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Editorial
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Minireviews
MinireviewUnderstanding and Addressing CLSI Breakpoint Revisions: a Primer for Clinical LaboratoriesThe Clinical and Laboratory Standards Institute (CLSI) has revised several breakpoints since 2010 for bacteria that grow aerobically. In 2019, these revisions include changes to the ciprofloxacin and levofloxacin breakpoints for the Enterobacteriaceae and Pseudomonas aeruginosa, daptomycin...
MinireviewBeyond Fever and Pain: Diagnostic Methods for Chikungunya VirusChikungunya virus (CHIKV) is an alphavirus that is primarily transmitted by Aedes species mosquitoes. Though reports of an illness consistent with chikungunya date back over 200 years, CHIKV only gained worldwide attention during a massive pandemic that began in East Africa in 2004.
MinireviewA Systematic Review and Meta-analysis of the Diagnostic Accuracy of Nucleic Acid Amplification Tests for Tuberculous MeningitisThe diagnosis of tuberculous meningitis (TBM) is difficult and poses a significant challenge to physicians worldwide. Recently, nucleic acid amplification (NAA) tests have shown promise for the diagnosis of TBM, although their performance has been variable.
Bacteriology
BacteriologyMethicillin-Resistant Staphylococcus aureus Harboring mecC Still Eludes Us in East London, United KingdomReports of methicillin-resistant Staphylococcus aureus (MRSA) harboring the mecC gene have increased in the UK since first being described. To our diagnostic S. aureus multiplex PCR, a mecC primer set was designed and implemented, and then the prevalence in our patient population...
BacteriologyMolecular Typing of Mycoplasma pneumoniae Strains in Sweden from 1996 to 2017 and the Emergence of a New P1 Cytadhesin Gene, Variant 2eMycoplasma pneumoniae causes respiratory infections, such as community-acquired pneumonia (CAP), with epidemics recurring every 3 to 7 years. In 2010 and 2011, many countries experienced an extraordinary epidemic peak.
BacteriologyMethodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology LaboratoryThere is growing evidence for the value of bacterial whole-genome sequencing in hospital outbreak investigations. Our aim was to develop methods that support efficient and accurate low-throughput clinical sequencing of methicillin-resistant Staphylococcus aureus (MRSA) isolates.
Bacteriologyhicap: In Silico Serotyping of the Haemophilus influenzae Capsule LocusHaemophilus influenzae exclusively colonizes the human nasopharynx and can cause a variety of respiratory infections as well as invasive diseases, including meningitis and sepsis. A key virulence determinant of H. influenzae is the polysaccharide capsule, of which six serotypes are known, each...
BacteriologyComparative Evaluation of Enteric Bacterial Culture and a Molecular Multiplex Syndromic Panel in Children with Acute GastroenteritisAlthough enteric multianalyte syndromic panels are increasingly employed, direct comparisons with traditional methods and the inclusion of host phenotype correlations are limited. Luminex xTAG gastrointestinal pathogen panel (GPP) and culture results are highly concordant.
BacteriologyEvaluation of the ELITe InGenius PCR Platform for Detection of Mycoplasma pneumoniaeMycoplasma pneumoniae is the leading cause of bacterial community-acquired pneumonia in persons of all ages. Due to the fastidious nature of this bacterium and the necessary specialized growth media, nucleic acid amplification testing is currently the most reliable means for patient diagnostics.
BacteriologyExtragenital Screening Is Essential for Comprehensive Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in the Pediatric PopulationChlamydia trachomatis and Neisseria gonorrhoeae are the two most common causes of sexually transmitted disease in the United States. Studies in adults, mostly in men who have sex with men, have shown that the prevalence of C. trachomatis...
BacteriologyEvaluation of the Liat Cdiff Assay for Direct Detection of Clostridioides difficile Toxin Genes within 20 MinutesClostridioides difficile is the main causative agent of antibiotic-associated diarrhea. Prompt diagnosis is required for initiation of timely infection control measures and appropriate adjustment of antibiotic treatment.
BacteriologyComparison of Three Nucleic Acid Amplification Tests and Culture for Detection of Group B Streptococcus from Enrichment BrothColonization of the gastrointestinal and genitourinary tracts of pregnant women with group B Streptococcus (GBS) can result in vertical transmission to neonates during labor/delivery. GBS infections in neonates can cause severe complications, such as sepsis, meningitis, and pneumonia.
BacteriologyFactors That Influence Confirmation of Neisseria gonorrhoeae Positivity by Molecular MethodsSeveral Neisseria gonorrhoeae nucleic acid amplification tests (NAATs) with high sensitivity exist. However, the specificity of N. gonorrhoeae NAATs may be suboptimal, particularly for extragenital biospecimens.
BacteriologyCulture of Rectal Swab Specimens for Enteric Bacterial Pathogens Decreases Time to Test Result While Preserving Assay Sensitivity Compared to Bulk Fecal SpecimensDiarrheal illness is a major cause of morbidity and mortality throughout the world, yet the etiologic agent of many cases of gastrointestinal illness remains unspecified, often due to the lack of convenient, timely, and sensitive diagnostic testing. Although bulk fecal specimens remain the recommended specimen type for enteric culture, rectal swabs may be an option preferred by clinicians and patients due to the convenience and timing...
