Table of Contents
Photo Quiz
Photo QuizAnswer to April 2021 Photo Quiz
Editorial
EditorialIs the Patient Infected with SARS-CoV-2?The U.S. Food and Drug Administration currently uses the nasopharyngeal swab specimen as the reference standard for evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assays. We propose that the patient-infected status algorithm is a superior way to classify whether an individual is infected or not infected.
The Brief Case
Point-Counterpoint
Point-CounterpointPoint-Counterpoint: Should Clinical Microbiology Laboratories Report Vancomycin MICs?Point-Counterpoint: Should Clinical Microbiology Laboratories Report Vancomycin MICs?Point-Counterpoint: Should Clinical Microbiology Laboratories Report Vancomycin MICs?Point-Counterpoint: Should Clinical Microbiology Laboratories Report Vancomycin MICs?With numerous reported challenges to reporting MICs for vancomycin, clinical laboratories are attempting to identify accurate methods for MIC testing. However, the issues of poor reproducibility, accuracy, and clinical utility remain a challenge. In this Point-Counterpoint, Dr. Sara Revolinski discusses the pros of reporting MICs for vancomycin, while Dr. Christopher Doern argues for the use of caution.
Minireviews
MinireviewUltrasensitive Diagnostics for Low-Density Asymptomatic Plasmodium falciparum Infections in Low-Transmission SettingsThe emergence of multidrug-resistant Plasmodium falciparum malaria in Southeast Asia (SEA) has accelerated regional malaria elimination efforts. Most malaria in this and other low-transmission settings exists in asymptomatic individuals, which conventional diagnostic tests lack the sensitivity to detect. This has led to the development of new ultrasensitive...
MinireviewValue of Xpert MTB/RIF Using Bronchoalveolar Lavage Fluid for the Diagnosis of Pulmonary Tuberculosis: a Systematic Review and Meta-analysisThe performance of Xpert MTB/RIF using bronchoalveolar lavage fluid (BAL) for the diagnosis of pulmonary tuberculosis (PTB) remains unclear. Therefore, a systematic review/meta-analysis was conducted.
MinireviewThe Importance and Challenges of Identifying SARS-CoV-2 Reinfections...Reports of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection have raised important questions about the strength and durability of the immune response to primary infection, which are key factors in predicting the course of the pandemic. Identifying reinfection requires detecting the virus at two different time points and using viral genomic data to distinguish reinfection from persistent viral carriage.
Bacteriology
BacteriologyA Test for the Rapid Detection of the Cefazolin Inoculum Effect in Methicillin-Susceptible Staphylococcus aureusThe cefazolin inoculum effect (CzIE) has been associated with therapeutic failures and mortality in invasive methicillin-susceptible Staphylococcus aureus (MSSA) infections. A diagnostic test to detect the CzIE is not currently available.
BacteriologyEvaluating the Rapid Emergence of Daptomycin Resistance in Corynebacterium: a Multicenter StudyMembers of the genus Corynebacterium are increasingly recognized as pathobionts and can be very resistant to antimicrobial agents. Previous studies have demonstrated that Corynebacterium striatum can rapidly develop high-level daptomycin resistance (HLDR) (MIC, ≥256 μg/ml).
BacteriologyTransmission and Antibiotic Resistance of Achromobacter in Cystic FibrosisAchromobacter species are increasingly being detected in patients with cystic fibrosis (CF), and this emerging pathogen is associated with antibiotic resistance and more-severe disease outcomes. Nonetheless, little is known about the extent of transmission and antibiotic resistance development in Achromobacter infections.
Mycobacteriology and Aerobic Actinomycetes
Mycobacteriology and Aerobic ActinomycetesLow-Level Rifampin Resistance and rpoB Mutations in Mycobacterium tuberculosis: an Analysis of Whole-Genome Sequencing and Drug Susceptibility Test Data in New YorkRapid and reliable detection of rifampin (RIF) resistance is critical for the diagnosis and treatment of drug-resistant and multidrug-resistant (MDR) tuberculosis. Discordant RIF phenotype/genotype susceptibility results remain a challenge due to the presence of rpoB mutations that do not confer high levels of RIF resistance, as have been exhibited in strains with mutations such as Ser450Leu.
