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Journal of Clinical Microbiology
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next-generation sequencing

  • Free
    Rapid High-Throughput Whole-Genome Sequencing of SARS-CoV-2 by Using One-Step Reverse Transcription-PCR Amplification with an Integrated Microfluidic System and Next-Generation Sequencing
    Virology
    Rapid High-Throughput Whole-Genome Sequencing of SARS-CoV-2 by Using One-Step Reverse Transcription-PCR Amplification with an Integrated Microfluidic System and Next-Generation Sequencing

    The long-lasting global COVID-19 pandemic demands timely genomic investigation of SARS-CoV-2 viruses. Here, we report a simple and efficient workflow for whole-genome sequencing utilizing one-step reverse transcription-PCR (RT-PCR) amplification on a microfluidic platform, followed by MiSeq amplicon sequencing.

    Tao Li, Hye Kyung Chung, Papa K. Pireku, Brett F. Beitzel, Mark A. Sanborn, Cynthia Y. Tang, Richard D. Hammer, Detlef Ritter, Xiu-Feng Wan, Irina Maljkovic Berry, Jun Hang
  • Deciphering an Adenovirus F41 Outbreak in Pediatric Hematopoietic Stem Cell Transplant Recipients by Whole-Genome Sequencing
    Virology
    Deciphering an Adenovirus F41 Outbreak in Pediatric Hematopoietic Stem Cell Transplant Recipients by Whole-Genome Sequencing

    Human adenovirus (HAdV) represents a major cause of mortality and morbidity in pediatric recipients of allogeneic hematopoietic stem cell transplants (HSCT). HAdV species F type 41 (HAdV-F41) infections in HSCT patients are scarce, whereas HAdV-F41 circulates commonly in healthy individuals. Between March and July 2018, HAdV-F41 infections were identified in four children (A, B, C, and E) who received allogeneic HSCT and one child...

    Caroline Lefeuvre, Maud Salmona, Linda Feghoul, Noémie Ranger, Séverine Mercier-Delarue, Laure Nizery, Aurélia Alimi, Jean-Hugues Dalle, Jérôme LeGoff
  • Free
    Low-Level Rifampin Resistance and <em>rpoB</em> Mutations in <span class="named-content genus-species" id="named-content-1">Mycobacterium tuberculosis</span>: an Analysis of Whole-Genome Sequencing and Drug Susceptibility Test Data in New York
    Mycobacteriology and Aerobic Actinomycetes
    Low-Level Rifampin Resistance and rpoB Mutations in Mycobacterium tuberculosis: an Analysis of Whole-Genome Sequencing and Drug Susceptibility Test Data in New York

    Rapid and reliable detection of rifampin (RIF) resistance is critical for the diagnosis and treatment of drug-resistant and multidrug-resistant (MDR) tuberculosis. Discordant RIF phenotype/genotype susceptibility results remain a challenge due to the presence of rpoB mutations that do not confer high levels of RIF resistance, as have been exhibited in strains with mutations such as Ser450Leu.

    Joseph Shea, Tanya A. Halse, Donna Kohlerschmidt, Pascal Lapierre, Herns A. Modestil, Cheryl H. Kearns, Felicia F. Dworkin, Jennifer L. Rakeman, Vincent Escuyer, Kimberlee A. Musser
  • A Bioinformatic Pipeline for Improved Genome Analysis and Clustering of Isolates during Outbreaks of Legionnaires' Disease
    Bacteriology
    A Bioinformatic Pipeline for Improved Genome Analysis and Clustering of Isolates during Outbreaks of Legionnaires' Disease

    Legionnaires’ disease, a severe lung infection caused by the bacterium Legionella pneumophila, occurs as single cases or in outbreaks that are actively tracked by public health departments. To determine the point source of an outbreak, clinical isolates need to be compared to environmental samples to find matching isolates.

    Wolfgang Haas, Pascal Lapierre, Kimberlee A. Musser
  • Retrospective Review of Clinical Utility of Shotgun Metagenomic Sequencing Testing of Cerebrospinal Fluid from a U.S. Tertiary Care Medical Center
    Bacteriology
    Retrospective Review of Clinical Utility of Shotgun Metagenomic Sequencing Testing of Cerebrospinal Fluid from a U.S. Tertiary Care Medical Center

    Shotgun metagenomic sequencing can detect nucleic acids from bacteria, fungi, viruses, and/or parasites in clinical specimens; however, little data exist to guide its optimal application to clinical practice. We retrospectively reviewed results of shotgun metagenomic sequencing testing requested on cerebrospinal fluid samples submitted to an outside reference laboratory from December 2017 through December 2019. Of the 53 samples from...

