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 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 Development and Validation of an in-House Library of Colombian Candida auris Strains with MALDI-TOF MS to Improve Yeast Identification

2020 ◽  
Vol 6 (2) ◽  
pp. 72 ◽  
Author(s):  
Andrés Ceballos-Garzon ◽  
Daniela Amado ◽  
Norida Vélez ◽  
María José Jiménez-A ◽  
Crescencio Rodríguez ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Candida Auris ◽  
Yeast Identification ◽  
Great Opportunity ◽  
Maldi Tof Ms ◽  
Identification Process ◽  
Clinical Strains ◽  
Maldi Tof ◽  
Development And Validation ◽  
Tof Ms

Background: Candida auris is characterized for having a high genetic variability among species. MALDI-TOF MS library contains spectra from only three strains of C. auris, which makes difficult the identification process and gives low scores at the species level. Our aim was to construct and validate an internal library to improve C. auris identification with Colombian clinical strains. Methods: From 30 clinical strains, 770 mass spectra were obtained for the construction of the database. The validation was performed with 300 strains to compare the identification results in the BDAL and C. auris Colombia libraries. Results: Our library allowed a complete, 100% identification of the evaluated strains and a significant improvement in the scores obtained, showing a better performance compared to the Bruker BDAL library. Conclusions: The strengthening of the database is a great opportunity to improve the scoring and C. auris identification. Library data are available via ProteomeXchange with identifier PXD016387.

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 Rapid antibiotic susceptibility testing on blood cultures using MALDI-TOF MS

PLoS ONE ◽  
2018 ◽  
Vol 13 (10) ◽  
pp. e0205603 ◽  
Author(s):  
Marlène Sauget ◽  
Xavier Bertrand ◽  
Didier Hocquet
Keyword(s):  
Antibiotic Susceptibility ◽  
Susceptibility Testing ◽  
Blood Cultures ◽  
Antibiotic Susceptibility Testing ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

scholarly journals Characterization of aliphatic hyperbranched polyesters by MALDI-TOF mass spectrometry

2007 ◽  
Vol 61 (6) ◽  
pp. 333-341
Author(s):  
Jasna Vukovic ◽  
Slobodan Jovanovic ◽  
Manfred Lechner
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectra ◽  
Degree Of Polymerization ◽  
Side Reactions ◽  
Maldi Tof Ms ◽  
Hyperbranched Polyesters ◽  
Maldi Tof ◽  
Maldi Tof Mass Spectra ◽  
Tof Ms

In this work, MALDI-TOF mass spectrometry was used for the characterization of aliphatic hyperbranched polyesters (AHBP), synthesized from 2,2-bis(hydroxymethyl)propionic acid (bis-MPA) and di-trimethylolpropane. From the obtained results it was concluded that it was not possible to take complete advantages of MALDI-TOF MS in this particular case, since the AHBP used in this work were polydisperse. The intensity of the signals from the high mass tail of these samples (pseudo generation higher than four) was underestimated and insufficient to distinguish it from the baseline and to use it for the analysis of the spectra. As a consequence of that, lower values of the Mn were obtained. At the same time, Mw were also underestimated, which led to very low values of the polydispersity index. On the other hand, it was possible to obtain molar masses of individual molecules from the MALDI-TOF mass spectra of AHBP and to qualitatively determine the extent of cyclization (side reactions) at each degree of polymerization. Using the adequate set of equations and results obtained from MALDI-TOF mass spectra of AHBP, every signal from the spectra was identified. The obtained results show that formation of poly(bis-MPA), intramolecular esterification and intramolecular etherification occurred as side reactions during the synthesis of these polyesters. The relative amount of the cycles increases with the number of pseudo generation (from the second up to the fifth pseudo generation). It was also observed that the relative proportion of the signals which represent cyclic structures increases with the increasing degree of polymerization. In this work the basic principles of MALDI-TOF MS are also presented, as well as, a review of adequate published articles.

scholarly journals Understanding the chemical basis for the preferential ionization of specific biomolecules in mass spectrometry analysis of microbial cells

2019 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectra ◽  
Mass Spectrometry Analysis ◽  
Chemical Pretreatment ◽  
Maldi Tof Ms ◽  
Spectrometry Analysis ◽  
Chemical Basis ◽  
Maldi Tof ◽  
Different Types ◽  
Tof Ms

Mass spectrometry-enabled microbial identification has successfully demonstrated the feasibility of using profiled biomolecules for identifying microorganisms based on a chemometric or proteome database search approach. However, mechanisms driving the preferential ionization and detection of particular biomolecules in various types of mass spectrometry remain poorly understood. Specifically, mass spectra obtained from different microbial species remain poorly annotated with respect to the specific types of biomolecules accounting for the peaks. For example, while ribosomal proteins are known to be a significant class of biomolecules that could partially account for the profiled mass peaks in mass spectra of microorganisms, other classes of proteins and biomolecules remain poorly annotated. This raises the important question of how different mass spectrometry approaches ionize different types of biomolecules from a cellular matrix. Specifically, mass spectra of microorganisms reveal that only a couple of mass peaks could capture the phylogeny of a species. However, the proteome of a cell is much larger and more complicated, and yet is not fully profiled by different types of mass spectrometry methods. For example, electrospray ionization mass spectrometry (ESI-MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) could only provide a small snapshot of the entire bacterial proteome. It could be argued that different mass spectrometry methods provide complementary views of a particular proteome. However, the question remains, how do proteins and biomolecules interact with the different sample preparation and mass spectrometry analysis methods for generating an ion cloud for separation in a mass spectrometer? Thus, efforts could be directed towards understanding how different types of proteins could be preferentially ionized by MALDI-TOF MS. Specifically, different reagents could be used to perform chemical pretreatment on the proteome, which would subsequently be analyzed by mass spectrometry. Thus, a correlative map between types of chemical pretreatment used and the corresponding mass spectra could be obtained. Collectively, knowledge gleaned from the research would illuminate the chemical basis by which specific biomolecules are preferentially ionized under particular conditions, which would inform the development of strategies for increasing the subset of biomolecules ionized from a cellular proteome. Such chemical rules would also aid in the interpretation of mass spectra obtained, particularly in understanding the biological context of the experiment. Overall, the key goal of this research is to help answer the question: what is the biological basis and context of the mass spectrum obtained from cells?

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