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Buszewski B, Błońska D, Kłodzińska E, Konop M, Kubesová A, Šalplachta J. Determination of Pathogens by Electrophoretic and Spectrometric Techniques. Crit Rev Anal Chem 2023:1-24. [PMID: 37326587 DOI: 10.1080/10408347.2023.2219748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In modern medical diagnostics, where analytical chemistry plays a key role, fast and accurate identification of pathogens is becoming increasingly important. Infectious diseases pose a growing threat to public health due to population growth, international air travel, bacterial resistance to antibiotics, and other factors. For instance, the detection of SARS-CoV-2 in patient samples is a key tool to monitor the spread of the disease. While there are several techniques for identifying pathogens by their genetic code, most of these methods are too expensive or slow to effectively analyze clinical and environmental samples that may contain hundreds or even thousands of different microbes. Standard approaches (e.g., culture media and biochemical assays) are known to be very time- and labor-intensive. The purpose of this review paper is to highlight the problems associated with the analysis and identification of pathogens that cause many serious infections. Special attention was paid to the description of mechanisms and the explanation of the phenomena and processes occurring on the surface of pathogens as biocolloids (charge distribution). This review also highlights the importance of electromigration techniques and demonstrates their potential for pathogen pre-separation and fractionation and demonstrates the use of spectrometric methods, such as MALDI-TOF MS, for their detection and identification.
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Affiliation(s)
- Bogusław Buszewski
- Prof. Jan Czochralski Kuyavian-Pomeranian Research & Development Centre, Torun, Poland
- Department of Environmental Chemistry and Bioanalytics, Nicolaus Copernicus University in Toruń, Torun, Poland
| | - Dominika Błońska
- Department of Environmental Chemistry and Bioanalytics, Nicolaus Copernicus University in Toruń, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Torun, Poland
| | - Ewa Kłodzińska
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Marek Konop
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Anna Kubesová
- Institute of Analytical Chemistry of the CAS, Brno, Czech Republic
| | - Jiří Šalplachta
- Institute of Analytical Chemistry of the CAS, Brno, Czech Republic
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Hleba L, Hlebova M, Kovacik A, Petrova J, Maskova Z, Cubon J, Massanyi P. Use of MALDI-TOF MS to Discriminate between Aflatoxin B1-Producing and Non-Producing Strains of Aspergillus flavus. Molecules 2022; 27:molecules27227861. [PMID: 36431961 PMCID: PMC9692738 DOI: 10.3390/molecules27227861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Aflatoxin B1 (AFB1) is one of the most toxic mycotoxins. One of the producers of AFB1 is Aspergillus flavus. Therefore, its rapid identification plays a key role in various sectors of the food and feed industry. MALDI-TOF mass spectrometry is one of the fastest and most accurate methods today. Therefore, the aim of this research was to develop the rapid identification of producing and non-producing strains of A. flavus based on the entire mass spectrum. To accomplish the main goal a different confirmatory MALDI-TOF MS and TLC procedures such as direct AFB1 identification by scraping from TLC plates, A. flavus mycelium, nutrient media around A. flavus growth, and finally direct AFB1 identification from infected wheat and barley grains had to be conducted. In this experiment, MALDI-TOF mass spectrometry with various modifications was the main supporting technology. All confirmatory methods confirmed the presence of AFB1 in the samples of aflatoxin-producing strains of A. flavus and vice versa; AFB1 was not detected in the case of non-producing strains. Entire mass spectra (from 2 to 20 kDa) of aflatoxin-producing and non-producing A. flavus strains were collected, statistically analyzed and clustered. An in-depth analysis of the obtained entire mass spectra showed differences between AFB1-producing and non-producing strains of A. flavus. Statistical and cluster analysis divided AFB1-producing and non-producing strains of A. flavus into two monasteries. The results indicate that it is possible to distinguish between AFB1 producers and non-producers by comparing the entire mass spectra using MALDI-TOF MS. Finally, we demonstrated that if there are established local AFB1-producing and non-producing strains of A. flavus, the entire mass spectrum database identification of aflatoxigenic A. flavus strains can be even faster and cheaper, without the need to identify the toxin itself.
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Affiliation(s)
- Lukas Hleba
- Faculty of Biotechnology and Food Sciences, Institute of Biotechnology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
- Correspondence:
| | - Miroslava Hlebova
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 917 01 Trnava, Slovakia
| | - Anton Kovacik
- Faculty of Biotechnology and Food Sciences, Institute of Applied Biology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Jana Petrova
- Faculty of Biotechnology and Food Sciences, Institute of Biotechnology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Zuzana Maskova
- Faculty of Biotechnology and Food Sciences, Institute of Biotechnology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Juraj Cubon
- Faculty of Biotechnology and Food Sciences, Institute of Food Sciences, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Peter Massanyi
- Faculty of Biotechnology and Food Sciences, Institute of Applied Biology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
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Forster MK, Sedaghatjoo S, Maier W, Killermann B, Niessen L. Discrimination of Tilletia controversa from the T. caries/T. laevis complex by MALDI-TOF MS analysis of teliospores. Appl Microbiol Biotechnol 2022; 106:1257-1278. [PMID: 35037998 PMCID: PMC8816839 DOI: 10.1007/s00253-021-11757-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/21/2021] [Accepted: 12/27/2021] [Indexed: 12/04/2022]
Abstract
The fungal genus Tilletia includes a large number of plant pathogens of Poaceae. Only a few of those cause bunt of wheat, but these species can lead to significant yield losses in crop production worldwide. Due to quarantine regulations and specific disease control using appropriate seed treatments for the different disease agents, it is of high importance to distinguish Tilletia caries and Tilletia laevis as causal agents of common bunt accurately from Tilletia controversa, the causal agent of the dwarf bunt. Several studies have shown that matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a useful tool to differentiate closely related fungal species. The aim of this study was to assess whether MALDI-TOF MS analysis is able to distinguish specimens of the three closely related pathogens T. caries, T. laevis, and T. controversa and whether it may constitute an alternative method to the morphology-based identification or germination tests. Spectral data are available via ProteomeXchange with identifier PXD030401. Spectra-based hierarchical cluster analysis (HCA) and discriminant analysis of principal components (DAPC) of the obtained mass spectra showed two main clusters. One cluster included specimens of T. controversa, whereas the second cluster comprised T. laevis and T. caries specimens. Even though main spectral profiles (MSPs) for species identification are missing, MALDI-TOF MS has proven to be a useful method for distinguishing between T. controversa and the two causal agents of common bunt, using direct analysis of teliospores, but was unable to separate T. caries and T. laevis species. KEY POINTS: • MALDI-TOF MS was developed to classify Tilletia species causing bunt of wheat. • Best results were achieved when combining HCA and DAPC analysis. • The method resulted in an accuracy of 98.51% testing 67 Tilletia specimens.
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Affiliation(s)
- Monika K Forster
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture (LfL), Voettinger Str. 38, 85354, Freising, Germany
- Chair of Microbiology, TUM School of Life Sciences, Technical University of Munich, Gregor-Mendel-Str. 4, 85354, Freising, Germany
| | - Somayyeh Sedaghatjoo
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
- Molecular Phytopathology and Mycotoxin Research, University of Goettingen, Grisebachstrasse 6, 37077, Goettingen, Germany
| | - Wolfgang Maier
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Berta Killermann
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture (LfL), Voettinger Str. 38, 85354, Freising, Germany
| | - Ludwig Niessen
- Chair of Microbiology, TUM School of Life Sciences, Technical University of Munich, Gregor-Mendel-Str. 4, 85354, Freising, Germany.
