Editors in Conversation

Avoiding HIV False Positives (JCM ed.) Feb 24, 2023

We can probably all agree that any false positive test result is bad, but I think it’s safe to say that some false positives, like a false positive HIV test for example, is much more anxiety provoking than others. And when it comes to HIV, there have been a number of key advances in the field over the past decade, include the development of improved diagnostics and optimized algorithmic approaches, all of which have allowed for earlier detection of infected patients, and particularly those with acute HIV. Among these advancements has been the development of 4th and 5th generation serologic assays, which offer multiple benefits over prior assay versions, but unfortunately, are not immune to the possibility of false positive results. So, confirmatory test remain a necessary – the challenge though is that depending on the institution and environment, the turnaround time for such confirmatory testing can be prolonged, leaving patients and clinicians in a kind of diagnostic limbo. So, is there a way to minimize the risk of false positive first-tier HIV serologic results? And that is the question will be the focus of our discussion today.

Watch this episode: https://youtu.be/kq61A3Jz67U

Guests:

Dr. Shivanjali Shankaran - Assistant Professor and ID Clinician in the Division of Infectious Diseases at Rush Medical Center in Chicago
Dr. Beverly Sha - Professor of Medicine, also in the Division of Infectious Diseases at Rush Medical Center

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.

Visit https://journals.asm.org/journal/jcm to read articles and/or submit a manuscript.

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

Discussing β-lactamase/β-lactamase inhibitors (AAC Ed.) Feb 10, 2023

Novel β-lactamase/β-lactamase inhibitors have become critical drugs to combat the most resistant Gram-negative infections. A series of new compounds with even more broad and potent activity are in the horizon to add to the therapeutic armamentarium. Today, we will discuss these drugs with experts in the field.

Topics discussed:

BL/BLI combinations that are currently available in clinical practice.
Future perspectives of BL/BLI armamentarium.
Resistance developing for this class of antibiotics.

Guests:

Robert Bonomo. Professor, Department of Medicine, Pharmacology and Molecular Biology and Microbiology, Case Western Reserve University, Director of VA CARES Center, Cleveland, OH
Patricia A. Bradford Antimicrobial Development Specialists LLC, Nyack, New York, USA

This episode is brought to you by the Antimicrobial Agents and Chemotherapy journal available at aac.asm.org. If you plan to publish in AAC, ASM Members get up to 50% off publishing fees. Visit asm.org/membership to sign up.

Visit journals.asm.org/journal/aac to browse issues and/or submit a manuscript.

Molecular Testing for Periprosthetic Joint Infections (JCM ed.) Jan 14, 2023

The applications of large multiplex panels for detection of pathogens have greatly expanded in the past several years. Initial tests were for detection of respiratory viruses, and the first such test was labor intensive and vulnerable to frequent contamination. Since then, additional sample types have been added, such as cerebrospinal fluid and positive blood culture broths, and tests are easier to perform and reasonably reliable. We discuss a research use only multiplex PCR assay for detection of pathogens in joint infections, and learning how it compares to targeted metagenomic sequencing and culture for detection of pathogens in periprosthetic joint infections.

Guests:

Dr. Marisa Azad - Assistant Professor of Medicine in the Division of Infectious Diseases at The Ottawa Hospital and an Associate Clinical Scientist at the Ottawa Hospital Research Institute.
Dr. Robin Patel - Co-Director of the Bacteriology Laboratory at the Mayo Clinic, where she is Professor of Medicine and Professor of Microbiology.

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.

Visit journals.asm.org/journal/jcm to read articles and/or submit a manuscript.

An Update on COVID-19 Therapeutics (AAC ed.) Dec 23, 2022

COVID-19 continues to pose major problems in the winter in the USA. Infections and hospitalizations are increasing and there is a fear of emergence of new variants. Therapeutic tools are also evolving. We discuss these new developments!

Watch the video version via: https://youtu.be/ElnahBl53e8

Topics discussed:

The latest facts on COVID
Current therapeutic approaches including antivirals and monoclonal antibodies
Future perspectives for the coming year on COVID-19.

Guests:

Adarsh Bhimraj, MD. Director of Education and Fellowships, Division of Infectious Diseases, Houston Methodsit Hospital. Chair IDSA Guidelines for COVID-19.

