scholarly journals Comparison of Three Commercial Systems for Identification of Yeasts Commonly Isolated in the Clinical Microbiology Laboratory

1999 ◽  
Vol 37 (6) ◽  
pp. 1967-1970 ◽  
Author(s):  
Jill K. Wadlin ◽  
Gayle Hanko ◽  
Rebecca Stewart ◽  
John Pape ◽  
Irving Nachamkin
Keyword(s):  
Clinical Microbiology ◽  
Reference Method ◽  
Clinical Microbiology Laboratory ◽  
Microbiology Laboratory ◽  
Diagnostic Systems ◽  
Routine Identification ◽  
Significant Difference ◽  
Additional Testing ◽  
Card System ◽  
Better Than

We evaluated three commercial systems (RapID Yeast Plus System; Innovative Diagnostic Systems, Norcross, Ga.; API 20C Aux; bioMerieux-Vitek, Hazelwood, Mo.; and Vitek Yeast Biochemical Card, bioMerieux-Vitek) against an auxinographic and microscopic morphologic reference method for the ability to identify yeasts commonly isolated in our clinical microbiology laboratory. Two-hundred one yeast isolates were compared in the study. The RapID Yeast Plus System was significantly better than either API 20C Aux (193 versus 167 correct identifications; P < 0.0001) or the Vitek Yeast Biochemical Card (193 versus 173 correct identifications;P = 0.003) for obtaining correct identifications to the species level without additional testing. There was no significant difference between results obtained with API 20C Aux and the Vitek Yeast Biochemical Card system (P = 0.39). The API 20C Aux system did not correctly identify any of the Candida krusei isolates (n = 23) without supplemental testing and accounted for the major differences between the API 20C Aux and RapID Yeast Plus systems. Overall, the RapID Yeast Plus System was easy to use and is a good system for the routine identification of clinically relevant yeasts.

scholarly journals Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

2020 ◽  
Vol 33 (4) ◽  
Author(s):  
Deirdre L. Church ◽  
Lorenzo Cerutti ◽  
Antoine Gürtler ◽  
Thomas Griener ◽  
Adrian Zelazny ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Clinical Microbiology ◽  
Clinical Microbiology Laboratory ◽  
Rrna Gene ◽  
Microbiology Laboratory ◽  
Cycle Sequencing ◽  
16S Sequencing ◽  
Routine Identification ◽  
Identification Of Bacteria

SUMMARY This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Prospective evaluation of the VITEK MS for the routine identification of bacteria and yeast in the clinical microbiology laboratory: assessment of accuracy of identification and turnaround time

2014 ◽  
Vol 63 (2) ◽  
pp. 235-241 ◽  
Author(s):  
Angella Charnot-Katsikas ◽  
Vera Tesic ◽  
Sue Boonlayangoor ◽  
Cindy Bethel ◽  
Karen M. Frank
Keyword(s):  
Clinical Microbiology ◽  
Clinical Care ◽  
Turnaround Time ◽  
Clinical Microbiology Laboratory ◽  
Microbiology Laboratory ◽  
Laboratory Assessment ◽  
16S Rrna Sequence ◽  
Routine Identification ◽  
Vitek 2 ◽  
Vitek Ms

This study assessed the accuracy of bacterial and yeast identification using the VITEK MS, and the time to reporting of isolates before and after its implementation in routine clinical practice. Three hundred and sixty-two isolates of bacteria and yeast, consisting of a variety of clinical isolates and American Type Culture Collection strains, were tested. Results were compared with reference identifications from the VITEK 2 system and with 16S rRNA sequence analysis. The VITEK MS provided an acceptable identification to species level for 283 (78 %) isolates. Considering organisms for which genus-level identification is acceptable for routine clinical care, 315 isolates (87 %) had an acceptable identification. Six isolates (2 %) were identified incorrectly, five of which were Shigella species. Finally, the time for reporting the identifications was decreased significantly after implementation of the VITEK MS for a total mean reduction in time of 10.52 h (P<0.0001). Overall, accuracy of the VITEK MS was comparable or superior to that from the VITEK 2. The findings were also comparable to other studies examining the accuracy of the VITEK MS, although differences exist, depending on the diversity of species represented as well as on the versions of the databases used. The VITEK MS can be incorporated effectively into routine use in a clinical microbiology laboratory and future expansion of the database should provide improved accuracy for the identification of micro-organisms.

