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The Brief Case
Minireviews
MinireviewHuman Bacterial Repertoire of the Urinary Tract: a Potential Paradigm ShiftThe aim of this article is to review the human repertoire of bacteria in urine already described by culture and metagenomic techniques and published in the literature. Our study led us to compare this repertoire with other available human repertoires.
MinireviewGenome-Based Prediction of Bacterial Antibiotic ResistanceClinical microbiology has long relied on growing bacteria in culture to determine antimicrobial susceptibility profiles, but the use of whole-genome sequencing for antibiotic susceptibility testing (WGS-AST) is now a powerful alternative. This review discusses the technologies that made this possible and presents results from recent studies to predict resistance based on genome sequences.
Bacteriology
BacteriologyA Prospective Study of Acinetobacter baumannii Complex Isolates and Colistin Susceptibility Monitoring by Mass Spectrometry of Microbial Membrane GlycolipidsAcinetobacter baumannii is a prevalent nosocomial pathogen with a high incidence of multidrug resistance. Treatment of infections due to this organism with colistin, a last-resort antibiotic of the polymyxin class, can result in the emergence of colistin-resistant strains.
BacteriologyReassessment of Routine Midstream Culture in Diagnosis of Urinary Tract InfectionMidstream urine (MSU) culture remains the gold standard diagnostic test for confirming urinary tract infection (UTI). We previously showed that patients with chronic lower urinary tract symptoms (LUTS) below the diagnostic cutoff on MSU culture may still harbor bacterial infection and that their antibiotic treatment was associated with symptom resolution.
BacteriologyBlood Smears Have Poor Sensitivity for Confirming Borrelia miyamotoi DiseaseBorrelia miyamotoi disease (BMD) is a newly recognized borreliosis that is cotransmitted by ticks wherever Lyme disease is zoonotic. Unlike Borrelia burgdorferi sensu lato, the agent of Lyme disease, B. miyamotoi is...
BacteriologyPublic Health Efforts Can Impact Adoption of Current Susceptibility Breakpoints, but Closer Attention from Regulatory Bodies Is NeededMicrobiological testing, including interpretation of antimicrobial susceptibility testing results using current breakpoints, is crucial for clinical care and infection control. Continued use of obsolete Enterobacteriaceae carbapenem breakpoints is common in clinical laboratories.
BacteriologyLevels of Mycoplasma genitalium Antimicrobial Resistance Differ by Both Region and Gender in the State of Queensland, Australia: Implications for Treatment GuidelinesMycoplasma genitalium is frequently associated with urogenital and rectal infections, with the number of cases of macrolide-resistant and quinolone-resistant M. genitalium infection continuing to increase. In this study, we examined the levels of resistance to these two common antibiotic treatments...
BacteriologyA Resazurin Reduction-Based Assay for Rapid Detection of Polymyxin Resistance in Acinetobacter baumannii and Pseudomonas aeruginosaA rapid test was developed for identification of polymyxin resistance in nonfermenting bacteria. This test detects viable cells after growth in a medium containing a defined concentration of colistin.
BacteriologyWhole-Genome Sequencing for Characterization of Capsule Locus and Prediction of Serogroup of Invasive Meningococcal IsolatesInvasive meningococcal disease is mainly caused by Neisseria meningitidis serogroups A, B, C, X, W, and Y. The serogroup is typically determined by slide agglutination serogrouping (SASG) and real-time PCR (RT-PCR).
BacteriologyA Core Genome Multilocus Sequence Typing Scheme for Enterococcus faecalisAmong enterococci, Enterococcus faecalis occurs ubiquitously, with the highest incidence of human and animal infections. The high genetic plasticity of E. faecalis complicates both molecular investigations and phylogenetic analyses.
BacteriologyEvaluation of the Accelerate Pheno System for Identification of Acinetobacter Clinical Isolates and Minocycline Susceptibility TestingThe Accelerate Pheno system (AXDX) is a rapid phenotypic bacterial identification and susceptibility testing system which is approved for use with positive blood cultures. Acinetobacter baumannii is a nosocomial pathogen for which the limited treatment options include minocycline in the case of multidrug resistance.
BacteriologyImpact of Gastrointestinal Panel Implementation on Health Care Utilization and OutcomesPCR-based multiplex gastrointestinal (GI) pathogen panels have started to replace stool culture and ova and parasite exam as a rapid and accurate means of diagnosing acute gastroenteritis. However, there are limited data on the impact of panel testing on patient outcomes.
BacteriologyEvaluation of Ciprofloxacin and Levofloxacin Disk Diffusion and Etest Using the 2019 Enterobacteriaceae CLSI BreakpointsIn 2019, the Clinical and Laboratory Standards Institute (CLSI) published revisions to the Enterobacteriaceae ciprofloxacin and levofloxacin breakpoints. We evaluated the performance of disk diffusion and Etest compared to that of reference broth microdilution by use of the revised breakpoints.
BacteriologyEvaluation of a Novel Stool Antigen Rapid Test Kit for Detection of Helicobacter pylori InfectionThe Quick Chaser H. pylori (QCP), which is a novel antigen detection kit for Helicobacter pylori, was developed recently. The previous examination kits targeted the catalase of H. pylori; however, this new test kit, to the best of...
