Microbe Magazine Podcast

Dr. Bobbi Pritt aka @parasitegal, creator of the blog Creepy Dreadful Wonderful Parasites, is a pathologist and clinical microbiologist with specialty interests in parasitic and vector-borne infections, and the pathology of infectious diseases. Dr. Pritt discusses her career and how she became an expert in clinical parasitology, her work internationally and how others can participate in global health work and how technology (digital pathology, AI, automation, etc.) will affect the lab and technicians in the future. This episode of Editors in Conversation is brought to you by the Journal of Clinical Microbiology and hosted by JCM Editor in Chief, Alex McAdam and Dr. Elli Theel. The Journal of Clinical Microbiology is available at asm.org/jcm. Follow EIC, Alex McAdam on twitter for JCM updates at twitter.com/JClinMicro and co-host, Elli Theel at twitter.com/ellitheelphd. Visit journals.asm.org/journal/jcm to read articles and/or submit a manuscript. Subscribe to Editors in Conversation (free) on Apple Podcas

Infections caused by Stenotrophomonas maltophilia appear to be increasing in frequency among the immunocompromised population and are challenging to treat. Moreover, resistance to traditional drugs used against these organisms is now becoming more common. Antibiotic options in these circumstances are scarce and new options are needed. We discuss this important topic with experts in the field. Recorded live in Washington DC at ASM Microbe 2022. Topics • Stenotrophomas maltophilia as an opportunistic pathogen and • The intrinsic ability of Stenotrophomonas maltophilia to resist common antimicrobials • Common mechanisms of resistance in Pseudomonas aeruginosa • Debate on treatment approaches and rationale for these strategies. Guests: Maria Fernanda Mojica PhD Senior Instructor, Case VA Center for Antimicrobial Resistance and Epidemiology. Case Western Reserve University Samuel Aitken, PharmD. Adjunct Clinical Professor of Pharmacy, University of Michigan. This episode of Editors in Conversation is brought to

We are just back from the Molecular Virology Workshop in West Palm Beach. This is a terrific meeting that is organized by the Pan-American Society for Clinical Virology or PASCV. The workshop immediately precedes the Clinical Virology Symposium that ASM organizes and many of us like to attend both. Today we’ll be talking about some of the high points of the Molecular Virology Workshop, with two members of the organizing committee from PASCV. Guests: Dr. Erin Graf, Director, Clinical Microbiology at Mayo Clinic in Phoenix Arizona. Dr. Stephanie Mitchell, Director of Medical Affairs at Cepheid. This episode of Editors in Conversation is brought to you by the Journal of Clinical Microbiology and hosted by JCM Editor in Chief, Alex McAdam and Dr. Elli Theel. JCM is available at https://jcm.asm.org and on https://twitter.com/JClinMicro. Links: On-demand sessions from PASCV https://www.pascv.org/page/MVW Visit journals.asm.org/journal/jcm to read articles and/or submit a manuscript. Follow JCM on Twitter via @J

Infections caused by multidrug-resistant Pseudomonas aeruginosa are considered a major public health problem. Antibiotic options are scarce but new drugs are emerging and more maybe available in the near future. Topics discussed: Pseudomonas aeruginosa as an important pathogen capable of developing resistance to multiple antibiotics Common mechanisms of resistance in Pseudomonas aeruginosa The current and future approaches for these MDR organisms. Guests: Michael Satlin, MD, Associate Professor of Medicine, Pathology and Laboratory Medicine, William Randolph Hearst Foundation Clinical Scholar in Microbiology and Infectious Diseases at Weill Cornell Medical College, New York, NY Alessandra Carattoli, PhD, Professor of Microbiology at the Sapienza University of Rome, Italy. Editor, AAC Visit journals.asm.org/journal/aac to browse issues and/or submit a manuscript.