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MALDI-TOF mass spectrometry–based identification of Eurotiales from different substrates and locations in Brazil. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01691-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Oyedeji AB, Green E, Adebiyi JA, Ogundele OM, Gbashi S, Adefisoye MA, Oyeyinka SA, Adebo OA. Metabolomic approaches for the determination of metabolites from pathogenic microorganisms: A review. Food Res Int 2021; 140:110042. [PMID: 33648268 DOI: 10.1016/j.foodres.2020.110042] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/04/2020] [Accepted: 12/13/2020] [Indexed: 12/30/2022]
Abstract
Metabolomics is a high precision analytical approach to obtaining detailed information of varieties of metabolites produced in biological systems, including foods. This study reviews the use of metabolomic approaches such as liquid chromatography mass spectrometry (LCMS), gas chromatography mass spectrometry (GC-MS), matrix assisted laser desorption /ionization tandem time of flight mass spectrometry (MALDI-TOF-MS) and nuclear magnetic resonance (NMR) for investigating the presence of foodborne pathogens and their metabolites. Pathogenic fungi and their notable metabolites (mycotoxins) have been studied more extensively using metabolomics as compared to bacteria, necessitating further studies in this regard. Nevertheless, such identified fungal and bacteria metabolites could be used as biomarkers for a more rapid detection of these pathogens in food. Other important compounds detected through metabolomics could also be correlated to functionality of these pathogenic strains, determined by the composition of the foods in which they exist, thereby providing insights into their metabolism. Considering the prevalence of these food pathogens, metabolomics still has potentials in the determination of food-borne pathogenic microorganisms especially for the determination of pathogenic bacteria toxins and is expected to generate research interests for further studies and applications.
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Affiliation(s)
- Ajibola Bamikole Oyedeji
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg Doornfontein Campus, P. O. Box 17011, Gauteng 2028, South Africa.
| | - Ezekiel Green
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg Doornfontein Campus, P. O. Box 17011, Gauteng 2028, South Africa
| | - Janet Adeyinka Adebiyi
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg Doornfontein Campus, P. O. Box 17011, Gauteng 2028, South Africa
| | - Opeolu Mayowa Ogundele
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg Doornfontein Campus, P. O. Box 17011, Gauteng 2028, South Africa
| | - Sefater Gbashi
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg Doornfontein Campus, P. O. Box 17011, Gauteng 2028, South Africa
| | - Martins Ajibade Adefisoye
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg Doornfontein Campus, P. O. Box 17011, Gauteng 2028, South Africa
| | - Samson Adeoye Oyeyinka
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg Doornfontein Campus, P. O. Box 17011, Gauteng 2028, South Africa
| | - Oluwafemi Ayodeji Adebo
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg Doornfontein Campus, P. O. Box 17011, Gauteng 2028, South Africa.
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Xu X, Xiao N, Yang M, Su Y, Guo Y. Discrimination of the microbial subspecies using the ribosomal protein spectra coupled with the metabolite high resolution mass spectra. Talanta 2020; 208:120361. [DOI: 10.1016/j.talanta.2019.120361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/01/2019] [Accepted: 09/14/2019] [Indexed: 10/26/2022]
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Reeve MA, Bachmann D, Caine TS. Identification of Penicillium species by MALDI-TOF MS analysis of spores collected by dielectrophoresis. Biol Methods Protoc 2019; 4:bpz018. [PMID: 32161810 PMCID: PMC6994048 DOI: 10.1093/biomethods/bpz018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 11/17/2022] Open
Abstract
In matrix-assisted laser-desorption and ionization mass spectrometry, spectral differences are frequently observed using different growth media on agar plates and/or different growth times in culture, which add undesirable analytical variance. In this article, we explore an approach to the above problem based upon the rationale that, while protein expression in fungal mycelium may well vary under different growth conditions, this might not apply to the same extent in fungal spores. To this end, we have exploited the fact that while mycelium is generally anchored to the fungal-growth substrate, some fungi produce physically-isolated spores which, as such, are amenable to manipulation using dielectrophoresis (the translational motion of charged or uncharged matter caused by polarization effects in a non-uniform electrical field). Such fields can be conveniently generated through the charging of an insulator using the triboelectric effect (the transfer of charge between two objects through friction when they are rubbed together). In this study, polystyrene microbiological inoculating loops were used in combination with nylon-fabric rubbing to harvest fungal spores from five species from within the genus Penicillium, which were grown on agar plates containing two different media over an extended time course. In terms of average Bruker spectral-comparison scores, our method generated higher scores in 80% of cases tested and, in terms of average coefficients of variation, our method generated lower spectral variability in 93% of cases tested. Harvesting of spores using a rapid, inexpensive and simple dielectrophoretic method, therefore, facilitates improved fungal identification for the Penicillium species tested.
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Becker P, Normand AC, Vanantwerpen G, Vanrobaeys M, Haesendonck R, Vercammen F, Stubbe D, Piarroux R, Hendrickx M. Identification of fungal isolates by MALDI-TOF mass spectrometry in veterinary practice: validation of a web application. J Vet Diagn Invest 2019; 31:471-474. [PMID: 30943879 DOI: 10.1177/1040638719835577] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a reliable method to identify fungal isolates. The success of this approach relies on the availability of exhaustive databases, but the latter were built with a focus on human pathogens. We assessed a large in-house database of reference spectra and a dedicated web application for their suitability for use in veterinary laboratories. A panel of 290 mold and yeast isolates representing 69 different fungal species was isolated from various animals (including pets, cattle, and zoo animals) and identified using both MALDI-TOF MS and conventional techniques. The performance of the 2 methods was compared, and identifications were confirmed by DNA sequencing. MALDI-TOF MS allowed distinction between some closely related species and achieved 89% correct identification at the species level. In comparison, only 60% of the isolates were correctly identified with conventional approaches. Using this online application, MALDI-TOF MS thus appears to be a relevant alternative for the identification of fungal isolates encountered by animal health professionals.
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Affiliation(s)
- Pierre Becker
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Anne-Cécile Normand
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Gerty Vanantwerpen
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Mia Vanrobaeys
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Roel Haesendonck
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Francis Vercammen
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Dirk Stubbe
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Renaud Piarroux
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Marijke Hendrickx
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
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Chan WK, Wildeboer D, Garelick H, Purchase D. Competition of As and other Group 15 elements for surface binding sites of an extremophilic Acidomyces acidophilus isolated from a historical tin mining site. Extremophiles 2018; 22:795-809. [PMID: 30039469 DOI: 10.1007/s00792-018-1039-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 07/09/2018] [Indexed: 11/30/2022]
Abstract
An arsenic-resistant fungal strain, designated WKC-1, was isolated from a waste roaster pile in a historical tin mine in Cornwall, UK and successfully identified to be Acidomyces acidophilus using matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry (MALDI-TOF/TOF MS) proteomic-based biotyping approach. WKC-1 showed considerable resistance to As5+ and Sb5+ where the minimal inhibitory concentration (MIC) were 22500 and 100 mg L-1, respectively, on Czapex-Dox Agar (CDA) medium; it was substantially more resistant to As5+ than the reference strains CBS 335.97 and CCF 4251. In a modified CDA medium containing 0.02 mg L-1 phosphate, WKC-1 was able to remove 70.30% of As5+ (100 mg L-1). Sorption experiment showed that the maximum capacity of As5+ uptake was 170.82 mg g-1 dry biomass as predicted by the Langmuir model. The presence of Sb5+ reduced the As5+ uptake by nearly 40%. Based on the Fourier-transform infrared spectroscopy (FT-IR) analysis, we propose that Sb is competing with As for these sorption sites: OH, NH, CH, SO3 and PO4 on the fungal cell surface. To our knowledge, this is the first report on the impact of other Group 15 elements on the biosorption of As5+ in Acidomyces acidophilus.
