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Avery EG, Zeppa JJ, Duncan DB, Barker KR, Fattouh R, Matukas LM, Rutherford C, Cabrera A, Sheth PM, Tran V, Goneau L, Katz K, Li XX, Kozak R. Evaluation of the utility and cost of secondary confirmatory testing for Neisseria gonorrhoeae identification from culture. Diagn Microbiol Infect Dis 2024; 109:116336. [PMID: 38723452 DOI: 10.1016/j.diagmicrobio.2024.116336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/17/2024] [Accepted: 04/27/2024] [Indexed: 05/28/2024]
Abstract
Current guideline recommends the use of two identification methods for Neisseria gonorrhoeae. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) is now used for primary identification and may be sufficient for definitive identification of N. gonorrhoeae. The performance of three secondary tests (BactiCard, RapID NH and NET test) were compared using 45 bacterial isolates, including 37 Neisseria species. These secondary tests demonstrated diminished specificity (67% - 88%) for N. gonorrhoeae compared with MALDI-TOF. Additionally, data from six clinical microbiology laboratories was used to compare confirmatory test costs and the agreement of results with MALDI-TOF. Discrepancies were documented for 9.4% of isolates, though all isolates (n= 288) identified by MALDI-TOF as N. gonorrhoeae were confirmed by the reference laboratory. These data demonstrate that MALDI-TOF alone is sufficient for N. gonorrhoeae identification, as secondary did not add diagnostic value but do add costs to the testing process.
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Affiliation(s)
- Ellen G Avery
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Joseph J Zeppa
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Donald Brody Duncan
- Division of Medical Microbiology, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada; Hamilton Regional Laboratory Medicine Program, Hamilton, ON, Canada
| | - Kevin R Barker
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Microbiology, Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, ON, Canada; Institute for Better Health, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Ramzi Fattouh
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Microbiology, Department of Laboratory Medicine, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Larissa M Matukas
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Microbiology, Department of Laboratory Medicine, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Candy Rutherford
- Hamilton Regional Laboratory Medicine Program, Hamilton, ON, Canada
| | - Ana Cabrera
- Pathology and Laboratory Medicine Department, London Health Sciences Centre, London, ON, Canada; Pathology and Laboratory Medicine Department, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada; Microbiology and Immunology Department, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Prameet M Sheth
- Division of Microbiology and Infectious Diseases, Kingston Health Sciences Center, Kingston, ON, Canada; Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Vanessa Tran
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Public Health Ontario, Toronto, ON, Canada
| | - Lee Goneau
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Dynacare Laboratory, Brampton, ON, Canada
| | - Kevin Katz
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Shared Hospital Laboratory, Toronto, ON, Canada; Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Xena X Li
- Shared Hospital Laboratory, Toronto, ON, Canada; Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Robert Kozak
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Shared Hospital Laboratory, Toronto, ON, Canada; Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.
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Trimpin S, Inutan ED, Pagnotti VS, Karki S, Marshall DD, Hoang K, Wang B, Lietz CB, Richards AL, Yenchick FS, Lee C, Lu IC, Fenner M, Madarshahian S, Saylor S, Chubatyi ND, Zimmerman T, Moreno-Pedraza A, Wang T, Adeniji-Adele A, Meher AK, Madagedara H, Owczarzak Z, Musavi A, Hendrickson TL, Peacock PM, Tomsho JW, Larsen BS, Prokai L, Shulaev V, Pophristic M, McEwen CN. Direct sub-atmospheric pressure ionization mass spectrometry: Evaporation/sublimation-driven ionization is amazing, fundamentally, and practically. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5018. [PMID: 38736378 DOI: 10.1002/jms.5018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/08/2023] [Accepted: 03/04/2024] [Indexed: 05/14/2024]
Abstract
This paper covers direct sub-atmospheric pressure ionization mass spectrometry (MS). The discovery, applications, and mechanistic aspects of novel ionization processes for use in MS that are not based on the high-energy input from voltage, laser, and/or high temperature but on sublimation/evaporation within a region linking a higher to lower pressure and modulated by heat and collisions, are discussed, including how this new reality has guided a series of discoveries, instrument developments, and commercialization. A research focus, inter alia, is on how best to understand, improve, and use these novel ionization processes, which convert volatile and nonvolatile compounds from solids (sublimation) or liquids (evaporation) into gas-phase ions for analysis by MS providing reproducible, accurate, sensitive, and prompt results. Our perception on how these unprecedented versus traditional ionization processes/methods relate to each other, how they can be made to coexist on the same mass spectrometer, and an outlook on new and expanded applications (e.g., clinical, portable, fast, safe, and autonomous) is presented, and is based on ST's Opening lecture presentation at the Nordic Mass spectrometry Conference, Geilo, Norway, January 2023. Focus will be on matrix-assisted ionization (MAI) and solvent-assisted ionization (SAI) MS covering the period from 2010 to 2023; a potential paradigm shift in the making.
