Evaluating and Improving Vitek MS for Identification of Clinically Relevant Species of Trichosporon and the Closely Related Genera Cutaneotrichosporon and Apiotrichum

ABSTRACT Trichosporon species are relevant etiologic agents of hospital-acquired infections. High mortality rates are attributed to Trichosporon deep-seated infections in immunocompromised individuals, making fast and accurate species identification relevant for hastening the discovery of best-targeted therapy. Recently, Trichosporon taxonomy has been reassessed, and three genera have been proposed for the pathogenic species: Trichosporon , Cutaneotrichosporon , and Apiotrichum . Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has replaced old phenotypic methods for microorganism identification in clinical laboratories, but spectral profile databases have to be evaluated and improved for optimal species identification performance. Vitek MS (bioMérieux) is one of the commercially available MALDI-TOF MS platforms for pathogen identification, and its spectral profile databases remain poorly evaluated for Trichosporon , Cutaneotrichosporon , and Apiotrichum species identification. We herein evaluated and improved Vitek MS for the identification of the main clinical relevant species of Trichosporon , Cutaneotrichosporon , and Apiotrichum using a large set of strains and isolates belonging to different yeast collections in Brazil and France.

Download Full-text

Evaluation of Vitek MS for Differentiation of Cryptococcus neoformans and Cryptococcus gattii Genotypes

Journal of Clinical Microbiology ◽

10.1128/jcm.01282-18 ◽

2018 ◽

Vol 57 (1) ◽

Cited By ~ 2

Author(s):

Lumena P. Machado Siqueira ◽

Viviane M. Favero Gimenes ◽

Roseli Santos de Freitas ◽

Márcia de Souza Carvalho Melhem ◽

Lucas Xavier Bonfietti ◽

...

Keyword(s):

Cryptococcus Neoformans ◽

Cryptococcus Gattii ◽

Correct Identification ◽

Content Type ◽

Maldi Tof Ms ◽

Mass Spectral ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Vitek Ms ◽

Tof Ms

ABSTRACT Cryptococcus neoformans and Cryptococcus gattii are the main pathogenic species of invasive cryptococcosis among the Cryptococcus species. Taxonomic studies have shown that these two taxa have different genotypes or molecular types with biological and ecoepidemiological peculiarities. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has been proposed as an alternative method for labor-intensive methods for C. neoformans and C. gattii genotype differentiation. However, Vitek MS, one of the commercial MALDI-TOF MS instruments, has not been yet been evaluated for this purpose. Thus, we constructed an in-house database with reference strains belonging to the different C. neoformans (VNI, VNII, VNIII, and VNIV) and C. gattii (VGI, VGII, VGIII, and VGIV) major molecular types by using the software Saramis Premium (bioMérieux, Marcy-l’Etoile, France). Then, this new database was evaluated for discrimination of the different genotypes. Our in-house database provided correct identification for all C. neoformans and C. gattii genotypes; however, due to the intergenotypic mass spectral similarities, a careful postanalytic evaluation is necessary to provide correct genotype identification.

Download Full-text

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

Journal of Clinical Microbiology ◽

10.1128/jcm.00825-16 ◽

2016 ◽

Vol 54 (8) ◽

pp. 2068-2073 ◽

Cited By ~ 36

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.

Download Full-text

Candida auris Clinical Isolates from South Korea: Identification, Antifungal Susceptibility, and Genotyping

Journal of Clinical Microbiology ◽

10.1128/jcm.01624-18 ◽

2019 ◽

Vol 57 (4) ◽

Cited By ~ 33

Author(s):

Yong Jun Kwon ◽

Jong Hee Shin ◽

Seung A Byun ◽

Min Ji Choi ◽

Eun Jeong Won ◽

...

Keyword(s):

Antifungal Susceptibility ◽

Diagnostic Tools ◽

Candida Auris ◽

Content Type ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Fluconazole Resistant ◽

