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Editorials
The Brief Case
Point-Counterpoint
Point-CounterpointPoint-Counterpoint: Differences between the European Committee on Antimicrobial Susceptibility Testing and Clinical and Laboratory Standards Institute Recommendations for Reporting Antimicrobial Susceptibility ResultsPoint-Counterpoint: Differences between the European Committee on Antimicrobial Susceptibility Testing and Clinical and Laboratory Standards Institute Recommendations for Reporting Antimicrobial Susceptibility ResultsPoint-Counterpoint: Differences between the European Committee on Antimicrobial Susceptibility Testing and Clinical and Laboratory Standards Institute Recommendations for Reporting Antimicrobial Susceptibility ResultsPoint-Counterpoint: Differences between the European Committee on Antimicrobial Susceptibility Testing and Clinical and Laboratory Standards Institute Recommendations for Reporting Antimicrobial Susceptibility ResultsAntibiotic susceptibility test results are among the most important results issued by clinical microbiology laboratories because they routinely guide critical treatment decisions. Interpretations of MIC or disk diffusion test results, such as “susceptible” or “resistant,” are easily understood. Clinical laboratories also need to determine whether and how their reports will reflect more complex situations.
Minireviews
MinireviewComparison of Respiratory Specimen Collection Methods for Detection of Influenza Virus Infection by Reverse Transcription-PCR: a Literature ReviewThe detection of influenza virus in respiratory specimens from ill individuals is the most commonly used method to identify influenza virus infection. A number of respiratory specimen types may be used, including swabs, brush, aspirate, and wash, and specimens may be collected from numerous sites, including the anterior and posterior nasopharynx, oropharynx, and nares.
MinireviewCost-Effective Respiratory Virus TestingThe timely and accurate diagnosis of respiratory virus infections has the potential to optimize downstream (posttesting) use of limited health care resources, including antibiotics, antivirals, ancillary testing, and inpatient and emergency department beds.
MinireviewClinical Utility of Advanced Microbiology Testing ToolsAdvanced microbiology technologies are rapidly changing our ability to diagnose infections, improve patient care, and enhance clinical workflow. These tools are increasing the breadth, depth, and speed of diagnostic data generated per patient, and testing is being moved closer to the patient through rapid diagnostic technologies, including point-of-care (POC) technologies.
Bacteriology
BacteriologyInteraction between Antibiotic Resistance, Resistance Genes, and Treatment Response for Urinary Tract Infections in Primary CareGiven increasing antimicrobial resistance, we aimed to determine antibiotic susceptibility and presence of resistance genes in uropathogens in primary care, factors associated with resistance to commonly prescribed antibiotics, and effect of treatment on early symptom resolution. We conducted a prospective study of primary care patients with urinary tract infection (UTI) symptoms and culture-confirmed UTI in Singapore from 2015 to 2016...
BacteriologyMolecular Diagnosis of Vaginitis: Comparing Quantitative PCR and Microbiome Profiling Approaches to Current Microscopy Scoring...Vaginitis is often diagnosed by microscopy and limited to testing for bacterial vaginosis (BV), vulvovaginal candidiasis, and trichomoniasis. Approximately 10% of vaginal swabs are negative but designated “altered flora” by BV Nugent score, leaving clinicians unsure how to treat patients. Accurate and comprehensive vaginitis diagnostics are needed to direct treatment and reduce risks of recurrent or more severe infections.
BacteriologyAnalysis of Infection Loads in Mycoplasma genitalium Clinical Specimens by Use of a Commercial Diagnostic TestMycoplasma genitalium is a common sexually transmitted infection with a propensity to acquire resistance to commonly used antimicrobial therapies. Bacterial load has been linked to patient symptoms and the success of treatment. In this study, we demonstrate methodology to estimate load from routine diagnostic assays using the ResistancePlus MG test (SpeeDx Pty Ltd.,...
BacteriologyDetermination of MIC Quality Control Ranges for the Novel Gyrase Inhibitor ZoliflodacinThis report describes the results of two different, multilaboratory quality control (QC) studies that were used to establish QC ranges for the novel gyrase inhibitor zoliflodacin against the ATCC strains recommended by the Clinical and Laboratory Standards Institute (CLSI).
BacteriologyEvaluation of BacterioScan 216Dx in Comparison to Urinalysis as a Screening Tool for Diagnosis of Urinary Tract Infections in ChildrenUrinalysis (UA) has routinely been used as a screening tool prior to urine culture set up. BacterioScan 216Dx is an FDA-cleared semiautomated system to detect bacterial growth in urine. The aim of this study was to evaluate 216Dx in comparison to UA for diagnosis of urinary tract infection (UTI) in children.