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Affiliation(s)
- Wai Kit Chan
- Department of Natural Science, Faculty of Science and Technology, Middlesex University, The Burroughs, London, NW4 4BT, UK
| | - Dirk Wildeboer
- Department of Natural Science, Faculty of Science and Technology, Middlesex University, The Burroughs, London, NW4 4BT, UK
| | - Hemda Garelick
- Department of Natural Science, Faculty of Science and Technology, Middlesex University, The Burroughs, London, NW4 4BT, UK
| | - Diane Purchase
- Department of Natural Science, Faculty of Science and Technology, Middlesex University, The Burroughs, London, NW4 4BT, UK.
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Quéro L, Girard V, Pawtowski A, Tréguer S, Weill A, Arend S, Cellière B, Polsinelli S, Monnin V, van Belkum A, Vasseur V, Nodet P, Mounier J. Development and application of MALDI-TOF MS for identification of food spoilage fungi. Food Microbiol 2018; 81:76-88. [PMID: 30910090 DOI: 10.1016/j.fm.2018.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/30/2018] [Accepted: 05/01/2018] [Indexed: 01/20/2023]
Abstract
Filamentous fungi are frequently involved in food spoilage and cause important food losses and substantial economic damage. Their rapid and accurate identification is a key step to better manage food safety and quality. In recent years, MALDI-TOF MS has emerged as a powerful tool to identify microorganisms and has successfully been applied to the identification of filamentous fungi especially in the clinical context. The aim of this study was to implement a spectral database representative of food spoilage molds. To this end, after application of a standardized extraction protocol, 6477 spectra were acquired from 618 fungal strains belonging to 136 species and integrated in the VITEK MS database. The performances of this database were then evaluated by cross-validation and ∼95% of correct identification to the species level was achieved, independently of the cultivation medium and incubation time. The database was also challenged with external isolates belonging to 52 species claimed in the database and 90% were correctly identified to the species level. To our best knowledge, this is the most comprehensive database of food-relevant filamentous fungi developed to date. This study demonstrates that MALDI-TOF MS could be an alternative to conventional techniques for the rapid and reliable identification of spoilage fungi in food and industrial environments.
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Affiliation(s)
- Laura Quéro
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France; BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Victoria Girard
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Audrey Pawtowski
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Sylvie Tréguer
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Amélie Weill
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France; Université de Bretagne Occidentale Culture Collection, Université de Brest, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Sandrine Arend
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Béatrice Cellière
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Sophie Polsinelli
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Valérie Monnin
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Alex van Belkum
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Valérie Vasseur
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Patrice Nodet
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Jérôme Mounier
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
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11
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Validation of a New Web Application for Identification of Fungi by Use of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2017. [PMID: 28637907 DOI: 10.1128/jcm.00263-17] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry has emerged as a reliable technique to identify molds involved in human diseases, including dermatophytes, provided that exhaustive reference databases are available. This study assessed an online identification application based on original algorithms and an extensive in-house reference database comprising 11,851 spectra (938 fungal species and 246 fungal genera). Validation criteria were established using an initial panel of 422 molds, including dermatophytes, previously identified via DNA sequencing (126 species). The application was further assessed using a separate panel of 501 cultured clinical isolates (88 mold taxa including dermatophytes) derived from five hospital laboratories. A total of 438 (87.35%) isolates were correctly identified at the species level, while 26 (5.22%) were assigned to the correct genus but the wrong species and 37 (7.43%) were not identified, since the defined threshold of 20 was not reached. The use of the Bruker Daltonics database included in the MALDI Biotyper software resulted in a much higher rate of unidentified isolates (39.76 and 74.30% using the score thresholds 1.7 and 2.0, respectively). Moreover, the identification delay of the online application remained compatible with real-time online queries (0.15 s per spectrum), and the application was faster than identifications using the MALDI Biotyper software. This is the first study to assess an online identification system based on MALDI-TOF spectrum analysis. We have successfully applied this approach to identify molds, including dermatophytes, for which diversity is insufficiently represented in commercial databases. This free-access application is available to medical mycologists to improve fungal identification.
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12
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Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry systems for the identification of clinical filamentous fungi. World J Microbiol Biotechnol 2017; 33:142. [PMID: 28608323 DOI: 10.1007/s11274-017-2297-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 05/22/2017] [Indexed: 10/19/2022]
Abstract
Infections caused by filamentous fungi have become a health concern, and require rapid and accurate identification in order for effective treatment of the pathogens. To compare the performance of two MALDI-TOF MS systems (Bruker Microflex LT and Xiamen Microtyper) in the identification of filamentous fungal species. A total of 374 clinical filamentous fungal isolates sequentially collected in the Clinical Laboratory at the Beijing Tongren Hospital between January 2014 and December 2015 were identified by traditional phenotypic methods, Bruker Microflex LT and Xiamen Microtyper MALDI-TOF MS, respectively. The discrepancy between these methods was resolved by sequencing for definitive identification. Bruker Microflex LT and Xiamen Microtyper had similar correct species ID (98.9 vs. 99.2%), genus ID (99.7 vs. 100%), mis-ID (0.3 vs. 0%) and no ID (0 vs. 0). The rate of correct species identification by both MALDI-TOF MS (98.9 and 99.2%, respectively) was much higher compared with phenotypic approach (91.9%). Both MALDI-TOF MS systems provide accurate identification of clinical filamentous fungi compared with conventional phenotypic method, and have the potential to replace identification for routine identification of these fungi in clinical mycology laboratories. Both systems have similar performance in the identification of clinical filamentous fungi.
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13
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Organic matrices, ionic liquids, and organic matrices@nanoparticles assisted laser desorption/ionization mass spectrometry. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.01.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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14
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Decision criteria for MALDI-TOF MS-based identification of filamentous fungi using commercial and in-house reference databases. BMC Microbiol 2017; 17:25. [PMID: 28143403 PMCID: PMC5282874 DOI: 10.1186/s12866-017-0937-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/17/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry protocols, which differ in identification criteria, have been developed for mold and dermatophyte identification. Currently, the most widely used approach is Bruker technology, although no consensus concerning the log(score) threshold has been established. Furthermore, it remains unknown how far increasing the number of spots to compare results might improve identification performance. In this study, we used in-house and Bruker reference databases as well as a panel of 422 isolates belonging to 126 species to test various thresholds. Ten distinct identification algorithms requiring one to four spots were tested. RESULTS Our findings indicate that optimal results were obtained by applying a decisional algorithm in which only the highest score of four spots was taken into account with a 1.7 log(score) threshold. Testing the entire panel enabled identification of 87.41% (in-house database) and 35.15% (Bruker database) of isolates, with a positive predictive value (PPV) of 1 at the genus level for both databases as well as 0.89 PPV (in-house database) and 0.72 PPV (Bruker database) at the species level. Applying the same rules to the isolates for which the species were represented by at least three strains in the database enabled identification of 92.1% (in-house database) and 46.6% (Bruker database) of isolates, with 1 PPV at the genus level for both databases as well as 0.95 PPV (in-house database) and 0.93 PPV (Bruker database) at the species level. CONCLUSIONS Depositing four spots per extract and lowering the threshold to 1.7, a threshold which is notably lower than that recommended for bacterial identification, decreased the number of unidentified specimens without altering the reliability of the accepted results. Nevertheless, regardless of the criteria used for mold and dermatophyte identification, commercial databases require optimization.
