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Minireviews
MinireviewUpdate on Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Identification of Filamentous FungiMatrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS)-based species identification has found its place in many clinical routine diagnostic laboratories over the past years, allowing significantly reduced turnaround times and high-precision results. With regard to MALDI-TOF MS for filamentous fungi, here, we discuss different approaches for sample processing and growth conditions before analysis. In...
MinireviewDiagnostic Approach for Arboviral Infections in the United StatesDomestic arthropod-borne viruses (arboviruses) are single-stranded RNA viruses, the most common of which include the mosquito-borne West Nile virus, St. Louis encephalitis virus, La Crosse virus, Jamestown Canyon virus, and eastern equine encephalitis virus, as well as the tick-borne Powassan virus. Previously considered rare infections, they have been detected with increasing frequency over the past 2 decades. Here, we present an...
Bacteriology
BacteriologyEvaluation of the Xpert Carba-R NxG Assay for Detection of Carbapenemase Genes in a Global Challenge Set of Pseudomonas aeruginosa IsolatesThe growing prevalence and diversity of carbapenemase producers among carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates warrants an expansion of detection capabilities. The purpose of this study was to evaluate the performance of the commercially available Xpert Carba-R (Carba-R) and the research-use-only Xpert Carba-R NxG (Carba-R NxG) in a global...
BacteriologyA Novel Platform Using RNA Signatures To Accelerate Antimicrobial Susceptibility Testing in Neisseria gonorrhoeaeThe rise of antimicrobial-resistant pathogens can be attributed to the lack of a rapid pathogen identification (ID) or antimicrobial susceptibility testing (AST), resulting in delayed therapeutic decisions at the point of care. Gonorrhea is usually empirically treated, with no AST results available before treatment, thus contributing to the rapid rise in drug resistance. Here, we present a rapid AST platform using RNA signatures for...
BacteriologyGenomic Serotyping, Clinical Manifestations, and Antimicrobial Resistance of Nontyphoidal Salmonella Gastroenteritis in Hospitalized Children in Ho Chi Minh City, VietnamNontyphoidal Salmonella (NTS) are among the most common etiological agents of diarrheal diseases worldwide and have become the most commonly detected bacterial pathogen in children hospitalized with diarrhea in Vietnam. Aiming to better understand the epidemiology, serovar distribution, antimicrobial resistance (AMR), and clinical manifestation of NTS gastroenteritis in Vietnam, we conducted a clinical genomics investigation of...
BacteriologySensitive Identification of Bacterial DNA in Clinical Specimens by Broad-Range 16S rRNA Gene EnrichmentThe broad-range detection and identification of bacterial DNA from clinical specimens are a foundational approach in the practice of molecular microbiology. However, there are circumstances under which conventional testing may yield false-negative or otherwise uninterpretable results, including the presence of multiple bacterial templates or degraded nucleic acids. Here, we describe an alternative, next-generation sequencing approach...
BacteriologyRetrospective Review of Clinical Utility of Shotgun Metagenomic Sequencing Testing of Cerebrospinal Fluid from a U.S. Tertiary Care Medical CenterShotgun metagenomic sequencing can detect nucleic acids from bacteria, fungi, viruses, and/or parasites in clinical specimens; however, little data exist to guide its optimal application to clinical practice. We retrospectively reviewed results of shotgun metagenomic sequencing testing requested on cerebrospinal fluid samples submitted to an outside reference laboratory from December 2017 through December 2019. Of the 53 samples from...
BacteriologyGram Staining: a Comparison of Two Automated Systems and Manual StainingVarious Gram staining automated systems are available to accelerate and standardize the staining process, but a systematic comparison of different systems is largely lacking. The objective of this study was to evaluate two devices in comparison to manual Gram staining. Clinical samples (n = 500; University Hospital Münster, Germany; May to June 2020) were simultaneously Gram stained manually and with two automated Gram stainers...