Mycobacteriology and Aerobic ActinomycetesMycobactericidal Effects of Different Regimens Measured by Molecular Bacterial Load Assay among People Treated for Multidrug-Resistant Tuberculosis in TanzaniaRifampin or multidrug-resistant tuberculosis (RR/MDR-TB) treatment has largely transitioned to regimens free of the injectable aminoglycoside component, despite the drug class’ purported bactericidal activity early in treatment. We tested whether Mycobacterium tuberculosis
Mycology
MycologyCategorizing Susceptibility of Clinical Isolates of Candida auris to Amphotericin B, Caspofungin, and Fluconazole by Use of the CLSI M44-A2 Disk Diffusion MethodWe evaluated the CLSI M44ed3E disk diffusion method compared with the CLSI M27ed4 broth microdilution method for caspofungin and fluconazole and the Etest method for amphotericin B to categorize susceptibility of 347 clinical isolates of Candida auris. Utilizing the zone diameter cutoffs established here, we observed overall categorical agreement between the two...
MycologyPerformance of Two Novel Chromogenic Media for the Identification of Multidrug-Resistant Candida auris Compared with Other Commercially Available FormulationsNon-albicans Candida species are emerging in the nosocomial environment, with the multidrug-resistant (MDR) species Candida auris being the most notorious example. Consequently, rapid and accurate species identification has become essential.
Virology
VirologyAssessment of Sample Pooling for Clinical SARS-CoV-2 TestingAccommodating large increases in sample workloads has presented a major challenge to clinical laboratories during the coronavirus disease 2019 (COVID-19) pandemic. Despite the implementation of automated detection systems and previous efficiencies, including barcoding, electronic data transfer, and extensive robotics, capacities have struggled to meet the demand.
VirologyPooling of Nasopharyngeal Swab Samples To Overcome a Global Shortage of Real-Time Reverse Transcription-PCR COVID-19 Test KitsThe global outbreak and rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created an urgent need for large-scale testing of populations. There is a demand for high-throughput testing protocols that can be used for efficient and rapid testing of clinical specimens. We evaluated a pooled PCR protocol for testing nasopharyngeal (NP) swabs using known positive/negative and untested clinical samples that were...
VirologyComparison of Antibody Class-Specific SARS-CoV-2 Serologies for the Diagnosis of Acute COVID-19Accurate diagnosis of acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is critical for appropriate management of patients with this disease. We examined the possible complementary role of laboratory-developed class-specific clinical serology in assessing SARS-CoV-2 infection in hospitalized patients.
VirologyA Scalable, Easy-to-Deploy Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic MaterialThe COVID-19 pandemic has created massive demand for widespread, distributed tools for detecting SARS-CoV-2 genetic material. The hurdles to scalable testing include reagent and instrument accessibility, availability of highly trained personnel, and large upfront investment.
VirologyA Fast and Accessible Method for the Isolation of RNA, DNA, and Protein To Facilitate the Detection of SARS-CoV-2Management of the coronavirus disease 2019 (COVID-19) pandemic requires widespread testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A main limitation for widespread SARS-CoV-2 testing is the global shortage of essential supplies, among them RNA extraction kits.
VirologySelf-Collected Saline Gargle Samples as an Alternative to Health Care Worker-Collected Nasopharyngeal Swabs for COVID-19 Diagnosis in OutpatientsWe assessed the performance, stability, and user acceptability of swab-independent self-collected saliva and saline mouth rinse/gargle sample types for the molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in adults and school-aged children. Outpatients who had recently been diagnosed with COVID-19 or were presenting with suspected COVID-19 were asked to have a nasopharyngeal (NP) swab collected and...
VirologyA New SARS-CoV-2 Dual-Purpose Serology Test: Highly Accurate Infection Tracing and Neutralizing Antibody Response DetectionMany severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serology tests have proven to be less accurate than expected and do not assess antibody function as neutralizing, correlating with protection from reinfection. A new assay technology measuring the interaction of the purified SARS-CoV-2 spike protein receptor binding domain (RBD) with the extracellular domain of the human angiotensin-converting enzyme 2 (hACE2) receptor...
