Join Dr. Ben Pinsky and Dr. Greg Berry as they dissect recent news stories, including the USDA's testing for H5N1 in ground beef and a surprising bubonic plague case in Oregon. They also tackle the resurgence of measles in the U.S., the local reappearance of malaria, and a curious study on Neosporin's potential to prevent viral infections.

• H5N1 Influenza Virus: Dr. Ben Pinsky provides an update on recent cases of H5N1 in humans and animals, including concerns about dairy cattle infections and the potential for human transmission.
• Bubonic Plague: Dr. Greg Berry discusses a recent case in Oregon, its transmission through cats, and the historical context of the plague.
• Measles: The resurgence of measles in the U.S. is addressed, with Dr. Pinsky noting an increase in cases compared to previous years and emphasizing the importance of vaccination.
• Malaria: The episode covers recent cases of locally acquired malaria in the U.S. and discusses the history of malaria in America.
• Neosporin and Viral Infections: The hosts examine a study suggesting Neosporin might prevent viral infections and discuss the implications and practicality of this claim.

• Dr. Ben Pinsky
• Dr. Greg Berry

• Join ASM for up to 50% off the publication fees when you publish in JCM or any of the ASM journals.

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.

Follow JCM on Twitter/𝕏 via @JClinMicro

The pipeline of antibiotic discovery is a major necessity due to the continuous evolution of resistance to currently used antimicrobials. This pipeline faces important challenges due to the lack of investment on antimicrobial research in the private sector and an economic model that discourages investment. In the last few years, however, encouraging signs are occurring but major gaps still remain. The World Health Organization has regularly assessed the preclinical and clinical antibacterial development pipeline and the latest report is now available in the journal, lets discuss it!

Watch this episode: https://youtu.be/IgqWmHDIx-0

• The process for review of the antibacterial pipeline.
• The progress and gaps in antibiotic discovery
• The opportunities to overcome the numerous hurdles in the early stages of the antibacterial research and development space

• Valeria Gigante Ph.D., Team Lead at the World Health Organization's (WHO) in the AMR Division, Geneva, Switzerland.

• Multi-year analysis of the global preclinical antibacterial pipeline: trends and gaps.

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.

Gonorrhea remains one of the more common sexually transmitted infections. In North America, the number of reported cases has generally risen for over ten years, with interruptions in the early days of the COVID-19 pandemic, followed by returns to rising rates of infection. Under the selective pressure of antimicrobial treatment, antimicrobial resistance has risen, which has led to limited options for treatment

Today, we will be discussing antimicrobial resistance in N. gonorrhoeae, including these questions:
    •    How accurate is gradient diffusion susceptibility testing when compared to agar-dilution results?
    •    Should we use analysis of whole genome sequencing results or agar dilution phenotypic results as the gold-standard for antibiotic susceptibility testing of N. gonorrhoeae?
    •    What is the utility of beta-lactamase testing for predicting penicillin susceptibility results in N. gonorrhoeae?

• Dr. Tanis Dingle, Clinical Microbiologist at Alberta Precision Laboratories and a Clinical Associate Professor in the Department of Pathology and Laboratory Medicine at the University of Calgary.
• Dr. Angela Ma., Clinical Microbiologist at Public Health Ontario.

• Use of genome sequencing to resolve differences in gradient diffusion and agar dilution antimicrobial susceptibility testing performance of Neisseria gonorrhoeae isolates in Alberta, Canada

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.

Follow JCM on Twitter via @JClinMicro

In the last few years we have witnessed the rise of very resistant fungal species some of them likely influenced by environmental conditions and climate change. Fortunately, there has been a bit of an explosion in the development of new antifungals and the pipeline has been strengthened in the last decade. We will have the ability to have new molecules with distinct and novel mechanisms of action in the near future that may contribute to combat recalcitrant fungal infections.