It is estimated that anywhere from 575,000 to 677,000 bloodstream infections occur annually in North America, with approximately 40,000 of those directly linked to patient mortality in the United States, making bloodstream infections the 11th most common cause of death in the US according to the Centers for Disease Control and Prevention. The detection of bloodstream infections and subsequent identification of the etiologic agent or agents is an essential role played by all clinical microbiology laboratories, day-in and day-out for routine patient care. So, today, we are going to dive into a recently published study in JCM, looking at organism-specific bloodstream infection prevalence rates and their individual mortality risks relative to patients with either negative blood cultures and in those for whom blood cultures were not ordered. Guests: - Dr. Nick Daneman - senior author on the manuscript, is a Clinical Scientists in the Division of Infectious Diseases at Sunnybrook Health Sciences Centre at the Unive

This episode is dedicated to the memory of the late George A. Jacoby, who was a pillar in the B-lactamase research community and a leader in the field of antimicrobial resistance. Assigning names to b-lactamase variants has been inconsistent and has led to confusion in the published literature. The common availability of whole genome sequencing has resulted in an exponential growth in the number of new b-lactamase genes. In November 2021 an international group of b-lactamase experts met virtually to develop a consensus for the way naturally-occurring b-lactamase genes should be named. Topics discussed: The inconsistencies in B-lactamase nomenclature Guidelines for publication of new alleles and newly discovered B-lactamases  Future needs of consensus among the b-lactamase community Guests: Patricia Bradford PhD., Antimicrobial Development Specialists LLC Karen Bush PhD, Professor of Practice, Biotechnology and Interim Director, Biotechnology Program, Indiana University. Robert Bonomo MD, Professor Case We

Antibiotic susceptibility testing is too slow. Faster identification of microorganisms is now common, as many laboratories use MALDI-TOF or molecular technologies for quick and definitive identification of bacteria. Improvements in susceptibility testing have lagged, as we continue to use tests that take a day for results, and which have not significantly changed in decades. Rapid phenotypic testing has can only be done on limited sample types, using a dedicated platform, and it has not been widely adopted. Tests for rapid genotypic testing usually include only a few genes and require confirmation by phenotypic testing. What are the prospects for fast susceptibility testing? Guests: Dr. Trish Simner. Trish, Associate Professor of Pathology at Johns Hopkins Medicine, where she is also Director of the Medical Bacteriology and Infectious Disease Sequencing. Dr. Dan Rhoads. Dan is the Section Head of Microbiology at the Cleveland Clinic, where he holds The Belinda Yen-Lieberman, PhD, and James M. Lieberman, MD, E

Bacteriophages are interesting viruses that target bacteria and have been used for therapeutic purposes. Recently, the emergence of antibiotic resistance has spurred a renewed interest in using these viruses or their products as therapeutic tools against recalcitrant human pathogens. AAC has also published a recent manuscript from ARLG to guide the use of phages in clinical practice. We will discuss with experts in the field the state-of-the-art in phage therapy. Objectives: • Understand the use of bacteriophages and their products for therapeutic purposes • Discuss the clinical applications of phages • Debate the barriers for developing of phages as therapeutic tools to treat multidrug-resistant infections Guests: • Vincent A. Fischetti, Ph.D, Professor and Director, Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY. • Saima Aslam, MBBS, Professor of Medicine, University of California San Diego, San Diego, CA. • Anthony Maresso, PhD. Professor and Founder of TAILOR

When most of us hear the word ‘CAPA’, these days we more than likely immediately start thinking about SARS-CoV-2 variants, trying to remember how important this particular one was in the grand scheme of the COVID-19 pandemic. But, that is not the ‘kappa’ we will be talking about today. Instead, we’ll be discussing the other CAPA, or COVID-19 Associated Pulmonary Aspergillosis, and we will cover a few areas on this topic, including: - Defining what CAPA is and how prevalent it is among ICU patients with COVID-19 - Discuss why identification of invasive aspergillosis in patients with COVID-19 differs compared to other at-risk patients - Review two recent publication in JCM that discuss specific assays and diagnostic approaches for optimal detection of invasive aspergillosis in patients with COVID-19. Guests: Dr. Martin Hoengil Prof. Alexandre Alanio This episode of Editors in Conversation is brought to you by the Journal of Clinical Microbiology and hosted by JCM Editor in Chief, Alex McAdam and Dr. Elli The

