scholarly journals Species Identification and Delineation of Pathogenic Mucorales by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

2018 ◽  
Vol 56 (4) ◽  
pp. e01886-17 ◽  
Author(s):  
Jin Shao ◽  
Zhe Wan ◽  
Ruoyu Li ◽  
Jin Yu
Keyword(s):  
Filamentous Fungi ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Reference Strains ◽  
Tof Ms

ABSTRACT This study aimed to validate the effectiveness of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS)-based identification of filamentous fungi of the order Mucorales. A total of 111 isolates covering six genera preserved at the Research Center for Medical Mycology of Peking University were selected for MALDI-TOF MS analysis. We emphasized the study of 23 strains of Mucor irregularis predominantly isolated from patients in China. We first used the Bruker Filamentous Fungi library (v1.0) to identify all 111 isolates. To increase the identification rate, we created a compensatory in-house database, the Beijing Medical University (BMU) database, using 13 reference strains covering 6 species, including M. irregularis, Mucor hiemalis, Mucor racemosus, Cunninghamella bertholletiae, Cunninghamella phaeospora, and Cunninghamella echinulata. All 111 isolates were then identified by MALDI-TOF MS using a combination of the Bruker library and BMU database. MALDI-TOF MS identified 55 (49.5%) and 74 (66.7%) isolates at the species and genus levels, respectively, using the Bruker Filamentous Fungi library v1.0 alone. A combination of the Bruker library and BMU database allowed MALDI-TOF MS to identify 90 (81.1%) and 111 (100%) isolates at the species and genus levels, respectively, with a significantly increased accuracy rate. MALDI-TOF MS poorly identified Mucorales when the Bruker library was used alone due to its lack of some fungal species. In contrast, this technique perfectly identified M. irregularis after main spectrum profiles (MSPs) of relevant reference strains were added to the Bruker library. With an expanded Bruker library, MALDI-TOF MS is an effective tool for the identification of pathogenic Mucorales.

scholarly journals Rapid Identification of Clinically Relevant Members of the Genus Exophiala by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry and Description of Two Novel Species, Exophiala campbellii and Exophiala lavatrina

2017 ◽  
Vol 55 (4) ◽  
pp. 1162-1176 ◽  
Author(s):  
Andrew M. Borman ◽  
Mark Fraser ◽  
Adrien Szekely ◽  
Daniel E. Larcombe ◽  
Elizabeth M. Johnson
Keyword(s):  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

ABSTRACT Exophiala is a ubiquitous pleomorphic genus comprising at least 40 species, many of which have been associated with superficial, visceral, or systemic infections in humans, other mammals, or cold-blooded animals. In this study, we investigated the potential of matrix-assisted laser desorption–ionization time of flight mass spectrometry (MALDI-TOF MS) for the identification of Exophiala species. A total of 89 isolates (including 50 human and 4 animal clinical isolates) stored in the National Collection of Pathogenic Fungi were identified by PCR amplification and sequencing of internal transcribed spacer region 1. Eighty-three of the isolates corresponded to 16 known species within Exophiala/Rhinocladiella . The remaining six isolates are shown by phylogenetic analyses based on four loci to represent two novel Exophiala species. Four isolates from domestic bathrooms which form a sister species with Exophiala lecanii-corni are described here as Exophiala lavatrina sp. nov. The remaining two isolates, both from subcutaneous infections, are distantly related to Exophiala oligosperma and are described here as Exophiala campbellii sp. nov. The triazoles and terbinafine exhibited low MICs against all Exophiala isolates in vitro . MALDI-TOF MS successfully distinguished all 18 species and identified all isolates after appropriate reference spectra were created and added to commercial databases. Intraspecific mean log scores ranged from 1.786 to 2.584 and were consistently significantly higher than interspecific scores (1.193 to 1.624), with the exception of E. lecanii-corni and E. lavatrina , for which there was considerable log score overlap. In summary, MALDI-TOF MS allows the rapid and accurate identification of a wide range of clinically relevant Exophiala species.