• The overall threat of fungal resistance.
• The antifungal pipeline in the last few years.
• New promising antifungals

• Andreas Groll, MD PhD, Professor of Pediatrics, Head of the Infectious Disease Research Programme and Deputy Director of the Department of Haematology/Oncology at the University Children's Hospital in Münster, Germany. Editor AAC

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

Despite the many advances in diagnostic testing for infectious diseases, detection of Coccidoides infections continues to rely on serologic assessment for anti-fungal antibodies, and what is perhaps more astonishing is that the serologic methods we use today, such as complement fixation and immunodiffusion, were first developed about a century ago. These assays are technically challenging to maintain and perform, and as a result few labs offer this testing, and even if performed on-site, testing can take up to 3 days complete, so there is definitely room for improvement.

So today, we are talking about a study that aimed to modernize and improve our current options and diagnostic approach for Valley Fever, using a simpler and definitely faster lateral flow immunoassay. And as an added bonus, the study was not homo sapien-centric.

• Dr. Francisca Grill, Chief Scientific Officer at Cactus Bio
• Dr. Tom Grys, Associate Professor of Laboratory Medicine and Pathology, and co-Director of the Clinical Microbiology laboratory at Mayo Clinic in Arizona

• Development of a rapid lateral flow assay for detection of anti-coccidioidal antibodies

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.

Follow JCM on Twitter via @JClinMicro

Climate change is possibly the major threat that planet earth is experiencing in this century with potential catastrophic consequences. As the planet warms, the change in weather patterns is affecting the microbial ecology in such a manner that humans are facing new health threats including emerging diseases and facing species of organisms that are more likely to survive these new climatic conditions and resist clinically useful antimicrobials.

• The global threat of global warming.
• Climate change and change sin microbial ecology.
• The consequences of climate change and emergence of new infectious diseases and antimicrobial resistance patterns.

• Arturo Casadeval MD, Bloomberg Distinguished Professor, Alfred & Jill Sommer Professor and Chair Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health. Editor in Chief of mBio, Member of the National Academy of Sciences

Fungi that are resistant to antifungal drugs have been very much in the news and even the subject of the hugely popular television program, The Last of Us. We talk with two experts in mycology and fungal susceptibility testing about the recent descriptions of terbinafine-resistant dermatophytes in the United States.

Some of the questions we will address include:
 • What are the manifestations of infections caused by terbinafine-resistant dermatophytes?
 • What species, including novel species, of dermatophytes are more commonly resistant to terbinafine?
 • How common is terbinafine resistance in dermatophytes in the U.S.?

Guests:

- Dr. Shawn Lockhart - Senior Advisor at the Centers for Disease Control

- Dr. Nathan Wiederhold - Director of the Fungus Testing Laboratory and a Professor at UT Health San Antonio.

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. Editors in conversation is supported by the American Society for Microbiology, which publishes JCM. If you are a member of ASM, you can get up to 50% off the publication fees when you publish in JCM or any of the ASM journals.

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/ETheelPhD.

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

Artificial intelligence (AI) has the potential to change the way we practice medicine and public health. The tools and AI approaches can substantially impact a broad range of fields from the manner we approach patient care to strategies to discover new antimicrobials, track pandemics and deploy public health measures.

AAC recently published a commentary on the impact of AI in infectious diseases and we have a conversation with the lead author of the manuscript and a expert guest who is applying these concepts in real time. 

• Basic concepts of AI and different applications.
• How AI can affect the practice of infectious diseases and antimicrobial research.
• Specific examples in which AI may have a transformative effect in the future.

• Lilian Abbo, MD MBA. Associate CMO Infectious Diseases, Professor of Clinical Infectious Diseases, Jackson Health System, University of Miami Miller School of Medicine, Miami Transplant Institute
• Masayuki Nigo, MD, MSc.  Associate Professor of Clinical Medicine, Houston Methodist Hospital, Section of Transplant Infectious Diseases.

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.

Dr. Elli Theel and Dr. Alex McAdam discuss recent viral outbreaks with expert virologists. Recorded before a live audience at ASM Microbe 2023.