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Affiliation(s)
- Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
- MSTM, LLC, Newark, Delaware, USA
| | - Ellen D Inutan
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
- MSTM, LLC, Newark, Delaware, USA
- Mindanao State University-Iligan Institute of Technology, Iligan City, Philippines
| | - Vincent S Pagnotti
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Santosh Karki
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
- MSTM, LLC, Newark, Delaware, USA
| | - Darrell D Marshall
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
- MSTM, LLC, Newark, Delaware, USA
| | - Khoa Hoang
- MSTM, LLC, Newark, Delaware, USA
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Beixi Wang
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | | | - Alicia L Richards
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Frank S Yenchick
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Chuping Lee
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - I-Chung Lu
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan
| | - Madeleine Fenner
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Sara Madarshahian
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Sarah Saylor
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Nicolas D Chubatyi
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Teresa Zimmerman
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | | | - Tongwen Wang
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Adetoun Adeniji-Adele
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Anil K Meher
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
- MSTM, LLC, Newark, Delaware, USA
| | - Hasini Madagedara
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Zachary Owczarzak
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Ahmed Musavi
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | | | | | - John W Tomsho
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | | | - Laszlo Prokai
- Department of Pharmacology and Neuroscience, The University of North Texas Health Science Center at Forth Worth, Fort Worth, Texas, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, The University of North Texas, Denton, Texas, USA
| | - Milan Pophristic
- MSTM, LLC, Newark, Delaware, USA
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
| | - Charles N McEwen
- MSTM, LLC, Newark, Delaware, USA
- Department of Chemistry & Biochemistry, Saint Joseph's University, Philadelphia, Pennsylvania, USA
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3
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Dela Cruz TEE, Behr JH, Geistlinger J, Grosch R, Witzel K. Monitoring of an Applied Beneficial Trichoderma Strain in Root-Associated Soil of Field-Grown Maize by MALDI-TOF MS. Microorganisms 2023; 11:1655. [PMID: 37512828 PMCID: PMC10384135 DOI: 10.3390/microorganisms11071655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
The persistence of beneficial microorganisms in the rhizosphere or surrounding soil following their application is a prerequisite for the effective interaction with the plant or indigenous microbial communities in the respective habitats. The goal of the study was to analyze the establishment and persistence of the applied beneficial Trichoderma harzianum (OMG16) strain in the maize root-associated soil depending on agricultural practice (soil management practice, N-fertilizer intensity) in a field experiment. A rapid identification of the inoculated strain OMG16 is essential for its monitoring. We used a culture-based approach coupled to matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis for the rapid identification of the inoculated Trichoderma strain as part of the beneficial microbe consortium (BMc). We isolated 428 fungal isolates from eight treatments of the field experiment. Forty eight percent of the isolated fungi equivalent to 205 fungal isolates were identified as Trichoderma, of which 87% (=179 isolates) were obtained from the fields inoculated with BMc. Gene sequence analysis showed a high similarity of the MALDI-TOF MS-identified Trichoderma, with that of the inoculated Trichoderma harzianum OMG16 confirming the re-isolation of the added beneficial fungus. This study highlighted the use of MALDI-TOF MS analysis as a quick, cost-effective detection and efficient monitoring tool for microbial-based bioinoculants in the field.