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15
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Lopes RB, Faria M, Souza DA, Bloch C, Silva LP, Humber RA. MALDI-TOF mass spectrometry applied to identifying species of insect-pathogenic fungi from the Metarhizium anisopliae complex. Mycologia 2017; 106:865-78. [DOI: 10.3852/13-401] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | | | - Luciano P. Silva
- Embrapa Genetic Resources and Biotechnology, Brasilia DF, CP 02372, 70770-917, Brazil
| | - Richard A. Humber
- USDA-ARS Biological Integrated Pest Management Research, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, New York 14853
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16
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Emerging and Future Applications of Matrix-Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry in the Clinical Microbiology Laboratory. J Mol Diagn 2016; 18:789-802. [DOI: 10.1016/j.jmoldx.2016.07.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 06/29/2016] [Accepted: 07/21/2016] [Indexed: 12/17/2022] Open
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17
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Cassagne C, Normand AC, L'Ollivier C, Ranque S, Piarroux R. Performance of MALDI-TOF MS platforms for fungal identification. Mycoses 2016; 59:678-690. [DOI: 10.1111/myc.12506] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/04/2016] [Accepted: 03/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Carole Cassagne
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Anne-Cécile Normand
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
| | - Coralie L'Ollivier
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Stéphane Ranque
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Renaud Piarroux
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
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18
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Proteomics of survival structures of fungal pathogens. N Biotechnol 2016; 33:655-665. [DOI: 10.1016/j.nbt.2015.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 12/09/2015] [Accepted: 12/16/2015] [Indexed: 11/21/2022]
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19
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Hamad I, Raoult D, Bittar F. Repertory of eukaryotes (eukaryome) in the human gastrointestinal tract: taxonomy and detection methods. Parasite Immunol 2016; 38:12-36. [PMID: 26434599 DOI: 10.1111/pim.12284] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 09/23/2015] [Indexed: 12/22/2022]
Abstract
Eukaryotes are an important component of the human gut, and their relationship with the human host varies from parasitic to commensal. Understanding the diversity of human intestinal eukaryotes has important significance for human health. In the past few decades, most of the multitudes of techniques that are involved in the diagnosis of the eukaryotic population in the human intestinal tract were confined to pathological and parasitological aspects that mainly rely on traditionally based methods. However, development of culture-independent molecular techniques comprised of direct DNA extraction from faeces followed by sequencing, offer new opportunities to estimate the occurrence of eukaryotes in the human gut by providing data on the entire eukaryotic community, particularly not-yet-cultured or fastidious organisms. Further broad surveys of the eukaryotic communities in the gut based on high throughput tools such as next generation sequencing might lead to uncovering the real diversity of these ubiquitous organisms in the human intestinal tract and discovering the unrecognized roles of these eukaryotes in modulating the host immune system and inducing changes in host gut physiology and ecosystem.
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Affiliation(s)
- I Hamad
- URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, Aix Marseille Université, Marseille, France
| | - D Raoult
- URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, Aix Marseille Université, Marseille, France
| | - F Bittar
- URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, Aix Marseille Université, Marseille, France
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20
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Ulrich S, Biermaier B, Bader O, Wolf G, Straubinger RK, Didier A, Sperner B, Schwaiger K, Gareis M, Gottschalk C. Identification of Stachybotrys spp. by MALDI-TOF mass spectrometry. Anal Bioanal Chem 2016; 408:7565-7581. [PMID: 27475444 DOI: 10.1007/s00216-016-9800-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/01/2016] [Accepted: 07/14/2016] [Indexed: 11/26/2022]
Abstract
Stachybotrys (S.) spp. are omnipresent cellulolytic molds. Some species are highly toxic owing to their ability to synthesize various secondary metabolites such as macrocyclic trichothecenes or hemolysins. The reliable identification of Stachybotrys at species level is currently limited to genome-based identification. This study aimed to establish a fast and reliable MALDI-TOF MS identification method by optimizing the pre-analytical steps for protein extraction for subsequent generation of high-quality fingerprint mass spectra. Eight reference strains of the American Type Culture Collection and the Technical University of Denmark were cultivated in triplicate (biological repetitions) for 2 days in malt extract broth. The mycelia (1.5 ml) were first washed with 75 % ethanol and an additional washing step with dimethyl sulfoxide (10 %) was added to remove unspecific low weight masses. Furthermore, mycelia were broken with roughened glass beads in formic acid (70 %) and acetonitrile. The method was successfully applied to a total of 45 isolates of Stachybotrys originating from three different habitats (indoor, feed, and food samples; n = 15 each): Twenty-seven isolates of S. chartarum and 18 isolates of S. chlorohalonata could be identified by MALDI-TOF MS. The data obtained exactly matched those obtained by genome-based identification. The mean score values for S. chartarum ranged from 2.509 to 2.739 and from 2.148 to 2.622 for S. chlorohalonata with a very good reproducibility: the relative standard deviations were between 0.3 % and 6.8 %. Thus, MALDI-TOF MS proved to be a fast and reliable alternative to identification of Stachybotrys spp. by nucleotide amplification and sequencing.
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Affiliation(s)
- Sebastian Ulrich
- Chair of Food Safety, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany.
| | - Barbara Biermaier
- Chair of Food Safety, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Goettingen, Kreuzbergring 57, 37075, Goettingen, Germany
| | - Georg Wolf
- Chair of Microbiology and Mycology, Department of Veterinary Sciences, LMU Munich, Veterinaerstr. 13, 80539, Munich, Germany
| | - Reinhard K Straubinger
- Chair of Microbiology and Mycology, Department of Veterinary Sciences, LMU Munich, Veterinaerstr. 13, 80539, Munich, Germany
| | - Andrea Didier
- Chair for Hygiene and Technology of Milk, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Brigitte Sperner
- Chair of Food Safety, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Karin Schwaiger
- Chair of Food Safety, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Manfred Gareis
- Chair of Food Safety, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Christoph Gottschalk
- Chair of Food Safety, Department of Veterinary Sciences, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
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21
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Debois D, Ongena M, Cawoy H, De Pauw E. In Situ Analysis of Bacterial Lipopeptide Antibiotics by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. Methods Mol Biol 2016; 1401:161-173. [PMID: 26831708 DOI: 10.1007/978-1-4939-3375-4_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a technique developed in the late 1990s enabling the two-dimensional mapping of a broad variety of biomolecules present at the surface of a sample. In many applications including pharmaceutical studies or biomarker discovery, the distribution of proteins, lipids or drugs, and metabolites may be visualized within tissue sections. More recently, MALDI MSI has become increasingly applied in microbiology where the versatility of the technique is perfectly suited to monitor the metabolic dynamics of bacterial colonies. The work described here is focused on the application of MALDI MSI to map secondary metabolites produced by Bacilli, especially lipopeptides, produced by bacterial cells during their interaction with their environment (bacteria, fungi, plant roots, etc.). This chapter addresses the advantages and challenges that the implementation of MALDI MSI to microbiological samples entails, including detailed protocols on sample preparation (from both microbiologist and mass spectrometrist points of view), matrix deposition, and data acquisition and interpretation. Lipopeptide images recorded from confrontation plates are also presented.
