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Minireviews
MinireviewMedical Parasitology Taxonomy Update, 2016–2017Parasite taxonomy continues to change as molecular and morphologic studies enhance our understanding of parasite relatedness. This minireview builds on the information provided in the last taxonomy update in this journal to summarize new and revised clinically relevant human parasite taxonomic changes that have occurred in 2016 and 2017.
MinireviewAn Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and...
MinireviewName Changes for Fungi of Medical Importance, 2016–2017This article lists proposed new or revised species names and classification changes associated with fungi of medical importance that were published in the years 2016 and 2017. While many of the revised names listed have been widely adopted without further discussion, some may take longer to achieve more general usage.
MinireviewTaxonomic Changes for Human and Animal Viruses, 2016 to 2018The classification of viruses provides the structure necessary to appreciate their biological diversity. Herein, we provide an update to our previous review of changes in viral taxonomy, covering changes between 2016 and 2018.
Bacteriology
BacteriologyToxin B PCR Amplification Cycle Threshold Adds Little to Clinical Variables for Predicting Outcomes in Clostridium difficile Infection: a Retrospective Cohort StudyThe objective of the present study was to evaluate the value of the PCR cycle threshold (CT) for predicting the recurrence/severity of infection compared to that of toxin detection plus clinical variables. First episodes of Clostridium difficile infection (CDI) diagnosed during 2015 at our institution were included.
BacteriologyTwo-Site Evaluation of the Colistin Broth Disk Elution Test To Determine Colistin In Vitro Activity against Gram-Negative BacilliLimited methods for colistin MIC determination are available to clinical microbiology laboratories. The purpose of this study was to evaluate the accuracy of the colistin broth disk elution (CBDE) test compared to that of broth microdilution (BMD) for identifying colistin MICs.
BacteriologyEvaluation of the CosmosID Bioinformatics Platform for Prosthetic Joint-Associated Sonicate Fluid Shotgun Metagenomic Data AnalysisWe previously demonstrated that shotgun metagenomic sequencing can detect bacteria in sonicate fluid, providing a diagnosis of prosthetic joint infection (PJI). A limitation of the approach that we used is that data analysis was time-consuming and specialized bioinformatics expertise was required, both of which are barriers to routine clinical use.
BacteriologyUsing Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal SalmonellaNontyphoidal Salmonella species are the leading bacterial cause of foodborne disease in the United States. Whole-genome sequences and paired antimicrobial susceptibility data are available for Salmonella strains because of surveillance efforts from public health agencies.
BacteriologyDirect Identification of 80 Percent of Bacteria from Blood Culture Bottles by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Using a 10-Minute Extraction ProtocolMatrix-assisted laser desorption ionization–time of flight mass spectrometry is not widely used to identify bacteria directly from positive blood culture bottles (BCBs) because of overlong protocols. The objective of this work was to develop and evaluate a simple extraction protocol for reliable identification from BCBs.
BacteriologyMulticenter Evaluation of NeuMoDx Group B Streptococcus Assay on the NeuMoDx 288 Molecular SystemGroup B Streptococcus (GBS) is the leading cause of neonatal sepsis and meningitis in developed countries. Recommendations for antepartum GBS detection include enriched culture with several options for identifying GBS, some of which are time-consuming.
BacteriologyMulticenter Clinical Evaluation of the Automated Aries Bordetella AssayMolecular methods offer superior sensitivity and specificity and reduce testing turnaround time from days to hours for detection of Bordetella pertussis and Bordetella parapertussis. In this study, we evaluated the performance of the automated PCR-based Aries Bordetella Assay, which detects...
BacteriologyMulticenter Clinical Evaluation of the Automated Aries Group A Strep PCR Assay from Throat SwabsGroup A Streptococcus (GAS) is one of the leading causes of bacterial pharyngitis. Early GAS diagnosis is critical for appropriate antibiotic administration that reduces the risk of GAS sequelae and limits spread of the infection.
BacteriologySonication Culture of Antimicrobial Agent-Containing Cement Spacers Removed during Staged Revisions for Arthroplasty InfectionDiagnosis of persistent infection at the time of reimplantation for staged revision of infected arthroplasties is challenging. Implant sonication culture for the diagnosis of prosthetic joint infection (PJI) has improved sensitivity compared to standard periprosthetic tissue culture.