Vitek 2 ◽

Vitek Ms ◽

Tof Ms

ABSTRACT Candida auris is an emerging worldwide fungal pathogen. Over the past 20 years, 61 patient isolates of C. auris (4 blood and 57 ear) have been obtained from 13 hospitals in Korea. Here, we reanalyzed those molecularly identified isolates using two matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) systems, including Biotyper and Vitek MS, followed by antifungal susceptibility testing, sequencing of the ERG11 gene, and genotyping. With a research-use-only (RUO) library, 83.6% and 93.4% of the isolates were correctly identified by Biotyper and Vitek MS, respectively. Using an in vitro diagnostic (IVD) library of Vitek MS, 96.7% of the isolates were correctly identified. Fluconazole-resistant isolates made up 62.3% of the isolates, while echinocandin- or multidrug-resistant isolates were not found. Excellent essential (within two dilutions, 96.7%) and categorical agreements (93.4%) between the Clinical and Laboratory Standards Institute (CLSI) and Vitek 2 (AST-YS07 card) methods were observed for fluconazole. Sequencing ERG11 for all 61 isolates revealed that only 3 fluconazole-resistant isolates showed the Erg11p amino acid substitution K143R. All 61 isolates showed identical multilocus sequence typing (MLST). Pulsed-field gel electrophoresis (PFGE) analyses revealed that both blood and ear isolates had the same or similar patterns. These results show that MALDI-TOF MS and Vitek 2 antifungal susceptibility systems can be reliable diagnostic tools for testing C. auris isolates from Korean hospitals. The Erg11p mutation was seldom found among Korean isolates of C. auris, and multidrug resistance was not found. Both MLST and PFGE analyses suggest that these isolates are genetically similar.

Download Full-text

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

Journal of Clinical Microbiology ◽

10.1128/jcm.02459-16 ◽

2017 ◽

Vol 55 (4) ◽

pp. 1162-1176 ◽

Cited By ~ 23

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.

Download Full-text

Clonal Diversification and Changes in Lipid Traits and Colony Morphology in Mycobacterium abscessus Clinical Isolates

Journal of Clinical Microbiology ◽

10.1128/jcm.02015-15 ◽

2015 ◽

Vol 53 (11) ◽

pp. 3438-3447 ◽

Cited By ~ 24

Author(s):

In Kwon Park ◽

Amy P. Hsu ◽

Hervé Tettelin ◽

Shamira J. Shallom ◽

Steven K. Drake ◽

...

Keyword(s):

Acid Fast Bacillus ◽

Mycobacterium Abscessus ◽

Colony Morphology ◽

Culture Methods ◽

Genetic Changes ◽

Content Type ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Tof Ms

The smooth-to-rough colony morphology shift inMycobacterium abscessushas been implicated in loss of glycopeptidolipid (GPL), increased pathogenicity, and clinical decline in cystic fibrosis (CF) patients. However, the evolutionary phenotypic and genetic changes remain obscure. Serial isolates from nine non-CF patients with persistentM. abscessusinfection were characterized by colony morphology, lipid profile via thin-layer chromatography and matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), sequencing of eight genes in the GPL locus, and expression level offadD23, a key gene involved in the biosynthesis of complex lipids. All 50 isolates were typed asM. abscessussubspeciesabscessusand were clonally related within each patient. Rough isolates, all lacking GPL, predominated at later disease stages, some showing variation within rough morphology. While most (77%) rough isolates harbored detrimental mutations inmps1andmps2, 13% displayed previously unreported mutations inmmpL4aandmmpS4, the latter yielding a putative GPL precursor. Two isolates showed no deleterious mutations in any of the eight genes sequenced. Mixed populations harboring different GPL locus mutations were detected in 5 patients, demonstrating clonal diversification, which was likely overlooked by conventional acid-fast bacillus (AFB) culture methods. Our work highlights applications of MALDI-TOF MS beyond identification, focusing on mycobacterial lipids relevant in virulence and adaptation. Later isolates displayed accumulation of triacylglycerol and reduced expression offadD23, sometimes preceding rough colony onset. Our results indicate that clonal diversification and a shift in lipid metabolism, including the loss of GPL, occur during chronic lung infection withM. abscessus. GPL loss alone may not account for all traits associated with rough morphology.

Download Full-text

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

Journal of Clinical Microbiology ◽

10.1128/jcm.02128-15 ◽

2015 ◽

Vol 54 (2) ◽

pp. 376-384 ◽

Cited By ~ 70

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.

