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Minireviews
MinireviewUnstimulated Pleural Fluid Interferon Gamma for Diagnosis of Tuberculous Pleural Effusion: a Systematic Review and Meta-analysisUnstimulated interferon gamma may be a useful pleural fluid biomarker in the diagnosis of tuberculous pleural effusion (TPE). However, the exact threshold of pleural fluid interferon gamma and its accuracy during routine clinical decision-making is not clear.
MinireviewImmunologic Testing for SARS-CoV-2 Infection from the Antigen PerspectiveCoronavirus disease 2019 (COVID-19), caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread globally as a severe pandemic. SARS-CoV-2 infection stimulates antigen-specific antibody responses.
MinireviewPerformance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysisNasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity.
Bacteriology
BacteriologyReflex Detection of Ciprofloxacin Resistance in Neisseria gonorrhoeae by Use of the SpeeDx ResistancePlus GC AssayResistance-guided therapy (RGT) for gonorrhoea may reduce unnecessary use of broad-spectrum antibiotics. When reflexed from the Aptima Combo 2 assay, the ResistancePlus GC assay demonstrated 94.8% sensitivity and 100.0% specificity for Neisseria gonorrhoeae detection.
BacteriologyEvaluation of the Accelerate Pheno System for Rapid Identification and Antimicrobial Susceptibility Testing of Positive Blood Culture Bottles Inoculated with Primary Sterile Specimens from Patients with Suspected Severe Infections...The Accelerate Pheno system is approved for rapid identification and phenotypic antimicrobial susceptibility testing (AST) of microorganisms grown from positive blood cultures inoculated with blood from septic patients. We evaluated the performance of the system for identification and AST from positive blood culture bottles inoculated with primary sterile nonblood specimens from patients with suspected severe infections.
BacteriologyGenomic Surveillance and Improved Molecular Typing of Bordetella pertussis Using wgMLSTMultilocus sequence typing (MLST) provides allele-based characterization of bacterial pathogens in a standardized framework. However, classical MLST schemes for Bordetella pertussis, the causative agent of whooping cough, seldom reveal diversity among the small number of gene targets and thereby fail to delineate population structure.
BacteriologyClinical Evaluation of a Real-Time PCR Assay for Simultaneous Detection of Helicobacter pylori and Genotypic Markers of Clarithromycin Resistance Directly from StoolHelicobacter pylori infection is mainly diagnosed noninvasively, with susceptibility testing traditionally requiring endoscopy. Treatment is empirical, with clarithromycin-based triple therapy recommended where resistance rates are below 15%. Rising rates of clarithromycin resistance, resulting in high therapy failure rates, are seen worldwide, but U.S. data are...
BacteriologyDetection of Tick-Borne Bacteria from Whole Blood Using 16S Ribosomal RNA Gene PCR Followed by Next-Generation SequencingReported cases of tick-borne diseases have steadily increased for more than a decade. In the United States, a majority of tick-borne infections are caused by bacteria.
BacteriologyHelicobacter pylori Antimicrobial Resistance and Gene Variants in High- and Low-Gastric-Cancer-Risk PopulationsColombia, South America has one of the world’s highest burdens of Helicobacter pylori infection and gastric cancer. While multidrug antibiotic regimens can effectively eradicate H. pylori, treatment efficacy is being jeopardized by the emergence of antibiotic-resistant...
Mycobacteriology and Aerobic Actinomycetes
Mycobacteriology and Aerobic ActinomycetesEvaluation of the Roche cobas MTB and MTB-RIF/INH Assays in Samples from Germany and Sierra LeoneThe cobas MTB and MTB-RIF/INH assays allow for detection of Mycobacterium tuberculosis complex (MTBC) nucleic acid and rifampicin (RIF) and isoniazid (INH) resistance-associated mutations in an automated, high-throughput workflow. In this study, we evaluated the performance of these assays, employing samples from settings of low and high tuberculosis (TB) burdens....
Parasitology
ParasitologyEvaluation of the Performance of the Loopamp Trypanosoma cruzi Detection Kit for the Diagnosis of Chagas Disease in an Area Where It Is Not Endemic, SpainIn Spain, PCR is the tool of choice for the diagnosis of congenital Chagas disease (CD) and serology for diagnosing chronic CD. A loop-mediated isothermal amplification test for Trypanosoma cruzi DNA detection showed good analytical performance and ease of use.
Virology
VirologyPerformance and Implementation Evaluation of the Abbott BinaxNOW Rapid Antigen Test in a High-Throughput Drive-Through Community Testing Site in MassachusettsRapid diagnostic tests (RDTs) for SARS-CoV-2 antigens (Ag) that can be performed at point of care (POC) can supplement molecular testing and help mitigate the COVID-19 pandemic. Deployment of an Ag RDT requires an understanding of its operational and performance characteristics under real-world conditions and in relevant subpopulations.
VirologyCopan eNAT Transport System To Address Challenges in COVID-19 Diagnostics in Regions with Limited Testing AccessCommunity-based health care clinics and hospital outreach services have the potential to expand coronavirus disease 2019 (COVID-19) diagnostics to rural areas. However, reduced specimen stability during extended transport, the absence of a cold chain to centralized laboratories, and biosafety concerns surrounding specimen handling have limited this expansion.
VirologyEvaluation of Specimen Types and Saliva Stabilization Solutions for SARS-CoV-2 TestingIdentifying SARS-CoV-2 infections through aggressive diagnostic testing remains critical to tracking and curbing the spread of the COVID-19 pandemic. Collection of nasopharyngeal swabs (NPS), the preferred sample type for SARS-CoV-2 detection, has become difficult due to the dramatic increase in testing and consequent supply strain.
