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Journal of Clinical Microbiology
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stool

  • Open Access
    Evaluation of Molecular Serotyping Assays for <span class="named-content genus-species" id="named-content-1">Shigella flexneri</span> Directly on Stool Samples
    Bacteriology
    Evaluation of Molecular Serotyping Assays for Shigella flexneri Directly on Stool Samples

    Shigella flexneri is prevalent worldwide and is the most common Shigella species in many countries. At least 19 S. flexneri serotypes exist, and serotype information is important for epidemiologic and vaccine development purposes.

    Jie Liu, Suporn Pholwat, Jixian Zhang, Mami Taniuchi, Rashidul Haque, Masud Alam, John Benjamin Ochieng, Jennifer A. Jones, James A. Platts-Mills, Sharon M. Tennant, Eric Houpt
  • Open Access
    Rapid and Sensitive Direct Detection and Identification of Poliovirus from Stool and Environmental Surveillance Samples by Use of Nanopore Sequencing
    Virology
    Rapid and Sensitive Direct Detection and Identification of Poliovirus from Stool and Environmental Surveillance Samples by Use of Nanopore Sequencing

    Global poliovirus surveillance involves virus isolation from stool and environmental samples, intratypic differential (ITD) by PCR, and sequencing of the VP1 region to distinguish vaccine (Sabin), vaccine-derived, and wild-type polioviruses and to ensure an appropriate response. This cell culture algorithm takes 2 to 3 weeks on average between sample receipt and sequencing. Direct detection of viral RNA using PCR allows faster detection...

    Alexander G. Shaw, Manasi Majumdar, Catherine Troman, Áine O’Toole, Blossom Benny, Dilip Abraham, Ira Praharaj, Gagandeep Kang, Salmaan Sharif, Muhammad Masroor Alam, Shahzad Shaukat, Mehar Angez, Adnan Khurshid, Nayab Mahmood, Yasir Arshad, Lubna Rehman, Ghulam Mujtaba, Ribqa Akthar, Muhammad Salman, Dimitra Klapsa, Yara Hajarha, Humayun Asghar, Ananda Bandyopadhyay, Andrew Rambaut, Javier Martin, Nicholas Grassly
  • Open Access
    Assessing the Use of PCR To Screen for Shedding of <span class="named-content genus-species" id="named-content-1">Salmonella enterica</span> in Infected Humans
    Bacteriology
    Assessing the Use of PCR To Screen for Shedding of Salmonella enterica in Infected Humans

    Recovery from enteric bacterial illness often includes a phase of organismal shedding over a period of days to months. The monitoring of this process through laboratory testing forms the foundation of public health action to prevent further transmission. Regulations in most jurisdictions in the United States exclude individuals who continue to shed certain organisms from sensitive occupations and situations, such as food handling,...

    Tyler Lloyd, Monica Bender, Sandra Huang, Robert Brown, Rita Shiau, Emily Yette, Munira Shemsu, Mark Pandori
  • Diagnostic Accuracy of a Noninvasive Test for Detection of <span class="named-content genus-species" id="named-content-1">Helicobacter pylori</span> and Resistance to Clarithromycin in Stool by the Amplidiag <span class="named-content genus-species" id="named-content-2">H. pylori</span>+ClariR Real-Time PCR Assay
    Bacteriology
    Diagnostic Accuracy of a Noninvasive Test for Detection of Helicobacter pylori and Resistance to Clarithromycin in Stool by the Amplidiag H. pylori+ClariR Real-Time PCR Assay

    The noninvasive detection of Helicobacter pylori and its resistance to clarithromycin could revolutionize the management of H. pylori-infected patients by tailoring eradication treatment without any need for endoscopy when histology is not necessary. Several real-time PCR tests performed on stools...