scholarly journals Evaluation of Matrix-Assisted Laser Desorption Ionization−Time of Flight Mass Spectrometry for Identification of Mycobacterium species, Nocardia species, and Other Aerobic Actinomycetes

2015 ◽  
Vol 54 (2) ◽  
pp. 376-384 ◽  
Author(s):  
S. P. Buckwalter ◽  
S. L. Olson ◽  
B. J. Connelly ◽  
B. C. Lucas ◽  
A. A. Rodning ◽  
...  
Keyword(s):  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Aerobic Actinomycetes ◽  
Tof Ms ◽  
Matrix Assisted Laser

The value of matrix-assisted laser desorption ionization−time of flight mass spectrometry (MALDI-TOF MS) for the identification of bacteria and yeasts is well documented in the literature. Its utility for the identification of mycobacteria andNocardiaspp. has also been reported in a limited scope. In this work, we report the specificity of MALDI-TOF MS for the identification of 162Mycobacteriumspecies and subspecies, 53Nocardiaspecies, and 13 genera (totaling 43 species) of other aerobic actinomycetes using both the MALDI-TOF MS manufacturer's supplied database(s) and a custom database generated in our laboratory. The performance of a simplified processing and extraction procedure was also evaluated, and, similar to the results in an earlier literature report, our viability studies confirmed the ability of this process to inactivateMycobacterium tuberculosisprior to analysis. Following library construction and the specificity study, the performance of MALDI-TOF MS was directly compared with that of 16S rRNA gene sequencing for the evaluation of 297 mycobacteria isolates, 148Nocardiaspecies isolates, and 61 other aerobic actinomycetes isolates under routine clinical laboratory working conditions over a 6-month period. MALDI-TOF MS is a valuable tool for the identification of these groups of organisms. Limitations in the databases and in the ability of MALDI-TOF MS to rapidly identify slowly growing mycobacteria are discussed.

scholarly journals Novel Strategy for Rapidly and Safely Distinguishing Bacillus anthracis and Bacillus cereus by Use of Peptide Mass Fingerprints Based on Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

2020 ◽  
Vol 59 (1) ◽  
pp. e02358-20
Author(s):  
Jianchun Wei ◽  
Huijuan Zhang ◽  
Huifang Zhang ◽  
Enmin Zhang ◽  
Binghua Zhang ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Bacillus Anthracis ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

ABSTRACTThe objective of this study was to construct a rapid, high-throughput, and biosafety-compatible screening method for Bacillus anthracis and Bacillus cereus based on matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). MALDI-TOF MS coupled to ClinProTools was used to discover MALDI-TOF MS biomarker peaks and generate a classification model based on a genetic algorithm (GA) to differentiate between different Bacillus anthracis and Bacillus cereus isolates. Thirty Bacillus anthracis and 19 Bacillus cereus strains were used to construct and analyze the model, and 40 Bacillus strains were used for validation. For the GA screening model, the cross-validation values, which reflect the ability of the model to handle variability among the test spectra, and the recognition capability values, which reflect the model’s ability to correctly identify its component spectra, were all 100%. This model contained 10 biomarker peaks (m/z 3,339.9, 3,396.3, 3,682.4, 5,476.7, 6,610.6, 6,680.1, 7,365.3, 7,792.4, 9,475.8, and 10,934.1) used to correctly identify 28 Bacillus anthracis and 12 Bacillus cereus isolates from 40 Bacillus isolates, with a sensitivity and specificity of 100%. With the obvious advantages of being rapid, highly accurate, and highly sensitive and having a low cost and high throughput, MALDI-TOF MS ClinProTools is a powerful and reliable tool for screening Bacillus anthracis and Bacillus cereus strains.

scholarly journals Fusobacterium nucleatum Subspecies Identification by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

