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Table of Contents

July 2020; Volume 58,Issue 7

Photo Quiz

  • Photo Quiz: Migrating Worm Naturally Exited through the Palate
    Photo Quiz
    Photo Quiz: Migrating Worm Naturally Exited through the Palate
    Kévin Brunet, Mélanie Catroux, Hélène Yera, Sophie Pasini, Marie-Hélène Rodier, Estelle Cateau
  • Answer to July 2020 Photo Quiz
    Photo Quiz
    Answer to July 2020 Photo Quiz
    Kévin Brunet, Mélanie Catroux, Hélène Yera, Sophie Pasini, Marie-Hélène Rodier, Estelle Cateau

The Brief Case

  • Free
    The Brief Case: Nystagmus in a 3-Month-Old Leading to a Diagnosis of Congenital Cytomegalovirus Infection
    The Brief Case
    The Brief Case: Nystagmus in a 3-Month-Old Leading to a Diagnosis of Congenital Cytomegalovirus Infection
    Priyanka Uprety, Erin H. Graf
  • Free
    Closing the Brief Case: Nystagmus in a 3-Month-Old Leading to a Diagnosis of Congenital Cytomegalovirus Infection
    The Brief Case
    Closing the Brief Case: Nystagmus in a 3-Month-Old Leading to a Diagnosis of Congenital Cytomegalovirus Infection
    Priyanka Uprety, Erin H. Graf

Minireviews

  • Sterility Testing for Cellular Therapies: What Is the Role of the Clinical Microbiology Laboratory?
    Minireview
    Sterility Testing for Cellular Therapies: What Is the Role of the Clinical Microbiology Laboratory?

    Sterility testing of cellular therapy products along with the associated environmental monitoring requirements for aseptic facilities, including compounding pharmacies, continues to impact clinical microbiology laboratories, as evidenced by the numerous discussions recurring on American Society for Microbiology Division C and ClinMicroNet listservs. This minireview provides an overview of this complex field of current good manufacturing...

    James E. T. Gebo, Anna F. Lau
  • Utility of Procalcitonin as a Biomarker for Sepsis in Children
    Minireview
    Utility of Procalcitonin as a Biomarker for Sepsis in Children

    Sepsis is a complex process defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. It is associated with significant morbidity and mortality rates in both adults and children, and emphasis has been placed on its early recognition and prompt provision of antimicrobials. Owing to limitations of current diagnostic tests (i.e., poor sensitivity and delayed results), significant research has been...

    Kevin J. Downes, Julie C. Fitzgerald, Scott L. Weiss

Bacteriology

  • Open Access
    Multicenter Evaluation of the BioFire FilmArray Pneumonia/Pneumonia Plus Panel for Detection and Quantification of Agents of Lower Respiratory Tract Infection
    Bacteriology
    Multicenter Evaluation of the BioFire FilmArray Pneumonia/Pneumonia Plus Panel for Detection and Quantification of Agents of Lower Respiratory Tract Infection

    The ability to provide timely identification of the causative agents of lower respiratory tract infections can promote better patient outcomes and support antimicrobial stewardship efforts. Current diagnostic testing options include culture, molecular testing, and antigen detection. These methods may require collection of various specimens, involve extensive sample treatment, and can suffer from low sensitivity and long turnaround times...

