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Editorial
EditorialWhen Should Asymptomatic Persons Be Tested for COVID-19?On 24 August 2020, the Centers for Disease Control and Prevention (CDC) updated its website to highlight that asymptomatic individuals, even those with exposure to a COVID-19-positive contact, do not necessarily need to be tested unless they have medical conditions associated with increased risk of severe illness from COVID-19. The CDC subsequently updated its guidance on 19 September 2020 to support testing of asymptomatic persons,...
The Brief Case
Minireview
MinireviewCefiderocol Antimicrobial Susceptibility Testing Considerations: the Achilles' Heel of the Trojan Horse?Cefiderocol (formerly S-649266) is a novel siderophore-conjugated cephalosporin with activity against a broad array of multidrug-resistant (MDR), aerobic Gram-negative bacilli. The siderophore component binds iron and uses active iron transport for drug entry into the bacterial periplasmic space. The cephalosporin moiety is the active antimicrobial component, structurally resembling a hybrid between ceftazidime and cefepime. Like other...
Bacteriology
BacteriologyMolecular Microbiological and Immune Characterization of a Cohort of Patients Diagnosed with Early Lyme DiseaseLyme disease is a tick-borne infection caused by the bacteria Borrelia burgdorferi. Current diagnosis of early Lyme disease relies heavily on clinical criteria, including the presence of an erythema migrans rash. The sensitivity of current gold-standard diagnostic tests relies upon antibody formation, which is typically delayed and thus of limited utility in early...
BacteriologyComparison of Agar Dilution to Broth Microdilution for Testing In Vitro Activity of Cefiderocol against Gram-Negative BacilliCefiderocol (CFDC) is a siderophore cephalosporin with activity against Gram-negative bacterial species that are resistant to carbapenems and other drugs. The MICs of CFDC were determined for 610 Gram-negative bacilli, including 302 multinational Enterobacterales isolates with characterized mechanisms of beta-lactam resistance, 180 clinical isolates from the Mayo Clinic and Mayo Clinic Laboratories not characterized for...
BacteriologyMulticenter Performance Evaluation of the Simplexa Bordetella Direct Kit in Nasopharyngeal Swab SpecimensDetection of Bordetella pertussis and Bordetella parapertussis using molecular methods is sensitive and specific with a short turnaround time compared to other diagnostic methods. In this multicenter study, we compared the performance of the Simplexa Bordetella Direct kit to those of other molecular...
BacteriologyEvaluation of the Biotoxis qPCR Detection Kit for Francisella tularensis Detection in Clinical and Environmental SamplesRapid and reliable detection and identification of Francisella tularensis (a tier 1 select agent) are of primary interest for both medical and biological threat surveillance purposes. The Biotoxis qPCR detection kit is a real-time quantitative PCR (qPCR) assay designed for the detection of Bacillus...
BacteriologyCefiderocol Antimicrobial Susceptibility Testing against Multidrug-Resistant Gram-Negative Bacilli: a Comparison of Disk Diffusion to Broth MicrodilutionAntimicrobial susceptibility testing (AST) of cefiderocol poses challenges because of its unique mechanism of action (i.e., requiring an iron-depleted state) and due to differences in interpretative criteria established by the Clinical and Laboratory Standards Institute (CLSI), U.S. Food and Drug Administration (FDA), and European Committee on Antimicrobial Susceptibility Testing (EUCAST). Our objective was to compare cefiderocol disk...
BacteriologySimple Phenotypic Tests To Improve Accuracy in Screening Chromosomal and Plasmid-Mediated Colistin Resistance in Gram-Negative BacilliCLSI and EUCAST recommend that only broth microdilution (BMD) should be used for routine colistin susceptibility testing; however, this technique can be difficult to perform in resource-poor settings. The purpose of this study was to evaluate the accuracy of a colistin agar spot test (COL-AS) and a colistin drop test (COL-DT) compared to BMD. COL-AS and COL-DT were assessed with a collection of 271 Gram-negative bacilli clinical...
BacteriologySequential Quadriplex Real-Time PCR for Identifying 20 Common emm Types of Group A StreptococcusWe developed a sequential quadriplex real-time PCR-based method for rapid identification of 20 emm types commonly found in invasive group A Streptococcus (iGAS) strains recovered through the Centers for Disease Control and Prevention’s Active Bacterial Core surveillance. Each emm real-time PCR assay showed high specificity and accurately identified the respective target emm type, including emm...