    Kyle G. Rodino, Michel Toledano, Andrew P. Norgan, Bobbi S. Pritt, Matthew J. Binnicker, Joseph D. Yao, Allen J. Aksamit, Robin Patel
  • Sensitive Identification of Bacterial DNA in Clinical Specimens by Broad-Range 16S rRNA Gene Enrichment
    Bacteriology
    Sensitive Identification of Bacterial DNA in Clinical Specimens by Broad-Range 16S rRNA Gene Enrichment

    The broad-range detection and identification of bacterial DNA from clinical specimens are a foundational approach in the practice of molecular microbiology. However, there are circumstances under which conventional testing may yield false-negative or otherwise uninterpretable results, including the presence of multiple bacterial templates or degraded nucleic acids. Here, we describe an alternative, next-generation sequencing approach...

    Sara Rassoulian Barrett, Noah G. Hoffman, Christopher Rosenthal, Andrew Bryan, Desiree A. Marshall, Joshua Lieberman, Alexander L. Greninger, Vikas Peddu, Brad T. Cookson, Stephen J. Salipante
  • Amino Acid Substitutions Associated with Treatment Failure for Hepatitis C Virus Infection
    Virology
    Amino Acid Substitutions Associated with Treatment Failure for Hepatitis C Virus Infection

    Despite the high virological response rates achieved with current directly acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 2% to 5% of treated patients do not achieve a sustained viral response. The identification of amino acid substitutions associated with treatment failure requires analytical designs, such as subtype-specific ultradeep sequencing (UDS) methods, for HCV characterization and patient management....

    María Eugenia Soria, Carlos García-Crespo, Brenda Martínez-González, Lucía Vázquez-Sirvent, Rebeca Lobo-Vega, Ana Isabel de Ávila, Isabel Gallego, Qian Chen, Damir García-Cehic, Meritxell Llorens-Revull, Carlos Briones, Jordi Gómez, Cristina Ferrer-Orta, Nuria Verdaguer, Josep Gregori, Francisco Rodríguez-Frías, María Buti, Juan Ignacio Esteban, Esteban Domingo, Josep Quer, Celia Perales
  • Whole-Genome Sequencing of Porcine Reproductive and Respiratory Syndrome Virus from Field Clinical Samples Improves the Genomic Surveillance of the Virus
    Clinical Veterinary Microbiology
    Whole-Genome Sequencing of Porcine Reproductive and Respiratory Syndrome Virus from Field Clinical Samples Improves the Genomic Surveillance of the Virus

    Porcine reproductive and respiratory syndrome virus (PRRSV) is a major economic concern worldwide. There are currently large data sets available about the ORF5 gene of the virus, with thousands of sequences available, but little data are currently available on the full-length genome of PRRSV. We hypothesized that whole-genome sequencing (WGS) of the PRRSV genome would allow better epidemiological monitoring than ORF5 gene sequencing....

    Christian Lalonde, Chantale Provost, Carl A. Gagnon
  • Open Access
    Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples
    Mycobacteriology and Aerobic Actinomycetes
    Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples

    Targeted next-generation sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samples for clinical diagnosis of drug-resistant tuberculosis (DR-TB). However, the complexity of sequencing platforms has limited their uptake in low-resource settings. The...

    Andrea M. Cabibbe, Andrea Spitaleri, Simone Battaglia, Rebecca E. Colman, Anita Suresh, Swapna Uplekar, Timothy C. Rodwell, Daniela M. Cirillo
  • Biennial Upsurge and Molecular Epidemiology of Enterovirus D68 Infection in New York, USA, 2014 to 2018
    Virology
    Biennial Upsurge and Molecular Epidemiology of Enterovirus D68 Infection in New York, USA, 2014 to 2018

    Enterovirus D68 (EV-D68) infection has been associated with outbreaks of severe respiratory illness and increased cases of nonpolio acute flaccid myelitis. The patterns of EV-D68 circulation and molecular epidemiology are not fully understood. In this study, nasopharyngeal (NP) specimens collected from patients in the Lower Hudson Valley, New York, from 2014 to 2018 were examined for rhinovirus/enterovirus (RhV/EV) by the FilmArray...

    Victoria L. Gilrane, Jian Zhuge, Weihua Huang, Sheila M. Nolan, Abhay Dhand, Changhong Yin, Christian Salib, Faariah Shakil, Helen Engel, John T. Fallon, Guiqing Wang

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