scholarly journals The Poisoned Well: Enhancing the Predictive Value of Antimicrobial Susceptibility Testing in the Era of Multidrug Resistance

2017 ◽  
Vol 55 (8) ◽  
pp. 2304-2308 ◽  
Author(s):  
Thea Brennan-Krohn ◽  
Kenneth P. Smith ◽  
James E. Kirby
Keyword(s):  
Antimicrobial Susceptibility ◽  
Clinical Microbiology ◽  
Predictive Power ◽  
Susceptibility Testing ◽  
Reference Method ◽  
Antimicrobial Susceptibility Testing ◽  
Clinical Microbiology Laboratory ◽  
Microbiology Laboratory ◽  
Laboratory Reference ◽  
Doubling Dilution

ABSTRACTAntimicrobial susceptibility testing (AST) is a fundamental mission of the clinical microbiology laboratory. Reference AST methods are based on bacterial growth in antibiotic doubling dilution series, which means that any error in the reference method inherently represents at least a 2-fold difference. We describe the origins of current AST reference methodology, highlight the sources of AST variability, and propose ideas for improving AST predictive power.

scholarly journals Kesesuaian Pemeriksaan jamur antara pewarnaan periodic acid schiff(PAS) dan KOH pada flour albus ibu hamil di RSUD dr Soetomo Surabaya

2020 ◽  
Vol 13 (01) ◽  
pp. 34-38
Author(s):  
Shinta Arya ◽  
Arthur pohan Kawilarang
Keyword(s):  
Pregnant Women ◽  
Clinical Microbiology ◽  
Vaginal Discharge ◽  
Periodic Acid ◽  
Clinical Microbiology Laboratory ◽  
Microbiology Laboratory ◽  
Childbearing Age ◽  
Periodic Acid Schiff ◽  
Significant Difference ◽  
Pas Staining

Background: Candidiasis vaginalis is a form of vaginal infection by Candida spp, estimated to occur in women of childbearing age in 70-75% of the cases. Clinical history, symptoms and laboratory examinations are very important to diagnose candidiasis vaginalis. Vaginal discharge examination can be done by direct or wet, and culture examination. Microscopic examination can be used to prove the existence of yeast form of Candida. This method is simple, can be applied in clinical microbiology laboratory with limited resources and is considered effective because it is cheap and results are obtained in a short time compared to culture. Detection of fungi by Periodic Acid Schiff (PAS) staining is visually better than KOH. The aim of this study is to analyze the concordance between Periodic Acid Schiff (PAS) staining and KOH method for fungal detection in flour albus from pregnant women. Method: This research is a descriptive observational study to figure out the suitability of Periodic Acid Schiff (PAS) staining and KOH method for fungal detection in flour albus from pregnant women with cross sectional approach. Samples were collected in the form of 30 vaginal discharge specimens taken from pregnant women and sent to the Clinical Microbiology Laboratory Dr. Soetomo Surabaya. The study was conducted in July - August 2019. Result: There was a significant difference in fungal detection between Periodic Acid Schiff (PAS) staining (56.7%, 17 samples) and 20% KOH method (6 samples) out of 30 samples (p=0.017). The concordance between Periodic Acid Schiff (PAS) staining and KOH method for fungal detection in flour albus from pregnant women is low (Kappa=0.321). Conclusion: Periodic Acid Schiff (PAS) staining detects more fungi when compared to KOH, and therefore is considered as a better method. Keywords: Flour albus, pregnancy, Periodic Acid Schiff (PAS), KOH.

scholarly journals Total Laboratory Automation and Three Shifts Reduce Turnaround Time of Cerebrospinal Fluid Culture Results in the Chinese Clinical Microbiology Laboratory

2021 ◽  
Vol 11 ◽  
Author(s):  
Weili Zhang ◽  
Siying Wu ◽  
Jin Deng ◽  
Quanfeng Liao ◽  
Ya Liu ◽  
...  
Keyword(s):  
Clinical Microbiology ◽  
Laboratory Data ◽  
Turnaround Time ◽  
Klebsiella Pneumonia ◽  
Clinical Microbiology Laboratory ◽  
Laboratory Automation ◽  
Microbiology Laboratory ◽  
Significant Difference ◽  
Total Laboratory Automation ◽  
The Difference