BacteriologyDigital Image Analysis for the Detection of Group B Streptococcus from ChromID Strepto B Medium Using PhenoMatrix AlgorithmsGroup B Streptococcus (GBS) can be found to colonize about 25% of all healthy, adult women and is the leading infectious cause of early neonatal morbidity and mortality in the United States. This study evaluated the clinical performance of PhenoMatrix (PM) chromogenic detection module (CDM) digital imaging software in detection of GBS from LIM broth plated on ChromID Strepto B chromogenic medium (ChromID) using the WASP...
BacteriologyEvaluation of Pneumococcal Serotyping of Nasopharyngeal-Carriage Isolates by Latex Agglutination, Whole-Genome Sequencing (PneumoCaT), and DNA Microarray in a High-Pneumococcal-Carriage-Prevalence Population in MalawiAccurate assessment of the serotype distribution associated with pneumococcal colonization and disease is essential for evaluating and formulating pneumococcal vaccines and for informing vaccine policy. For this reason, we evaluated the concordance between pneumococcal serotyping results by latex agglutination, whole-genome sequencing (WGS) with PneumoCaT, and DNA microarray for samples from community carriage surveillance in Blantyre,...
BacteriologyMeningococcal Deduced Vaccine Antigen Reactivity (MenDeVAR) Index: a Rapid and Accessible Tool That Exploits Genomic Data in Public Health and Clinical Microbiology ApplicationsAs microbial genomics makes increasingly important contributions to clinical and public health microbiology, the interpretation of whole-genome sequence data by nonspecialists becomes essential. In the absence of capsule-based vaccines, two protein-based vaccines have been used for the prevention of invasive serogroup B meningococcal disease (IMD) since their licensure in 2013 and 2014. These vaccines have different components and...
BacteriologyEvaluation of Surrogate Tests for the Presence of mecA-Mediated Methicillin Resistance in Staphylococcus capitis, Staphylococcus haemolyticus, Staphylococcus hominis, and Staphylococcus warneriTesting of staphylococci other than Staphylococcus aureus (SOSA) for mecA-mediated resistance is challenging. Isolates of Staphylococcus capitis, Staphylococcus haemolyticus,...
BacteriologyNovel Strategy for Rapidly and Safely Distinguishing Bacillus anthracis and Bacillus cereus by Use of Peptide Mass Fingerprints Based on Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass SpectrometryThe objective of this study was to construct a rapid, high-throughput, and biosafety-compatible screening method for Bacillus anthracis and Bacillus cereus based on matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). MALDI-TOF MS coupled to ClinProTools was...
Mycobacteriology and Aerobic Actinomycetes
Mycobacteriology and Aerobic ActinomycetesAssessing Nanopore Sequencing for Clinical Diagnostics: a Comparison of Next-Generation Sequencing (NGS) Methods for Mycobacterium tuberculosisNext-generation sequencing technologies are being rapidly adopted as a tool of choice for diagnostic and outbreak investigation in public health laboratories. However, costs of operation and the need for specialized staff remain major hurdles for laboratories with limited resources for implementing these technologies. This project aimed to assess the feasibility of using Oxford Nanopore MinION whole-genome sequencing data of...
Mycology
MycologyCOVID-19-Associated Invasive Aspergillosis: Data from the UK National Mycology Reference LaboratoryCOVID-19-associated pulmonary aspergillosis (CAPA) was recently reported as a potential infective complication affecting critically ill patients with acute respiratory distress syndrome following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, with incidence rates varying from 8 to 33% depending on the study. However, definitive diagnosis of CAPA is challenging. Standardized diagnostic algorithms and definitions...
MycologyDiagnostic Accuracy of the Biosynex CryptoPS Cryptococcal Antigen Semiquantitative Lateral Flow Assay in Patients with Advanced HIV DiseaseHigh cryptococcal antigen (CrAg) titers in blood are associated with subclinical meningitis and mortality in CrAg-positive individuals with advanced HIV disease (AHD). We evaluated a novel semiquantitative lateral flow assay (LFA), CryptoPS, that may be able to identify individuals with high CrAg titers in a cohort of AHD patients undergoing CrAg screening. In a prospective cohort of patients with AHD (CD4 cell count, ≤200/μl) receiving...
