Pushing the Limits of MALDI-TOF Mass Spectrometry: Beyond Fungal Species Identification
16 Oct 2015-Journal of Fungi (Multidisciplinary Digital Publishing Institute)-Vol. 1, Iss: 3, pp 367-383
TL;DR: In this article, a review of the use of MALDI-TOF in the clinical mycology laboratory is presented, focusing on present and future applications of this versatile analytical tool in the field of bioinformatics.
Abstract: Matrix assisted laser desorption ionization time of flight (MALDI-TOF) is a powerful analytical tool that has revolutionized microbial identification. Routinely used for bacterial identification, MALDI-TOF has recently been applied to both yeast and filamentous fungi, confirming its pivotal role in the rapid and reliable diagnosis of infections. Subspecies-level identification holds an important role in epidemiological investigations aimed at tracing virulent or drug resistant clones. This review focuses on present and future applications of this versatile tool in the clinical mycology laboratory.
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TL;DR: The importance and practicality of a more inclusive approach to evaluate and characterise novel yeast strains used for winemaking is highlighted by deploying traditional and modern chemical and organoleptic evaluation techniques of wines in conjunction with cutting-edge omics approaches towards enhancing white wine varietal aroma.
15 citations
TL;DR: The diagnosis of this infection in non-endemic countries is hampered by the lack of clinical suspicion and a dearth of available diagnostic tools adequate to offer rapid and accurate results, so non-culture-based assays present as a suitable alternative in this situation.
Abstract: Human histoplasmosis is a fungal infection caused by the inhalation of microconidia of the thermally dimorphic fungi Histoplasma capsulatum. Autochthonous cases of histoplasmosis have been diagnosed in almost every country, but it is considered an endemic infection in specific areas of the world. Many of them are popular travel destinations or the source of migratory movements. Thus, the vast majority of the registered cases in non-endemic countries are imported. They correspond to people having been exposed to the fungus in endemic locations as immigrants, expatriates, transient workers or tourists, with reported cases also associated to organ donation. Misdiagnosis and delays in initiation of treatment are not uncommon in cases of imported histoplasmosis. They are associated to high fatality-rates specially in patients with compromised cellular immunity in which progressive disseminated forms develop. The diagnosis of this infection in non-endemic countries is hampered by the lack of clinical suspicion and a dearth of available diagnostic tools adequate to offer rapid and accurate results. Non-culture-based assays such as nucleic-acid amplification tests present as a suitable alternative in this situation, offering improved sensitivity and specificity, shortened turnaround time, and increased biosafety by avoiding culture manipulation. In non-endemic regions, molecular techniques are being used mainly in laboratories from countries that have registered an increase in the incidence of imported cases. However, the number of published techniques is limited and lack consensus. Efforts are currently under way to standardize nucleic acid amplification-based techniques for its implementation in areas registering a rising number of imported cases.
12 citations
Cites background from "Pushing the Limits of MALDI-TOF Mas..."
...capsulatum can grow in mycological media of common use in routine laboratories, and current MALDI-TOF systems can provide a presumptive identification (Panda et al., 2015; Rizzato et al., 2015; Rychert et al., 2018; Valero et al., 2018)....
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31 Dec 2019
TL;DR: This investigation highlights the potential of MalDI-TOF MS technique as a fast and cost-efficient alternative for clinical Fusarium identification, however, MALDI-toF MS requires a more accurate and larger database.
Abstract: The aim of this study was to compare the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), phenotypic and molecular methods for the identification of Fusarium species complexes isolated from clinical cases in the State of Sao Paulo (Brazil) between the years 2001 and 2017. Sequencing of ITS region of ribosomal DNA and elongation factor 1 alpha gene (ET1α) were used as reference method in the analysis of a total of 108 Fusarium spp. clinical strains isolated from human hosts with superficial and systemic infections. Agreement between MALDI-TOF-MS and molecular data was observed for 97 out of 108 clinical isolates (89.8%), whereas five (4.6%) and six (5.5%) clinical isolates were misidentified and were not identified by MALDI-TOF MS, respectively. ITS region sequences and MALDI-TOF MS mass spectra identified and grouped correctly most of Fusarium clinical isolates at species complex level. This investigation highlights the potential of MALDI-TOF MS technique as a fast and cost-efficient alternative for clinical Fusarium identification. However, MALDI-TOF MS requires a more accurate and larger database. This work is the first comprehensive report for Fusarium population, based on phenotypic analyses, proteomic profile by MALDI-TOF and phylogenetic analyses of Fusarium species complexes isolated from clinical cases in the State of Sao Paulo, Brazil.