VirologyEvaluation of the Xpert Xpress SARS-CoV-2/Flu/RSV Assay for Simultaneous Detection of SARS-CoV-2, Influenza A and B Viruses, and Respiratory Syncytial Virus in Nasopharyngeal SpecimensPatients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A (flu A), influenza B (flu B), and respiratory syncytial virus (RSV) have overlapping clinical presentations, but the approaches to treatment and management of infections caused by these viruses are different. Therefore, rapid diagnosis in conjunction with infection prevention measures is important to prevent transmission of the diseases....
VirologyPerformance of Saliva Specimens for the Molecular Detection of SARS-CoV-2 in the Community Setting: Does Sample Collection Method Matter?Data on the performance of saliva specimens for diagnosing coronavirus disease 2019 (COVID-19) in ambulatory patients are scarce and inconsistent. We assessed saliva-based specimens for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse transcriptase PCR (RT-PCR) in the community setting and compared three different collection methods.
VirologyCorrelation of SARS-CoV-2 Nucleocapsid Antigen and RNA Concentrations in Nasopharyngeal Samples from Children and Adults Using an Ultrasensitive and Quantitative Antigen AssayDiagnosis of COVID-19 by PCR offers high sensitivity, but the utility of detecting samples with high cycle threshold (CT) values remains controversial. Currently available rapid diagnostic tests (RDTs) for SARS-CoV-2 nucleocapsid antigens (Ag) have sensitivity well below PCR.
VirologyPerformance Characteristics of BinaxNOW COVID-19 Antigen Card for Screening Asymptomatic Individuals in a University SettingWe compared the performance of the Abbott BinaxNOW COVID-19 antigen card to that of a standard reverse transcription-PCR (RT-PCR) assay (Thermo Fisher TaqPath COVID-19 Combo kit) for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2,645 asymptomatic students presenting for screening at the University of Utah. SARS-CoV-2 RNA was detected in 1.7% of the study participants by RT-PCR.
Immunoassays
ImmunoassaysPerformance Characteristics of the Vidas SARS-CoV-2 IgM and IgG Serological AssaysThe COVID-19 pandemic, caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to spread worldwide. Serological testing for SARS-CoV-2-specific antibodies plays an important role in understanding and controlling the pandemic, notably through epidemiological surveillance.
ImmunoassaysNovel Genetic Constructs for Production of Recombinant HTLV-1/2 Antigens and Evaluation of Their Reactivity to Plasma Samples from HTLV-1-Infected PatientsHuman T-cell leukemia virus type 1 (HTLV-1) can cause life-threatening diseases for which there are no effective treatments. Prevention of HTLV-1 infection requires massive testing of pregnant women, blood for transfusion, and organs for transplantation, as well as safe sex.
ImmunoassaysQuantitative Measurement of Anti-SARS-CoV-2 Antibodies: Analytical and Clinical EvaluationThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). While molecular-based testing is used to diagnose COVID-19, serologic testing of antibodies specific to SARS-CoV-2 is used to detect past infection.
Epidemiology
EpidemiologyGenetic Evaluation of Nosocomial Candida auris TransmissionWhole-genome sequences of Candida auris isolates from nosocomial and nonnosocomial infections were compared. The average numbers of single nucleotide variations were different between the two groups. The small amount of genetic variability between intra- or interhost isolates suggests recovery of all colonizing or infecting genomes for comparison is required for...
Letters to the Editor
Letter to the EditorBordetella hinzii: an Unusual Pathogen in Human Urinary Tract Infection
Letter to the EditorNeglecting Genetic Diversity Hinders Timely Diagnosis of Cryptococcus Infections
Erratum
Masthead
Commentaries
In a recent report of a systematic review of critical concentrations (CCs), the World Health Organization (WHO) lowered the rifampin (RIF) CC for antimicrobial susceptibility testing (AST) of the Mycobacterium tuberculosis complex using Middlebrook 7H10 medium and the Bactec mycobacterial growth indicator tube (MGIT) 960 system from 1 to 0.5 μg/ml. The previous RIF CC...
The coronavirus disease 2019 (COVID-19) pandemic has put the clinical laboratory in the spotlight. The news media is regularly seeking out interviews with microbiologists, infectious disease specialists, and pathologists.