BackgroundTotal laboratory automation (TLA) has the potential to reduce specimen processing time, optimize workflow, and decrease turnaround time (TAT). The purpose of this research is to investigate whether the TAT of our laboratory has changed since the adoption of TLA, as well as to optimize laboratory workflow, improve laboratory testing efficiency, and provide better services of clinical diagnosis and treatment.Materials and MethodsLaboratory data was extracted from our laboratory information system in two 6-month periods: pre-TLA (July to December 2019) and post-TLA (July to December 2020), respectively.ResultsThe median TAT for positive cultures decreased significantly from pre-TLA to post-TLA (65.93 vs 63.53, P&lt;0.001). For different types of cultures, The TAT of CSF changed the most (86.76 vs 64.30, P=0.007), followed by sputum (64.38 vs 61.41, P&lt;0.001), urine (52.10 vs 49,57, P&lt;0.001), blood (68.49 vs 66.60, P&lt;0.001). For Ascites and Pleural fluid, there was no significant difference (P&gt;0.05). Further analysis found that the incidence of broth growth only for pre-TLA was 12.4% (14/133), while for post-TLA, it was 3.4% (4/119). The difference was statistically significant (P=0.01). The common isolates from CSF samples were Cryptococcus neoformans, coagulase-negative Staphylococcus, Acinetobacter baumannii, and Klebsiella pneumonia.ConclusionUsing TLA and setting up three shifts shortened the TAT of our clinical microbiology laboratory, especially for CSF samples.

scholarly journals Decrease in Enteroviral Meningitis - An Unexpected Benefit of COVID-19 Mitigation?

2020 ◽  
Author(s):  
Kami D Kies ◽  
Amber S Thomas ◽  
Matthew J Binnicker ◽  
Kelli L Bashynski ◽  
Robin Patel
Keyword(s):  
Cerebrospinal Fluid ◽  
Laboratory Testing ◽  
Clinical Microbiology ◽  
Late Summer ◽  
Mitigation Strategies ◽  
Clinical Microbiology Laboratory ◽  
Microbiology Laboratory ◽  
Testing Data ◽  
Early Fall ◽  
Enteroviral Meningitis

Abstract Enteroviral meningitis is seasonal, typically exhibiting a rise in prevalence in late summer/early fall. Based on clinical microbiology laboratory testing data of cerebrospinal fluid, the expected August/September/October peak in enteroviral meningitis did not occur in 2020, possibly related to COVID-19 mitigation strategies.

scholarly journals Implementation and evaluation of a novel real-time multiplex assay for SARS-CoV-2: in-field learnings from a clinical microbiology laboratory

Pathology ◽  
2020 ◽  
Vol 52 (7) ◽  
pp. 754-759 ◽  
Author(s):  
Eloise Williams ◽  
Katherine Bond ◽  
Brian Chong ◽  
Dawn Giltrap ◽  
Malcolm Eaton ◽  
...  
Keyword(s):  
Real Time ◽  
Clinical Microbiology ◽  
Multiplex Assay ◽  
Clinical Microbiology Laboratory ◽  
Microbiology Laboratory

scholarly journals One Small Step for the Gram Stain, One Giant Leap for Clinical Microbiology

2016 ◽  
Vol 54 (6) ◽  
pp. 1416-1417 ◽  
Author(s):  
Richard B. Thomson
Keyword(s):  
Clinical Microbiology ◽  
Rapid Test ◽  
Error Rates ◽  
Clinical Microbiology Laboratory ◽  
Microbiology Laboratory ◽  
Gram Stain ◽  
Small Step ◽  
Link Type ◽  
Giant Leap

The Gram stain is one of the most commonly performed tests in the clinical microbiology laboratory, yet it is poorly controlled and lacks standardization. It was once the best rapid test in microbiology, but it is no longer trusted by many clinicians. The publication by Samuel et al. (J. Clin. Microbiol. 54:1442–1447, 2016,http://dx.doi.org/10.1128/JCM.03066-15) is a start for those who want to evaluate and improve Gram stain performance. In an age of emerging rapid molecular results, is the Gram stain still relevant? How should clinical microbiologists respond to the call to reduce Gram stain error rates?

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