• What are the recent epidemiologic and diagnostic findings with Mpox? 
• What are the reservoirs for influenza A H5N1 and how is it transmitted to humans?
• Why was there such a large number of cases of human metapneumovirus this past respiratory virus season?

• Dr. Ben Pinsky, Director of the Clinical Virology laboratory and Professor of Pathology and Medicine at Stanford Health Care and the Stanford University School of Medicine
• Dr. Ryan Relich, Director of Clinical Microbiology and the Special Pathogens Unit laboratory at IU Health and Eskenazi Health and an Associate Professor of Clinical Pathology and Laboratory Medicine at the Indiana University School of Medicine

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.

Follow JCM on Twitter via @JClinMicro

In response to the global burden of antimicrobial resistance (AMR) and the critical role antimicrobial stewardship plays in optimizing antibiotic use and reducing the subsequent emergence of AMR, Antimicrobial Agents and Chemotherapy is excited to add a new section to the journal focused on antimicrobial stewardship studies. Combatting the devastating burden of AMR requires novel, multipronged approaches from clinicians and scientists alike. Launching this new section is an important step in disseminating cutting-edge research that will have notable implications in the global fight against antimicrobial-resistant pathogens.

• The role of antimicrobial stewardship in preventing emerging of resistance.
• The types of high-quality manuscripts that AAC is seeking in this area.
• Encourage excellence in antimicrobial stewardship research.

• Pranita Tamma, MD MPH, Associate Professor of Pediatrics Director, Pediatric Antimicrobial Stewardship Program, Johns Hopkins University, Baltimore MA, Editor AAC.
• Ryan Shields PharmD, MS.  Associate Professor of Medicine, Co-Director, Antibiotic Management Program, University of Pittsburgh, Pittsburgh, PA. Editor AAC.

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 combination of aztreonam with ceftazidime-avibactam is increasingly used for treatment of antimicrobial-resistant Gram-negative bacilli. Clinical laboratories are asked to perform susceptibility testing using this combination, but many laboratory directors have been unsure how to approach this. Today, we’ll discuss a recent paper in the Journal of Clinical Microbiology in which the investigators evaluated a promising method for testing this combination of two antimicrobials and a beta-lactamase inhibitor. We will also discuss the rational for combining these agents, as well as what lab directors should consider before validating and offering this susceptibility testing.

• Dr. Trish Simner - Director of the Medical Bacteriology and Infectious Disease Sequencing Laboratories, Johns Hopkins Hospital
• Dr. Romney Humphries - Director of the Division of Laboratory Medicine and the Medical Director of the Microbiology Laboratory at Vanderbilt University Medical Center.

• Multicenter Evaluation of an MIC-Based Aztreonam and Ceftazidime-Avibactam Broth Disk Elution Test

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.

Follow JCM on Twitter via @JClinMicro

Recorded at ASM Microbe 2023, Cesar has a conversation with Dr. Maria Elena Bottazzi about the role of minority women in science and discovery, the journey of Hispanic women in science and the current challenges posed by society to deliver science and global health equity.

• Dr. Maria Elena Bottazzi - Sr. Associate Dean of the National School of Tropical Medicine at Baylor College of Medicine, Distinguished Professor of Biology at Baylor University, Waco

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 European alchemists of the 12th century sought to find the philosopher’s stone, a substance that would transmute base metals, such as lead, into precious metals, such as silver and gold. Today, we discuss whether data analysis, including machine learning, can transmute base laboratory data into precious clinical tools. We will use antimicrobial susceptibility testing as a case-study for new applications of data analysis. Some of the questions we will address include:

• How can relatively simple data analyses be used to build upon current methods of verification of antimicrobial susceptibility testing?
• How do commercial systems analyze individual susceptibility results and can we improve on this analysis using new methods?
• Finally, what is the long-term potential for leveraging laboratory data and other clinical data to improve and support clinical decision making? And what needs to happen to realize this goal?

