests: Prof. Pam Silver and Prof. Danielle Tullman-Ercek. Visit msystems.asm.org to read articles and/or submit a manuscript. Subscribe to Editors in Conversation (free) on Apple Podcasts, Google Podcasts, Android, Spotify, Email.

The speed of development of vaccines for COVID-19 has been unprecedented, exceeding expectations. A reflection of the process and lessons for the future. A conversation with Dr. Carol Baker.  Topics discussed: The vaccine development for COVID-19 and key elements in the initial success Understand the clinical data leading to approval of the vaccines  Comment on the future of vaccines with implementation of new technologies Guest: Dr. Carol Baker: Professor of Pediatrics and University of Texas Health Science Center, McGovern Medical School. 2019 Albert B. Sabin Gold Medal Recipient and member of the National Academy of Medicine. Visit aac.asm.org to browse issues and/or submit a manuscript. Subscribe to Editors in Conversation (free) on Apple Podcasts, Google Podcasts, Android, Spotify, Email.

2020 was a great year… for research in clinical microbiology. The COVID-19 pandemic presented unprecedented challenges, including challenges to clinical laboratories. Clinical microbiologists rapidly created a variety of tests for SARS-CoV-2, figured out innovative ways to collect and transport samples for SARS-CoV-2 testing, and also continued their research in areas outside of the pandemic. In this episode of the podcast, three editors of JCM are each going to discuss three of the most important papers published in the journal during 2020. Links: Dr. Simner’s Selections Bacteremia and Blood Culture Utilization during COVID-19 Surge in New York City. https://jcm.asm.org/content/58/8/e00875-20 Evaluation of Optimal Blood Culture Incubation Time to Maximize Clinically Relevant Results from a Contemporary Blood Culture Instrument and Media System. https://jcm.asm.org/content/early/2020/11/24/JCM.02459-20  Detection of Intestinal Protozoa in Trichrome-Stained Stool Specimens by Use of a Deep Convolutional Ne

The emergence COVID-19 changed the entire world, a look back to one of the most difficult years for public health in modern history. Objectives: • Summarize the key events leading to the COVID-19 pandemic • Discuss the missteps and successes on the COVID-19 fight in the US • Comment on the future and what 2021 is likely to bring in relation t the COVID-19 pandemic Guest: • Dr. Jeanne Marrazzo: The C. Glenn Cobbs Professor in Infectious Diseases and Director, Division of Infectious Diseases, UAB | The University of Alabama at Birmingham. Visit https://aac.asm.org to read the current Antimicrobial Agents and Chemotherapy

The COVID-19 pandemic has brought more media attention to clinical laboratories than at any time in recent history. Today we’ll talk about media coverage of diagnostic testing for COVID-19 with two experts. Some of the questions we’ll discuss include: How has the media coverage of tests for COVID-19 affected the public’s view of these tests? What is the role of social media in talking about testing for COVID-19? How do reporters covering COVID-19 testing work with clinical microbiologists to get the story right?

ARLG is changing the field of clinical research in antimicrobial resistance. We will talk with the Principal Investigators of the ARLG to discuss their strategy Objectives: • Review the history and accomplishments of ARLG • Discuss the missions of ARLG including training new clinical investigators focused on antibiotic resistance • Comment of the future of ARLG and clinical research on antibiotic resistance Joining me to talk about ARLG are the principal investigators of this ambitious effort: • Dr. Vance Fowler: Professor of Medicine, Florence McAlister Distinguished Professor of Medicine, Professor in Molecular Genetics and Microbiology, Duke University. • Dr. Henry “Chip” Chambers: Professor of Medicine, Emeritus. University of California, San Francisco Visit aac.asm.org to read the current issue.

Let’s talk about total laboratory automation in the clinical microbiology laboratory. Highly automated systems are fairly common in the clinical chemistry and hematology labs, and they are increasingly common in clinical microbiology. Here are some of the questions we’ll answer today. What does total laboratory automation look like in the clinical microbiology laboratory? Are there still manual steps required? In other words, how total is total? What are the benefits of total laboratory automation? Is it good for the lab staff, the caregivers, or, best of all, the patients? What is like to convert your lab to total laboratory automation? What kind of time and resources are needed? Guests: Dr. Carey-Ann Burnham, Dr. Erin McElvania Links mentioned: Machine Learning Takes Laboratory Automation to the Next Level by B. Ford and E. McElvania Evaluation of the WASPLab Segregation Software To Automatically Analyze Urine Cultures Using Routine Blood and MacConkey Agars by M. Faron et al. Enhanced Recovery of Fast