    Caitlin N. Murphy, Randal Fowler, Joan Miquel Balada-Llasat, Amanda Carroll, Hanna Stone, Oluseun Akerele, Blake Buchan, Sam Windham, Amanda Hopp, Shira Ronen, Ryan F. Relich, Rebecca Buckner, Del A. Warren, Romney Humphries, Shelly Campeau, Holly Huse, Suki Chandrasekaran, Amy Leber, Kathy Everhart, Amanda Harrington, Christina Kwong, Andrew Bonwit, Jennifer Dien Bard, Samia Naccache, Cynthia Zimmerman, Barbara Jones, Cory Rindlisbacher, Maggie Buccambuso, Angela Clark, Margarita Rogatcheva, Corrin Graue, Kevin M. Bourzac
  • Open Access
    Practical Comparison of the BioFire FilmArray Pneumonia Panel to Routine Diagnostic Methods and Potential Impact on Antimicrobial Stewardship in Adult Hospitalized Patients with Lower Respiratory Tract Infections
    Bacteriology
    Practical Comparison of the BioFire FilmArray Pneumonia Panel to Routine Diagnostic Methods and Potential Impact on Antimicrobial Stewardship in Adult Hospitalized Patients with Lower Respiratory Tract Infections

    Lower respiratory tract infections, including hospital-acquired and ventilator-associated pneumonia, are common in hospitalized patient populations. Standard methods frequently fail to identify the infectious etiology due to the polymicrobial nature of respiratory specimens and the necessity of ordering specific tests to identify viral agents. The potential severity of these infections combined with a failure to clearly identify the...

    Blake W. Buchan, Sam Windham, Joan-Miquel Balada-Llasat, Amy Leber, Amanda Harrington, Ryan Relich, Caitlin Murphy, Jennifer Dien Bard, Samia Naccache, Shira Ronen, Amanda Hopp, Derya Mahmutoglu, Matthew L. Faron, Nathan A. Ledeboer, Amanda Carroll, Hannah Stone, Oluseun Akerele, Kathy Everhart, Andrew Bonwit, Christina Kwong, Rebecca Buckner, Del Warren, Randal Fowler, Sukantha Chandrasekaran, Holly Huse, Shelley Campeau, Romney Humphries, Corrin Graue, Angela Huang
  • Open Access
    Characteristics of <span class="named-content genus-species" id="named-content-1">Mycoplasma genitalium</span> Urogenital Infections in a Diverse Patient Sample from the United States: Results from the Aptima <span class="named-content genus-species" id="named-content-2">Mycoplasma genitalium</span> Evaluation Study (AMES)
    Bacteriology
    Characteristics of Mycoplasma genitalium Urogenital Infections in a Diverse Patient Sample from the United States: Results from the Aptima Mycoplasma genitalium Evaluation Study (AMES)

    Data from a large prospective multicenter clinical validation study of a nucleic acid amplification in vitro diagnostic test for Mycoplasma genitalium were analyzed to describe the prevalence of M. genitalium infection, risk factors, and disease associations in female and male patients...

    Lisa E. Manhart, Charlotte A. Gaydos, Stephanie N. Taylor, Rebecca A. Lillis, Edward W. Hook, Jeffrey D. Klausner, Carmelle V. Remillard, Melissa Love, Byron McKinney, Damon K. Getman
    and on behalf of the AMES Clinical Study Group
  • 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
  • Evaluation of the BioFire FilmArray Pneumonia Panel for Detection of Viral and Bacterial Pathogens in Lower Respiratory Tract Specimens in the Setting of a Tertiary Care Academic Medical Center
    Bacteriology
    Evaluation of the BioFire FilmArray Pneumonia Panel for Detection of Viral and Bacterial Pathogens in Lower Respiratory Tract Specimens in the Setting of a Tertiary Care Academic Medical Center

    Our objective was to evaluate the diagnostic yield and accuracy of the BioFire FilmArray pneumonia panel (BFPP) for identification of pathogens in lower respiratory tract specimens (n = 200) from emergency department (ED) and intensive care unit (ICU) patients at a tertiary care academic medical center. Specimens were collected between January and November 2018, from patients ≥18 years of age, and culture was performed as part...

