scholarly journals An alternative for urine cultures: Direct identification of uropathogens from urine by MALDI-TOF MS

2020 ◽  
Author(s):  
Arzu Akşit İlki ◽  
Sevim Özsoy ◽  
Gulşen Gelmez ◽  
Burak Aksu ◽  
Güner Söyletir
Keyword(s):  
Flow Cytometry ◽  
Antibiotic Susceptibility ◽  
Clinical Microbiology ◽  
Urine Samples ◽  
Clinical Microbiology Laboratory ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Susceptibility Tests ◽  
Tract Infections ◽  
Tof Ms

AbstractUrinary tract infections are one of the most common bacterial infections and rapid diagnosis of the infection is essential for appropriate antibiotic therapy. The goal of our study was to identify urinary pathogens directly by MALDI-TOF MS and to perform antibiotic susceptibility tests in order to shorten the period spent for culturing.Urine samples submitted for culture to the Clinical Microbiology Laboratory were enrolled in this study. Urine samples were screened for leukocyte and bacteria amount by flow cytometry. Samples with bacterial load of 106–107/mL were tested directly by MALDI-TOF MS and antibiotic susceptibility tests (AST) were performed.In total, 538 positive urine samples were evaluated in our study. MALDI-TOF MS identified the microorganism directly from the urine sample in 91.8% of these samples and the concordance rate of conventional identification and direct detection was 95.8% for Gram-negatives at the genus and species level. Escherichia coli (n:401) was the most frequently isolated microorganism, followed by Klebsiella pneumoniae (n:57). AST results were generated for 111 of these urine samples and the concordance was 90% and 87% for E. coli and K. pneumoniae, respectively.Our results showed that screening of urine samples with flow cytometry to detect positive samples and identification of uropathogens directly by MALDI-TOF MS with an accuracy of over 90% can be a suitable method particularly for Gram-negative bacteria in clinical microbiology laboratories.

scholarly journals Performances and Reliability of Bruker Microflex LT and VITEK MS MALDI-TOF Mass Spectrometry Systems for the Identification of Clinical Microorganisms

2015 ◽  
Vol 2015 ◽  
pp. 1-18 ◽  
Author(s):  
Kivanc Bilecen ◽  
Gorkem Yaman ◽  
Ugur Ciftci ◽  
Yahya Rauf Laleli
Keyword(s):  
Mass Spectrometry ◽  
Clinical Microbiology ◽  
Identification Accuracy ◽  
Clinical Microbiology Laboratory ◽  
Maldi Tof Ms ◽  
Microbial Identification ◽  
Phenotypic Identification ◽  
Maldi Tof ◽  
Vitek Ms ◽  
Tof Ms

In clinical microbiology laboratories, routine microbial identification is mostly performed using culture based methodologies requiring 24 to 72 hours from culturing to identification. Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) technology has been established as a cost effective, reliable, and faster alternative identification platform. In this study, we evaluated the reliability of the two available MALDI-TOF MS systems for their routine clinical level identification accuracy and efficiency in a clinical microbiology laboratory setting. A total of 1,341 routine phenotypically identified clinical bacterial and fungal isolates were selected and simultaneously analyzed using VITEK MS (bioMérieux, France) and Microflex LT (Bruker Diagnostics, Germany) MALDI-TOF MS systems. For any isolate that could not be identified with either of the systems and for any discordant result, 16S rDNA gene or ITS1/ITS2 sequencing was used. VITEK MS and Microflex LT correctly identified 1,303 (97.17%) and 1,298 (96.79%) isolates to the species level, respectively. In 114 (8.50%) isolates initial phenotypic identification was inaccurate. Both systems showed a similar identification efficiency and workflow robustness, and they were twice as more accurate compared to routine phenotypic identification in our sample pool. MALDITOF systems with their accuracy and robustness offer a good identification platform for routine clinical microbiology laboratories.

Identification and diversity of Actinomyces species in a clinical microbiology laboratory in the MALDI-TOF MS era

Anaerobe ◽  
2018 ◽  
Vol 54 ◽  
pp. 151-158 ◽  
Author(s):  
Peivern Fong ◽  
Michelle J. Francis ◽  
John F. Hamblin ◽  
Tony M. Korman ◽  
Maryza Graham
Keyword(s):  
Clinical Microbiology ◽  
Clinical Microbiology Laboratory ◽  
Microbiology Laboratory ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Actinomyces Species ◽  
Tof Ms

scholarly journals MALDI-TOF MS in the clinical microbiology laboratory

2013 ◽  
Vol 49 (4) ◽  
pp. 256-259 ◽  
Author(s):  
Marcelo Jenne Mimica ◽  
Marines Dalla Valle Martino ◽  
Jacyr Pasternak
Keyword(s):  
Clinical Microbiology ◽  
Clinical Microbiology Laboratory ◽  
Microbiology Laboratory ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

scholarly journals Rapidly predicting vancomycin resistance of Enterococcus faecium through MALDI-TOF MS spectrum obtained in real-world clinical microbiology laboratory