• Dr. Sanjat Kanjilal (twitter/𝕏)

The modern alchemy of clinical pathology: turning the output of microbiology laboratory operations into gold

• Join ASM for up to 50% off the publication fees when you publish in JCM or any of the ASM journals.
• Watch this episode: youtu.be/rWuQ0nSWL1Y

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.

As many of you are likely aware, May is recognized as Women’s Health Care Month by the National Cervical Cancer Coalition, and this year, the CDC has identified the week of May 14th as National Women’s Health Week. So, what better way to recognize these national events on the podcast than to talk about diagnostics for a number of extremely common and uniquely female issues – of course, I’m talking about infectious causes of vaginitis and vaginosis. Classically, diagnosis of these infections has been done at the point-of-care using wet mount microscopy and assessment for various clinical criteria, all approaches associated with some interpretive subjectivity, and let’s say imperfect performance characteristics. As a result, molecular solutions for detection of the various pathogens associated with vaginitis and vaginosis are now increasingly available for use in clinical laboratories, and also at the point-of-care, and as is the post-COVID trend, a number of these assays, including the one we are going to discuss today, can be performed on both clinician and patient self-collected samples

• Dr. Rebecca Lillis - Associate Professor of Clinical Medicine at Louisiana State University Health Science Center and the Medical Director of the LSU-CrescentCare Sexual Health Center in New Orleans.
• Dr. Barbara Van Der Pol - Professor of Medicine and Public Health at the University of Alabama at Birmingham

• Clinical Evaluation of a New Molecular Test for the Detection of Organisms Causing Vaginitis and Vaginosis

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.

Follow JCM on Twitter via @JClinMicro

As the number of immunocompromised patients rise in our hospitals, the presentation of severe infections caused by HSV and CMV are rising. Most importantly, lack of response and documented resistance are becoming more frequently observed.

• The clinical problems caused by resistant HSV and CMV infections.
• Mechanisms of resistance in these organisms.
• Insights into novel therapeutic approaches to treat resistant gonococcal infections.

• Christine M. Johnston, MD, MPH - Associate Professor Department of Medicine, Division of Allergy and Infectious Diseases. Adjunct Associate Professor, Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA.
• Roy Chemaly, MD, MPH - Professor of Medicine, Chief Infection Control Officer, Director, Clinical Virology Research, University of Texas MD Anderson Cancer Center, 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.

Susceptibility testing for piperacillin-tazobactam has undergone rapid evolution, largely driven by some surprising results from the MERINO trial, which compared the efficacy of piperacillin-tazobactam and meropenem for treatment of patients with ceftriaxone-resistant E. coli or Klebsiella pneumoniae bacteremia. We discuss how the results of the MERINO trial led to reconsideration of breakpoints for pipercillin-tazobactam at the Clinical Laboratory Standards Institute, or CLSI, how the breakpoints were changed, and how well commercial platforms perform piperacillin-tazobactam testing using FDA or CLSI breakpoints. Spoiler alert: the news isn’t great.

If you are interested in beta-lactam/beta lactamase combinations, you should check out the previous episode of this podcast, hosted by our friend Dr. Cesar Arias, the Editor-in-Chief of Antimicrobial Agents and Chemotherapy. Cesar and the guests did a great review of recent developments in this fast-moving area.

• Dr. Trish Simner - Director of the Medical Bacteriology and Infectious Disease Sequencing Laboratories, Johns Hopkins Hospital
• Dr. Romney Humphries - Director of the Division of Laboratory Medicine and the Medical Director of the Microbiology Laboratory at Vanderbilt University Medical Center.

The Center of Diseases Control and Prevention (CDC) has categorized emergent resistance in Neisseria gonorrhoeae as an “urgent” public health problem. We discuss the emerging problem of gonorrhea and implications for public health with experts in the field

• The clinical implications of resistance to B-lactams and quinolones in Neisseria gonorrhoeae
• Mechanisms of resistance in these organisms
• Insights into therapeutic approaches to treat resistant gonococcal infections.