10 citations
01 Jan 2017
TL;DR: In this article, the development of yeast for the production of varietal aromatic Sauvignon blanc with lower volatile-acidity (VA) was identified as a South African industry priority.
Abstract: Wine yeast Saccharomyces cerevisiae and wild yeasts e.g. Torulaspora delbrueckii forms an integral
part of wine production by converting relatively 'neutral' flavoured Sauvignon blanc grape must into
varietal aromatic wines. Yeast derived and mediated metabolites which contribute to Sauvignon blanc
wine aroma and flavour, are regulated by yeast proteins (enzymes) that are differentially expressed
during the course of fermentation. Inoculation with an appropriate yeast strain can, therefore, increase
commercial wines sales as resultant wines will have sought-after aromas and flavours. Likewise,
inoculation with the incorrect strain can have an undesirable effect on wine quality. Subsequently, the
development of yeasts for the production of varietal aromatic Sauvignon blanc with lower volatile
acidity (VA) was also identified as a South African industry priority. Although genetic modification can
address this, the use of genetically modified organisms (GMO) is illegal.
6 citations
Cites background or methods from "Pushing the Limits of MALDI-TOF Mas..."
...Identification of unknown yeasts are achieved by comparing their mass spectra to a Bruker Daltonics BioTyper library database (Rizzato et al., 2016)....
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...A novel database can, however, be developed from scratch to accodomate spectra originating from excluded or novel microbes (Rizzato et al., 2016)....
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01 Jan 2017
TL;DR: The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) mass spectra show congruency with the genealogy of microorganisms, and can be implemented as a valuable analytical tool for polyphasic approaches in microbial systematics.
Abstract: Traditional methods for identifying microorganisms in microbiology laboratories are based on microscopic and biochemical methods (phenotyping) and gene sequencing identification techniques (genotyping). However in the past decade, the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been established as a new reliable, rapid, and inexpensive automatable method for identifying a wide array of bacteria, archaea, fungi, dermatophytes and even viruses. Its “molecular-phenotypic”-based methodology is based on the reproducible detection of protein mass patterns (proteomic profile) obtained from whole cells, cell lysates, or crude bacterial extracts. Microbial MALDI-TOF MS mass spectra can be regarded as snapshots of the protein composition of the strains under study. Many of the mass spectral signals have been assigned as high-abundance proteins with housekeeping functions, such as basic ribosomal proteins or DNA-binding proteins. These proteins are highly conserved and consistently expressed under nearly all growth conditions. They can thus be regarded as robust biomarker candidates of the respective microorganism and their identification. As ribosomal protein genealogies mirror the rRNA genes reconstructed phylogenies, the mass spectra show congruency with the genealogy of microorganisms, and hence, can be implemented as a valuable analytical tool for polyphasic approaches in microbial systematics.
2 citations
References
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TL;DR: How basic science studies are elucidating the molecular details of the crosstalk that occurs at the host–pathogen interface, as well as the consequences of these interactions for the pathophysiology of UTIs is discussed.
Abstract: Urinary tract infections (UTIs) are a severe public health problem and are caused by a range of pathogens, but most commonly by Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Enterococcus faecalis and Staphylococcus saprophyticus. High recurrence rates and increasing antimicrobial resistance among uropathogens threaten to greatly increase the economic burden of these infections. In this Review, we discuss how basic science studies are elucidating the molecular details of the crosstalk that occurs at the host-pathogen interface, as well as the consequences of these interactions for the pathophysiology of UTIs. We also describe current efforts to translate this knowledge into new clinical treatments for UTIs.
2,251 citations
TL;DR: In this article, the authors used matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) to identify both selected bacteria and bacteria in select clinical situations.