BacteriologyRapid and Easy Detection of Carbapenemases in Enterobacterales in the Routine Laboratory Using the New GenePOC Carba/Revogene Carba C AssayThe novel, real-time PCR-based GenePOC Carba assay on the microfluidic revogene platform (GenePOC, Québec, Canada; now Meridian Bioscience, Cincinnati, OH, USA) was recently designed for the detection of blaKPC, blaNDM, blaVIM, blaOXA-48-like, and blaIMP.
BacteriologyOptimization of Turnaround Time for Group A Streptococcus PCRThe use of some nucleic acid amplification tests (NAATs) for the diagnosis of group A Streptococcus (GAS) pharyngitis allows laboratories to adopt single-tiered testing without reflex culture. However, centralization may delay the delivery of actionable information to the bedside, particularly in the outpatient setting. We describe two novel workflows at our institution and their effect on in-lab turnaround time (TAT) at a...
BacteriologyWhole-Genome Sequencing Reveals a Prolonged and Persistent Intrahospital Transmission of Corynebacterium striatum, an Emerging Multidrug-Resistant PathogenCorynebacterium striatum is an emerging multidrug-resistant (MDR) pathogen that occurs primarily among immunocompromised and chronically ill patients. However, little is known about the genomic diversity of C. striatum, which contributes to its long-term persistence and transmission in hospitals.
BacteriologyA Multicenter Study To Evaluate Ceftaroline Breakpoints: Performance in an Area with High Prevalence of Methicillin-Resistant Staphylococcus aureus Sequence Type 5 LineageCeftaroline (CPT) is a broad-spectrum agent with potent activity against methicillin-resistant Staphylococcus aureus (MRSA). The sequence type 5 (ST5) Chilean-Cordobés clone, associated with CPT nonsusceptibility, is dominant in Chile, a region with high rates of MRSA infections.
Mycobacteriology and Aerobic Actinomycetes
Mycobacteriology and Aerobic ActinomycetesSame-Day Tools, Including Xpert Ultra and IRISA-TB, for Rapid Diagnosis of Pleural Tuberculosis: a Prospective Observational StudyThe diagnosis of pleural tuberculosis (TB) is problematic. The comparative performance of newer same-day tools for pleural TB, including Xpert MTB/RIF Ultra (ULTRA), has hitherto not been comprehensively studied. Adenosine deaminase (ADA), IRISA-TB (interferon gamma ultrasensitive rapid immunosuspension assay), Xpert MTB/RIF, and ULTRA performance outcomes were evaluated in pleural fluid samples from 149 patients with suspected pleural...
Mycology
MycologySpecies Distinction in the Trichophyton rubrum ComplexThe Trichophyton rubrum species complex comprises commonly encountered dermatophytic fungi with a worldwide distribution. The members of the complex usually have distinct phenotypes in culture and cause different clinical symptoms, despite high genome similarity. In order to better delimit the species within the complex, molecular, phenotypic, and physiological...
MycologyA Novel Broad Allele-Specific TaqMan Real-Time PCR Method To Detect Triazole-Resistant Strains of Aspergillus fumigatus, Even with a Very Low Percentage of Triazole-Resistant Cells Mixed with Triazole-Susceptible CellsInvasive aspergillosis caused by triazole-resistant strains of Aspergillus fumigatus is a growing public health concern, as is the occurrence of mixed infections with triazole-resistant and -susceptible A. fumigatus strains. Therefore, it is crucial to develop robust methods to identify triazole-...
Parasitology
ParasitologyAssessing Performance of HRP2 Antigen Detection for Malaria Diagnosis in MozambiqueRapid diagnostic tests (RDTs) that detect the Plasmodium falciparum-specific histidine-rich protein 2 (PfHRP2) antigen are the primary methods for malaria diagnosis in Mozambique. However, these tests do not detect infections with non-falciparum malaria or Pfhrp2- and Pfhrp3-deleted P....
Virology
VirologyMulticenter Clinical Validation of the Molecular BD Max Enteric Viral Panel for Detection of Enteric PathogensThe conventional methodology for gastrointestinal pathogen detection remains time-consuming, expensive, and of limited sensitivity. The objective of this study was to evaluate the performance of the BD Max enteric viral panel (Max EVP) assay for identification of viral pathogens in stool specimens from individuals with symptoms of acute gastroenteritis, enteritis, or colitis.
VirologyViruses in Vietnamese Patients Presenting with Community-Acquired Sepsis of Unknown CauseCommunity-acquired (CA) sepsis is a major public health problem worldwide, yet the etiology remains unknown for >50% of the patients. Here we applied metagenomic next-generation sequencing (mNGS) to characterize the human virome in 492 clinical samples (384 sera, 92 pooled nasal and throat swabs, 10 stools, and 6 cerebrospinal fluid samples) from 386 patients (213 adults and 173 children) presenting with CA sepsis who were recruited...