2020 ◽  
Author(s):  
Hsin-Yao Wang ◽  
Ko-Pei Lu ◽  
Chia-Ru Chung ◽  
Yi-Ju Tseng ◽  
Tzong-Yi Lee ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Antibiotic Susceptibility ◽  
Body Fluid ◽  
Mass Spectra ◽  
External Validation ◽  
Antibiotic Use ◽  
Clinical Microbiology Laboratory ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

AbstractEnterococcus faecium is one of the leading pathogens in the world. In this study, we proposed a strategy to rapidly and accurately distinguish vancomycin-resistant Enterococcus faecium (VREfm) and vancomycin-susceptible E. faecium (VSEfm) to help doctors correctly determine the use of vancomycin by a machine learning (ML)-based algorithm. A predictive model was developed and validated to distinguish VREfm and VSEfm by analyzing MALDI-TOF MS spectra of unique E. faecium isolates from different specimen types. Firstly, 5717 mass spectra, including 2795 VREfm and 2922 VSEfm, were used to develop the algorithm. And 2280 mass spectra of isolates, namely 1222 VREfm and 1058 VSEfm, were used to externally validate the algorithm. The random forest-based algorithm demonstrated good classification performances for overall specimens, whose mean AUROC in 5-fold cross validation, time-wise validation, and external validation was all greater than 0.84. For the detection of VREfm in blood, sterile body fluid, urinary tract, and wound, the AUROC in external validation was also greater than 0.84. The predictions with algorithms were significantly more accurate than empirical antibiotic use. The accuracy of antibiotics administration could be improved by 30%. And the algorithm could provide rapid antibiotic susceptibility results at least 24 hours ahead of routine laboratory tests. The turn-around-time of antibiotic susceptibility could be reduced by 50%. In conclusion, a ML algorithm using MALDI-TOF MS spectra obtained in routine workflow accurately differentiated VREfm from VSEfm, especially in blood and sterile body fluid, which can be applied to facilitate the clinical testing process due to its accuracy, generalizability, and rapidness.

scholarly journals MALDI-TOF MS for the Diagnosis of Infectious Diseases

2015 ◽  
Vol 61 (1) ◽  
pp. 100-111 ◽  
Author(s):  
Robin Patel
Keyword(s):  
Clinical Microbiology ◽  
Anaerobic Bacteria ◽  
Automated Analysis ◽  
Accurate Method ◽  
Clinical Microbiology Laboratory ◽  
Microbiology Laboratory ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Bacteria And Fungi ◽  
Tof Ms

Abstract BACKGROUND First introduced into clinical microbiology laboratories in Europe, MALDI-TOF MS is being rapidly embraced by laboratories around the globe. Although it has multiple applications, its widespread adoption in clinical microbiology relates to its use as an inexpensive, easy, fast, and accurate method for identification of grown bacteria and fungi based on automated analysis of the mass distribution of bacterial proteins. CONTENT This review provides a historical perspective on this new technology. Modern applications in the clinical microbiology laboratory are reviewed with a focus on the most recent publications in the field. Identification of aerobic and anaerobic bacteria, mycobacteria, and fungi are discussed, as are applications for testing urine and positive blood culture bottles. The strengths and limitations of MALDI-TOF MS applications in clinical microbiology are also addressed. SUMMARY MALDI-TOF MS is a tool for rapid, accurate, and cost-effective identification of cultured bacteria and fungi in clinical microbiology. The technology is automated, high throughput, and applicable to a broad range of common as well as esoteric bacteria and fungi. MALDI-TOF MS is an incontrovertibly beneficial technology for the clinical microbiology laboratory.

scholarly journals Diagnostic accuracy of MALDI-TOF mass spectrometry for the direct identification of clinical pathogens from urine

Open Medicine ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. 266-273
Author(s):  
Min Tang ◽  
Jia Yang ◽  
Ying Li ◽  
Luhua Zhang ◽  
Ying Peng ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Likelihood Ratio ◽  
Meta Analysis ◽  
Positive Likelihood Ratio ◽  
Negative Likelihood Ratio ◽  
Urine Samples ◽  
Direct Identification ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

AbstractMatrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) has become one of the most popular methods for the rapid and cost-effective detection of clinical pathogenic microorganisms. This study aimed to evaluate and compare the diagnostic performance of MALDI-TOF MS with that of conventional approaches for the direct identification of pathogens from urine samples. A systematic review was conducted based on a literature search of relevant databases. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and area under the summary receiver operating characteristic (SROC) curve of the combined studies were estimated. Nine studies with a total of 3920 subjects were considered eligible and included in the meta-analysis. The pooled sensitivity was 0.85 (95% CI 0.79-0.90), and the pooled specificity was 0.93 (95% CI 0.82-0.97). The PLR and NLR were 11.51 (95% CI 4.53-29.26) and 0.16 (95% CI 0.11-0.24), respectively. The area under the SROC curve was 0.93 (95% CI 0.91-0.95). Sensitivity analysis showed that the results of this meta-analysis were stable. MALDI-TOF MS could directly identify microorganisms from urine samples with high sensitivity and specificity.

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