VirologyComparison of 16 Serological SARS-CoV-2 Immunoassays in 16 Clinical LaboratoriesSerological assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to support clinical diagnosis and epidemiological investigations. Recently, assays for large-scale detection of total antibodies (Ab), immunoglobulin G (IgG), and IgM against SARS-CoV-2 antigens have been developed, but there are limited data on the diagnostic accuracy of these assays.
VirologyRapid 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 SequencingThe 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.
VirologyPortable RT-PCR System: a Rapid and Scalable Diagnostic Tool for COVID-19 TestingCombating the ongoing coronavirus disease 2019 (COVID-19) pandemic demands accurate, rapid, and point-of-care testing with fast results to triage cases for isolation and treatment. The current testing relies on reverse transcriptase PCR (RT-PCR), which is routinely performed in well-equipped laboratories by trained professionals at specific locations.
VirologyVerification and Validation of SARS-CoV-2 Assay Performance on the Abbott m2000 and Alinity m SystemsWe verified the analytical performance of the Abbott RealTime SARS-CoV-2 assay on the m2000 system and compared its clinical performance to the CDC 2019-nCoV real-time PCR diagnostic panel and the Thermo Fisher TaqPath RT-PCR COVID-19 kit. We also performed a bridging study comparing the RealTime SARS-CoV-2 assay with the new Abbott Alinity m SARS-CoV-2 assay.
VirologyDeciphering an Adenovirus F41 Outbreak in Pediatric Hematopoietic Stem Cell Transplant Recipients by Whole-Genome SequencingHuman 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...
VirologyAnti-Human T-Cell Leukemia Virus Type 1 (HTLV-1) Antibody Assays in Cerebrospinal Fluid for the Diagnosis of HTLV-1-Associated Myelopathy/Tropical Spastic ParaparesisThe anti-human T-cell leukemia virus type 1 (HTLV-1) antibody assay in common use has changed from the particle agglutination (PA) method to chemiluminescent immunoassay (CLIA) and chemiluminescent enzyme immunoassay (CLEIA). These assays were validated in serum but not in cerebrospinal fluid (CSF). However, anti-HTLV-1 antibody positivity in CSF is a requisite for diagnosing HTLV-1-associated myelopathy/tropical spastic paraparesis (...
Immunoassays
ImmunoassaysImpact of T-Cell Xtend on T-SPOT.TB Assay in High-Risk Individuals after Delayed Blood Sample ProcessingT-SPOT.TB (T-SPOT) is an interferon gamma release assay (IGRA) used to detect infection with Mycobacterium tuberculosis based on the number of spot-forming T cells; however, delays in sample processing have been shown to reduce the number of these spots that are detected following laboratory processing. Adding T-Cell Xtend (XT) into blood samples before...
ImmunoassaysPerformance of Four IgM Antibody Assays in the Diagnosis of Measles Virus Primary Infection and Cases with a Serological Profile Indicating ReinfectionThe object of this study was to determine the diagnostic performance of four commercially available IgM tests in the diagnosis of measles virus (MeV) primary infection and cases with a serological profile indicating reinfection. Sera from 187 patients with MeV primary infection, 30 patients with suspected reinfection (after vaccine failure), and 153 patients with rash-like symptoms after exclusion of MeV infection were retested with...
ImmunoassaysAssessment of S1-, S2-, and NCP-Specific IgM, IgA, and IgG Antibody Kinetics in Acute SARS-CoV-2 Infection by a Microarray and Twelve Other ImmunoassaysIn this study, we comprehensively analyzed multispecific antibody kinetics of different immunoglobulins in hospitalized patients with acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Three hundred fifty-four blood samples longitudinally obtained from 81 IgG-seroconverting progressed coronavirus disease 2019 (CoVID-19) patients were quantified for spike 1 (S1), S2, and nucleocapsid protein (NCP)-specific IgM...
Epidemiology
EpidemiologyAntibody Responses to Two Recombinant Treponemal Antigens (rp17 and TmpA) before and after Azithromycin Treatment for Yaws in Ghana and Papua New GuineaWHO and its partners aim to interrupt yaws transmission in countries of endemicity and to certify others as being yaws-free. Transmission can be assessed using rapid plasma reagin (RPR) tests, reflecting current or recent infection, but RPR is operationally impractical.
EpidemiologyEvaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance StudyWhile influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure.
EpidemiologyMycoplasma hyopneumoniae Surveillance in Pig Populations: Establishing Sampling Guidelines for Detection in Growing PigsAntemortem detection of Mycoplasma hyopneumoniae infection in swine production systems has relied on antibody testing, but the availability of tests based on DNA detection and novel diagnostic specimens, e.g., tracheal swabs and oral fluids, has the potential to improve M. hyopneumoniae surveillance...
Letters to the Editor
Letter to the EditorTaxonomy Revision of Leishmania spp. in Thailand
Letter to the EditorNew Pneumococcal Serotype 15D
Letter to the EditorReply to Mungthin et al., “Taxonomy Revision of Leishmania spp. in Thailand”
Author Correction
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Journal of Clinical Microbiology® (JCM) publishes the most current research related to the laboratory diagnosis of human and animal infections and the role of the laboratory in both the management of infectious diseases and the elucidation of the epidemiology of infections.
Editor in Chief: Dr. Alexander J. McAdam
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Reconciling Genotypic and Phenotypic Susceptibility Tests with Dr. Patricia Simner and Dr. Jennifer Dien Bard. Hosted by Journal of Clinical Microbiology Editor in Chief, Dr. Alexander McAdam.
Commentary
In light of the present pandemic of novel coronavirus disease 2019 (COVID-19) and the unprecedented high demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing worldwide, there are shortages of established specimen collection devices for respiratory viral testing for diagnostic microbiology laboratories. This creates the need to validate unverified collection devices from manufacturers that may not be a...