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Affiliation(s)
- Thomas Edison E Dela Cruz
- Department of Biological Sciences, College of Science, University of Santo Tomas (UST), España Blvd., Manila 1015, Philippines
| | - Jan Helge Behr
- Department of Plant-Microbes Systems, Leibniz Institute of Vegetables and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Joerg Geistlinger
- Department of Agriculture, Landscape Development and Ecotrophology, Anhalt University of Applied Sciences (AUAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Rita Grosch
- Department of Plant-Microbes Systems, Leibniz Institute of Vegetables and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Katja Witzel
- Department of Plant-Microbes Systems, Leibniz Institute of Vegetables and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
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4
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Volokhov DV, Zagorodnyaya TA, Furtak VA, Nattanmai G, Randall L, Jose S, Gao Y, Gulland FM, Eisenberg T, Delmonte P, Blom J, Mitchell KK. Neisseria montereyensis sp. nov., Isolated from Oropharynx of California Sea Lion (Zalophus californianus): Genomic, Phylogenetic, and Phenotypic Study. Curr Microbiol 2023; 80:253. [PMID: 37354372 DOI: 10.1007/s00284-023-03380-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Abstract
A novel Neisseria strain, designated CSL10203-ORH2T, was isolated from the oropharynx of a wild California sea lion (Zalophus californianus) that was admitted to The Marine Mammal Center in California, USA. The strain was originally cultured from an oropharyngeal swab on BD Phenylethyl Alcohol (PEA) agar with 5% sheep blood under aerobic conditions. Phylogenetic analyses based on 16S rRNA, rplF, and rpoB gene sequences and the core genome sequences indicated that the strain was most closely related to only N. zalophi CSL 7565T. The average nucleotide identity and digital DNA-DNA hybridization values between strain CSL10203-ORH2T and the closely related species N. zalophi CSL 7565T were 89.84 and 39.70%, respectively, which were significantly lower than the accepted species-defined thresholds for describing novel prokaryotic species at the genomic level. Both type strains were phenotypically similar but can be easily and unambiguously distinguished between each other by the analysis of their housekeeping genes, e.g., rpoB, gyrB, or argF. The major fatty acids in both type strains were C12:0, C16:0, C16:1-c9, and C18:1-c11. Based on the genomic, phenotypic, and phylogenetic properties, the novel strain represents a novel species of the genus Neisseria, for which the name Neisseria montereyensis sp. nov. with the type strain CSL10203-ORH2T (= DSM 114706T = CCUG 76428T = NCTC 14721T) is proposed. The genome G + C content is 45.84% and the complete draft genome size is 2,310,535 bp.
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Affiliation(s)
- Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, Laboratory of Method Development, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Building 52, Room 1120, Silver Spring, MD, 20993-0002, USA.
| | - Tatiana A Zagorodnyaya
- Center for Biologics Evaluation and Research, Laboratory of Method Development, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Building 52, Room 1120, Silver Spring, MD, 20993-0002, USA
| | - Vyacheslav A Furtak
- Center for Biologics Evaluation and Research, Laboratory of Method Development, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Building 52, Room 1120, Silver Spring, MD, 20993-0002, USA
| | - Geetha Nattanmai
- Bacteriology Laboratory, Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY, 12208, USA
| | - Linnell Randall
- Bacteriology Laboratory, Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY, 12208, USA
| | - Sherly Jose
- Bacteriology Laboratory, Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY, 12208, USA
| | - Yamei Gao
- Center for Biologics Evaluation and Research, Laboratory of Method Development, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Building 52, Room 1120, Silver Spring, MD, 20993-0002, USA
| | - Frances M Gulland
- Wildlife Health Center, University of California, Davis, CA, 95616, USA
| | - Tobias Eisenberg
- Department of Veterinary Medicine, Hessian State Laboratory (LHL), Schubertstrasse 60, 35392, Giessen, Germany
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Frankfurter Strasse 89-91, 35392, Giessen, Germany
| | - Pierluigi Delmonte
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Campus Drive, College Park, MD, 20740, USA
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Heinrich Buff Ring 58, 35392, Giessen, Germany
| | - Kara K Mitchell
- Bacteriology Laboratory, Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY, 12208, USA
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5
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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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6
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Khoder M, Osman M, Kassem II, Rafei R, Shahin A, Fournier PE, Rolain JM, Hamze M. Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity. Int J Mol Sci 2022; 23:13456. [PMID: 36362240 PMCID: PMC9657967 DOI: 10.3390/ijms232113456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 10/27/2023] Open
Abstract
Genome sequencing facilitates the study of bacterial taxonomy and allows the re-evaluation of the taxonomic relationships between species. Here, we aimed to analyze the draft genomes of four commensal Neisseria clinical isolates from the semen of infertile Lebanese men. To determine the phylogenetic relationships among these strains and other Neisseria spp. and to confirm their identity at the genomic level, we compared the genomes of these four isolates with the complete genome sequences of Neisseria gonorrhoeae and Neisseria meningitidis and the draft genomes of Neisseria flavescens, Neisseria perflava, Neisseria mucosa, and Neisseria macacae that are available in the NCBI Genbank database. Our findings revealed that the WGS analysis accurately identified and corroborated the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) species identities of the Neisseria isolates. The combination of three well-established genome-based taxonomic tools (in silico DNA-DNA Hybridization, Ortho Average Nucleotide identity, and pangenomic studies) proved to be relatively the best identification approach. Notably, we also discovered that some Neisseria strains that are deposited in databases contain many taxonomical errors. The latter is very important and must be addressed to prevent misdiagnosis and missing emerging etiologies. We also highlight the need for robust cut-offs to delineate the species using genomic tools.