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

The Best Clinical Microbiology Papers of 2022 (JCM Ed.) Dec 07, 2022

As we enter into the holiday season, many of us look forward to celebrating long-standing traditions with family and friends, which is no different from us here on the podcast! While not necessarily as long-standing as some of the other classic holiday traditions, after 2.5 years on air, we on this podcast have established our own end-of-year tradition, which is to take a look back at some of our favorite papers or more intriguing manuscripts published in the Journal of Clinical Microbiology over the past year. And so as you’ll see, thanks to the different areas of expertise and general interest among our panel today, we’ve selected quite a variety of papers to discuss, ranging from evaluation of new blood culture systems to use of metagenomics for infective endocarditis and to the potential application of interferon gamma release assays for detection of Histoplasma infections. And so, suffice it to say, there will be something of interest for everyone listening. But, for those watching today, you are clearly getting an extra special treat as you get to see us do this episode wearing our best holiday gear and accessories.

Guest:

Dr. Trish Simner.

Links:

Nasal Swab Performance by Collection Timing, Procedure, and Method of Transport for Patients with SARS-CoV-2. DOI: https://doi.org/10.1128/JCM.00569-21

Multicenter Postimplementation Assessment of the Positive Predictive Value of SARS-CoV-2 Antigen-Based Point-of-Care Tests Used for Screening of Asymptomatic Continuing Care Staff. DOI: https://doi.org/10.1128/JCM.01411-21

Laboratory Safety: Handling Burkholderia pseudomallei Isolates without a Biosafety Cabinet. DOI: https://doi.org/10.1128/JCM.00424-21

The clinical utility of 2 high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in MALDI-TOF MS. DOI: https://doi.org/10.1128/JCM.01769-21

Performance of Fully Automated Antimicrobial Disk Diffusion Susceptibility Testing Using Copan WASP Colibri Coupled to the Radian In-Line Carousel and Expert System. DOI: 10.1128/JCM.00777-21

Benefits Derived from Full Laboratory Automation in Microbiology: A Tale of Four Laboratories. DOI https://doi.org/10.1128/JCM.01969-20

Reflex Detection of Ciprofloxacin Resistance in Neisseria gonorrhoeae by Use of the SpeeDx ResistancePlus GC Assay. DOI: https://doi.org/10.1128/JCM.00089-21

Comparative Performance of Latest-Generation and FDA-Cleared Serology Tests for the Diagnosis of Chagas Disease. DOI: https://doi.org/10.1128/JCM.00158-21

Diagnosing Pulmonary Tuberculosis by Using Sequence-Specific Purification of Urine Cell-Free DNA. DOI: https://doi.org/10.1128/JCM.00074-21

Indeterminate QuantiFERON Gold Plus Results Reveal Deficient Interferon Gamma Responses in Severely Ill COVID-19 Patients. DOI: https://doi.org/10.1128/JCM.00811-21

Visit journals.asm.org/journal/jcm to read articles and/or submit a manuscript.

Follow JCM on Twitter via @JClinMicro

How Can Clinical Microbiology Labs Contribute to Antimicrobial Stewardship? (JCM ed.) Nov 18, 2022

Deciding how extensively to work up and report respiratory cultures is the worst. There are useful guidelines on how to approach this. But, in my experience, very few laboratories strictly follow these guidelines. That can be because of concerns about under-reporting pathogens or about over-reporting microbiota, or it can be the result of pressure from clinical staff to report more organisms than the guidelines suggest. Today, we’ll be talking with two guests about their study on how over-reporting of organisms from respiratory tract cultures can lead to over treatment with antimicrobials.

Guests:

Dr. Sarah Parker, pediatric infectious disease specialist at Children’s Hospital Colorado and the Medical Director of the Antimicrobial Stewardship Program.
Dr. Andrea Prinzi, infectious disease medical science liason with bioMerieux.

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.

Research Careers in Antimicrobial Resistance (AAC ed.) Nov 05, 2022

Antimicrobial resistance is the ‘silent pandemic’ and to tackle this challenging public health problem we need to attract the best and brightest. Today we will discuss pathways to work on this field with trainees who will be the next generation of outstanding researchers in the field, currently as part of different T32 training programs in the United States. Welcome to Editors in Conversation

Topics discussed:

Different pathways to follow careers in antimicrobial research
The challenges to follow an academic and research pathways
Future perspectives and guidance for early stage investigators who want to pursue research on antimicrobial resistance.