    Maxime Pichon, Benoit Pichard, Thierry Barrioz, Chloé Plouzeau, Vincent Croquet, Ginette Fotsing, Alexandre Chéron, Éric Vuillemin, Marc Wangermez, Paul-Arthur Haineaux, Philippe Vasseur, Quentin Thiebault, Clémence Lefèvre, Anaïs de Singly, Julie Cremniter, Lauranne Broutin, Anthony Michaud, Christine Silvain, Christophe Burucoa
  • Whole-Genome Single-Nucleotide Polymorphism (SNP) Analysis Applied Directly to Stool for Genotyping Shiga Toxin-Producing <span class="named-content genus-species" id="named-content-1">Escherichia coli</span>: an Advanced Molecular Detection Method for Foodborne Disease Surveillance and Outbreak Tracking
    Bacteriology
    Whole-Genome Single-Nucleotide Polymorphism (SNP) Analysis Applied Directly to Stool for Genotyping Shiga Toxin-Producing Escherichia coli: an Advanced Molecular Detection Method for Foodborne Disease Surveillance and Outbreak Tracking

    Whole-genome sequencing (WGS) of pathogens from pure culture provides unparalleled accuracy and comprehensive results at a cost that is advantageous compared with traditional diagnostic methods. Sequencing pathogens directly from a primary clinical specimen would help circumvent the need for culture and, in the process, substantially shorten the time to diagnosis and public health reporting.

    Navjot Singh, Pascal Lapierre, Tammy M. Quinlan, Tanya A. Halse, Samantha Wirth, Michelle C. Dickinson, Erica Lasek-Nesselquist, Kimberlee A. Musser
  • Open Access
    Diagnostic Accuracy of Stool Xpert MTB/RIF for Detection of Pulmonary Tuberculosis in Children: a Systematic Review and Meta-analysis
    Epidemiology
    Diagnostic Accuracy of Stool Xpert MTB/RIF for Detection of Pulmonary Tuberculosis in Children: a Systematic Review and Meta-analysis

    Invasive collection methods are often required to obtain samples for the microbiological evaluation of children with presumptive pulmonary tuberculosis (PTB). Nucleic acid amplification testing of easier-to-collect stool samples could be a noninvasive method of diagnosing PTB.

    Emily MacLean, Giorgia Sulis, Claudia M. Denkinger, James C. Johnston, Madhukar Pai, Faiz Ahmad Khan
  • Comparison of Loop-Mediated Isothermal Amplification and Real-Time PCR Assays for Detection of <span class="named-content genus-species" id="named-content-1">Strongyloides</span> Larvae in Different Specimen Matrices
    Parasitology
    Comparison of Loop-Mediated Isothermal Amplification and Real-Time PCR Assays for Detection of Strongyloides Larvae in Different Specimen Matrices

    Strongyloides stercoralis can cause disease that ranges from asymptomatic chronic infection to fatal hyperinfection. Diagnosis from stool can be challenging because the most sensitive conventional tests require live larvae to be effective and there can be low larval output in chronic infection.

    Matthew R. Watts, Rady Kim, Vishal Ahuja, Gemma J. Robertson, Yasmin Sultana, Michael C. Wehrhahn, Richard S. Bradbury, Gwendolyn L. Gilbert, Rogan Lee
  • Open Access
    Mycobacteriology and Aerobic Actinomycetes
    Molecular Detection of Mycobacterium tuberculosis from Stools in Young Children by Use of a Novel Centrifugation-Free Processing Method
    Elisabetta Walters, Lesley Scott, Pamela Nabeta, Anne-Marie Demers, Gary Reubenson, Corné Bosch, Anura David, Marieke van der Zalm, Joshua Havumaki, Megan Palmer, Anneke C. Hesseling, Jabulani Ncayiyana, Wendy Stevens, David Alland, Claudia Denkinger, Padmapriya Banada
  • Bacteriology
    A Novel Stool PCR Test for Helicobacter pylori May Predict Clarithromycin Resistance and Eradication of Infection at a High Rate
    Erin Beckman, Ilaria Saracino, Giulia Fiorini, Courtney Clark, Vladimir Slepnev, Denise Patel, Clarissa Gomez, Reddy Ponaka, Vecheslav Elagin, Dino Vaira
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