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Affiliation(s)
- May Khoder
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
- Institut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, France
| | - Marwan Osman
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Issmat I Kassem
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA 30223-1797, USA
| | - Rayane Rafei
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Ahmad Shahin
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Pierre Edouard Fournier
- Institut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, France
| | - Jean-Marc Rolain
- Institut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, France
| | - Monzer Hamze
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
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7
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Identification of Epigallocatechin-3-Gallate (EGCG) from Green Tea Using Mass Spectrometry. SEPARATIONS 2022. [DOI: 10.3390/separations9080209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In an era where humanity is reinstating its lost hope and expectation on natural products, green tea occupies quite a position for what it has proven to be, in its endeavors for human welfare and health. Epigallocatechin-3-gallate (EGCG) is the key to the vast biological activities of green tea. Green tea is no longer in the backdrop; it has emerged as the most viral, trending bioactive molecule when it comes to health benefits for human beings. This review focuses on the use of various analytical techniques for the analysis of EGCG. That which has been achieved so far, in terms of in vitro, pure component analysis, as well as those spikes in biological fluids and those in vivo in animal and human samples, was surveyed and presented. The use of MS-based techniques for the analysis of EGCG is elaborately reviewed and the need for improvising the applications is explained. The review emphasizes that there is plenty of room to explore matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) applications in this subject area.
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8
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Limitation of
ctrA
as a Target for Neisseria meningitidis Identification and Potential Alternative Targets. J Clin Microbiol 2022; 60:e0015222. [DOI: 10.1128/jcm.00152-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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9
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MALDI-Based Mass Spectrometry in Clinical Testing: Focus on Bacterial Identification. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12062814] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The term “proteome” refers to the total of all proteins expressed in an organism. The term “proteomics” refers to the field of research that includes not only information on the expression levels of individual proteins, but also their higher-order structures, intermolecular interactions, and post-translational modifications. The core technology, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), is available for protein analysis thanks to the work of Koichi Tanaka and John Fenn, who were awarded the Nobel Prize in Chemistry in 2002. The most successful proteome analysis in clinical practice is rapid microbial identification. This method determines the bacterial species by comparing the proteome profile of the bacteria obtained by matrix-assisted laser desorption ionization-time of flight MS (MALDI-TOF MS) with a database. MS is superior in simplicity, speed, and accuracy to classic speciation by staining and phenotyping. In clinical microbiology, MS has had a large impact on the diagnosis and treatment of infectious disease. Early diagnosis and treatment of infectious disease are important, and rapid identification by MALDI-TOF MS has made a major contribution to this field.