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Affiliation(s)
- Delphine Debois
- Mass Spectrometry Laboratory (LSM-GIGA-R), Chemistry Department, University of Liege - Allee du 6 aout, 11 - B6c - Chimie Licence et Recherche - Quartier Agora, Liege-1 (Sart Tilman), B-4000, Belgium.
| | - Marc Ongena
- Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Hélène Cawoy
- Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory (LSM-GIGA-R), Chemistry Department, University of Liege - Allee du 6 aout, 11 - B6c - Chimie Licence et Recherche - Quartier Agora, Liege-1 (Sart Tilman), B-4000, Belgium
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22
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Albataineh MT, Sutton DA, Fothergill AW, Wiederhold NP. Update from the Laboratory: Clinical Identification and Susceptibility Testing of Fungi and Trends in Antifungal Resistance. Infect Dis Clin North Am 2015; 30:13-35. [PMID: 26739605 DOI: 10.1016/j.idc.2015.10.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Despite the availability of new diagnostic assays and broad-spectrum antifungal agents, invasive fungal infections remain a significant challenge to clinicians and are associated with marked morbidity and mortality. In addition, the number of etiologic agents of invasive mycoses has increased accompanied by an expansion in the immunocompromised patient populations, and the use of molecular tools for fungal identification and characterization has resulted in the discovery of several cryptic species. This article reviews various methods used to identify fungi and perform antifungal susceptibility testing in the clinical laboratory. Recent developments in antifungal resistance are also discussed.
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Affiliation(s)
- Mohammad T Albataineh
- Fungus Testing Laboratory, Department of Pathology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Deanna A Sutton
- Fungus Testing Laboratory, Department of Pathology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Annette W Fothergill
- Fungus Testing Laboratory, Department of Pathology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Nathan P Wiederhold
- Fungus Testing Laboratory, Department of Pathology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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23
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Al-Hatmi AMS, Normand AC, van Diepeningen AD, Hendrickx M, de Hoog GS, Piarroux R. Rapid identification of clinical members of Fusarium fujikuroi complex using MALDI-TOF MS. Future Microbiol 2015; 10:1939-52. [DOI: 10.2217/fmb.15.108] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: To develop the matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF MS) method for identification of Fusarium species within Fusarium fujikuroi complex for use in clinical microbiology laboratories. Materials & methods: A total of 24 reference and 60 clinical and environmental isolates belonging to the F. fujikuroi complex were subjected to MALDI-TOF MS identification. Protein extracts of Fusarium isolates were obtained using formic acid extraction. Multilocus sequence analysis was used as a gold standard. Results: The MALDI-TOF MS Biotyper correctly identified 93.6% of the strains down to the species level, while the remaining isolates (6.4%) were identified at the genus level when using scores of ≥ 2.0 as cut-off values. Correct identification was obtained despite large intraspecific heterogeneities in MALDI-TOF spectra. Conclusion: MALDI-TOF MS is a rapid identification tool for the recognition of species within F. fujikuroi complex, provided a database is available.
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Affiliation(s)
- Abdullah MS Al-Hatmi
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Institute of Biodiversity & Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Directorate General of Health Services, Ministry of Health, Ibri Hospital, Ibri, Oman
| | - Anne-Cécile Normand
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, France
| | | | - Marijke Hendrickx
- BCCM/IHEM: Scientific Institute of Public Health, Mycology & Aerobiology Section, Bruxelles, Belgium
| | - G Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Institute of Biodiversity & Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Peking University Health Science Center, Research Center for Medical Mycology, Beijing, China
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Renaud Piarroux
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, France
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24
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Singhal N, Kumar M, Kanaujia PK, Virdi JS. MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 2015; 6:791. [PMID: 26300860 PMCID: PMC4525378 DOI: 10.3389/fmicb.2015.00791] [Citation(s) in RCA: 778] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/21/2015] [Indexed: 01/13/2023] Open
Abstract
Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.
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Affiliation(s)
- Neelja Singhal
- Department of Microbiology, University of Delhi New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi New Delhi, India
| | - Pawan K Kanaujia
- Department of Microbiology, University of Delhi New Delhi, India
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25
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Gruenwald M, Rabenstein A, Remesch M, Kuever J. MALDI-TOF mass spectrometry fingerprinting: A diagnostic tool to differentiate dematiaceous fungi Stachybotrys chartarum and Stachybotrys chlorohalonata. J Microbiol Methods 2015; 115:83-8. [PMID: 26036596 DOI: 10.1016/j.mimet.2015.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/27/2015] [Accepted: 05/29/2015] [Indexed: 11/17/2022]
Abstract
Stachybotrys chartarum and Stachybotrys chlorohalonata are two closely related species. Unambiguous identification of these two species is a challenging task if relying solely on morphological criteria and therefore smarter and less labor-intensive approaches are needed. Here we show that even such closely related species of fungi as S. chartarum and S. chlorohalonata are unequivocally discriminated by their highly reproducible MALDI-TOF-MS fingerprints (matrix assisted laser desorption/ionization time-of-flight mass spectrometry fingerprints). We examined 19 Stachybotrys and one Aspergillus isolate by MALDI-TOF-MS. All but one isolate produced melanin containing conidia on malt extract agar. Mass spectra were obtained in good quality from the analysis of hyaline and darkly pigmented conidia by circumventing the property of melanin which causes signal suppression. MALDI-TOF fingerprint analysis clearly discriminated not only the two morphologically similar species S. chartarum and S. chlorohalonata from each other but separated them precisely from Stachybotrys bisbyi and Aspergillus versicolor isolates. Furthermore, even S. chartarum chemotypes A and S could be differentiated into two distinct groups by their MALDI-TOF fingerprints. The chemotypes of S. chartarum isolates were identified by trichodiene synthase 5 (tri5) sequences prior to mass spectra analysis. Additionally, species identities of all isolates were verified by their 18S rRNA and tri5 gene sequences.
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Affiliation(s)
- Maike Gruenwald
- Bremen Institute for Materials Testing, Microbiology Department, Paul-Feller-Straße 1, 28199 Bremen, Germany.
| | - Andreas Rabenstein
- Bremen Institute for Materials Testing, Microbiology Department, Paul-Feller-Straße 1, 28199 Bremen, Germany.
| | - Markko Remesch
- Bremen Institute for Materials Testing, Microbiology Department, Paul-Feller-Straße 1, 28199 Bremen, Germany.
| | - Jan Kuever
- Bremen Institute for Materials Testing, Microbiology Department, Paul-Feller-Straße 1, 28199 Bremen, Germany.
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26
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Becker PT, Stubbe D, Claessens J, Roesems S, Bastin Y, Planard C, Cassagne C, Piarroux R, Hendrickx M. Quality control in culture collections: Confirming identity of filamentous fungi by MALDI-TOF MS. MYCOSCIENCE 2015. [DOI: 10.1016/j.myc.2014.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Helmel M, Marchetti-Deschmann M, Raus M, Posch AE, Herwig C, Šebela M, Allmaier G. Intact cell mass spectrometry as a progress tracking tool for batch and fed-batch fermentation processes. Anal Biochem 2015; 470:25-33. [PMID: 25447465 DOI: 10.1016/j.ab.2014.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 10/12/2014] [Accepted: 10/14/2014] [Indexed: 11/25/2022]
Abstract
Penicillin production during a fermentation process using industrial strains of Penicillium chrysogenum is a research topic permanently discussed since the accidental discovery of the antibiotic. Intact cell mass spectrometry (ICMS) can be a fast and novel monitoring tool for the fermentation progress during penicillin V production in a nearly real-time fashion. This method is already used for the characterization of microorganisms and the differentiation of fungal strains; therefore, the application of ICMS to samples directly harvested from a fermenter is a promising possibility to get fast information about the progress of fungal growth. After the optimization of the ICMS method to penicillin V fermentation broth samples, the obtained ICMS data were evaluated by hierarchical cluster analysis or an in-house software solution written especially for ICMS data comparison. Growth stages of a batch and fed-batch fermentation of Penicillium chrysogenum are differentiated by one of those statistical approaches. The application of two matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) instruments in the linear positive ion mode from different vendors demonstrated the universal applicability of the developed ICMS method. The base for a fast and easy-to-use method for monitoring the fermentation progress of P. chrysogenum is created with this ICMS method developed especially for fermentation broth samples.