AAC just published a review from the WHO advisory panel on the antibacterial pipeline analyzing ‘traditional’ and ‘non-traditional’ antibacterial agents and modulators in clinical development current on 30 June 2021 with activity against the WHO priority pathogens, mycobacteria and Clostridioides difficile. Today, we will dissect this important publication Objectives: • Understand the role of the WHO in antimicrobial resistance • Discuss the analysis of the antibacterial pipeline • Deliberate on important highlights from the review and the future of antibacterial research. Guests: - Dr. Peter Beyer, Senior Advisor for the Antimicrobial Resistance Division at the World Health Organization. - Dr. Mark Butler, MSBChem Consulting, Brisbane, Queensland, Australia - Dr. Prabhavathi Fernandes. Member, Scientific Advisory Committee, GARDP, Geneva, Switzerlandand The National Biodefense Science 17Board, Health and Human Services, Washington DC, USA This episode of Editors in Conversation is brought to you by the Antim

In less than two months since it was discovered, the omicron variant of SARS-CoV-2 has become the dominant variant of the virus, causing an unprecedented rise in the number of cases of COVID-19 in the U.S. and elsewhere. The emergence of this variant has quickly led to some surprising claims about diagnostic testing for omicron and a renewed appreciation of the importance of sequencing the viral genome for typing purposes. We will address several questions about testing for omicron, including: • Are rapid antigen tests sensitive for detection of omicron? And should people swab their throats to increase the sensitivity of these tests? • How does the emergence of omicron change our use of polymerase chain reaction tests for SARS-CoV-2? • How can we definitively identify the omicron variant and do we have the needed capacity for this? This episode of Editors in Conversation is brought to you by the Journal of Clinical Microbiology and hosted by JCM Editor in Chief, Alex McAdam and Dr. Elli Theel. JCM is availabl

As we round out yet another year of this pandemic, clinical microbiologists have not slowed down. We have not slowed down in our response to the pandemic or other day-to-day testing needs, despite the constant reagent backorders and personnel shortages, and equally as important, we have not slowed down in publishing high quality, informative and clinically relevant papers, which have really spanned the gamut of clinical microbiology - from antimicrobial susceptibility testing, to next generation sequencing assays and AI, to evaluation of new high throughput assays for a variety of pathogens, the field continues to expand at an impressive pace. Three Journal of Clinical Microbiology (JCM) editors discuss some of their favorite and most impactful papers published in the Journal in 2021. Welcome to Editors in Conversation. This episode is brought to you by the Journal of Clinical Microbiology, available at https://jcm.asm.org and on https://twitter.com/JClinMicro and is supported by the American Society for Micr

Infections caused by carbapenem-resistant Acinetobacter spp. are considered an urgent public health problem. Antibiotic options are scarce but new drugs may be available in the near future. We discuss this important topic with experts in the field. Topics discussed: Acinetobacter as an opportunistic pathogen Therapeutic approaches for Acinetobacter infections The future approach for this MDR organisms. Guests: Dr. Yohei Doi, Professor and Director, Center for Innovative Antimicrobial Therapy, University of Pittsburgh Medical Center, Pittsburgh, PA Dr. Joseph Patrick Hornak. Fellow, Infectious Diseases, University of Texas Medical Branch, Galveston, TX 

Is sequencing the SARS-CoV-2 genome useful for patient care? What about institutional infection control? And if clinical labs decide to perform SARS-CoV-2 sequencing, how should they do it? How should they report the results? And will they get paid? Until recently, sequencing of SARS-CoV-2 genomes has mainly been done in public health or research laboratories. Now, there is increasing interest in sequencing the viral genome in healthcare settings for uses in patient care and infection control. We’ll be talking about a new guideline that can help clinical labs and institutions decide whether to perform SARS-CoV-2 sequencing. Guest: Dr. Alex Greninger Dr. Francesca Lee Links: Clinical and Infection Prevention Applications of SARS-CoV-2 Genotyping: an IDSA/ASM Consensus Review Document https://journals.asm.org/doi/10.1128/JCM.01659-21

