Microbe Magazine Podcast

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

AAC Launches a new section. New perspectives on antimicrobial agents seeks to provide a clinically-oriented, concise summary supported by emerging clinical trial and/or real-world data. Our first article will be focused on remdesivir Objectives: • Review the rationale for the use of remdesivir against SARS-CoV-2 • Discuss the clinical data supporting the use of remdesivir for COVID-19 • Elaborate on future studies and knowledge gaps for the use of remdesivir New Perspectives on Antimicrobial Agents are brief invited reviews (limit of 4,000 words, exclusive of references) of antimicrobial agents that have been recently introduced into clinical practice. The aim is to provide a clinically-oriented, concise summary supported by emerging clinical trial and/or real-world data. Reviews should include a discussion on the importance of new findings in advancing the field and perspective on the agent’s place in therapy. Opinions and commentary may be included. Multidisciplinary authors are highly encouraged We have de

Laboratory testing for COVID-19, what’s new since we talked about this in August? A lot. Here are some of the questions we’ll talk about. • Do positive antibody tests indicate that people are immune to infection by SARS-CoV-2, the virus that causes COVID-19? • What sample types might replace the dreaded nasopharyneal swab for more comfortable sample collection? • What are the new rapid tests for COVID-19, and how should they be used? Alex is joined by two expert guests to discuss diagnostic testing for SARS-CoV-2. - Dr. Melissa Miller, who is the Director of both the Clinical Molecular Microbiology Laboratory and the Clinical Microbiology Laboratory at University of North Carolina School of Medicine. Dr. Miller is also an Editor of JCM. - Dr. Elitza Theel, who is the Director of the Infectious Diseases Serology laboratory at Mayo Clinic in Rochester, Minnesota. Dr. Theel is a member of the Editorial Board of JCM. Links: Antibody Testing and Serology “Neutralizing antibodies correlate with protection from

How are we discovering new antibiotics in the 21st, How is science responding to the antibiotic crisis? Objectives: • Discuss the challenges on discovering new antibiotics in the modern era • Debate the current strategies to find new molecules against the most recalcitrant pathogens • Understand the multiple approaches that could lead to antibiotic development. Visit aac.asm.org to read the latest issue of Antimicrobial Agents and Chemotherapy.

Let’s talk about parasites. Parasites are shocking. Some of them are large enough to be seen without magnification as they crawl across eyeballs, wriggle under the skin or exit from various orifices of the body. But parasites are fascinating and diverse creatures which live in association with a host, such as a human, and they cause the host harm. Many parasites have complicated life cycles that can involve multiple hosts and different developmental stages of the parasite within each host. Links mentioned: Dr. Pritt’s Blog, Creepy, Dreadful, Wonderful Parasites: https://parasitewonders.blogspot.com/ Dr. Couturier’s Paper, Detection of Intestinal Protozoa in Trichrome-Stained Stool Specimens by Use of a Deep Convolutional Neural Network, https://jcm.asm.org/content/58/6/e02053-19

Why are we running out of antibiotics? A look at the pharmaceutical development of one of the most life-saving class of drugs. Topics discussed: The reasons behind the stagnant and declining antibiotic development pipeline New initiatives focused on stimulating the antibiotic market Strategies to spur the antibiotic development Guests: Helen Boucher, MD. Professor of Medicine and Chief, Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Editor of AAC Karen Bush, PhD. Professor of Practice & Interim Director, Biotechnology Program Indiana University. Former Editor AAC. Visit aac.asm.org to read current and archived issues of the Antimicrobial Agents and Chemotherapy journal.

• How can the clinical laboratory detect carbapenemases, which are enzyme that can make bacteria resistant to some of the most potent or broad-spectrum antibiotics available? • What is the clinical significance of detecting such an enzyme? Does it affect the care of the patient? • Finally, what practical advice can we give to help labs decide which of the many available tests is the best one for them? The antibiotics we discuss are the “carbapenems,” such as imipenem and meropenem. These are among the broadest spectrum antibiotics available. Bacteria that are resistant to carbapenems were identified as “urgent threats” by the CDC in 2019. Some bacteria produce enzymes which destroy these antibiotics, and these enzymes are called “carbapenemases.” By producing a carbapenemase, bacteria become resistant to these antibiotics, making carbapenems useless for treatment of infections caused by such bacteria. I am joined by an expert guest to discuss detection of carbapenemases, Dr. Patricia Simner. Dr. Simner is an

Discussing new guidelines on the use of vancomycin for severe Staphylocccus aureus infections. The August issue of AAC includes interesting papers about mechanism of resistance to metronidazole in C. difficile, a variant of KPC resistant to ceftazidime-avibactam and description of a new “ultra-broad spectrum B-lactamase inhibitor” among others! You can find the issue at https://aac.asm.org.

The state of the art treatment of COVID-19, understand the role of some medications currently used for COVID-19 and dissecting novel approaches and strategies for the treatment of COVID-19 likely to become available in the short term. Guests: Henry Masur MD and Adarsh Bhimraj MD. Read the current issue of Antimicrobial Agents and Chemotherapy at https://aac.asm.org