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Affiliation(s)
- Michaela Helmel
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, A-1060 Vienna, Austria
| | | | - Martin Raus
- Department of Protein Biochemistry and Proteomics, Centrum of the Region Hana for Biotechnological and Agricultural Research, Faculty of Sciences, Palacký University, CZ-78371 Olomouc, Czech Republic
| | - Andreas E Posch
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, A-1060 Vienna, Austria
| | - Christoph Herwig
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, A-1060 Vienna, Austria
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Centrum of the Region Hana for Biotechnological and Agricultural Research, Faculty of Sciences, Palacký University, CZ-78371 Olomouc, Czech Republic
| | - Günter Allmaier
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, A-1060 Vienna, Austria.
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Becker PT, de Bel A, Martiny D, Ranque S, Piarroux R, Cassagne C, Detandt M, Hendrickx M. Identification of filamentous fungi isolates by MALDI-TOF mass spectrometry: clinical evaluation of an extended reference spectra library. Med Mycol 2014; 52:826-34. [DOI: 10.1093/mmy/myu064] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Helmel M, Marchetti-Deschmann M, Allmaier G. Improved sample preparation for intact cell mass spectrometry (biotyping) of mycelium samples taken from a batch fermentation process of Penicillium chrysogenum. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:957-964. [PMID: 24623701 DOI: 10.1002/rcm.6849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 01/21/2014] [Accepted: 01/21/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE Penicillium chrysogenum is an important species in biotechnology and an improved production rate for penicillin drug variants is of utmost interest. Intact cell mass spectrometry (ICMS) or biotyping can be a novel and time-saving tool to monitor a fermentation process of Penicillium strains for fast intervention during penicillin production. METHODS Fermentation broth was collected directly from a fermenter at specific time points known to show significantly different penicillin production rates. The mycelium was purified by washing multiple times with water and recovered by centrifugation. The mycelium was further mixed with matrix-assisted laser desorption/ionization (MALDI) MS matrix and immediately spotted on different types of targets. ICMS spectra were obtained by MALDI time-of-flight (TOF) MS in the positive ion linear mode in the m/z range 3000 to 16 000. RESULTS An ICMS method for culture broth samples of P. chrysogenum was developed. It was shown that ferulic acid mixed with sinapinic acid (2.5 mg and 22.5 mg/mL) is the most appropriate matrix combination. The matrices were dissolved in acetonitrile/0.1% trifluoroacetic acid (70/30, v/v) and spotted together with the sample on various target types. Sample preparation was thoroughly studied for homogeneity and reproducibility. CONCLUSIONS Culture broth directly collected from a bioreactor could be analyzed applying the optimized approach. The ideal choice of matrix, the adequate preparation technique and the type of target were the focus of this work showing that samples collected at different times during fermentation exhibit a characteristic pattern using the developed method.
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Affiliation(s)
- Michaela Helmel
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, A-1060, Vienna, Austria
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Dong H, Marchetti-Deschmann M, Allmaier G. Characterization of on-target generated tryptic peptides from Giberella zeae conidia spore proteins by means of matrix-assisted laser desorption/ionization mass spectrometry. Mol Cell Probes 2014; 28:91-8. [DOI: 10.1016/j.mcp.2013.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/15/2013] [Accepted: 10/17/2013] [Indexed: 11/24/2022]
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Chalupová J, Raus M, Sedlářová M, Sebela M. Identification of fungal microorganisms by MALDI-TOF mass spectrometry. Biotechnol Adv 2013; 32:230-41. [PMID: 24211254 DOI: 10.1016/j.biotechadv.2013.11.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 10/24/2013] [Accepted: 11/03/2013] [Indexed: 12/26/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a reliable tool for fast identification and classification of microorganisms. In this regard, it represents a strong challenge to microscopic and molecular biology methods. Nowadays, commercial MALDI systems are accessible for biological research work as well as for diagnostic applications in clinical medicine, biotechnology and industry. They are employed namely in bacterial biotyping but numerous experimental strategies have also been developed for the analysis of fungi, which is the topic of the present review. Members of many fungal genera such as Aspergillus, Fusarium, Penicillium or Trichoderma and also various yeasts from clinical samples (e.g. Candida albicans) have been successfully identified by MALDI-TOF MS. However, there is no versatile method for fungi currently available even though the use of only a limited number of matrix compounds has been reported. Either intact cell/spore MALDI-TOF MS is chosen or an extraction of surface proteins is performed and then the resulting extract is measured. Biotrophic fungal phytopathogens can be identified via a direct acquisition of MALDI-TOF mass spectra e.g. from infected plant organs contaminated by fungal spores. Mass spectrometric peptide/protein profiles of fungi display peaks in the m/z region of 1000-20000, where a unique set of biomarker ions may appear facilitating a differentiation of samples at the level of genus, species or strain. This is done with the help of a processing software and spectral database of reference strains, which should preferably be constructed under the same standardized experimental conditions.
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Affiliation(s)
- Jana Chalupová
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - Martin Raus
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - Michaela Sedlářová
- Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - Marek Sebela
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic.
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Chan PH, Wong SY, Lin SH, Chen YC. Lysozyme-encapsulated gold nanocluster-based affinity mass spectrometry for pathogenic bacteria. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2143-2148. [PMID: 23996387 DOI: 10.1002/rcm.6674] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/24/2013] [Accepted: 07/02/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Bacterial infections can be difficult to treat and can lead to irreversible damage to patients if proper treatment is not provided in time. Additionally, the emerging threat from antibiotic-resistant bacterial strains makes medical treatment even more difficult. Thus, rapid identification of infected bacterial strains is essential to assist diagnostics and medical treatment. METHODS Lysozymes are glycoside hydrolases that can bind with peptidoglycans on bacterial cell walls. In this work, we demonstrated that lysozyme-encapsulated gold nanoclusters (lysozyme-AuNCs) with red photoluminescence can be used as affinity probes to concentrate pathogenic bacteria. After bacteria had been probed by the lysozyme-AuNCs in a sample solution, the lysozyme-AuNC-bacteria conjugates were readily spun down at a low centrifugation speed. The red emission from the AuNCs on the conjugates could be visualized with the naked eye under illumination of ultraviolet light. The bacteria in the conjugates can be identified by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) combined with principal component analysis (PCA). RESULTS We demonstrated that pathogenic bacteria including Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, pandrug-resistant Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecalis, and vancomycin-resistant Enterococcus faecalis (VRE) can be readily concentrated by the lysozyme-AuNCs and distinguished by the results combining MALDI-MS and PCA. Additionally, the possibility of using the current approach to differentiate E. faecalis from VRE was also demonstrated. The lowest detection concentration for E. coli using the current approach is ~10(6) cells/mL. CONCLUSIONS The results indicated that the lysozyme-AuNCs are effective affinity probes for Gram-positive and Gram-negative bacteria. By combining the results from MALDI-MS and PCA, different bacteria can be easily distinguished. The current approach can be potentially used to assist the identification of bacteria from biological fluids.