BacteriologyComprehensive Evaluation of Compendial USP<71>, BacT/Alert Dual-T, and Bactec FX for Detection of Product Sterility Testing ContaminantsThe emergence of cell therapy programs in large academic centers has led to an increasing demand for clinical laboratories to assist with product sterility testing. Automated blood culture systems have shown promise as alternatives to the manual USP<71> compendial method, but current published data are limited by small organism test sets, particularly for molds.
BacteriologyEvaluation of the ePlex Blood Culture Identification Panels for Detection of Pathogens in Bloodstream InfectionsRapid identification and susceptibility testing results are of importance for the early appropriate therapy of bloodstream infections. The ePlex (GenMark Diagnostics) blood culture identification (BCID) panels are fully automated PCR-based assays designed to identify Gram-positive and Gram-negative bacteria, fungi, and bacterial resistance genes within 1.5 h from positive blood culture.
BacteriologyAssessment of Test Performance and Potential for Environmental Contamination Associated with a Point-of-Care Molecular Assay for Group A Streptococcus in an End User SettingAlthough U.S. Food and Drug Administration-approved and CLIA-waived point-of-care (POC) molecular systems are being implemented in routine clinical practice, instrument reliability, test performance in the hands of end users, and the potential for environmental contamination resulting from use of POC molecular systems have not been extensively evaluated.
Mycobacteriology and Aerobic Actinomycetes
Mycobacteriology and Aerobic ActinomycetesMycobacterium talmoniae, a Potential Pulmonary Pathogen Isolated from Multiple Patients with Bronchiectasis in the United States, Including the First Case of Clinical Disease in a Patient with Cystic FibrosisWe characterize three respiratory isolates of the recently described species Mycobacterium talmoniae recovered in Texas, Louisiana, and Massachusetts, including the first case of disease in a patient with underlying cystic fibrosis. The three isolates had a 100% match to M. talmoniae NE-TNMC-100812...
Mycobacteriology and Aerobic ActinomycetesMODS-Wayne, a Colorimetric Adaptation of the Microscopic-Observation Drug Susceptibility (MODS) Assay for Detection of Mycobacterium tuberculosis Pyrazinamide Resistance from Sputum SamplesAlthough pyrazinamide (PZA) is a key component of first- and second-line tuberculosis treatment regimens, there is no gold standard to determine PZA resistance. Approximately 50% of multidrug-resistant tuberculosis (MDR-TB) and over 90% of extensively drug-resistant tuberculosis (XDR-TB) strains are also PZA resistant.
Mycobacteriology and Aerobic ActinomycetesPerformance of RGM Medium for Isolation of Nontuberculous Mycobacteria from Respiratory Specimens from Non-Cystic Fibrosis PatientsA new selective medium for rapidly growing mycobacteria (RGM medium) was evaluated on respiratory specimens from non-cystic fibrosis patients and compared to the mycobacterial growth indicator tube (MGIT) system and Middlebrook 7H11 agar for the isolation of all nontuberculous mycobacteria (NTM). A total of 203 mucolyzed respiratory specimens collected from 163 patients were inoculated on RGM medium and incubated at both 30°C (RGM30)...
Mycobacteriology and Aerobic ActinomycetesAdded Value of Xpert MTB/RIF Ultra for Diagnosis of Pulmonary Tuberculosis in a Low-Prevalence SettingXpert MTB/RIF (Xpert) for direct molecular detection of Mycobacterium tuberculosis and rifampin resistance from clinical specimens has dramatically improved the diagnosis of tuberculosis (TB). Xpert MTB/RIF Ultra (Ultra) is proposed as a substitute of Xpert with increased sensitivity and improved rifampin resistance detection.
Mycology
MycologyEmydomyces testavorans, a New Genus and Species of Onygenalean Fungus Isolated from Shell Lesions of Freshwater Aquatic TurtlesThe fungal order Onygenales includes many pathogens of humans and animals, and recent studies have shown some onygenalean fungi to be significant emerging pathogens of reptiles. Although many of these fungi have similar morphological features in histologic tissue sections, recent molecular analyses have revealed a genetically complex and diverse group of reptile pathogens comprising several genera, most notably ...