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10
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Paulini F, Araujo MS, Silva LP, Lucci CM. Initial steps on mapping differentially expressed proteins in bovine preantral follicles and ovarian tissue: An approach using single-follicle MALDI-MS and mass spectrometry imaging (MSI) analysis. Reprod Domest Anim 2021; 57:19-32. [PMID: 34626135 DOI: 10.1111/rda.14025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/07/2021] [Indexed: 12/15/2022]
Abstract
The molecular mechanisms regulating follicular development and ensuring primordial follicle activation remain undefined. To help elucidate these mechanisms, this proteomic study of bovine ovarian tissue identified the differential molecular profiles of preantral follicles together with the spatial distribution of the most abundant molecular components in the tissue. Isolated primordial, primary and secondary follicles were individually placed on a MALDI target plate for mass spectral acquisitions, with detection of different m/z ranges. Ovarian tissue was sectioned and analysed in the m/z 400-2,000 range. Results of the first analysis indicated a similarity pattern in the molecular protein profile among different follicular classes in the m/z ranges of 100-1000 and 25,000-200,000, but in the m/z ranges of 800-4000, 4000-20,000 and 15,000-70,000, primary and secondary follicles shared similar clustering profiles which were different from primordial follicles (p < .05). In the second analysis, it was possible to correlate some intense molecular components in the tissue from global mass spectrum with the ions detected in the first analysis. Molecular components at m/z 11,325 (±230) were also detected in primary and secondary follicles in the experiment with isolated follicles, in addition to ions at m/z 4,029 (±120), 13,799 (±70), 5,547 (±9), 15,313 (±200), 7,018 (±40) and 7,663 (±90) which were also intensely detected in primary and secondary follicles. The present proteomic approaches evaluated different mass ranges of preantral follicles in bovine ovarian tissue and also indicated the spatial distribution of the most abundant molecular components. This study hopes to pave the way for future research identifying and characterizing specific proteins involved in follicle activation in bovine follicles, in order to better understand folliculogenesis and potentially improve mammalian follicle culture systems.
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Affiliation(s)
- Fernanda Paulini
- Department of Physiological Sciences, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Michelle Silva Araujo
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Luciano Paulino Silva
- Laboratory of Nanobiotechnology (LNANO), Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - Carolina Madeira Lucci
- Department of Physiological Sciences, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
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AlMasoud N, Muhamadali H, Chisanga M, AlRabiah H, Lima CA, Goodacre R. Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing. Analyst 2021; 146:770-788. [DOI: 10.1039/d0an01482f] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review compares and contrasts MALDI-MS, FT-IR spectroscopy and Raman spectroscopy for whole organism fingerprinting and bacterial typing.
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Affiliation(s)
- Najla AlMasoud
- Department of Chemistry
- College of Science
- Princess Nourah bint Abdulrahman University
- Riyadh 11671
- Saudi Arabia
| | - Howbeer Muhamadali
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Malama Chisanga
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Haitham AlRabiah
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Cassio A. Lima
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
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Testing the Applicability of MALDI-TOF MS as an Alternative Stock Identification Method in a Cryptic Species Complex. Molecules 2020; 25:molecules25143214. [PMID: 32674457 PMCID: PMC7397217 DOI: 10.3390/molecules25143214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/01/2020] [Accepted: 07/12/2020] [Indexed: 11/16/2022] Open
Abstract
Knowledge of intraspecific variability of a certain species is essential for their long-term survival and for the development of conservation plans. Nowadays, molecular/genetic methods are the most frequently used for this purpose. Although, the Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) technique has become a promising alternative tool to specify intraspecific variability, there is a lack of information about the limitations of this method, and some methodological issues need to be resolved. Towards this goal, we tested the sensitivity of this method on an intraspecific level, using genetically identified individuals of a cryptic fish species complex collected from five distinct populations. Additionally, some methodologic issues, such as the effect of (1) delayed sample preparation, (2) clove oil anaesthetization, and (3) different tissue types (muscle, and brain) were investigated using the MS analysis results. Our results show that the delayed sample preparation has a fundamental effect on the result of MS analysis, while at the same time the clove oil did not affect the results considerably. Both the brain and muscle samples were usable for cryptic species identification, but in our opinion this method has limited applicability for population-level segregation. The application of MALDI-TOF MS to the exploitable toolkit of phylogenetic and taxonomic researches could be used to broaden conclusions.
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Abstract
The bacterium Neisseria gonorrhoeae causes the sexually transmitted infection (STI) gonorrhoea, which has an estimated global annual incidence of 86.9 million adults. Gonorrhoea can present as urethritis in men, cervicitis or urethritis in women, and in extragenital sites (pharynx, rectum, conjunctiva and, rarely, systemically) in both sexes. Confirmation of diagnosis requires microscopy of Gram-stained samples, bacterial culture or nucleic acid amplification tests. As no gonococcal vaccine is available, prevention relies on promoting safe sexual behaviours and reducing STI-associated stigma, which hinders timely diagnosis and treatment thereby increasing transmission. Single-dose systemic therapy (usually injectable ceftriaxone plus oral azithromycin) is the recommended first-line treatment. However, a major public health concern globally is that N. gonorrhoeae is evolving high levels of antimicrobial resistance (AMR), which threatens the effectiveness of the available gonorrhoea treatments. Improved global surveillance of the emergence, evolution, fitness, and geographical and temporal spread of AMR in N. gonorrhoeae, and improved understanding of the pharmacokinetics and pharmacodynamics for current and future antimicrobials in the treatment of urogenital and extragenital gonorrhoea, are essential to inform treatment guidelines. Key priorities for gonorrhoea control include strengthening prevention, early diagnosis, and treatment of patients and their partners; decreasing stigma; expanding surveillance of AMR and treatment failures; and promoting responsible antimicrobial use and stewardship. To achieve these goals, the development of rapid and affordable point-of-care diagnostic tests that can simultaneously detect AMR, novel therapeutic antimicrobials and gonococcal vaccine(s) in particular is crucial.
