2020: A Bad Year with Great Papers in Clinical Microbiology (JCM ed.)

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