    Daniel M. Webber, Meghan A. Wallace, Carey-Ann D. Burnham, Neil W. Anderson
  • Evaluation of NG-Test Carba 5 for Rapid Phenotypic Detection and Differentiation of Five Common Carbapenemase Families: Results of a Multicenter Clinical Evaluation
    Bacteriology
    Evaluation of NG-Test Carba 5 for Rapid Phenotypic Detection and Differentiation of Five Common Carbapenemase Families: Results of a Multicenter Clinical Evaluation

    NG-Test Carba 5 is a rapid in vitro multiplex immunoassay for the phenotypic detection and differentiation of five common carbapenemase families (KPC, OXA-48-like, VIM, IMP, and NDM) directly from bacterial colonies. The assay is simple to perform and has recently received U.S. Food and Drug Administration clearance. A method comparison study was performed at geographically diverse medical centers (n = 3) in the United...

    Stephen Jenkins, Nathan A. Ledeboer, Lars F. Westblade, Carey-Ann D. Burnham, Matthew L. Faron, Yehudit Bergman, Rebecca Yee, Brian Mesich, Derek Gerstbrein, Meghan A. Wallace, Amy Robertson, Kathy A. Fauntleroy, Anna S. Klavins, Rianna Malherbe, Andre Hsiung, Patricia J. Simner
  • Assessment of the Clinical Utility of Plasma Metagenomic Next-Generation Sequencing in a Pediatric Hospital Population
    Bacteriology
    Assessment of the Clinical Utility of Plasma Metagenomic Next-Generation Sequencing in a Pediatric Hospital Population

    Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA (cfDNA) is commercially available, but its role in the workup of infectious diseases is unclear. To understand the clinical utility of plasma mNGS, we retrospectively reviewed patients tested at a pediatric institution over 2 years to evaluate the clinical relevance of the organism(s) identified and the impact on antimicrobial management. We also investigated the...

    Rose A. Lee, Fatima Al Dhaheri, Nira R. Pollock, Tanvi S. Sharma
  • Open Access
    Multicenter Clinical Evaluation of the Revogene Strep A Molecular Assay for Detection of <span class="named-content genus-species" id="named-content-1">Streptococcus pyogenes</span> from Throat Swab Specimens
    Bacteriology
    Multicenter Clinical Evaluation of the Revogene Strep A Molecular Assay for Detection of Streptococcus pyogenes from Throat Swab Specimens

    Group A streptococcus (GAS) species cause bacterial pharyngitis in both adults and children. Early and accurate diagnosis of GAS is important for appropriate antibiotic therapy to prevent GAS sequalae. The Revogene Strep A molecular assay (Meridian Bioscience Canada Inc, Quebec City, QC, Canada) is an automated real-time PCR assay for GAS detection from throat swab specimens within approximately 70 min. This multicenter prospective...

    D. Banerjee, J. Michael, B. Schmitt, H. Salimnia, N. Mhaissen, D. M. Goldfarb, P. Lachance, M. L. Faron, T. Aufderheide, N. Ledeboer, A. Weissfeld, R. Selvarangan
  • Adapting Microarray Gene Expression Signatures for Early Melioidosis Diagnosis
    Bacteriology
    Adapting Microarray Gene Expression Signatures for Early Melioidosis Diagnosis

    Melioidosis is caused by Burkholderia pseudomallei and is predominantly seen in tropical regions. The clinical signs and symptoms of the disease are nonspecific and often result in misdiagnosis, failure of treatment, and poor clinical outcome. Septicemia with septic shock is the most common cause of death, with mortality rates above 40%. Bacterial culture is the gold...

    Ornuma Sangwichian, Toni Whistler, Arnone Nithichanon, Chidchamai Kewcharoenwong, Myint Myint Sein, Chawitar Arayanuphum, Narisara Chantratita, Ganjana Lertmemongkolchai

Mycobacteriology and Aerobic Actinomycetes

  • Genomic Analysis of <span class="named-content genus-species" id="named-content-1">Mycobacterium abscessus</span> Complex Isolates Collected in Ireland between 2006 and 2017
    Mycobacteriology and Aerobic Actinomycetes
    Genomic Analysis of Mycobacterium abscessus Complex Isolates Collected in Ireland between 2006 and 2017

    Members of the Mycobacterium abscessus complex (MABC) are multidrug-resistant nontuberculous mycobacteria and cause opportunistic pulmonary infections in individuals with cystic fibrosis (CF). In this study, genomic analysis of MABC isolates was performed to gain greater insights into the epidemiology of circulating strains in Ireland. Whole-genome sequencing (WGS)...