2015 ◽  
Vol 53 (4) ◽  
pp. 1399-1402 ◽  
Author(s):  
Shuping Nie ◽  
Baoyu Tian ◽  
Xiaowei Wang ◽  
David H. Pincus ◽  
Martin Welker ◽  
...  
Keyword(s):  
Fusobacterium Nucleatum ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms ◽  
Matrix Assisted Laser

We explored the use of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for identification ofFusobacterium nucleatumsubspecies. MALDI-TOF MS spectra of fiveF. nucleatumsubspecies (animalis,fusiforme,nucleatum,polymorphum, andvincentii) were analyzed and divided into four distinct clusters, including subsp.animalis,nucleatum,polymorphum, andfusiforme/vincentii. MALDI-TOF MS with the modified SARAMIS database further correctly identified 28 of 34F. nucleatumclinical isolates to the subspecies level.

scholarly journals Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Molds of the Fusarium Genus

2014 ◽  
Vol 53 (2) ◽  
pp. 465-476 ◽  
Author(s):  
David Triest ◽  
Dirk Stubbe ◽  
Koen De Cremer ◽  
Denis Piérard ◽  
Anne-Cécile Normand ◽  
...  
Keyword(s):  
Species Complex ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Species Complexes ◽  
Tof Ms

The rates of infection withFusariummolds are increasing, and a diverse number ofFusariumspp. belonging to different species complexes can cause infection. Conventional species identification in the clinical laboratory is time-consuming and prone to errors. We therefore evaluated whether matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a useful alternative. The 289Fusariumstrains from the Belgian Coordinated Collections of Microorganisms (BCCM)/Institute of Hygiene and Epidemiology Mycology (IHEM) culture collection with validated sequence-based identities and comprising 40 species were used in this study. An identification strategy was developed, applying a standardized MALDI-TOF MS assay and an in-house reference spectrum database.In vitroantifungal testing was performed to assess important differences in susceptibility between clinically relevant species/species complexes. We observed that no incorrect species complex identifications were made by MALDI-TOF MS, and 82.8% of the identifications were correct to the species level. This success rate was increased to 91% by lowering the cutoff for identification. Although the identification of the correct species complex member was not always guaranteed, antifungal susceptibility testing showed that discriminating betweenFusariumspecies complexes can be important for treatment but is not necessarily required between members of a species complex. With this perspective, someFusariumspecies complexes with closely related members can be considered as a whole, increasing the success rate of correct identifications to 97%. The application of our user-friendly MALDI-TOF MS identification approach resulted in a dramatic improvement in both time and accuracy compared to identification with the conventional method. A proof of principle of our MALDI-TOF MS approach in the clinical setting using recently isolatedFusariumstrains demonstrated its validity.

Leptospira ainlahdjerensis sp. nov., Leptospira ainazelensis sp. nov., Leptospira abararensis sp. nov. and Leptospira chreensis sp. nov., four new species isolated from water sources in Algeria

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Anissa Amara Korba ◽  
Hakim Lounici ◽  
Malia Kainiu ◽  
Antony T. Vincent ◽  
Jean-François Mariet ◽  
...  
Keyword(s):  
Novel Species ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Link Type ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Leptospira strains were isolated from freshwater sampled at four sites in Algeria and characterized by whole-genome sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The cells were spiral-shaped and motile. Phylogenetic and MALDI-TOF MS analyses showed that the strains can be clearly distinguished from the other described species in the genus Leptospir a, therefore representing two novel species of the pathogen subclade P1 and two novel species of the saprophyte subclade S1. The names Leptospira ainlahdjerensis sp. nov. (type strain 201903070T=KIT0297T=CIP111912T), Leptospira ainazelensis sp. nov. (201903071T=KIT0298T=CIP111913T), Leptospira abararensis sp. nov. (201903074T=KIT0299T=CIP111914T) and Leptospira chreensis (201903075T=KIT0300T=CIP111915T) are proposed.

scholarly journals Typing and Species Identification of ClinicalKlebsiellaIsolates by Fourier Transform Infrared Spectroscopy and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