MycologyInvasive Infections Due to Trichosporon: Species Distribution, Genotyping, and Antifungal Susceptibilities from a Multicenter Study in ChinaA total of 133 clinical Trichosporon isolates were collected in the National China Hospital Invasive Fungal Surveillance Net (CHIF-NET) program in 2009 to 2016. Accurate identification was performed by sequencing of the intergenic spacer 1 (IGS1) region.
Parasitology
ParasitologyRole of Toxoplasma IgA as Part of a Reference Panel for the Diagnosis of Acute Toxoplasmosis during PregnancyThis study evaluated the usefulness of adding the Toxoplasma gondii IgA antibody enzyme-linked immunosorbent assay (ELISA) to the serologic panel of tests done for the diagnosis of acute toxoplasmosis in pregnant women in a reference laboratory in the United States. We conducted a retrospective study of 690 consecutive pregnant women with positive...
Virology
VirologyMultiplex Droplet Digital PCR Assay for Quantification of Human T-Cell Leukemia Virus Type 1 Subtype c DNA Proviral Load and T Cells from Blood and Respiratory Exudates Sampled in a Remote SettingDuring human T-cell leukemia virus type 1 (HTLV-1) infection, the frequency of cells harboring an integrated copy of viral cDNA, the proviral load (PVL), is the main risk factor for progression of HTLV-1-associated diseases. Accurate quantification of provirus by droplet digital PCR (ddPCR) is a powerful diagnostic tool with emerging uses for monitoring viral expression.
VirologyClinical Validation of the cobas HPV Test on the cobas 6800 System for the Purpose of Cervical ScreeningThis study demonstrates that the clinical sensitivity, specificity, and reproducibility of the novel cobas human papillomavirus (HPV) test on the cobas 6800 system for high-risk HPV types fulfills the criteria for use in population-based cervical screening. The criteria were formulated by an international consortium, using the cobas 4800 HPV test as a validated reference assay.
VirologyCombination of Nonstructural Protein 1-Based Enzyme-Linked Immunosorbent Assays Can Detect and Distinguish Various Dengue Virus and Zika Virus InfectionsThe recent outbreaks of Zika virus (ZIKV) and associated birth defects in regions of dengue virus (DENV) endemicity emphasize the need for sensitive and specific serodiagnostic tests. We reported previously that enzyme-linked immunosorbent assays (ELISAs) based on the nonstructural protein 1 (NS1) of DENV serotype 1 (DENV1) and ZIKV can distinguish primary DENV1, secondary DENV, and ZIKV infections.
VirologyMissing Cases of Herpes Simplex Virus (HSV) Infection of the Central Nervous System When the Reller Criteria Are Applied for HSV PCR Testing: a Multicenter StudyPrevious studies suggested that herpes simplex virus (HSV) PCR testing can be safely deferred in patients with normal cerebrospinal fluid (CSF) white blood cell (WBC) counts and protein levels as long as they are older than 2 years of age and are not immunocompromised, the so-called Reller criteria. In this multicenter study, we retrospectively assessed the validity of these screening criteria in our setting.
Immunoassays
ImmunoassaysField Performance and Diagnostic Accuracy of a Low-Cost Instrument-Free Point-of-Care CD4 Test (Visitect CD4) Performed by Different Health Worker Cadres among Pregnant WomenMeasuring CD4 counts remains an important component of HIV care. The Visitect CD4 is the first instrument-free low-cost point-of-care CD4 test with results interpreted visually after 40 min, providing a result of ≥350 CD4 cells/mm3.
Letters to the Editor
Letter to the EditorIndustry Perspectives on the WHO Essential Diagnostics List
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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
Commentaries
Polymyxins are relied upon for the treatment of carbapenem-resistant Gram-negative bacterial infections, but polymyxin resistance is increasing. Only broth microdilution is recommended for polymyxin susceptibility testing, but this method is impractical for most clinical microbiology laboratories.
Thanks to the genomics revolution, thousands of strain-specific whole-genome sequences are now accessible for a wide range of pathogenic bacteria. This availability enables big data informatics approaches to be used to study the spread and acquisition of antimicrobial resistance (AMR).