BacteriologyVariability in Zinc Concentration among Mueller-Hinton Broth Brands: Impact on Antimicrobial Susceptibility Testing of Metallo-β-Lactamase-Producing EnterobacteriaceaeZinc concentrations in cation-adjusted Mueller-Hinton broth (caMHB) from different manufacturers have been found to differ. Here, we evaluated the impact of utilizing different brands and lots of commercially available caMHB on the classification of the antimicrobial susceptibility of metallo-β-lactamase (MBL)-harboring Enterobacteriaceae. We also evaluated the addition of EDTA to caMHB as a means of achieving zinc-limited...
Chlamydiology and Rickettsiology
Chlamydiology and RickettsiologyThe Isolation of Orientia tsutsugamushi and Rickettsia typhi from Human Blood through Mammalian Cell Culture: a Descriptive Series of 3,227 Samples and Outcomes in the Lao People’s Democratic RepublicIn the Lao People’s Democratic Republic (Laos), rickettsial infections, including scrub and murine typhus, account for a significant burden of fevers. The Mahosot Hospital Microbiology Laboratory in Vientiane, Laos, routinely performs rickettsial isolation from hospitalized patients with suspected rickettsioses using mammalian cell culture systems. We review the clinical and laboratory factors associated with successful...
Mycobacteriology and Aerobic Actinomycetes
Mycobacteriology and Aerobic ActinomycetesAntimicrobial Susceptibility and Phylogenetic Relations in a German Cohort Infected with Mycobacterium abscessusMycobacterium abscessus is a highly antibiotic-resistant opportunistic pathogen causing clinically challenging infections in patients with preexisting lung diseases or under immunosuppression. Hence, reliable antibiotic susceptibility data are required for effective treatment. Aims of this study were to investigate (i) the congruence of genotypic and phenotypic...
Mycobacteriology and Aerobic ActinomycetesMycobacterium septicum: a 6-Year Clinical Experience from a Tertiary Hospital and Reference LaboratoryMycobacterium septicum is a rarely identified nontuberculous mycobacterium capable of causing infections in both healthy and immunocompromised individuals. Only a few cases of M. septicum infections have been reported, which makes recognizing corresponding clinical disease more challenging for...
Mycology
MycologyAn Evaluation of the Performance of the IMMY Aspergillus Galactomannan Enzyme-Linked Immunosorbent Assay When Testing Serum To Aid in the Diagnosis of Invasive AspergillosisThe objectives of this study were to evaluate the performance of the recently released IMMY Aspergillus galactomannan enzyme immunoassay (IMMY GM-EIA) when testing serum samples and to identify the optimal galactomannan index (GMI) positivity threshold for the diagnosis of invasive aspergillosis (IA). This was a retrospective case/control study, comprising 175 serum samples obtained from 131 patients, 35 of whom had probable or...
MycologySpiromastigoides asexualis: Phylogenetic Analysis and Evaluation as a Cause of False-Positive Blastomyces DNA Probe Test ResultsThis is the first case of Spiromastigoides asexualis human infection, and it notably gave a false-positive Blastomyces DNA probe laboratory result. We further investigated other Spiromastigoides isolates as a cause of false-positive testing results, their phylogenetic relationship, and their susceptibility profiles to clinically available antifungal...
MycologyEvaluation of the Amplex eazyplex Loop-Mediated Isothermal Amplification Assay for Rapid Diagnosis of Pneumocystis jirovecii PneumoniaQuantitative PCR (qPCR) assays are the gold standard for diagnosis of Pneumocystis jirovecii pneumonia (PCP). However, they are laborious and require skilled personnel. Therefore, execution outside regular working hours of the molecular biology laboratory is limited. The eazyplex P. jirovecii assay...
MycologyNanopore Sequencing of the Fungal Intergenic Spacer Sequence as a Potential Rapid Diagnostic AssayFungal infections are being caused by a broadening spectrum of fungi, yet in many cases, identification to the species level is required for proper antifungal selection. We investigated the fungal intergenic spacer (IGS) sequence in combination with nanopore sequencing for fungal identification. We sequenced isolates from two Cryptococcus species complexes, C....
Parasitology
ParasitologyRapid Diagnostic Tests for Trypanosoma cruzi Infection: Field Evaluation of Two Registered Kits in a Region of Endemicity and a Region of Nonendemicity in ArgentinaInfection by Trypanosoma cruzi (Chagas disease [ChD]) affects around 7 million people in the Americas, most of whom are unaware of their status due to lack of clinical manifestations and poor access to diagnosis. Rapid diagnostic tests (RDTs) are widely used for screening for different infections (HIV, hepatitis B, and syphilis), and their application for ChD would...