    Natalia Redondo, Simone Mok, Lorraine Montgomery, Peter R. Flanagan, Eleanor McNamara, Edmond G. Smyth, Niamh O'Sullivan, Kirsten Schaffer, Thomas R. Rogers, Margaret M. Fitzgibbon
  • Open Access
    Long Noncoding RNA and Predictive Model To Improve Diagnosis of Clinically Diagnosed Pulmonary Tuberculosis
    Mycobacteriology and Aerobic Actinomycetes
    Long Noncoding RNA and Predictive Model To Improve Diagnosis of Clinically Diagnosed Pulmonary Tuberculosis

    Clinically diagnosed pulmonary tuberculosis (PTB) patients lack microbiological evidence of Mycobacterium tuberculosis, and misdiagnosis or delayed diagnosis often occurs as a consequence. We investigated the potential of long noncoding RNAs (lncRNAs) and corresponding predictive models to diagnose these patients. We enrolled 1,764 subjects, including clinically...

    Xuejiao Hu, Shun Liao, Hao Bai, Shubham Gupta, Yi Zhou, Juan Zhou, Lin Jiao, Lijuan Wu, Minjin Wang, Xuerong Chen, Yanhong Zhou, Xiaojun Lu, Tony Y. Hu, Zhaolei Zhang, Binwu Ying

Mycology

  • Human Infections Caused by Clonally Related African Clade (Clade III) Strains of <span class="named-content genus-species" id="named-content-1">Candida auris</span> in the Greater Houston Region
    Mycology
    Human Infections Caused by Clonally Related African Clade (Clade III) Strains of Candida auris in the Greater Houston Region

    Candida auris is a pathogen of considerable public health importance. It was first reported in 2009. Five clades, determined by genomic analysis and named by the distinct regions where they were initially identified, have been defined. We previously completed a draft genome sequence of an African clade (clade III) strain cultured from the urine of a patient...

    S. Wesley Long, Matthew Ojeda Saavedra, Paul A. Christensen, James M. Musser, Randall J. Olsen

Immunoassays

  • Chimeric Protein Designed by Genome-Scale Immunoinformatics Enhances Serodiagnosis of Bovine Neosporosis
    Immunoassays
    Chimeric Protein Designed by Genome-Scale Immunoinformatics Enhances Serodiagnosis of Bovine Neosporosis

    Neosporosis has become a concern since it is associated with abortion in cattle. Currently, in situ diagnosis is determined through anamnesis, evaluation of the history, and perception of the clinical signs of the herd. There is no practical and noninvasive test adapted to a large number of samples, which represents a gap for the use of new approaches that provide information about infections and the risks of herds. Here, we...

    Higor Sette Pereira, Ludmila Tavares e Almeida, Vitória Fernandes, Renato Lima Senra, Patrícia Pereira Fontes, Eustáquio Resende Bittar, Andréa de Oliveira Barros Ribon, Polyana Pizzi Rotta, Daniel Menezes-Souza, Joely Ferreira Figueiredo Bittar, Tiago Antônio de Oliveira Mendes
  • Performance of a Modified Two-Tiered Testing Enzyme Immunoassay Algorithm for Serologic Diagnosis of Lyme Disease in Nova Scotia
    Immunoassays
    Performance of a Modified Two-Tiered Testing Enzyme Immunoassay Algorithm for Serologic Diagnosis of Lyme Disease in Nova Scotia

    Compared to the standard two-tiered testing (STTT) algorithm for Lyme disease serology using an enzyme immunoassay (EIA) followed by Western blotting, data from the United States suggest that a modified two-tiered testing (MTTT) algorithm employing two EIAs has improved sensitivity to detect early localized Borrelia burgdorferi infections without compromising...