2018 ◽  
Vol 56 (11) ◽  
Author(s):  
Ariane G. Dinkelacker ◽  
Sophia Vogt ◽  
Philipp Oberhettinger ◽  
Norman Mauder ◽  
Jörg Rau ◽  
...  
Keyword(s):  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
High Discriminatory Power ◽  
Tof Ms ◽  
Matrix Assisted Laser

ABSTRACTKlebsiella pneumoniaeand related species are frequent causes of nosocomial infections and outbreaks. Therefore, quick and reliable strain typing is crucial for the detection of transmission routes in the hospital. The aim of this study was to evaluate Fourier transform infrared spectroscopy (FTIR) and matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) as rapid methods for typing clinicalKlebsiellaisolates in comparison to whole-genome sequencing (WGS), which was considered the gold standard for typing and identification. Here, 68 clinicalKlebsiellastrains were analyzed by WGS, FTIR, and MALDI-TOF MS. FTIR showed high discriminatory power in comparison to the WGS reference, whereas MALDI-TOF MS exhibited a low ability to type the isolates. MALDI-TOF mass spectra were further analyzed for peaks that showed high specificity for differentKlebsiellaspecies. Phylogenetic analysis revealed that theKlebsiellaisolates comprised three different species:K. pneumoniae,K. variicola, andK. quasipneumoniae. Genome analysis showed that MALDI-TOF MS can be used to distinguishK. pneumoniaefromK. variicoladue to shifts of certain mass peaks. The peaks were tentatively identified as three ribosomal proteins (S15p, L28p, L31p) and one stress response protein (YjbJ), which exhibit amino acid differences between the two species. Overall, FTIR has high discriminatory power to recognize the clonal relationship of isolates, thus representing a valuable tool for rapid outbreak analysis and for the detection of transmission events due to fast turnaround times and low costs per sample. Furthermore, specific amino acid substitutions allow the discrimination ofK. pneumoniaeandK. variicolaby MALDI-TOF MS.

scholarly journals Improved Short-Sequence-Repeat Genotyping of Mycobacterium avium subsp. paratuberculosis by Using Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

2013 ◽  
Vol 80 (2) ◽  
pp. 534-539 ◽  
Author(s):  
Christina Ahlstrom ◽  
Herman W. Barkema ◽  
Jeroen De Buck
Keyword(s):  
Sanger Sequencing ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms ◽  
Matrix Assisted Laser

ABSTRACTAccurate sequence analysis of mononucleotide repeat regions is difficult, complicating the use of short sequence repeats (SSRs) as a tool for bacterial strain discrimination. Although multiple SSR loci in the genome ofMycobacterium aviumsubsp.paratuberculosisallow genotyping ofM. aviumsubsp.paratuberculosisisolates with high discriminatory power, further characterization of the most discriminatory loci is limited due to inherent difficulties in sequencing mononucleotide repeats. Here, a method was evaluated using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) as an alternative to Sanger sequencing to further differentiate the dominant mycobacterial interspersed repetitive-unit (MIRU)–variable-number tandem-repeat (VNTR)M. aviumsubsp.paratuberculosistype (n= 37) in Canadian dairy herds by targeting a highly discriminatory mononucleotide SSR locus. First, PCR-amplified DNA was digested with two restriction enzymes to yield a sufficiently small fragment containing the SSR locus. Second, MALDI-TOF MS was performed to identify the mass, and thus repeat length, of the target. Sufficiently intense, discriminating spectra were obtained to determine repeat lengths up to 15, an improvement over the limit of 11 using traditional sequencing techniques. Comparison to synthetic oligonucleotides and Sanger sequencing results confirmed a valid and reproducible assay that increased discrimination of the dominantM. aviumsubsp.paratuberculosisMIRU-VNTR type. Thus, MALDI-TOF MS was a reliable, fast, and automatable technique to accurately resolveM. aviumsubsp.paratuberculosisgenotypes based on SSRs.

scholarly journals Multicenter Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Study for Identification of Clinically Relevant Nocardia spp.

