Table of Contents
Photo Quiz
Photo QuizAnswer to March 2020 Photo Quiz
Editorial
The Brief Case
Biographical Feature
Point-Counterpoint
Point-CounterpointPoint-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?With established applications of next-generation sequencing in inherited diseases and oncology, clinical laboratories are evaluating the use of metagenomics for identification of infectious agents directly from patient samples, to aid in the diagnosis of infections. Metagenomic next-generation sequencing for infectious diseases promises an unbiased approach to detection of microbes that does not depend on growth in culture or the...
Bacteriology
BacteriologyComparison of Three Commercial Tools for Metagenomic Shotgun Sequencing AnalysisMetagenomic shotgun sequencing for the identification of pathogens is being increasingly utilized as a diagnostic method. Interpretation of large and complicated data sets is a significant challenge, for which multiple commercial tools have been developed. Three commercial metagenomic shotgun sequencing tools, CosmosID, One Codex, and IDbyDNA, were compared to determine whether they result in similar interpretations of the same...
BacteriologyMethod Comparison of the ImmuView L. pneumophila and L. longbeachae Urinary Antigen Test with the BinaxNOW Legionella Urinary Antigen Card for Detection of Legionella pneumophila Serogroup 1 Antigen in UrineWe compared the clinical performance of the ImmuView L. pneumophila and L. longbeachae urinary antigen test (SSI Diagnostica A/S, Hillerød, Denmark) to that of the BinaxNOW Legionella urinary antigen card (Binax; Abbott, Lake Buff, IL) using urine specimens from patients suspected of having pneumonia. In total, 100 frozen urine samples (derived from...
BacteriologyPhenotypic Detection of Plasmid-Mediated Colistin Resistance in EnterobacteriaceaeThe aim of this work was to evaluate an easy-to-perform assay based upon inhibition of mobile colistin resistance (MCR) activity by EDTA. We included 92 nonrelated isolates of Enterobacteriaceae (74 Escherichia coli, 17 Klebsiella pneumoniae, and 1...
BacteriologyHelicobacter pylori Infections in the Bronx, New York: Surveying Antibiotic Susceptibility and Strain Lineage by Whole-Genome SequencingThe emergence of drug resistance in Helicobacter pylori has resulted in a greater need for susceptibility-guided treatment. While the alleles associated with resistance to clarithromycin and levofloxacin have been defined, there are limited data regarding the molecular mechanisms underlying resistance to other antimicrobials. Using...
BacteriologyCerebrospinal Fluid Findings Are Poor Predictors of Appropriate FilmArray Meningitis/Encephalitis Panel Utilization in Pediatric PatientsMolecular testing of cerebrospinal fluid (CSF) using the BioFire FilmArray meningitis/encephalitis (FA-M/E) panel permits rapid, simultaneous pathogen detection. Due to the broad spectrum of targeted organisms, FA-M/E testing may be restricted to patients with abnormal CSF findings. We sought to determine if restriction is appropriate in our previously healthy and/or immunocompromised pediatric patients.
BacteriologyValidation of a New Rapid Detection Test for Detection of Neisseria meningitidis A/C/W/X/Y Antigens in Cerebrospinal FluidMeningococcal meningitis remains a life-threatening disease worldwide, with high prevalence in the sub-Saharan meningitis belt. A rapid diagnosis is crucial for implementing adapted antimicrobial treatment. We describe the performances of a new immunochromatographic test (MeningoSpeed, BioSpeedia, France) for detecting and grouping Neisseria meningitidis....
BacteriologyPerformance of the QIAstat-Dx Gastrointestinal Panel for Diagnosing Infectious GastroenteritisDetection and identification of enteropathogens that cause infectious gastroenteritis are essential steps for appropriate patient treatment and effective isolation precautions. Several syndrome-based tests have recently become available, with the gastrointestinal panel (GIP) assay on the QIAstat-Dx as the most recent addition to the syndromic testing landscape.
BacteriologyOptimizing DNA Extraction Methods for Nanopore Sequencing of Neisseria gonorrhoeae Directly from Urine SamplesEmpirical gonorrhea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnostics to select an effective treatment. There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance. We investigated if Nanopore sequencing can detect sufficient...
BacteriologyEvaluation of the ResistancePlus MG FleXible Assay for Detection of Wild-Type and 23S rRNA-Mutated Mycoplasma genitalium StrainsAntibiotic resistance in Mycoplasma genitalium is rising globally, and resistance-guided diagnostics can facilitate targeted and timely treatment. The ResistancePlus MG FleXible (RPMG Flex) assay for the detection of M. genitalium and macrolide resistance-mediating mutations (MRMM) was evaluated for...
Mycology
MycologyEvaluation of a Rapid Fungal Detection Panel for Identification of Candidemia at an Academic Medical CenterThis study was conducted to assess the utility of the T2Candida panel across an academic health center and identify potential areas for diagnostic optimization. A retrospective chart review was conducted on patients with a T2Candida panel and mycolytic/fungal (myco/f lytic) blood culture collected simultaneously during hospitalizations from February 2017 to March 2018.