Mycobacteriology and Aerobic Actinomycetes
Mycobacteriology and Aerobic ActinomycetesImpact of External Quality Assurance on the Quality of Xpert MTB/RIF Testing in Viet NamFollowing the endorsement of the Xpert MTB/RIF assay (Cepheid, Sunnyvale, CA, USA) by the World Health Organization (WHO) in 2010, Viet Nam’s National Tuberculosis Control Program (NTP) began using GeneXpert instruments in NTP laboratories. In 2013, Viet Nam’s NTP implemented an Xpert MTB/RIF external quality assurance (EQA) program in collaboration with the U.S.
Mycobacteriology and Aerobic ActinomycetesNoninvasive Detection of Tuberculosis by Oral Swab AnalysisDiagnostic tests for tuberculosis (TB) usually require collection of sputum, a viscous material derived from human airways. Sputum can be difficult and hazardous to collect and challenging to process in the laboratory.
Mycology
MycologyUtility of Serum and Bronchoalveolar Lavage Fluid Galactomannan in Diagnosis of Chronic Pulmonary AspergillosisThe value of serum and bronchoalveolar lavage fluid galactomannan (BALF-GM) in diagnosing chronic pulmonary aspergillosis (CPA) remains unclear. Here, we study the diagnostic efficacy of GM in the diagnosis of CPA.
Parasitology
ParasitologyPerformance of Antigen Concentration Thresholds for Attributing Fever to Malaria among Outpatients in AngolaThe density of malaria parasites is a key determinant of whether an infected individual develops fever. While the pyrogenic threshold for malaria parasite density has been well studied, there are no analogous data on the antigen levels associated with fever during infection.
Virology
VirologyClinical Impact of Rapid Point-of-Care PCR Influenza Testing in an Urgent Care Setting: a Single-Center StudySeasonal influenza virus causes significant morbidity and mortality each year. Point-of-care (POC) testing using rapid influenza diagnostic tests (RIDTs), immunoassays that detect viral antigens, are often used for diagnosis by physician offices and urgent care centers.
VirologyA Simpler and More Sensitive Single-Copy HIV-1 RNA Assay for Quantification of Persistent HIV-1 Viremia in Individuals on Suppressive Antiretroviral TherapyA real-time quantitative reverse transcriptase PCR assay with single-copy sensitivity targeting the integrase region of HIV-1 (integrase single-copy assay [iSCA] v1.0) has been widely used to quantify plasma viremia in individuals on antiretroviral therapy (ART). iSCA v1.0 requires the use of an ultracentrifuge, and only about half of the nucleic acid extracted from plasma is assayed for HIV-1 RNA.
Immunoassays
ImmunoassaysEvaluation of a Rapid Immunochromatographic Assay and Two Enzyme-Linked Immunosorbent Assays for Detection of IgM-Class Antibodies to Zika VirusThere are currently five serologic assays available for detection of anti-Zika virus (ZIKV) IgM-class antibodies with U.S. Food and Drug Administration emergency use authorization.
ImmunoassaysComprehensive Evaluation of Differential Serodiagnosis between Zika and Dengue Viral InfectionsDiagnostic testing for Zika virus (ZIKV) or dengue virus (DENV) infection can be accomplished by a nucleic acid detection method; however, a negative result does not exclude infection due to the low virus titer during infection depending on the timing of sample collection. Therefore, a ZIKV- or DENV-specific serological assay is essential for the accurate diagnosis of patients and to mitigate potential severe health outcomes.
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ImmunoassaysAn Automated Immunoblot Method for Detection of IgG Antibodies to Hepatitis C Virus: a Potential Supplemental Antibody Confirmatory AssayAn estimated 41,200 people were newly infected with hepatitis C virus (HCV) in 2016 in the United States. Screening tests for antibodies to HCV may generate up to 32% false positivity in low-risk populations.
Clinical Veterinary Microbiology
Clinical Veterinary MicrobiologyTest Agreement among Biochemical Methods, Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry, and 16S rRNA Sequencing for Identification of Microorganisms Isolated from Bovine Milk...The objective of this prospective study was a blinded comparison of three methods for the identification of bacteria isolated on Columbia blood agar from milk samples of dairy cows. Basic biochemical testing, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), and 16S rRNA partial genome sequence analysis were compared for bacterial identification to the genus or species level.
Clinical Veterinary MicrobiologyDetection and Differentiation of Two Koala Gammaherpesviruses by Use of High-Resolution Melt (HRM) Analysis Reveals Differences in Viral Prevalence and Clinical Associations in a Large Study of Free-Ranging KoalasThe iconic koala (Phascolarctos cinereus) is host to two divergent gammaherpesviruses, phascolarctid gammaherpesviruses 1 and 2 (PhaHV-1 and -2), but the clinical significance of the individual viruses is unknown and current diagnostic methods are unsuitable for differentiating between the viruses in large-scale studies. To address this, we modified a pan-herpesvirus...
Letters to the Editor
Letter to the EditorValue of Patient Population Selection and Lyme Borreliosis Tests
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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
Commentary
Expansion of technologies, changing infrastructure, and dwindling resources have produced the need for health care reform and changes in clinical laboratories. The health care model will have to shift increasingly from a fee-for-service model to a value-based model.