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Khoder M, Osman M, Diene SM, Okdah L, Lalaoui R, Al Achkar M, Mallat H, Hamze M, Rolain JM. Evaluation of different testing tools for the identification of non-gonococcal Neisseria spp. isolated from Lebanese male semen: a strong and significant association with infertility. J Med Microbiol 2019; 68:1012-1020. [DOI: 10.1099/jmm.0.000990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- May Khoder
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
- Aix-Marseille University, IRD, APHM, MEPHI, IHU Méditerranée infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Seydina M. Diene
- Aix-Marseille University, IRD, APHM, MEPHI, IHU Méditerranée infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Liliane Okdah
- Aix-Marseille University, IRD, APHM, MEPHI, IHU Méditerranée infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Rym Lalaoui
- Aix-Marseille University, IRD, APHM, MEPHI, IHU Méditerranée infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | | | - Hassan Mallat
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Jean-Marc Rolain
- Aix-Marseille University, IRD, APHM, MEPHI, IHU Méditerranée infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
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Advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs. Parasitology 2019; 145:537-542. [PMID: 29900810 DOI: 10.1017/s0031182018000884] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA barcoding is now a common tool in parasitology and epidemiology, which require good methods for identification not only of parasites and pathogens but vectors and reservoirs. This special issue presents some advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs. DNA barcoding found new applications in disease ecology, conservation parasitology, environmental parasitology and in paleoparasitology. New technologies such as next-generation sequencing and matrix-assisted laser desorption-ionization time-of-flight have made it now possible to investigate large samples of specimens. By allowing the investigation of parasites at the interface between environment, biodiversity, animal and human health, barcoding and biobanking have important policy outcomes as well as ethics and legal implications. The special issue 'Advances and challenges in the barcoding of parasites, vectors and reservoirs' illustrates some recent advances and proposes new avenues for research in barcoding in parasitology.
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Pellegrino FLPC, Chagas TPG, Alves MS, Carvalho-Assef APD, Chapeaurouge A, Asensi MD. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Applications in Bacteriology: brazilian contributions. HU REVISTA 2018. [DOI: 10.34019/1982-8047.2017.v43.2859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among its innumerous applications in Bacteriology, the Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) technique is evolving as a powerful tool for bacterial identification and antimicrobial resistance investigation. Publications have evaluated the MALDI-TOF MS performance in the identification of a series of bacterial pathogens, including the most common severe infectious agents, emergent pathogens involved with outbreaks of healthcare-associated infections, rare pathogens, and those whose isolation in culture media is difficult. As compared to conventional methods of bacterial identification, MALDI-TOF MS has proven to be a fast, accurate and cost-effective technique. Currently, MALDI-TOF MS has been used in antimicrobial resistance studies, since it has shown to be an efficient tool in detecting specific resistance mechanisms in bacteria, such as beta-lactamases production, for example. Here, we describe the advances in this growing field of mass spectrometry applied to Bacteriology, including Brazilian contributions.