Candida auris is an urgent and high-priority antimicrobial resistant organisms. COVID-19 appears to have increased the identification of this pathogen in vulnerable patients. We discuss with experts the emergence of Candida auris and its relationship with COVID-19. Guests: Dr. Sevtap Arikan-Akdagli, Director, Department of Medical Microbiology, Head of Mycology Laboratory, Hacettepe University Medical School, Ankara, Turkey Dr. Bhavarth Shukla. Assistant Professor of Medicine, University of Miami Miller School of Medicine and Director of Stewardship, Jackson Memorial Health System. Miami, FL. Dr. Dimitrios P. Kontoyiannis,  Robert C Hickey Chair in Clinical Care, Deputy Head, Division of Internal Medicine, MD Anderson Cancer Center, Houston, TX.

Today we’re talking about testing in schools for COVID-19, and about recalls of SARS-CoV-2 tests due to false positive results, and, about whether we are ready to go to in-person scientific and medical meetings. Joining me for this roundtable discussion are two frequent guests on the podcast, Dr. Melissa Miller, from UNC School of Medicine, and Dr. Elli Theel, from Mayo Clinic. Links: School Testing for COVID-19. https://www.cp24.com/news/toronto-school-parents-set-up-diy-covid-19-surveillance-testing-program-1.5590772 and https://www.nytimes.com/2021/09/19/health/coronavirus-school-quarantine-testing.html False positive COVID-19 tests. https://www.nbcnews.com/news/us-news/view-hosts-say-they-had-false-positive-covid-tests-during-n1280183 and https://www.nytimes.com/2021/10/05/health/at-home-covid-tests-recall.html Return to In-Person Meetings? https://blogs.jwatch.org/hiv-id-observations/

How can we determine whether someone who has COVID-19 can transmit the virus to other people? Tests in routine clinical use, such as reverse-transcription polymerase chain reaction and antigen tests, are designed to determine whether SARS-CoV-2 is present or not, but many people have proposed that these tests be used to determine whether a patient is infectious. Furthermore, tests for SARS-CoV-2 that are not routinely used in clinical laboratories, such as viral culture and detection of sub-genomic viral RNAs, have also been discussed as indicators of infectivity. But how accurate are any of these tests for determining whether someone is infectious? Guest: Dr. Matthew Binnicker, Director of Clinical Virology and Professor of Laboratory Medicine and Pathology at Mayo Clinic. Twitter: @DrMattBinnicker Links: Can Testing Predict SARS-CoV-2 Infectivity? The Potential for Certain Methods to be a Surrogate for Replication-Competent Virus https://journals.asm.org/doi/10.1128/JCM.00469-21 Visit https://asm.org/jcm to

Enterococci, particularly vancomycin-resistant isolates tend to affect the most vulnerable and immunocompromised patients and are one of the most difficult bacteria to treat. In absence of robust clinical data, we will discuss therapeutic approaches for these recalcitrant organism.  

Tests for antibodies, or serological testing, for SARS-CoV-2 have come a long way since the early days of the COVID-19 pandemic. There are now several commercial tests available and some laboratories have developed tests for specific purposes. Tests can determine whether a person has had COVID-19 in the past, or whether someone has had an antibody response to vaccination or even whether someone has antibodies that can neutralize the virus, preventing it from infecting host cells. Guests: - Dr. Elitza Theel, Director of the Infectious Diseases Serology laboratory at Mayo Clinic in Rochester, Minnesota. - Dr. Alex Greninger, Assistant Director of the Clinical Virology Laboratory at the University of Washington Clinical Virology Laboratory, where he is also an Assistant Professor of Laboratory Medicine. Visit asm.org/eic for links mentioned

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.