Guests:

Cheyenne Lee. 4th Year Ph.D. Candidate | McBride Lab, Microbiology and Molecular Genetics (MMG) Program Initiative for Maximizing Student Development (IMSD) Graduate Student Representative, Emory University, Atlanta, GA. T32 predoctoral fellow
Edwin Chen, MD, PhD. Infectious Diseases Fellow, Postdoctoral T32 Fellow, University of Pittsburgh. Pittsburgh, PA.
Kara Hood, PhD. Pos-doctoral T32 Fellow, Texas Medical Center Program in Antimicrobial Resistance, Houston Methodist Research Institute, Houston, TX.

This episode is brought to you by the Antimicrobial Agents and Chemotherapy journal available at aac.asm.org. If you plan to publish in AAC, ASM Members get up to 50% off publishing fees. Visit asm.org/membership to sign up.

Visit journals.asm.org/journal/aac to browse issues and/or submit a manuscript.

Machine Learning and Artificial Intelligence in the Clinical Microbiology Laboratory (JCM ed.) Oct 08, 2022

The idea of applying machine learning and digital pathology platforms to everyday workflows in the clinical microbiology laboratory has become increasing intriguing and appealing, especially as labs continue to optimize efficiency in the midst of workforce shortages. The promise of this new digital frontier is multifold, including decreasing turnaround time and potentially cost, and freeing up technologist time to focus on higher yield activities in the lab. Many labs have now taken the initial leap into automated culture and imaging systems, but what’s next? Are the digital pathology AI algorithms ready for prime-time in clinical microbiology labs? Is the future now?

Guests:

Dr. Niaz Banaei, Medical Director of the Stanford Health Care Clinical Microbiology Laboratory and Professor of Pathology and Medicine at Stanford University
Dr. Dan Rhoads, Section Head of Microbiology at Cleveland Clinic

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/Refences:

Evaluation of MetaSystems automated fluorescent microscopy system for the machine-assisted detection of acid-fast bacilli in clinical samples. https://journals.asm.org/doi/10.1128/jcm.01131-22
Computer vision and artifical intelligence are emerging diagnostic tools for the clinical microbiologist. https://journals.asm.org/doi/10.1128/JCM.00511-20?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed

Visit journals.asm.org/journal/jcm to read articles and/or submit a manuscript.

Follow JCM on Twitter via @JClinMicro

How Proposed Change to US Regulation Could Impact Clinical Microbiology Labs Sep 16, 2022

There are a number of regulatory proposals under consideration which could have important effects on clinical microbiology labs, and clinical labs more generally. First, the VALID act would change how clinical tests are regulated with particularly important implications for laboratory-developed tests. Second, the Centers for Medicare and Medicaid Services has proposed changes to the educational requirements for lab directors under CLIA and additional changes that would increase the fees that clinical labs pay to CMS. If you have been waiting for someone to explain these changes and how they could affect your lab, you’ve come to the right podcast.

Guests:

Dr. Melissa Miller, Director of the Clinical Microbiology Laboratory and a Professor at the University Of North Carolina School Of Medicine
Mary Lee Watts, Director of Federal Affairs at ASM

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:

ASM Submits Concerns On VALID Act. https://asm.org/Articles/Policy/2022/May-2022/VALID-Act
ASM Submits Comments to CMS on Proposed Rule for CLIA-Labs. https://asm.org/Articles/Policy/2022/Aug2022/ASM-Comments-on-CMS-Proposed-Rules-for-CLIA-Certif

Visit journals.asm.org/journal/jcm to read articles and/or submit a manuscript.

Follow JCM on Twitter via @JClinMicro

Management of Mycobacterium Abscessus Infections: The Rise of a Superbug Sep 02, 2022

Infections caused by Mycobacterium abscessus appear to be increasing in frequency among the immunocompromised population and are challenging to treat. Antibiotic options in these cases are scarce, prolonged therapy is required and new options are needed. We will discuss this important topic with experts in the field.

Topics discussed:

Define M. abscessus as an opportunistic pathoge
The intrinsic phenotypic characteristics of M. abscessus, including resistance to common antimicrobials
Treatment approaches and rationale for these strategies

Guests:

Kelly Dooley, MD. PhD, MPH. Professor of Medicine, Johns Hopkins University and Editor of AAC
Charles L. Daley, MD, Professor and Chief of the Division of Mycobacterial and Respiratory Infections. National Jewish Health
Thomas Dick, PhD. Professor, Center for Discovery and Innovation, Hackensack Meridian Health

This episode is brought to you by the Antimicrobial Agents and Chemotherapy journal available at aac.asm.org. If you plan to publish in AAC, ASM Members get up to 50% off publishing fees. Visit asm.org/membership to sign up

Visit journals.asm.org/journal/aac to browse issues and/or submit a manuscript.