• William M. Shafer, Professor, Department of Microbiology and Immunology, Emory University School of Medicine, Co-Director, Emory Antibiotic Resistance Center
• Yonatan Grad, Melvin J. and Geraldine L. Glimcher Associate Professor of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public 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.

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

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.

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

• 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.

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.

• 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.

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

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

• 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

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

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.

• 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.

Antimicrobial resistance is a priority public health problem with complex roots and connotations. However, due to a lack of focus on this topic, research training programs, specifically those focused on AMR are limited. Additionally, scientific meetings that particularly highlight the science of antimicrobial resistance are scarce. We recently published a commentary that evaluates the state-of-the-art of the training programs in AMR in the US. We discuss this topic with the leading author and discussed the issue with leaders in the field.

• The challenges that training in AMR poses and how to approach them.
• The current status of training programs in the USA
• Specific strategies that could improve the access and dissemination of AMR research 

• William M Shafer, PhD,  Professor, Department of Microbiology and Immunology; Director
  Antimicrobial Resistance and Therapeutic Discovery Training Program.
• Lee H. Harrison, M.D. Professor of Medicine and Epidemiology, Associate chief of epidemiology and education Division of Infectious Diseases, University of Pittsburgh School of Medicine. Director University of Pittsburgh Antimicrobial Resistance T32 Program

• Ensuring a sustained workforce to combat antibiotic resistance in the 21st century: the critical need for training the next-gen of scientists at the pre-doctoral level

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.

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

• 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.

• 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.

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?

• 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.

• 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

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.

• 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.

• 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

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.

• 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

• 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 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?

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.

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.

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

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.

• 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.

• 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

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.

• 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.

• 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.

Rhodococcus infections are uncommon, however they can cause serious disease in certain patients. There are a number of challenges though when dealing with Rhodococcus infections, including the fact that much of what we know around their susceptibility profiles and the clinical management of infected individuals actually comes from a number case series and in some situations, from the veterinary literature.  So today, our two guests are going to tell us about their experiences with Rhodococcus over a 10-year period and bring us up-to-speed on things like:

• Which species of Rhodococcus are most commonly isolated and associated with clinical disease
• What is the recommended approach to susceptibility testing for Rhodococcus and what sorts of susceptibility trends do we see at both the genus and species levels
• And also, of course, we’re going to talk about the clinical manifestations and outcomes of clinically significant Rhodococcus infections

• Adi S. Shah, M.B.B.S., Mayo Clinic
• Nancy L. Wengenack, Ph.D., Mayo Clinic

Rhodococcus infection: a 10-year retrospective analysis of clinical experience and antimicrobial susceptibility profile | Journal of Clinical 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.

Follow JCM on Twitter via @JClinMicro

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

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.

• 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

• 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

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.

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

Phage therapy has gained a lot of traction but the challenges created by this approach have not been properly assessed at a big scale. We often read about therapy successes on isolated cases but, rarely, we read or hear about failures. AAC recently published a case series of patients who failed phage therapy. Today, we will discuss this topic with the principal investigator on the research.

• Phage therapy as an approach for MDR bacteria.
• The challenges of phage therapies.
• Issues that can influence the success of phage therapy

• Saima Aslam, MBBS. Director, Solid Organ Transplant Infectious Diseases Service, Professor of Medicine, University of California, San Diego.

Pseudomonas aeruginosa ventricular assist device infections: findings from ineffective phage therapies in five cases https://journals.asm.org/doi/10.1128/aac.01728-23

• How are we doing with phage therapy at this point?
• What are the challenges to deploy phage therapy in clinical settings?
• The 5 cases of failure of phage therapy in patients with LVADs summarized
• What factors did Dr. Aslam identify that were related with the failure?
• How do you develop neutralization against phages and how can you prevent it?  
• Bacterial isolates with varying phage susceptibility, how can this be detected?
• What did Dr. Aslam learn?
• Future research

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.

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/

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

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.