Parasitology
ParasitologyA Real-Time PCR Assay for Simultaneous Detection and Differentiation of Four Common Entamoeba Species That Infect HumansThere are over 40 species within the genus Entamoeba, eight of which infect humans. Of these, four species (Entamoeba histolytica, E. dispar, E. moshkovskii, and E. bangladeshi) are morphologically indistinguishable from each other, and yet differentiation is important for appropriate treatment decisions. Here, we developed a...
Virology
VirologyPerformance Evaluation of the SAMBA II SARS-CoV-2 Test for Point-of-Care Detection of SARS-CoV-2Nucleic acid amplification for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in respiratory samples is the standard method for diagnosis. The majority of this testing is centralized and therefore has turnaround times of several days. Point-of-care (POC) testing with rapid turnaround times would allow more effective triage in settings where patient management and infection control decisions need to be...
VirologyDiagnostic Accuracy of Four Commercial Triplex Immunochromatographic Tests for Rapid Detection of Rotavirus, Adenovirus, and Norovirus in Human Stool SamplesNoroviruses (NoV), rotaviruses (RVA), and adenoviruses (AdV) are the main viral agents responsible for acute gastroenteritis (AGE) in humans. We aimed to determine the diagnostic accuracy of four commercial immunochromatographic tests (ICTs) intended for the rapid and simultaneous detection of these three pathogens. Diagnostic accuracy of bioNexia Noro/Rota-Adeno (bioMérieux), Immunoquick NoRotAdeno (Biosynex), Rota+Adeno+Noro combo...
VirologyEvaluation of Three Commercial SARS-CoV-2 Serologic Assays and Their Performance in Two-Test AlgorithmsSensitive and specific severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serologic assays are needed to inform diagnostic, therapeutic, and public health decision-making. We evaluated three commercial serologic assays as stand-alone tests and as components of two-test algorithms. Two nucleocapsid antibody tests (Abbott IgG and Roche total antibody) and one spike protein antibody test (DiaSorin IgG) were included. We assessed...
VirologyAnalytical and Clinical Sample Performance Characteristics of the Onclarity Assay for the Detection of Human PapillomavirusThe objective of this study was to determine the result reproducibility and performance of the BD Onclarity human papillomavirus (HPV) assay (Onclarity) on the BD Viper LT platform using both contrived and clinical specimens. Reproducibility was assessed in BD SurePath liquid-based cytology (LBC) medium (SurePath) using contrived panels (HPV genotype 16 [HPV16] positive, HPV18 positive, or HPV45 positive) or clinical specimens (HPV16, -...
VirologyPositive Impact of Routine Testing for Enterovirus and Parechovirus on Length of Hospitalization and Antimicrobial Use among Inpatients ≤6 Months of AgeEnterovirus (EV) and parechovirus (PeV) are leading viral causes of central nervous system (CNS) infection among hospitalized neonates and young infants, yet testing for PeV is not routinely performed. The goal of our study was to determine how EV and PeV CSF RT-PCR testing impacted the duration of antibiotic use and the length of hospitalization (LOS) in children ≤6 months old with suspected CNS infection. This retrospective cohort...
VirologyMetagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19Broad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of...
VirologyA Clinical Epidemiology and Molecular Attribution Evaluation of Adenoviruses in Pediatric Acute Gastroenteritis: a Case-Control StudyThe objective of this study was to characterize the etiological role of human adenovirus (HAdV) serotypes in pediatric gastroenteritis. Using a case-control design, we compared the frequencies of HAdV serotypes between children with ≥3 episodes of vomiting or diarrhea within 24 h and <7 days of symptoms (i.e., cases) and those with no infectious symptoms (i.e., controls). Stool samples and/or rectal swabs underwent molecular...
VirologyHIV-2 Drug Resistance Genotyping from Dried Blood SpotsThe treatment of HIV-2 in resource-limited settings (RLS) is complicated by the limited availability of HIV-2-active antiretroviral drugs and inadequate access to HIV-2 viral load and drug resistance testing. Dried blood spots (DBS)-based drug resistance testing, widely studied for HIV-1, has not been reported for HIV-2 and could present an opportunity to improve care for HIV-2-infected individuals. We selected 150 DBS specimens from...