Abstract: Background. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry accurately identifies both selected bacteria and bacteria in select clinical situations. It has not been evaluated for routine use in the clinic. Methods. We prospectively analyzed routine MALDI-TOF mass spectrometry identification in parallel with conventional phenotypic identification of bacteria regardless of phylum or source of isolation. Discrepancies were resolved by 16S ribosomal RNA and rpoB gene sequence-based molecular identification. Colonies (4 spots per isolate directly deposited on the MALDI-TOF plate) were analyzed using an Autoflex II Bruker Daltonik mass spectrometer. Peptidic spectra were compared with the Bruker BioTyper database, version 2.0, and the identification score was noted. Delays and costs of identification were measured. Results. Of 1660 bacterial isolates analyzed, 95.4% were correctly identified by MALDI-TOF mass spectrometry; 84.1% were identified at the species level, and 11.3% were identified at the genus level. In most cases, absence of identification (2.8% of isolates) and erroneous identification (1.7% of isolates) were due to improper database entries. Accurate MALDI-TOF mass spectrometry identification was significantly correlated with having 10 reference spectra in the database (P = .01). The mean time required for MALDI-TOF mass spectrometry identification of 1 isolate was 6 minutes for an estimated 22%-32% cost of current methods of identification. Conclusions. MALDI-TOF mass spectrometry is a cost-effective, accurate method for routine identification of bacterial isolates in <1 h using a database comprising ≥10 reference spectra per bacterial species and a ≥1.9 identification score (Brucker system). It may replace Gram staining and biochemical identification in the near future.
1,695 citations
"Pushing the Limits of MALDI-TOF Mas..." refers background in this paper
...In the past few years matrix-assisted laser desorption ionization time of flight (MALDI-TOF) has revolutionized medical microbiology [8], enabling rapid and accurate bacterial species identification (within a few minutes) with simple and reliable procedures [9]....
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TL;DR: The prognosis is poor and is determined largely by degree of immunosuppression and extent of infection, with virtually a 100% death rate among persistently neutropenic patients with disseminated disease.
Abstract: Fusarium species cause a broad spectrum of infections in humans, including superficial, locally invasive, and disseminated infections. The clinical form of fusariosis depends largely on the immune status of the host and the portal of entry, with superficial and localized disease occurring mostly in immunocompetent patients and invasive and disseminated disease affecting immunocompromised patients. Risk factors for severe fusariosis include prolonged neutropenia and T-cell immunodeficiency, especially in hematopoietic stem cell transplant recipients with severe graft-versus-host disease. The most frequent presentation of disseminated fusariosis is a combination of characteristic cutaneous lesions and positive blood cultures, with or without lung or sinus involvement. The prognosis is poor and is determined largely by degree of immunosuppression and extent of infection, with virtually a 100% death rate among persistently neutropenic patients with disseminated disease. These infections may be clinically suspected on the basis of a constellation of clinical and laboratory findings, which should lead to prompt therapy. Treatment options include the lipid formulations of amphotericin B, voriconazole, and posaconazole. Prevention of fusarial infection among high-risk patients should be considered.
827 citations
TL;DR: The application of MALDI mass spectrometry to desorb protein biomarkers from intact viruses, bacteria, fungus, and spores is the focus of this review.
Abstract: The application of MALDI mass spectrometry to desorb protein biomarkers from intact viruses, bacteria, fungus, and spores is the focus of this review. Instrumentation, sample collection, sample preparation, and algorithms for data analysis are summarized. Optimally these analyses should be carried out in less than five minutes. Successful applications are discussed from biotechnology, cell biology, and the pharmaceutical industry.
801 citations
TL;DR: MALDI-TOF MS has been used successfully for microbial typing and identification at the subspecies level, demonstrating that this technology is a potential efficient tool for epidemiological studies and for taxonomical classification.
Abstract: Until recently, microbial identification in clinical diagnostic laboratories has mainly relied on conventional phenotypic and gene sequencing identification techniques. The development of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) devices has revolutionized the routine identification of microorganisms in clinical microbiology laboratories by introducing an easy, rapid, high throughput, low-cost, and efficient identification technique. This technology has been adapted to the constraint of clinical diagnostic laboratories and has the potential to replace and/or complement conventional identification techniques for both bacterial and fungal strains. Using standardized procedures, the resolution of MALDI-TOF MS allows accurate identification at the species level of most Gram-positive and Gram-negative bacterial strains with the exception of a few difficult strains that require more attention and further development of the method. Similarly, the routine identification by MALDI-TOF MS of yeast isolates is reliable and much quicker than conventional techniques. Recent studies have shown that MALDI-TOF MS has also the potential to accurately identify filamentous fungi and dermatophytes, providing that specific standardized procedures are established for these microorganisms. Moreover, MALDI-TOF MS has been used successfully for microbial typing and identification at the subspecies level, demonstrating that this technology is a potential efficient tool for epidemiological studies and for taxonomical classification.
744 citations
"Pushing the Limits of MALDI-TOF Mas..." refers background in this paper
...In the past few years matrix-assisted laser desorption ionization time of flight (MALDI-TOF) has revolutionized medical microbiology [8], enabling rapid and accurate bacterial species identification (within a few minutes) with simple and reliable procedures [9]....
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