    Ian R. C. Davis, Shelly A. McNeil, Wanda Allen, Donna MacKinnon-Cameron, L. Robbin Lindsay, Katarina Bernat, Antonia Dibernardo, Jason J. LeBlanc, Todd F. Hatchette

Clinical Veterinary Microbiology

  • Resolution of <span class="named-content genus-species" id="named-content-1">Streptococcus suis</span> Serotypes 1/2 versus 2 and 1 versus 14 by PCR-Restriction Fragment Length Polymorphism Method
    Clinical Veterinary Microbiology
    Resolution of Streptococcus suis Serotypes 1/2 versus 2 and 1 versus 14 by PCR-Restriction Fragment Length Polymorphism Method

    Streptococcus suis is an important pathogen of pigs but is also transmissible to humans, with potentially fatal consequences. Among 29 serotypes currently recognized, some are clinically and epidemiologically more important than others. This is particularly true for serotypes 2 and 14, which have a large impact on pig production and also on human health. Conventional...

    Jan Matiasovic, Monika Zouharova, Katerina Nedbalcova, Natalie Kralova, Katarina Matiaskova, Bronislav Simek, Ivana Kucharovicova, Marcelo Gottschalk

Epidemiology

  • Open Access
    Species Identification and Antibiotic Resistance Prediction by Analysis of Whole-Genome Sequence Data by Use of ARESdb: an Analysis of Isolates from the Unyvero Lower Respiratory Tract Infection Trial
    Epidemiology
    Species Identification and Antibiotic Resistance Prediction by Analysis of Whole-Genome Sequence Data by Use of ARESdb: an Analysis of Isolates from the Unyvero Lower Respiratory Tract Infection Trial

    Whole-genome sequencing (WGS) is now routinely performed in clinical microbiology laboratories to assess isolate relatedness. With appropriately developed analytics, the same data can be used for prediction of antimicrobial susceptibility. We assessed WGS data for identification using open-source tools and antibiotic susceptibility testing (AST) prediction using ARESdb compared to matrix-assisted laser desorption ionization-time of...

    Ines Ferreira, Stephan Beisken, Lukas Lueftinger, Thomas Weinmaier, Matthias Klein, Johannes Bacher, Robin Patel, Arndt von Haeseler, Andreas E. Posch

Author Corrections

  • Free
    Correction for Mathison and Pritt, “Medical Parasitology Taxonomy Update, 2016–2017”
    Author Correction
    Correction for Mathison and Pritt, “Medical Parasitology Taxonomy Update, 2016–2017”
    Blaine A. Mathison, Bobbi S. Pritt
  • Free
    Correction for Han et al., “<em>In Vitro</em> Susceptibility of Hepatitis C Virus Genotype 1 through 6 Clinical Isolates to the Pangenotypic NS3/4A Inhibitor Voxilaprevir”
    Author Correction
    Correction for Han et al., “In Vitro Susceptibility of Hepatitis C Virus Genotype 1 through 6 Clinical Isolates to the Pangenotypic NS3/4A Inhibitor Voxilaprevir”
    Bin Han, Bandita Parhy, Julia Lu, Eric Zhou, David Hsieh, Gregory Camus, Ross Martin, Evguenia S. Svarovskaia, Hongmei Mo, Hadas Dvory-Sobol

Masthead

  • Free
    Editorial Board
    Masthead
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Journal of Clinical Microbiology: 58 (7)

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volume 58, issue 7
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  • When To Retest: an Examination of Repeat COVID-19 PCR Patterns in an Ambulatory Population
  • Laboratory Diagnosis of COVID-19: Current Issues and Challenges
  • 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
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