2016 ◽  
Vol 54 (5) ◽  
pp. 1251-1258 ◽  
Author(s):  
Sara J. Blosser ◽  
Steven K. Drake ◽  
Jennifer L. Andrasko ◽  
Christina M. Henderson ◽  
Kamal Kamboj ◽  
...  
Keyword(s):  
Species Complex ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Level Identification ◽  
Tof Ms

This multicenter study analyzedNocardiaspp., including extraction, spectral acquisition, Bruker matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) identification, and score interpretation, using threeNocardialibraries, the Bruker, National Institutes of Health (NIH), and The Ohio State University (OSU) libraries, and compared the results obtained by each center. A standardized study protocol, 150Nocardiaisolates, and NIH and OSUNocardiaMALDI-TOF MS libraries were distributed to three centers. Following standardized culture, extraction, and MALDI-TOF MS analysis, isolates were identified using score cutoffs of ≥2.0 for species/species complex-level identification and ≥1.8 for genus-level identification. Isolates yielding a score of <2.0 underwent a single repeat extraction and analysis. The overall score range for all centers was 1.3 to 2.7 (average, 2.2 ± 0.3), with common species generally producing higher average scores than less common ones. Score categorization and isolate identification demonstrated 86% agreement between centers; 118 of 150 isolates were correctly identified to the species/species complex level by all centers. Nine strains (6.0%) were not identified by any center, and six (4.0%) of these were uncommon species with limited library representation. A categorical score discrepancy among centers occurred for 21 isolates (14.0%). There was an overall benefit of 21.2% from repeat extraction of low-scoring isolates and a center-dependent benefit for duplicate spotting (range, 2 to 8.7%). Finally, supplementation of the BrukerNocardiaMALDI-TOF MS library with both the OSU and NIH libraries increased the genus-level and species-level identification by 18.2% and 36.9%, respectively. Overall, this study demonstrates the ability of diverse clinical microbiology laboratories to utilize MALDI-TOF MS for the rapid identification of clinically relevantNocardiaspp. and to implement MALDI-TOF MS libraries developed by single laboratories across institutions.

scholarly journals Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Clinically Relevant Filamentous Fungi

2016 ◽  
Vol 54 (8) ◽  
pp. 2068-2073 ◽  
Author(s):  
Allison R. McMullen ◽  
Meghan A. Wallace ◽  
David H. Pincus ◽  
Kathy Wilkey ◽  
Carey-Ann D. Burnham
Keyword(s):  
Filamentous Fungi ◽  
Species Level ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Vitek Ms ◽  
Tof Ms

Invasive fungal infections have a high rate of morbidity and mortality, and accurate identification is necessary to guide appropriate antifungal therapy. With the increasing incidence of invasive disease attributed to filamentous fungi, rapid and accurate species-level identification of these pathogens is necessary. Traditional methods for identification of filamentous fungi can be slow and may lack resolution. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and accurate method for identification of bacteria and yeasts, but a paucity of data exists on the performance characteristics of this method for identification of filamentous fungi. The objective of our study was to evaluate the accuracy of the Vitek MS for mold identification. A total of 319 mold isolates representing 43 genera recovered from clinical specimens were evaluated. Of these isolates, 213 (66.8%) were correctly identified using the Vitek MS Knowledge Base, version 3.0 database. When a modified SARAMIS (Spectral Archive and Microbial Identification System) database was used to augment the version 3.0 Knowledge Base, 245 (76.8%) isolates were correctly identified. Unidentified isolates were subcultured for repeat testing; 71/319 (22.3%) remained unidentified. Of the unidentified isolates, 69 were not in the database. Only 3 (0.9%) isolates were misidentified by MALDI-TOF MS (includingAspergillus amoenus[n= 2] andAspergillus calidoustus[n= 1]) although 10 (3.1%) of the original phenotypic identifications were not correct. In addition, this methodology was able to accurately identify 133/144 (93.6%)Aspergillussp. isolates to the species level. MALDI-TOF MS has the potential to expedite mold identification, and misidentifications are rare.

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