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Morel F, Jacquier H, Desroches M, Fihman V, Kumanski S, Cambau E, Decousser JW, Berçot B. Use of Andromas and Bruker MALDI-TOF MS in the identification of Neisseria. Eur J Clin Microbiol Infect Dis 2018; 37:2273-2277. [DOI: 10.1007/s10096-018-3368-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/27/2018] [Indexed: 10/28/2022]
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Barreiro JR, Gonçalves JL, Grenfell R, Leite RF, Juliano L, Santos MV. Direct identification of bovine mastitis pathogens by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in pre-incubated milk. Braz J Microbiol 2018; 49:801-807. [PMID: 30177270 PMCID: PMC6175725 DOI: 10.1016/j.bjm.2018.04.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 02/09/2018] [Accepted: 04/16/2018] [Indexed: 11/21/2022] Open
Abstract
The present study aimed to compare two MALDI-TOF identification methods [(a) direct sample identification after pre-incubation; or (b) use of bacteria isolated on pre-culture)] to standard, traditional bench microbiology. A total of 120 quarter milk samples from 40 Holstein lactating cows were screened based on culture-positive results obtained by microbiological culture (reference method) with the following numbers of quarters positive per cow: 4 cows with 1, 8 cows with 2, 12 cows with 3 and 16 cows with 4 infected quarters per cow. For direct identification method, quarter milk samples (n = 120) were skimmed by centrifugation (10,000 × g/10 min) and pre-incubated at 37 °C for 12 h. After pre-incubation, quarter milk samples were submitted to total bacterial count by flow cytometry and for a preparation protocol for bacterial ribosomal protein extraction followed by MALDI-TOF MS analysis. The direct MALDI-TOF MS identification method compared to microbiological culture correctly identified isolates of coagulase-negative Staphylococci (27.2%), Streptococcus agalactiae (21.8%), Staphylococcus aureus (14.2%), and Streptococcus uberis (5.2%). The pre-incubation protocol of milk samples, associated to the direct identification method by MALDI-TOF MS, did not increase the identification at species level (score >2.0) of pathogens causing subclinical mastitis in comparison to the method without previous incubation.
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Affiliation(s)
- Juliana R Barreiro
- Universidade de São Paulo (USP), Faculdade de Medicina Veterinária e Zootecnia, Departamento de Nutrição e Produção animal, Pirassununga, SP, Brazil
| | - Juliano L Gonçalves
- Universidade de São Paulo (USP), Faculdade de Medicina Veterinária e Zootecnia, Departamento de Nutrição e Produção animal, Pirassununga, SP, Brazil
| | - Rafaella Grenfell
- Universidade Federal de São Paulo, Departamento de Biofísica, São Paulo, SP, Brazil
| | - Renata F Leite
- Universidade de São Paulo (USP), Faculdade de Medicina Veterinária e Zootecnia, Departamento de Nutrição e Produção animal, Pirassununga, SP, Brazil
| | - Luiz Juliano
- Universidade Federal de São Paulo, Departamento de Biofísica, São Paulo, SP, Brazil
| | - Marcos V Santos
- Universidade de São Paulo (USP), Faculdade de Medicina Veterinária e Zootecnia, Departamento de Nutrição e Produção animal, Pirassununga, SP, Brazil.
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Bronzato GF, Oliva MS, Alvin MG, Pribul BR, Rodrigues DP, Coelho SM, Coelho IS, Souza MM. MALDI-TOF MS as a tool for the identification of Vibrio alginolyticus from Perna perna mussels (Linnaeus, 1758). PESQUISA VETERINARIA BRASILEIRA 2018. [DOI: 10.1590/1678-5150-pvb-5233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
ABSTRACT: Vibrio species are ubiquitous in aquatic environments, including coastal and marine habitats. Vibrio alginolyticus is an opportunistic pathogen for fish, crustaceans and mussels and their identification by biochemical tests may be impaired due their nutritional requirements. The study used Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to identify 49 Vibrio spp. isolates associated with mussels (Perna perna) from different locations along the Rio de Janeiro coast. The rpoA gene was used as a genus-specific marker of Vibrio spp. and was positive in all 209 isolates. MALDI-TOF MS confirmed 87.8% of V. alginolyticus when compared to the results of the biochemical tests. Four isolates were identified as Shewanella putrefaciens (8.16%) and one was identified as V. parahaemolyticus (2.0%). Just one isolate was not identified by this technique (2.0%). The pyrH sequencing confirmed 75% of the proteomic technique results. MALDI-TOF MS is an excellent option for characterization of bacterial species, as it is efficient, fast and easy to apply. In addition, our study confirms its high specificity and sensitivity in these marine bacteria identification.