The Inoculum Effect of Antibiotic Susceptibility Testing Aug 20, 2022

The inoculum effect of antibiotic susceptibility testing is often discussed at playgrounds and infectious diseases conferences, but many of us don’t really have a clear definition of what it is or a good understanding of its importance.

We’ll be talking about the inoculum effect and susceptibility testing of Staphylococcus aureus with cefazolin.

Some of the questions we’ll discuss are: • What exactly is the inoculum effect and how is it measured? • Does the inoculum effect have clinical significance? • How common is the inoculum effect with Staph aureus and cefazolin?

Diagnosis and Treatment of Monkeypox Aug 05, 2022

As July 26, the world has documented 19,188 cases of monkeypox, with 3,591 cases in the US alone, making the US the country with the most known infections amid the global outbreak. The WHO has declared monkeypox a public health emergency. Although this disease has been known for years, certain features suggest that we are facing a unique outbreak of monkeypox with the potential for worldwide spreading.

In this special podcast edition of Editors in Conversation we will discuss the diagnosis and treatment of monkeypox with experts in the field who have dealt with significant number of cases in the US.

Topics:

• The significance of the monkeypox outbreak • The approach for the diagnosis of monkeypox • The treatment approaches and prevention tools for monkeypox

This special episode is brought to you by Journal of Clinical Microbiology and Antimicrobial Agents and Chemotherapy journals.

Hosts: - Cesar A. Arias, Editor in Chief of AAC, - Dr. Elli Theel, Editor of JCM

This podcast is supported by the American Society for Microbiology, which publishes both JCM and AAC. Don’t forget to check the latest issues of JCM and AAC with outstanding papers on microbial diagnostics, mechanisms of resistance, pharmacology of antimicrobial agents, epidemiology and clinical therapeutics, among others.

Joining us to discuss this important topic are:

• Jason Zucker, MD. Assistant Professor of Medicine at Columbia University Medical Center and Infectious Diseases physician at New York-Presbyterian / Columbia University Irving Medical Center • Benjamin Pinsky, MD, PhD, Associate Professor of Pathology and of Medicine (Infectious Diseases). Stanford University, palo Alto, CA. Medical Director of the Clinical Virology Laboratory for Stanford Health Care and the Stanford Children’s Health.

Dynamite Parasites, with Dr. Bobbi Pritt (JCM ed.) Jul 02, 2022

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 Podcasts, Google Podcasts, Android, Spotify, Email.

Stenotrophomonas maltophilia: The Silent Rise of a Superbug (AAC ed.) Jun 18, 2022

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 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

What’s New in Molecular Virology? (JCM ed.) May 28, 2022

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 @JClinMicro

Treatment of Resistant Pseudomonas Aeruginosa Infections (AAC ed.) May 14, 2022

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.

Prevalence and Mortality Associated with Bloodstream Infections (JCM ed.) Apr 29, 2022

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 University of Toronto, and a Adjunct Physician at Public Health Ontario. - Dr. Kevin Brown is a Scientist at Public Health Ontario and Assistant Professor at the University of Toronto

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.

Links Prevalence and Mortality Associated with Bloodstream Organisms: a Population-Wide Retrospective Cohort Study. https://journals.asm.org/doi/epub/10.1128/jcm.02429-21

Consensus on B-lactamases (AAC ed.) Apr 05, 2022

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 Western Reserve University, Director VA CARES Research Collaborative

Links:

Consensus on β-Lactamase Nomenclature https://journals.asm.org/doi/10.1128/aac.00333-22

Visit journals.asm.org/journal/aac to browse issues and/or submit a manuscript.

Multiplex PCR for Predicting Antibiotic Susceptibility (JCM ed.) Mar 19, 2022

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

Phages as Therapeutic Tools Against Multidrug Resistant Bacteria (AAC ed.) Mar 05, 2022

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

COVID-19 Associated Pulmonary Aspergillosis - The Other CAPA (JCM ed.) Feb 18, 2022

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:

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

WHO Critical Review of the Antibacterial Pipeline (AAC ed.) Jan 28, 2022

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

Testing for COVID-19 During the Age of Omicron (JCM ed.) Jan 21, 2022

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

Best Clinical Microbiology Papers of 2021 (JCM ed.) Dec 28, 2021

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.

