Editors in Conversation

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 Neural Network. Deep Neural Networks Offer Morphologic Classification and Diagnosis of Bacterial Vaginosis. https://jcm.asm.org/content/early/2020/11/02/JCM.02236-20 Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples. https://jcm.asm.org/content/58/1/e00963-19 A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing. https://jcm.asm.org/content/58/6/e00060-20 Nanopore Sequencing of the Fungal Intergenic Spacer Sequence as a Potential Rapid Diagnostic Assay. https://jcm.asm.org/content/58/12/e01972-20 Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples https://jcm.asm.org/content/58/10/e00632-20 Dr. Miller's Selections Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription–Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19. https://jcm.asm.org/content/58/9/e01438-20 A Direct Comparison of Enhanced Saliva to Nasopharyngeal Swab for the Detection of SARS-CoV-2 in Symptomatic Patients. https://jcm.asm.org/content/58/11/e01946-20 Targeted Metagenomics for Clinical Detection and Discovery of Bacterial Tick-Borne Pathogens. Retrospective Review of Clinical Utility of Shotgun Metagenomic Sequencing Testing of Cerebrospinal Fluid from a U.S. Tertiary Care Medical Center. https://jcm.asm.org/content/58/12/e01729-20 Plasma Metagenomic Next-Generation Sequencing Assay for Identifying Pathogens: a Retrospective Review of Test Utilization in a Large Children's Hospital. https://jcm.asm.org/content/58/11/e00794-20 Dr. McAdam's Selections Neutralizing Antibodies Correlate with Protection from SARS-CoV-2 in Humans during a Fishery Vessel Outbreak with a High Attack Rate. https://jcm.asm.org/content/58/11/e02107-20 Performance of Abbott ID Now COVID-19 Rapid Nucleic Acid Amplification Test Using Nasopharyngeal Swabs Transported in Viral Transport Media and Dry Nasal Swabs in a New York City Academic Institution. https://jcm.asm.org/content/58/8/e01136-20 3. Reduced In Vitro Susceptibility of Streptococcus pyogenes to β-Lactam Antibiotics Associated with Mutations in the pbp2x Gene Is Geographically Widespread. https://jcm.asm.org/content/58/4/e01993-19

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 Fastidious Organisms from Urine Culture in the Setting of Total Laboratory Automation by W. Lainhart and C-A Burnham Total Laboratory Automation: a Micro-Comic Strip by C-A Burnham and A. McAdam Subscribe to Editors in Conversation (free) on Apple Podcasts, Google Podcasts, Android, Spotify.

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 decided to launch the section with a special focus on remdesivir, currently the only FDA-approved drug to treat COVID-19. Joining me today to discuss this are the proud lead authors of the firs paper of the new section. Ryan please introduce our guests • Dr. Muneerah Aleissa: Postdoctoral research fellow, Brigham's and Women Hospital, Harvard Medical School. • Dr. Francisco Marty: Associate Physician, Brigham and Women's Hospital and Associate Professor of Medicine, Harvard Medical School. Visit aac.asm.org to read the current issue of Antimicrobial Agents and Chemotherapy.

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 SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate" by Addetia et al. https://jcm.asm.org/content/early/2020/08/21/JCM.02107-20/article-info "Humoral Immune Response to SARS-CoV-2 in Iceland" by Gudbjartsson et al. https://www.nejm.org/doi/full/10.1056/NEJMoa2026116 Molecular Testing "When Should Asymptomatic Persons Be Tested for COVID-19?" By Schuetz et al. https://jcm.asm.org/content/early/2020/10/05/JCM.02563-20 CDC Testing recommendations: https://www.cdc.gov/coronavirus/2019-ncov/hcp/testing-overview.html FDA SARS-CoV-2 Reference Panel Comparative Data https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-reference-panel-comparative-data?utm_medium=email&utm_source=govdelivery CDC Wastewater Surveillance for SARS-CoV-2 https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/wastewater-surveillance.html NY Times article, "Your coronavirus test is positive. Maybe it shouldn't be.": https://www.nytimes.com/2020/08/29/health/coronavirus-testing.html Frequent, community based testing "Rethinking Covid-19 Test Sensitivity — A Strategy for Containment" by Mina et al. https://www.nejm.org/doi/full/10.1056/NEJMp2025631?query=featured_coronavirus "Can We Test Our Way Out of the COVID-19 Pandemic?" by Pettengill and McAdam. https://jcm.asm.org/content/early/2020/08/24/JCM.02225-20/article-info

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 Associate Professor of Pathology at Johns Hopkins University and an Associate Director of in the Medical Microbiology laboratory there. She is also a newly-appointed editor of JCM. Dr. Simner wrote an outstanding review in JCM called "Phenotypic Detection of Carbapenemase-Producing Organisms from Clinical Isolates" in 2018. It's a few years old, but I think it is still the best available overview of these tests. We also talk about one of her more recent articles.

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

A conversation with Lou Rice about his career and his experience of being the Editor of Chief for the AAC Journal for the past decade. Visit aac.asm.org to read the current issue.

A discussion about laboratory testing for COVID-19 with two experts, Dr. Melissa Miller and Dr. Elitza Theel. Hosted by Journal of Clinical Microbiology Editor in Chief, Dr. Alexander McAdam. Get the current issue of the Journal of Clinical Microbiology at https://jcm.asm.org/

Objectives: • Discuss the therapeutic options currently being used for COVID-19 • Evaluate some clinical data supporting the use of these drugs • Comment on clinical trials and enrollment Participants: • Andre Kalil, Professor, University of Nebraska Medical Center, Omaha, NB, USA. Lead Investigator, NIH Clinical Trial for COVId-19 • Miguel A. Martinez, Editor AAC. Professor, AIDS Research Institute-IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain. Visit https://aac.asm.org/ to browse issues and/or submit a manuscript.