Editors in Conversation

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, Endowed Chair in Clinical Microbiology.

Trish and Dan are first and last authors on a paper in press at JCM. The title is "Multicenter Evaluation of the Acuitas AMR Gene Panel for Detection of an Extended Panel of Antimicrobial Resistance Genes among Bacterial Isolates."

Topics of Discussion • Scope of the AST problem • Conventional AST – how long does it take? • General approaches to reducing the time for AST – targeted genotypic (PCR), whole genome sequencing, and faster phenotypic methods. What do you see as potential for each? • What is the Acuitas AMR Gene Panel and how does it work? • Study design • Summary of results • Discrepant results • Workflow • Where do you see this fitting into current laboratory testing

Links • Multicenter Evaluation of the Acuitas AMR Gene Panel for Detection of an Extended Panel of Antimicrobial Resistance Genes among Bacterial Isolates. https://journals.asm.org/doi/10.1128/JCM.02098-21

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://asm.org/jcm. Follow EIC Alex McAdam on twitter for JCM updates via https://twitter.com/JClinMicro and co-host, Elli Theel at https://twitter.com/ellitheelphd.

Subscribe to the podcast at https://asm.org/eic

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 Labs, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX.

This episode of Editors in Conversation is brought to you by the Antimicrobial Agents and Chemotherapy Journal and hosted by AAC Editor in Chief, Cesar Arias. AAC is available at https://asm.org/aac. Follow Cesar on twitter at https://twitter.com/SuperBugDoc for AAC updates.

Subscribe to the podcast at https://asm.org/eic

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 Hoenigl
• 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 Theel. JCM is available at https://jcm.asm.org. Follow EIC Alex McAdam on twitter for JCM updates via https://twitter.com/JClinMicro and co-host, Elli Theel at https://twitter.com/ellitheelphd.

Subscribe to the podcast at https://asm.org/eic

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 Antimicrobial Agents and Chemotherapy Journal and hosted by AAC Editor in Chief, Cesar Arias. AAC is available at https://aac.asm.org. Follow Cesar on twitter at https://twitter.com/SuperBugDoc for AAC updates.

Subscribe to the podcast at https://asm.org/eic

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 available at https://jcm.asm.org and on https://twitter.com/JClinMicro.

Guests: Dr. S. Wesley Long, Dr. Melissa Miller

Links:

Discordant SARS-CoV-2 PCR and Rapid Antigen Test Results When Infectious: A December 2021 Occupational Case Series. Preprint at https://www.medrxiv.org/content/10.1101/2022.01.04.22268770v1

Assessment of the analytical sensitivity of ten lateral flow devices against the SARS-CoV-2 omicron variant. In press at Journal of Clinical Microbiology. https://journals.asm.org/doi/10.1128/jcm.02479-21

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 Microbiology, which publishes JCM.

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.

• Acinetobacter as an opportunistic pathogen
• Therapeutic approaches for Acinetobacter infections
• The future approach for this MDR organisms.

• 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.

• 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/