Treatment of Acinetobacter spp. Infections (AAC ed.) Dec 11, 2021

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

SARS-CoV-2 Sequencing for Clinical Care and Infection Control Nov 29, 2021

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 at the Intersection of the COVID-19 Pandemic Oct 29, 2021

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.

COVID-19 Testing - Schools, False Positives, and In-Person Meetings (JCM ed.) Oct 22, 2021

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/

Testing for COVID-19 Infectivity (JCM ed.) Aug 20, 2021

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 read articles and/or submit a manuscript.

Follow JCM on Twitter via https://twitter.com/JClinMicro

Subscribe to ASM's YouTube channel at https://goo.gl/mOVHlK

Treatment of VRE Infections (AAC ed.) Jul 31, 2021

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.

Advances in Serologic Testing for COVID-19 (JCM ed.) Jul 23, 2021

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

Innovative Clinical Trials for COVID-19 (AAC ed.) Jul 02, 2021

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.

Mythbusting in Susceptibility Testing (JCM ed.) Jun 25, 2021

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.

Antimalarial Drug-Resistance (AAC ed.) Jun 04, 2021

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

Staphylococcus argenteus: another coagulase positive Staphylococcus (JCM ed.) May 28, 2021

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

β-lactam/β-lactamase inhibitor combinations (AAC ed.) May 07, 2021

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

Reconciling Genotypic and Phenotypic Susceptibility Tests (JCM ed.) Apr 30, 2021

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

Gaps in Laboratory Diagnosis of Fungal Diseases (JCM ed.) Apr 02, 2021

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

Pandemic Built Environment (mSystems ed.) Mar 29, 2021

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 group

Visit msystems.asm.org to read articles and/or submit a manuscript.

Developing Non-Traditional Antibiotics (AAC ed.) Mar 19, 2021

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.

Fermentative Food Microbiome (mSystems ed.) Mar 13, 2021

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.

Optimizing Blood Cultures with Dr. Eric Ransom and Dr. Valeria Fabre (JCM ed.) Mar 05, 2021

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/content/58/10/e01053-20

Evaluation of Optimal Blood Culture Incubation Time To Maximize Clinically Relevant Results from a Contemporary Blood Culture Instrument and Media System at https://jcm.asm.org/content/59/3/e02459-20

Read more at https://jcm.asm.org

Top Non-COVID-19 AAC Papers of 2020: A discussion with early stage investigators (AAC ed.) Feb 26, 2021

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 (JCM ed.) Feb 12, 2021

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:

Subscribe to Editors in Conversation (free) on Apple Podcasts, Google Podcasts, Android, Spotify.

Synthetic Microbiology (mSystems ed.) Jan 29, 2021

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.

Vaccines for COVID19: A Critical Appraisal with Dr. Carol Baker (AAC ed.) Jan 25, 2021

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: A Bad Year with Great Papers in Clinical Microbiology (JCM ed.) Jan 09, 2021

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

2020: The year of COVID-19 (AAC ed.) Dec 18, 2020

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

COVID-19: Clinical Labs in the Media Spotlight with Dr. Katherine Wu and Dr. Susan Butler-Wu (JCM ed.) Dec 11, 2020

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?

The Antimicrobial Resistance Leadership Group (ARLG) (AAC ed.) Nov 30, 2020

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.

Total Laboratory Automation in Clinical Microbiology (JCM ed.) Nov 13, 2020

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:

Subscribe to Editors in Conversation (free) on Apple Podcasts, Google Podcasts, Android, Spotify.

The use of remdesivir against SARS-CoV-2 (AAC ed.) Nov 02, 2020

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.

COVID-19 Diagnostic Testing Redux (JCM ed.) Oct 16, 2020

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

Discovering new antibiotics (AAC ed.) Oct 05, 2020

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.

Parasites (JCM ed.) Sep 18, 2020

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

The dearth of antibiotic development (AAC ed.) Sep 02, 2020

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.

Detection of carbapenemases (JCM ed.) Aug 21, 2020

• 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.

New Vancomycin Guidelines (AAC ed.) Aug 13, 2020

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.

COViD-19: Therapeutic Update (AAC ed.) Aug 10, 2020

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

Antimicrobial Agents and Chemotherapy Journal - Past, Present and Future (AAC ed.) Aug 10, 2020

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.

Diagnostic Tests for COVID-19 (JCM ed.) Aug 05, 2020

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/

Therapeutic approaches for COVID-19: Myths and facts (AAC ed.) Aug 04, 2020

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.

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