VirologyNew Subgenotyping and Consensus Real-Time Reverse Transcription-PCR Assays for Hepatitis A Outbreak SurveillanceLaboratory surveillance plays an important role in the detection and control of hepatitis A outbreaks and requires the application of rapid and accurate molecular diagnostic tools for hepatitis A virus (HAV) RNA detection, subgenotype identification, and sequence-based genotyping.
VirologyMolecular Subtyping of Human Rhinovirus in Children from Three Sub-Saharan African CountriesThe pathogenesis of human rhinovirus (HRV) during severe respiratory disease remains undefined; thus, we aimed to explore the relationship between the HRV molecular subtyping results obtained during severe and asymptomatic childhood infections. Nasopharyngeal/oropharyngeal swabs from children (1 to 59 months of age) hospitalized with pneumonia and from age-frequency-matched controls were collected between August 2011 and August 2013....
VirologyMetagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the CongoWe applied metagenomic next-generation sequencing (mNGS) to detect Zaire Ebola virus (EBOV) and other potential pathogens from whole-blood samples from 70 patients with suspected Ebola hemorrhagic fever during a 2014 outbreak in Boende, Democratic Republic of the Congo (DRC) and correlated these findings with clinical symptoms. Twenty of 31 patients (64.5%) tested in Kinshasa, DRC, were EBOV positive by quantitative reverse...
Immunoassays
ImmunoassaysEvaluation of LDBio Aspergillus ICT Lateral Flow Assay for IgG and IgM Antibody Detection in Chronic Pulmonary AspergillosisDetecting Aspergillus-specific IgG is critical to diagnosing chronic pulmonary aspergillosis (CPA). Existing assays are often cost- and resource-intensive and not compatible with resource-constrained laboratory settings. LDBio Diagnostics has recently commercialized a lateral flow assay based on immunochromatographic technology (ICT) that detects Aspergillus antibodies (IgG and IgM) in less than 30 min, requiring...
ImmunoassaysAntibodies to Borrelia turicatae in Experimentally Infected Dogs Cross-React with Borrelia burgdorferi Serologic AssaysTick-borne relapsing fever (TBRF) is caused by several Borrelia spp. (including Borrelia turicatae), which are primarily transmitted by Ornithodoros ticks. Relapsing fever group species are found worldwide, except for Antarctica. Approximately 500 human cases were reported between 1990 and 2011 in the United States (likely an underestimate), while...
Clinical Veterinary Microbiology
Clinical Veterinary MicrobiologyMatrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Is a Superior Diagnostic Tool for the Identification and Differentiation of Mycoplasmas Isolated from AnimalsIn veterinary diagnostic laboratories, identification of mycoplasmas is achieved by demanding, cost-intensive, and time-consuming methods that rely on antigenic or genetic identification.
Clinical Veterinary MicrobiologySerotype and Genotype (Multilocus Sequence Type) of Streptococcus suis Isolates from the United States Serve as Predictors of PathotypeStreptococcus suis is a significant cause of mortality in piglets and growing pigs worldwide. The species contains pathogenic and commensal strains, with pathogenic strains causing meningitis, arthritis, endocarditis, polyserositis, and septicemia. Serotyping and multilocus sequence typing (MLST) are primary methods to differentiate strains, but the information is...
Epidemiology
EpidemiologyPatterns and Predictors of Staphylococcus aureus Carriage during the First Year of Life: a Longitudinal StudyWe sought here to investigate the patterns of Staphylococcus aureus carriage in the first year of life, its determinants, and the dynamics of transmission between mothers and infants. A prospective longitudinal cohort study of S. aureus carriage among mothers and their infants was performed,...
EpidemiologyClostridioides difficile Whole-Genome Sequencing Reveals Limited Within-Host Genetic Diversity in a Pediatric CohortWhole-genome sequencing (WGS) is a highly sensitive method for identifying genetic relatedness and transmission of Clostridioides difficile strains. Previous studies suggest that as few as 3 core genome single-nucleotide variants (SNVs) discriminate between genetically distinct isolates. Because a single C...
EpidemiologyGenomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing Enterobacterales in Victoria, Australia, 2012 to 2016Carbapenemase-producing Enterobacterales (CPE) are being increasingly reported in Australia, and integrated clinical and genomic surveillance is critical to effectively manage this threat. We sought to systematically characterize CPE in Victoria, Australia, from 2012 to 2016.
Letters to the Editor
Letter to the EditorSusceptibility Categories Should Be Agreed Upon
Letter to the EditorReply to Molitor, “Susceptibility Categories Should Be Agreed Upon”
Letter to the EditorComparative Performance of BD MAX MDR-TB and Cepheid Xpert MTB/RIF Assays
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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.
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Dr. Alexander J. McAdam, Editor in Chief
September 2019 Photo Quiz
Video for Answer to September a Photo Quiz in the Journal of Clinical Microbiology (JCM) https://doi.org/10.1128/JCM.00480-19.