Episode Summary


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, 3 JCM editors each discuss 3 of the most important papers published in the journal during 2020.

Guests: Melissa Miller, Patricia Simner

Links mentioned:

Dr. Simner's Selections

1. 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

2. 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

3. 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

1. 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

2. Targeted Metagenomics for Clinical Detection and Discovery of Bacterial Tick-Borne Pathogens.

3. 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

1. 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

2. 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

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