VirologyClinical Evaluation of BD Veritor SARS-CoV-2 Point-of-Care Test Performance Compared to PCR-Based Testing and versus the Sofia 2 SARS Antigen Point-of-Care TestThe clinical performance of the BD Veritor System for Rapid Detection of SARS-CoV-2 nucleocapsid antigen (Veritor), a chromatographic immunoassay used for SARS-CoV-2 point-of-care testing, was evaluated using nasal specimens from individuals with COVID-19 symptoms. Two studies were completed to determine clinical performance. In the first study, nasal specimens and either nasopharyngeal or oropharyngeal specimens from 251 participants...
VirologyComparison of Upper Respiratory Viral Load Distributions in Asymptomatic and Symptomatic Children Diagnosed with SARS-CoV-2 Infection in Pediatric Hospital Testing ProgramsThe distribution of upper respiratory viral loads (VL) in asymptomatic children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unknown. We assessed PCR cycle threshold (Ct) values and estimated VL in infected asymptomatic children diagnosed in nine pediatric hospital testing programs. Records for asymptomatic and symptomatic patients with positive clinical SARS-CoV-2 tests were reviewed. Ct values were (i...
Immunoassays
ImmunoassaysComparison of the Clinical Performances of the Abbott Alinity IgG, Abbott Architect IgM, and Roche Elecsys Total SARS-CoV-2 Antibody AssaysCritical evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serologic assays is needed to guide clinical decision-making and ensure that these assays provide optimal benefit to patients and the public. Here, three commercially available assays with widespread distribution capabilities are compared. A total of 667 specimens, 103 from patients with confirmed SARS-CoV-2 infections and 564 collected prior to the...
ImmunoassaysCOVID-19 Serology at Population Scale: SARS-CoV-2-Specific Antibody Responses in SalivaSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of an ongoing pandemic that has infected over 36 million and killed over 1 million people. Informed implementation of government public health policies depends on accurate data on SARS-CoV-2 immunity at a population scale. We hypothesized that detection of SARS-CoV-2 salivary antibodies could serve as a noninvasive alternative to serological testing for monitoring...
Clinical Veterinary Microbiology
Clinical Veterinary MicrobiologyEvaluation of a Fecal Shedding Test To Detect Badger Social Groups Infected with Mycobacterium bovisBovine tuberculosis (bTB) is an economically important disease affecting the cattle industry in England and Wales. bTB, caused by Mycobacterium bovis, also causes disease in the Eurasian badger (Meles meles), a secondary maintenance host. Disease transmission between these two species is...
Epidemiology
EpidemiologyGlobal Molecular Epidemiology of Respiratory Syncytial Virus from the 2017−2018 INFORM-RSV StudyRespiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection among infants and young children, resulting in annual epidemics worldwide. INFORM-RSV is a multiyear clinical study designed to describe the global molecular epidemiology of RSV in children under 5 years of age by monitoring temporal and geographical evolution of current circulating RSV strains, F protein antigenic sites, and their relationships...
EpidemiologyC-Reactive Protein Testing for Active Tuberculosis among Inpatients without HIV in Uganda: a Diagnostic Accuracy StudyThe objective of this prospective cross-sectional study, conducted at a national referral hospital in Kampala, Uganda, was to determine diagnostic performance of serum C-reactive protein (CRP) as a triage test for tuberculosis (TB) among HIV-seronegative inpatients. We calculated the sensitivity, specificity, positive and negative likelihood ratios, and positive and negative predictive values to determine the diagnostic performance of a...
EpidemiologyGlobal Epidemiology and Evolutionary History of Staphylococcus aureus ST45Staphylococcus aureus ST45 is a major global MRSA lineage with huge strain diversity and a high clinical impact. It is one of the most prevalent carrier lineages but also frequently causes severe invasive disease, such as bacteremia. Little is known about its evolutionary history. In this study, we used whole-genome sequencing to analyze a large collection of 451...
Letters to the Editor
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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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Commentary
Interest continues to grow regarding the role of serologic assays for the detection of prior infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The U.S. Food and Drug Administration (FDA) has granted emergency use authorization (EUA) status to many SARS-CoV-2 serologic assays. In this document, expert recommendations from clinical microbiologist members of the American Society for Microbiology (ASM) concerning...