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Affiliation(s)
- Po-Han Chan
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
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Posteraro B, De Carolis E, Vella A, Sanguinetti M. MALDI-TOF mass spectrometry in the clinical mycology laboratory: identification of fungi and beyond. Expert Rev Proteomics 2013; 10:151-64. [PMID: 23573782 DOI: 10.1586/epr.13.8] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
MALDI-TOF mass spectrometry (MS) is becoming essential in most clinical microbiology laboratories throughout the world. Its successful use is mainly attributable to the low operational costs, the universality and flexibility of detection, as well as the specificity and speed of analysis. Based on characteristic protein spectra obtained from intact cells - by means of simple, rapid and reproducible preanalytical and analytical protocols - MALDI-TOF MS allows a highly discriminatory identification of yeasts and filamentous fungi starting from colonies. Whenever used early, direct identification of yeasts from positive blood cultures has the potential to greatly shorten turnaround times and to improve laboratory diagnosis of fungemia. More recently, but still at an infancy stage, MALDI-TOF MS is used to perform strain typing and to determine antifungal drug susceptibility. In this article, the authors discuss how the MALDI-TOF MS technology is destined to become a powerful tool for routine mycological diagnostics.
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Jeong YS, Lee J, Kim SJ. Discrimination of Bacillus anthracis Spores by Direct in-situ Analysis of Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.9.2635] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ranque S, Normand AC, Cassagne C, Murat JB, Bourgeois N, Dalle F, Gari-Toussaint M, Fourquet P, Hendrickx M, Piarroux R. MALDI-TOF mass spectrometry identification of filamentous fungi in the clinical laboratory. Mycoses 2013; 57:135-40. [PMID: 23895114 DOI: 10.1111/myc.12115] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 06/29/2013] [Accepted: 07/08/2013] [Indexed: 11/27/2022]
Abstract
This study aimed to validate the effectiveness of a standardised procedure for the MALDI-TOF mass spectrometry (MS)-based identification on a large sample of filamentous fungi routinely identified in university hospitals' laboratories. Non-dermatophyte filamentous fungi prospectively isolated in the routine activity of five teaching hospitals in France were first identified by conventional methods in each laboratory and then by MS in one centre. DNA sequence-based identification resolved discrepancies between both methods. In this study, of the 625 analysed filamentous fungi of 58 species, 501 (80%) and 556 (89%) were correctly identified by conventional methods and MS respectively. Compared with the conventional method, MS dramatically enhanced the performance of the identification of the non-Aspergillus filamentous fungi with a 31-61% increase in correct identification rate. In conclusion, this study on a large sample of clinical filamentous fungi taxa demonstrates that species identification is significantly improved by MS compared with the conventional method. The main limitation is that MS identification is possible only if the species is included in the reference spectra library. Nevertheless, for the routine clinical laboratory, MS provides the means to attain markedly accurate results in filamentous fungi identification, which was previously restricted to only a few reference laboratories.
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Affiliation(s)
- Stéphane Ranque
- UMR MD3, Aix-Marseille Université, Marseille, France; Laboratoire de Parasitologie-Mycologie, APHM Timone, Marseille, France
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Normand AC, Cassagne C, Ranque S, L'ollivier C, Fourquet P, Roesems S, Hendrickx M, Piarroux R. Assessment of various parameters to improve MALDI-TOF MS reference spectra libraries constructed for the routine identification of filamentous fungi. BMC Microbiol 2013; 13:76. [PMID: 23565856 PMCID: PMC3691839 DOI: 10.1186/1471-2180-13-76] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 03/25/2013] [Indexed: 01/06/2023] Open
Abstract
Background The poor reproducibility of matrix-assisted desorption/ionization time-of-flight (MALDI-TOF) spectra limits the effectiveness of the MALDI-TOF MS-based identification of filamentous fungi with highly heterogeneous phenotypes in routine clinical laboratories. This study aimed to enhance the MALDI-TOF MS-based identification of filamentous fungi by assessing several architectures of reference spectrum libraries. Results We established reference spectrum libraries that included 30 filamentous fungus species with various architectures characterized by distinct combinations of the following: i) technical replicates, i.e., the number of analyzed deposits for each culture used to build a reference meta-spectrum (RMS); ii) biological replicates, i.e., the number of RMS derived from the distinct subculture of each strain; and iii) the number of distinct strains of a given species. We then compared the effectiveness of each library in the identification of 200 prospectively collected clinical isolates, including 38 species in 28 genera. Identification effectiveness was improved by increasing the number of both RMS per strain (p<10-4) and strains for a given species (p<10-4) in a multivariate analysis. Conclusion Addressing the heterogeneity of MALDI-TOF spectra derived from filamentous fungi by increasing the number of RMS obtained from distinct subcultures of strains included in the reference spectra library markedly improved the effectiveness of the MALDI-TOF MS-based identification of clinical filamentous fungi.
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Posch AE, Koch C, Helmel M, Marchetti-Deschmann M, Macfelda K, Lendl B, Allmaier G, Herwig C. Combining light microscopy, dielectric spectroscopy, MALDI intact cell mass spectrometry, FTIR spectromicroscopy and multivariate data mining for morphological and physiological bioprocess characterization of filamentous organisms. Fungal Genet Biol 2013; 51:1-11. [DOI: 10.1016/j.fgb.2012.11.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/22/2012] [Accepted: 11/23/2012] [Indexed: 10/27/2022]
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Bader O. MALDI-TOF-MS-based species identification and typing approaches in medical mycology. Proteomics 2013; 13:788-99. [DOI: 10.1002/pmic.201200468] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 11/17/2012] [Accepted: 11/24/2012] [Indexed: 12/26/2022]
Affiliation(s)
- Oliver Bader
- Institute for Medical Microbiology and German National Reference Center for Systemic Mycoses; University Medical Center Göttingen; Göttingen Germany
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Braga PAC, Tata A, Gonçalves dos Santos V, Barreiro JR, Schwab NV, Veiga dos Santos M, Eberlin MN, Ferreira CR. Bacterial identification: from the agar plate to the mass spectrometer. RSC Adv 2013. [DOI: 10.1039/c2ra22063f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Vermeulen E, Verhaegen J, Indevuyst C, Lagrou K. Update on the Evolving Role of MALDI-TOF MS for Laboratory Diagnosis of Fungal Infections. CURRENT FUNGAL INFECTION REPORTS 2012. [DOI: 10.1007/s12281-012-0093-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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De Carolis E, Posteraro B, Lass-Flörl C, Vella A, Florio A, Torelli R, Girmenia C, Colozza C, Tortorano A, Sanguinetti M, Fadda G. Species identification of Aspergillus, Fusarium and Mucorales with direct surface analysis by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Microbiol Infect 2012; 18:475-84. [DOI: 10.1111/j.1469-0691.2011.03599.x] [Citation(s) in RCA: 197] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Manikandan M, Wu HF, Hasan N. Cell population based mass spectrometry using platinum nanodots for algal and fungal studies. Biosens Bioelectron 2012; 35:493-497. [DOI: 10.1016/j.bios.2012.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 02/29/2012] [Accepted: 03/12/2012] [Indexed: 10/28/2022]
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Croxatto A, Prod'hom G, Greub G. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev 2012; 36:380-407. [DOI: 10.1111/j.1574-6976.2011.00298.x] [Citation(s) in RCA: 581] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 07/06/2011] [Accepted: 07/07/2011] [Indexed: 11/30/2022] Open