MycologyHuman Blastomycosis in South Africa Caused by Blastomyces percursus and Blastomyces emzantsi sp. nov., 1967 to 2014We reevaluated 20 cases of blastomycosis diagnosed in South Africa between 1967 and 2014, with Blastomyces dermatitidis considered to be the etiological agent, in light of newly described species and the use of more advanced technologies. In addition to histopathological and/or culture-based methods, all 20 isolates were phenotypically and genotypically characterized...
Parasitology
ParasitologyEvaluation of a Novel High-Definition PCR Multiplex Assay for Simultaneous Detection of Tick-Borne Pathogens in Human Clinical SpecimensThe incidence of tick-borne infections in the United States has risen significantly in the past decade. Ticks can transmit a variety of pathogens, including bacteria, protozoa, and viruses, that can cause serious illnesses. Therefore, the use of rapid, sensitive, and specific multiplex tests is important to identify the pathogen(s) in the acute phase and determine appropriate treatment to minimize the severity of the disease.
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Virology
VirologyBayesian Evaluation of Solana HSV 1+2/VZV Assay Compared to Viral Culture and Commercial PCR Assay for Cutaneous or Mucocutaneous SpecimensResults from the Solana HSV 1+2/VZV assay for the detection of herpes simplex virus 1 (HSV-1), HSV-2, and varicella-zoster virus (VZV) in cutaneous or mucocutaneous specimens were compared with that of viral culture and a commercial PCR assay (RealStar alpha herpesvirus PCR kit).
VirologyComparison of the ID Now Influenza A & B 2, Cobas Influenza A/B, and Xpert Xpress Flu Point-of-Care Nucleic Acid Amplification Tests for Influenza A/B Virus Detection in ChildrenEarly diagnosis of influenza (Flu) is critical for patient management and infection control. The ID Now influenza A & B 2 (ID Now) assay (Abbott Laboratories), Cobas influenza A/B nucleic acid test (LIAT; Roche Molecular Systems, Inc.), and Xpert Xpress Flu (Xpert; Cepheid) are rapid, point-of-care molecular assays for Flu virus detection. The study aim was to compare the performances of these three commercially available Clinical...
Immunoassays
ImmunoassaysDiagnostic Value of Galactomannan in Bronchoalveolar Lavage Fluid for Chronic Respiratory Disease with Pulmonary AspergillosisThe objective of this study was to explore the diagnostic value of the bronchoalveolar lavage fluid galactomannan (BALF GM) test for chronic respiratory disease with pulmonary aspergillosis and to establish the optimal cutoff value. Samples from a total of 309 chronic respiratory disease patients seen at the respiratory medicine department of Peking University Shenzhen Hospital from September 2016 to September 2019 were analyzed.
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ImmunoassaysDevelopment and Evaluation of a Novel VHH-Based Immunocapture Assay for High-Sensitivity Detection of Shiga Toxin Type 2 (Stx2) in Stool SamplesShiga toxin (Stx)-producing Escherichia coli (STEC) is the main cause of postdiarrheal hemolytic-uremic syndrome (HUS), a life-threatening clinical complication characterized by hemolytic anemia, thrombocytopenia, and acute renal failure that mainly affects children. A relevant feature of STEC strains is the production of Stx, and all of them express Stx1 and/or Stx2...
Clinical Veterinary Microbiology
Clinical Veterinary MicrobiologySingle-Cell-Based Digital PCR Detection and Association of Shiga Toxin-Producing Escherichia coli Serogroups and Major Virulence GenesEscherichia coli serogroups O157, O26, O45, O103, O111, O121, and O145, when carrying major virulence genes, the Shiga toxin genes stx1 and stx2 and the intimin gene eae, are important foodborne pathogens. They are referred to as the “top 7” Shiga toxin-producing...
Epidemiology
EpidemiologyTest Accuracy of Human Papillomavirus in Urine for Detection of Cervical Intraepithelial NeoplasiaThe objective was to assess the diagnostic test accuracy of high-risk human papillomavirus (hrHPV) testing of self-collected urine and cervicovaginal samples for the detection of cervical intraepithelial neoplasia grade 2 or higher (CIN2+). We recruited a convenience sample of women 25 to 65 years of age who were undergoing clinically indicated colposcopy at two medical centers in North Carolina between November 2016 and January 2019....
EpidemiologyPredictors of Clostridioides difficile Infection-Related Complications and Treatment Patterns among Nucleic Acid Amplification Test-Positive/Toxin Enzyme Immunoassay-Negative PatientsThe addition of toxin enzyme immunoassay (EIA) to nucleic acid amplification tests, including PCR, creates challenges in the diagnosis and management of Clostridioides difficile infection (CDI). There are limited data in large cohorts, with discordant results, that is, PCR-positive/EIA-negative (PCR+/EIA−) results. We conducted a retrospective...
Letters to the Editor
Retraction
Masthead
Commentary
The Clinical and Laboratory Standards Institute (CLSI) Subcommittee on Antimicrobial Susceptibility Testing (AST SC) is a volunteer-led, multidisciplinary consensus body that develops and publishes standards and guidelines (among other products) for antimicrobial susceptibility testing (AST) methods and results interpretation in the United States and internationally. The Subcommittee (SC) meets face-to-face twice yearly, and its working...