Download Full-text

Novel attempt at discrimination of a bullet-shaped siphonophore (Family Diphyidae) using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-ToF MS)

Scientific Reports ◽

10.1038/s41598-021-98724-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Nayeon Park ◽

Jisu Yeom ◽

Raehyuk Jeong ◽

Wonchoel Lee

Keyword(s):

Species Identification ◽

Morphological Characteristics ◽

Kuroshio Current ◽

Northwest Pacific ◽

Maldi Tof Ms ◽

Protein Mass ◽

Maldi Tof ◽

Morphological Findings ◽

Flight Mass Spectrometry ◽

Tof Ms

AbstractOne major difficulty in identifying the gelatinous bodied bullet-shaped Siphonophore, Diphyids, is that their shape is deformed following ethanol fixation. Ethanol often is preferred over other fixatives, since samples fixed in ethanol can be used for molecular studies that can supplement morphological findings. To overcome this problem, we obtained protein mass spectra of ten species of Diphyidae found in the waters of the Kuroshio Current (Northwest Pacific and South Coast of South Korea) to test whether MALDI-ToF MS could be used as a methodology for species identification. In addition, a number of morphological characteristics that can be used with ethanol-treated samples was summarized. Concatenated phylogenetic analysis was also performed to determine the phylogenetic relationship by obtaining partial sequences of four genes (mtCOI, 16S rRNA, 18S rRNA, and ITS regions). Based on our integrative analysis, MALDI-ToF MS was evaluated as a potentially fast, inexpensive, and accurate tool for species identification along with conventional morphological and DNA barcoding for Diphyidae.

Download Full-text

Identification of Nocardia species using Autof MS 1000 and Bruker MALDI-TOF MS systems: A comparison

10.1101/2021.01.11.426310 ◽

2021 ◽

Author(s):

Bing Ma ◽

Yunqi Tian ◽

Yungang Han ◽

Lifang Ban ◽

Junwen Yang ◽

...

Keyword(s):

Species Identification ◽

Protein Extraction ◽

Reference Method ◽

Invasive Disease ◽

Species Level ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Significant Difference ◽

Tof Ms

ABSTRACTNocardia is an important cause of clinically invasive disease, but for most clinical laboratories, identification of these isolates to the species level is challenging. Recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used for identification of most bacterial and fungal isolates. In this multicenter study, we evaluated the identification of Nocardia isolates using Autof MS1000 and Bruker Biotyper. A total of 86 non-duplicate Nocardia isolates from 7 hospital laboratories were evaluated. Further, we carried out sequence analysis of 16S rRNA, gyrB, secA1, hsp65, and rpoB genes as a reference method for Nocardia species identification. The 86 isolates were directly spotted on the target plate and plate protein extraction was performed. Data were analyzed by SPSS 19.0. In total, 72 (83.7%) strains (score ≥ 9.0) and 70 (81.4%) strains (score ≥ 2.0) were correctly identified by the Autof MS1000 and Bruker Biotyper systems, respectively, at the species level. There was no significant difference (P > 0.05) between the two systems using the same protein extraction method. In conclusion, the Autof MS 1000 and Bruker MALDI-TOF systems showed no difference in identification of Nocardia spp. to the species level and could meet the most important clinical requirement for species identification.

Download Full-text

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

Journal of Clinical Microbiology ◽

10.1128/jcm.02358-20 ◽

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.

Download Full-text

Rapid and cost-effective identification of Bartonella species using mass spectrometry

Journal of Medical Microbiology ◽

10.1099/jmm.0.009647-0 ◽

2009 ◽

Vol 58 (9) ◽

pp. 1154-1159 ◽

Cited By ~ 43

Author(s):

Pierre-Edouard Fournier ◽

Carine Couderc ◽

Sylvain Buffet ◽

Christophe Flaudrops ◽

Didier Raoult

Keyword(s):

Mass Spectrometry ◽

Species Identification ◽

Chemical Reactivity ◽

Bacterial Species ◽

Cost Effective ◽

Molecular Techniques ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Tof Ms

Bacteria of the genus Bartonella are emerging zoonotic bacteria recognized in a variety of human diseases. Due to their poor chemical reactivity, these fastidious bacteria are poorly characterized using routine phenotypic laboratory tests. Identification is usually achieved using molecular techniques that are time-consuming, expensive and technically demanding. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a new technique for bacterial species identification. This study evaluated the use of MALDI-TOF MS for rapid genus and species identification of Bartonella species. Reference strains representing 17 recognized Bartonella species were studied. For each species, MS spectra for four colonies were analysed. The consensus spectrum obtained for each species was unique among spectra obtained for 2843 bacteria within the Bruker database, including 109 alphaproteobacteria. Thirty-nine additional blind-coded Bartonella strains were correctly identified at the species level, including 36 with a significant score. Altogether, these data demonstrate that MS is an accurate and reproducible tool for rapid and inexpensive identification of Bartonella species.

Download Full-text