Virology
VirologyReplicate Aptima Assay for Quantifying Residual Plasma Viremia in Individuals on Antiretroviral TherapyDetection of residual plasma viremia in antiretroviral therapy (ART)-suppressed HIV-infected individuals is critical for characterizing the latent reservoir and evaluating the impact of cure interventions. Ultracentrifugation-based single-copy assays are sensitive but labor intensive. Fully automated replicate testing using a standard clinical viral load assay was evaluated as a high-throughput alternative for the quantification of low-...
VirologyAutomated Multireplicate Quantification of Persistent HIV-1 Viremia in Individuals on Antiretroviral TherapyClearance of low-level viremia that persists in most HIV-1-positive individuals on antiretroviral therapy (ART) is an important milestone for efforts to cure HIV-1 infection. The level of persistent viremia on ART is generally below the lower limit of quantification (LOQ) of current FDA-cleared plasma HIV-1 RNA assays (20 to 40 copies/ml) but can be quantified by reverse transcriptase PCR (RT-PCR) assays with single-copy sensitivity....
VirologyNovel Use of Rapid Antigen Influenza Testing in the Outpatient Setting To Provide an Early Warning Sign of Influenza Activity in the Emergency Departments of an Integrated Health SystemSeasonal influenza virus is associated with high morbidity and mortality especially in vulnerable patient populations. Here, we demonstrate the novel use of Sofia influenza A+B fluorescent immunoassay (FIA), a rapid antigen-based influenza point-of-care test (POCT), combined with Virena software for automatic deidentified tracking of influenza activity across the Los Angeles area and for predicting surges of influenza cases in the...
VirologyAmino Acid Substitutions Associated with Treatment Failure for Hepatitis C Virus InfectionDespite the high virological response rates achieved with current directly acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 2% to 5% of treated patients do not achieve a sustained viral response. The identification of amino acid substitutions associated with treatment failure requires analytical designs, such as subtype-specific ultradeep sequencing (UDS) methods, for HCV characterization and patient management....
Immunoassays
ImmunoassaysPerformance of Commercial Mycoplasma hyopneumoniae Serum Enzyme-Linked Immunosorbent Assays under Experimental and Field ConditionsMycoplasma hyopneumoniae is an economically significant pathogen of swine. M. hyopneumoniae serum antibody detection via commercial enzyme-linked immunosorbent assays (ELISAs) is widely used for routine surveillance in commercial swine production systems. Samples from two studies were used to...
ImmunoassaysSerological Assays Estimate Highly Variable SARS-CoV-2 Neutralizing Antibody Activity in Recovered COVID-19 PatientsThe development of neutralizing antibodies (NAbs) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) following infection or vaccination is likely to be critical for the development of sufficient population immunity to drive cessation of the coronavirus disease of 2019 (COVID-19) pandemic. A large number of serologic tests, platforms, and methodologies are being employed to determine seroprevalence in populations to...
Clinical Veterinary Microbiology
Clinical Veterinary MicrobiologyA Novel Real-Time PCR-Based Screening Test with Pooled Fecal Samples for Bovine Johne’s DiseaseJohne’s disease (JD) is an economically important infectious disease in livestock farming caused by Mycobacterium avium subsp. paratuberculosis. As an alternative to serological tests, which are used mainly for the screening of whole herds, we developed a novel ResoLight-based real-time PCR (RL-PCR) assay with pooled fecal samples for the detection of fecal...
Epidemiology
EpidemiologyFull Molecular Typing of Neisseria meningitidis Directly from Clinical Specimens for Outbreak InvestigationNeisseria meningitidis is a leading cause of bacterial meningitis and sepsis worldwide and an occasional cause of meningococcal urethritis. When isolates are unavailable for surveillance or outbreak investigations, molecular characterization of pathogens needs to be performed directly from clinical specimens, such as cerebrospinal fluid (CSF), blood, or urine. However...
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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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