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Horká M, Kubesová A, Šalplachta J, Zapletalová E, Horký J, Šlais K. Capillary and gel electromigration techniques and MALDI-TOF MS – Suitable tools for identification of filamentous fungi. Anal Chim Acta 2012; 716:155-62. [DOI: 10.1016/j.aca.2011.12.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 12/14/2011] [Accepted: 12/15/2011] [Indexed: 10/14/2022]
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Cassagne C, Ranque S, Normand AC, Fourquet P, Thiebault S, Planard C, Hendrickx M, Piarroux R. Mould routine identification in the clinical laboratory by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. PLoS One 2011; 6:e28425. [PMID: 22194834 PMCID: PMC3237453 DOI: 10.1371/journal.pone.0028425] [Citation(s) in RCA: 192] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 11/08/2011] [Indexed: 11/29/2022] Open
Abstract
Background MALDI-TOF MS recently emerged as a valuable identification tool for bacteria and yeasts and revolutionized the daily clinical laboratory routine. But it has not been established for routine mould identification. This study aimed to validate a standardized procedure for MALDI-TOF MS-based mould identification in clinical laboratory. Materials and Methods First, pre-extraction and extraction procedures were optimized. With this standardized procedure, a 143 mould strains reference spectra library was built. Then, the mould isolates cultured from sequential clinical samples were prospectively subjected to this MALDI-TOF MS based-identification assay. MALDI-TOF MS-based identification was considered correct if it was concordant with the phenotypic identification; otherwise, the gold standard was DNA sequence comparison-based identification. Results The optimized procedure comprised a culture on sabouraud-gentamicin-chloramphenicol agar followed by a chemical extraction of the fungal colonies with formic acid and acetonitril. The identification was done using a reference database built with references from at least four culture replicates. For five months, 197 clinical isolates were analyzed; 20 were excluded because they were not identified at the species level. MALDI-TOF MS-based approach correctly identified 87% (154/177) of the isolates analyzed in a routine clinical laboratory activity. It failed in 12% (21/177), whose species were not represented in the reference library. MALDI-TOF MS-based identification was correct in 154 out of the remaining 156 isolates. One Beauveria bassiana was not identified and one Rhizopus oryzae was misidentified as Mucor circinelloides. Conclusions This work's seminal finding is that a standardized procedure can also be used for MALDI-TOF MS-based identification of a wide array of clinically relevant mould species. It thus makes it possible to identify moulds in the routine clinical laboratory setting and opens new avenues for the development of an integrated MALDI-TOF MS-based solution for the identification of any clinically relevant microorganism.
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Affiliation(s)
- Carole Cassagne
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, France.
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Ho YP, Reddy PM. Advances in mass spectrometry for the identification of pathogens. MASS SPECTROMETRY REVIEWS 2011; 30:1203-24. [PMID: 21557290 PMCID: PMC7168406 DOI: 10.1002/mas.20320] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 08/06/2010] [Accepted: 08/06/2010] [Indexed: 05/25/2023]
Abstract
Mass spectrometry (MS) has become an important technique to identify microbial biomarkers. The rapid and accurate MS identification of microorganisms without any extensive pretreatment of samples is now possible. This review summarizes MS methods that are currently utilized in microbial analyses. Affinity methods are effective to clean, enrich, and investigate microorganisms from complex matrices. Functionalized magnetic nanoparticles might concentrate traces of target microorganisms from sample solutions. Therefore, nanoparticle-based techniques have a favorable detection limit. MS coupled with various chromatographic techniques, such as liquid chromatography and capillary electrophoresis, reduces the complexity of microbial biomarkers and yields reliable results. The direct analysis of whole pathogenic microbial cells with matrix-assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high-throughput measurements. The MS detection of polymerase chain reaction (PCR)-amplified microbial nucleic acids provides an alternative to biomarker analysis. This review will conclude with some current applications of MS in the identification of pathogens.
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Affiliation(s)
- Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan.
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Dermatophyte identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2011; 49:4067-71. [PMID: 21956979 DOI: 10.1128/jcm.01280-11] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometer (MS) for the identification of dermatophytes from clinical cultures was compared to that of dermatophyte identification using 28S rRNA gene sequencing. The MALDI Biotyper library (MBL; version 3.0) was used alone and in combination with a supplemented library containing an additional 20 dermatophyte spectra (S-MBL). Acquired spectra were interpreted using both the manufacturer-recommended scores (genus, ≥1.7; species, ≥2.0) and adjusted cutoff values established by this study (genus, ≥1.5; species, ≥1.7); identifications required a minimum 10% difference in scores between the top two different organisms to be considered correct. One hundred well-characterized, archived dermatophyte isolates and 71 fresh dermatophyte cultures were evaluated using both libraries and both sets of cutoff criteria. Collectively, the S-MBL significantly outperformed the MBL at both the genus (93% versus 37.4%; P < 0,0001) and species (59.6% versus 20.5%; P < 0.0001) levels when using the adjusted score criteria. Importantly, application of the lowered cutoff values significantly improved genus (P = 0.005)- and species (P < 0.0001)-level identification for the S-MBL, without leading to an increase in misidentifications. MALDI-TOF MS is a cost-effective and rapid alternative to traditional or molecular methods for dermatophyte identification, provided that the reference library is supplemented to sufficiently encompass clinically relevant, intraspecies strain diversity.
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Coulibaly O, Marinach-Patrice C, Cassagne C, Piarroux R, Mazier D, Ranque S. Pseudallescheria/Scedosporium complex species identification by Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry. Med Mycol 2011; 49:621-6. [PMID: 21281060 DOI: 10.3109/13693786.2011.555424] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Because timely and accurate identification of members of the Pseudallescheria/ Scedosporium species complex (PSC) is clinically relevant, the objective of this investigation was to study the stability and influence of the main variable factors in the routine clinical laboratory to the potential use the Matrix-Assisted Laser Desorption Ionization-Time-Of-Flight (MALDI-TOF MS) in the identification of these fungi. Twenty-two PSC reference strains, three clinical isolates, an αHCCA matrix, and an Autoflex I spectrometer with BioTyper software (Bruker) were employed in this study. Intra-and inter-specimen composite correlation indices for each MS spectrum as compared to a reference spectrum were computed. MS identification was stable after the fungi were subcultured over a 1-month period. While neither culture medium (Sabouraud vs. Malt extract) nor protein extraction methods (formic acid vs. trifluoroacetic acid) significantly influenced the quality of the MS identifications, they were considerably increased from day 3 to day 6 of incubation. MALDI-TOF MS can be used in the routine clinical laboratory in the identification of members of the complex provided that valid spectra libraries are developed. Although preliminary results are encouraging, further studies are warranted to demonstrate whether MS can distinguish the species that have recently been described using multilocus sequence analysis within P. boydii sl. and to validate its use in the routine clinical laboratory for identifying clinically relevant moulds.
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Affiliation(s)
- Oumar Coulibaly
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, France
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Dong H, Shen W, Cheung MTW, Liang Y, Cheung HY, Allmaier G, Kin-Chung Au O, Lam YW. Rapid detection of apoptosis in mammalian cells by using intact cell MALDI mass spectrometry. Analyst 2011; 136:5181-9. [DOI: 10.1039/c1an15750g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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