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Journal of Clinical Microbiology
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DNA sequencing

  • Nanopore Sequencing of the Fungal Intergenic Spacer Sequence as a Potential Rapid Diagnostic Assay
    Mycology
    Nanopore Sequencing of the Fungal Intergenic Spacer Sequence as a Potential Rapid Diagnostic Assay

    Fungal infections are being caused by a broadening spectrum of fungi, yet in many cases, identification to the species level is required for proper antifungal selection. We investigated the fungal intergenic spacer (IGS) sequence in combination with nanopore sequencing for fungal identification. We sequenced isolates from two Cryptococcus species complexes, C....

    Gretchen A. Morrison, Jianmin Fu, Grace C. Lee, Nathan P. Wiederhold, Connie F. Cañete-Gibas, Evelien M. Bunnik, Brian L. Wickes
  • Open Access
    DNA Thermo-Protection Facilitates Whole-Genome Sequencing of Mycobacteria Direct from Clinical Samples
    Mycobacteriology and Aerobic Actinomycetes
    DNA Thermo-Protection Facilitates Whole-Genome Sequencing of Mycobacteria Direct from Clinical Samples

    Mycobacterium tuberculosis is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole-genome sequencing, are required. Our aim was to develop a simple, low-cost method of preparing DNA for sequencing direct from M....

    Sophie George, Yifei Xu, Gillian Rodger, Marcus Morgan, Nicholas D. Sanderson, Sarah J. Hoosdally, Samantha Thulborn, Esther Robinson, Priti Rathod, A. Sarah Walker, Timothy E. A. Peto, Derrick W. Crook, Kate E. Dingle
  • Whole-Genome Sequencing of <span class="named-content genus-species" id="named-content-1">Corynebacterium diphtheriae</span> Isolates Recovered from an Inner-City Population Demonstrates the Predominance of a Single Molecular Strain
    Epidemiology
    Whole-Genome Sequencing of Corynebacterium diphtheriae Isolates Recovered from an Inner-City Population Demonstrates the Predominance of a Single Molecular Strain

    In some parts of the world, Corynebacterium diphtheriae has reemerged as a pathogen, especially as a cause of infections among impoverished and marginalized populations. We performed whole-genome sequencing (WGS) on all cutaneous C. diphtheriae isolates (n = 56) from Vancouver’s inner-city...

    Samuel D. Chorlton, Gordon Ritchie, Tanya Lawson, Marc G. Romney, Christopher F. Lowe
  • Open Access
    Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples
    Virology
    Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples

    Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential for a diagnostic test for influenza virus which also provides insights on transmission, evolution, and drug resistance and simultaneously detects other viruses. We therefore set out to apply the Oxford Nanopore Technologies sequencing method to...

    Kuiama Lewandowski, Yifei Xu, Steven T. Pullan, Sheila F. Lumley, Dona Foster, Nicholas Sanderson, Alison Vaughan, Marcus Morgan, Nicole Bright, James Kavanagh, Richard Vipond, Miles Carroll, Anthony C. Marriott, Karen E. Gooch, Monique Andersson, Katie Jeffery, Timothy E. A. Peto, Derrick W. Crook, A. Sarah Walker, Philippa C. Matthews
  • Utility of DNA Next-Generation Sequencing and Expanded Quantitative Urine Culture in Diagnosis and Management of Chronic or Persistent Lower Urinary Tract Symptoms
    Minireview
    Utility of DNA Next-Generation Sequencing and Expanded Quantitative Urine Culture in Diagnosis and Management of Chronic or Persistent Lower Urinary Tract Symptoms

    Many patients suffer from chronic, irritative lower urinary tract symptoms (LUTS). The evaluation and management of these patients have proven difficult with the use of standard diagnostic tools, including urinalysis and urine culture. The growing body of literature on the urinary microbiome has looked at the possible implications of the bladder microbiome and dysbiosis, or perturbations in the microbiome, in conditions associated with...

    Monika Gasiorek, Michael H. Hsieh, Catherine S. Forster
  • Open Access
    Metagenomic Next-Generation Sequencing for Identification and Quantitation of Transplant-Related DNA Viruses
    Virology
    Metagenomic Next-Generation Sequencing for Identification and Quantitation of Transplant-Related DNA Viruses

    Infections with DNA viruses are frequent causes of morbidity and mortality in transplant recipients.

    Meredith L. Carpenter, Susanna K. Tan, Thomas Watson, Rowena Bacher, Vaishnavi Nagesh, Alain Watts, Gordon Bentley, Jenna Weber, ChunHong Huang, Malaya K. Sahoo, Armin Hinterwirth, Thuy Doan, Theodore Carter, Queeny Dong, Stéphane Gourguechon, Eric Harness, Sean Kermes, Srihari Radhakrishnan, Gongbo Wang, Alejandro Quiroz-Zárate, Jesus Ching, Benjamin A. Pinsky
  • Improved Species-Level Clinical Identification of <span class="named-content genus-species" id="named-content-1">Enterobacteriaceae</span> through Broad-Range <em>dnaJ</em> PCR and Sequencing
    Bacteriology
    Improved Species-Level Clinical Identification of Enterobacteriaceae through Broad-Range dnaJ PCR and Sequencing

    Enterobacteriaceae represent a diverse and medically important family of bacteria that are difficult to identify to the species level using the standard molecular method of 16S rRNA gene sequencing. Prior work has demonstrated the value of dnaJ gene sequence analysis in resolving different members of the family. However, existing protocols are not optimized...

    Kathryn McLean, Christopher A. Rosenthal, Dhruba Sengupta, Jennifer Owens, Brad T. Cookson, Noah G. Hoffman, Stephen J. Salipante
  • <span class="named-content genus-species" id="named-content-1">Helicobacter pylori</span> Mutations Detected by Next-Generation Sequencing in Formalin-Fixed, Paraffin-Embedded Gastric Biopsy Specimens Are Associated with Treatment Failure
    Bacteriology
    Helicobacter pylori Mutations Detected by Next-Generation Sequencing in Formalin-Fixed, Paraffin-Embedded Gastric Biopsy Specimens Are Associated with Treatment Failure

    Helicobacter pylori antibiotic resistance is widespread and increasing worldwide. Routine detection of H. pylori mutations that invoke antimicrobial resistance may be a useful approach to guide antimicrobial therapy and possibly avert treatment failure.

    Behtash G. Nezami, Mehul Jani, David Alouani, Daniel D. Rhoads, Navid Sadri
  • Open Access
    Bacteriology
    Accurate and Rapid Differentiation of Acinetobacter baumannii Strains by Raman Spectroscopy: a Comparative Study
    Meron Ghebremedhin, Rae Heitkamp, Shubha Yesupriya, Bradford Clay, Nicole J. Crane
  • Bacteriology
    Bifidobacterium Bacteremia: Clinical Characteristics and a Genomic Approach To Assess Pathogenicity
    Eirin Esaiassen, Erik Hjerde, Jorunn Pauline Cavanagh, Gunnar Skov Simonsen, Claus Klingenberg
    and Norwegian Study Group on Invasive Bifidobacterial Infections

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