Mycobacteriology and Aerobic Actinomycetes
Mycobacteriology and Aerobic ActinomycetesPhylogenetic Analysis of Mycobacterium tuberculosis Strains in Wales by Use of Core Genome Multilocus Sequence Typing To Analyze Whole-Genome Sequencing DataAn inability to standardize the bioinformatic data produced by whole-genome sequencing (WGS) has been a barrier to its widespread use in tuberculosis phylogenetics. The aim of this study was to carry out a phylogenetic analysis of tuberculosis in Wales, United Kingdom, using Ridom SeqSphere software for core genome multilocus sequence typing (cgMLST) analysis of whole-genome sequencing data.
Mycology
MycologyBeta-d-Glucan for Diagnosing Pneumocystis Pneumonia: a Direct Comparison between the Wako β-Glucan Assay and the Fungitell AssayMeasuring serum beta-d-glucan (BDG) is a useful tool for supporting a quantitative PCR (qPCR)-based diagnosis of suspected Pneumocystis pneumonia (PCP) with bronchoalveolar lavage (BAL) fluid. Since the 2000s, the Fungitell assay was the only BDG assay which was FDA cleared and Conformité Européenne (CE) marked.
MycologyGenotyping of Pneumocystis jirovecii by Use of a New Simplified Nomenclature System Based on the Internal Transcribed Spacer Regions and 5.8S rRNA Gene of the rRNA OperonGenotyping based on internal transcribed spacer 1 (ITS1) and ITS2 of the rRNA operon has played an important role in understanding the transmission and epidemiology of Pneumocystis jirovecii, one of the major opportunistic pathogens in individuals with AIDS and other immunocompromised individuals. The widespread use of this typing system has resulted in several...
Immunoassays
ImmunoassaysEvaluation of the Bio-Rad Geenius HIV 1/2 Assay as Part of a Confirmatory HIV Testing Strategy for Quebec, Canada: Comparison with Western Blot and Inno-Lia AssaysThe rapid confirmatory Bio-Rad Geenius HIV 1/2 assay was evaluated as an alternative to the HIV-1 Western blot (WB) confirmatory assay. A total of 370 retrospective samples collected from 356 patients were tested.
Clinical Veterinary Microbiology
Clinical Veterinary MicrobiologyDevelopment of Molecular Methods for Rapid Differentiation of Mycoplasma gallisepticum Vaccine Strains from Field IsolatesMycoplasma gallisepticum is among the most economically significant mycoplasmas causing production losses in poultry. Seven melt-curve and agarose gel-based mismatch amplification mutation assays (MAMAs) and one PCR are provided in the present study to distinguish the M. gallisepticum vaccine...
Epidemiology
EpidemiologyPigment Visibility on Rectal Swabs Used To Detect Enteropathogens: a Prospective Cohort StudyData are lacking regarding the impact of visible pigment on rectal swab diagnostic accuracy. We describe the test characteristics of rectal swabs with and without pigment in children with gastroenteritis.
EpidemiologyEvidence of Sharing of Klebsiella pneumoniae Strains between Healthy Companion Animals and Cohabiting HumansThis study aimed to characterize the fecal colonization and sharing of Klebsiella pneumoniae strains between companion animals and humans living in close contact. Fecal samples were collected from 50 healthy participants (24 humans, 18 dogs, and 8 cats) belonging to 18 households.
EpidemiologyComparing Patient Risk Factor-, Sequence Type-, and Resistance Locus Identification-Based Approaches for Predicting Antibiotic Resistance in Escherichia coli Bloodstream InfectionsRapid diagnostic tests for antibiotic resistance that identify the presence or absence of antibiotic resistance genes/loci are increasingly being developed. However, these approaches usually neglect other sources of predictive information which could be identified over shorter time periods, including patient epidemiologic risk factors for antibiotic resistance and markers of lineage.
EpidemiologySummary and Trends of the Russian Gonococcal Antimicrobial Surveillance Programme, 2005 to 2016The Russian Gonococcal Antimicrobial Surveillance Programme (RU-GASP) was established in 2004 and operated continuously during the years from 2005 to 2016. The aims of this study were to summarize the RU-GASP results over this 12-year period and evaluate the trends in Neisseria gonorrhoeae antimicrobial resistance in Russia.
EpidemiologyDiagnostic Accuracy of Stool Xpert MTB/RIF for Detection of Pulmonary Tuberculosis in Children: a Systematic Review and Meta-analysisInvasive collection methods are often required to obtain samples for the microbiological evaluation of children with presumptive pulmonary tuberculosis (PTB). Nucleic acid amplification testing of easier-to-collect stool samples could be a noninvasive method of diagnosing PTB.
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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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Commentaries
The use of nucleic acid amplification tests (NAATs) for the diagnosis of Clostridium (Clostridioides) difficile infection (CDI) leads to overdiagnosis. To improve the clinical specificity of NAATs, there has been a recent interest in using toxin gene cycle thresholds (CTs) to predict the presence and absence of toxins.
The growth of pathogen genomics shows no signs of abating. Whole-genome sequencing of clinical viral and bacterial isolates continues to grow in nearly exponential bounds.