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Picaud V, Giovannelli JF, Truntzer C, Charrier JP, Giremus A, Grangeat P, Mercier C. Linear MALDI-ToF simultaneous spectrum deconvolution and baseline removal. BMC Bioinformatics 2018; 19:123. [PMID: 29621971 PMCID: PMC5887234 DOI: 10.1186/s12859-018-2116-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 03/13/2018] [Indexed: 11/10/2022] Open
Abstract
Background Thanks to a reasonable cost and simple sample preparation procedure, linear MALDI-ToF spectrometry is a growing technology for clinical microbiology. With appropriate spectrum databases, this technology can be used for early identification of pathogens in body fluids. However, due to the low resolution of linear MALDI-ToF instruments, robust and accurate peak picking remains a challenging task. In this context we propose a new peak extraction algorithm from raw spectrum. With this method the spectrum baseline and spectrum peaks are processed jointly. The approach relies on an additive model constituted by a smooth baseline part plus a sparse peak list convolved with a known peak shape. The model is then fitted under a Gaussian noise model. The proposed method is well suited to process low resolution spectra with important baseline and unresolved peaks. Results We developed a new peak deconvolution procedure. The paper describes the method derivation and discusses some of its interpretations. The algorithm is then described in a pseudo-code form where the required optimization procedure is detailed. For synthetic data the method is compared to a more conventional approach. The new method reduces artifacts caused by the usual two-steps procedure, baseline removal then peak extraction. Finally some results on real linear MALDI-ToF spectra are provided. Conclusions We introduced a new method for peak picking, where peak deconvolution and baseline computation are performed jointly. On simulated data we showed that this global approach performs better than a classical one where baseline and peaks are processed sequentially. A dedicated experiment has been conducted on real spectra. In this study a collection of spectra of spiked proteins were acquired and then analyzed. Better performances of the proposed method, in term of accuracy and reproductibility, have been observed and validated by an extended statistical analysis.
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Affiliation(s)
- Vincent Picaud
- University of Bordeaux, IMS, UMR 5218, Talence, 33400, France.
| | | | - Caroline Truntzer
- CLIPP, Pôle de Recherche Université de Bourgogne, Dijon, 21000, France
| | - Jean-Philippe Charrier
- Technology Research Department, Innovation Unit, Marcy l'Étoile, bioMérieux SA, Marcy l'Étoile, 69280, France
| | - Audrey Giremus
- University of Bordeaux, IMS, UMR 5218, Talence, 33400, France
| | - Pierre Grangeat
- Université Grenoble Alpes, Grenoble, 38000, France.,CEA, LETI, MINATEC Campus, DTBS, 17 Rue des Martyrs, Grenoble, 38054, France
| | - Catherine Mercier
- Service de Biostatistique, Hospices Civils de Lyon, Lyon, 69000, France.,Université Lyon 1, Villeurbanne, 69100, France.,CNRS UMR5558, Laboratoire de Biométrie et Biologie Évolutive, Équipe Biostatistique-Santé, Villeurbanne, 69100, France
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El-Bouri K, Johnston S, Rees E, Thomas I, Bome-Mannathoko N, Jones C, Reid M, Ben-Ismaeil B, Davies AP, Harris LG, Mack D. Comparison of bacterial identification by MALDI-TOF mass spectrometry and conventional diagnostic microbiology methods: agreement, speed and cost implications. Br J Biomed Sci 2018. [DOI: 10.1080/09674845.2012.12002436] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- K. El-Bouri
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - S. Johnston
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - E. Rees
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - I. Thomas
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - N. Bome-Mannathoko
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - C. Jones
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - M. Reid
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - B. Ben-Ismaeil
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - A. P. Davies
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - L. G. Harris
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - D. Mack
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
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Grégory D, Chaudet H, Lagier JC, Raoult D. How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota. Expert Rev Proteomics 2018; 15:217-229. [PMID: 29336192 DOI: 10.1080/14789450.2018.1429271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.
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Affiliation(s)
- Dubourg Grégory
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Hervé Chaudet
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Jean-Christophe Lagier
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
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Maasz G, Takács P, Boda P, Varbiro G, Pirger Z. Mayfly and fish species identification and sex determination in bleak (Alburnus alburnus) by MALDI-TOF mass spectrometry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 601-602:317-325. [PMID: 28558278 DOI: 10.1016/j.scitotenv.2017.05.207] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
Besides food quality control of fish or cephalopods, the novel mass spectrometry (MS) approaches could be effective and beneficial methods for the investigation of biodiversity in ecological research. Our aims were to verify the applicability of MALDI-TOF MS in the rapid identification of closely related species, and to further develop it for sex determination in phenotypically similar fish focusing on the low mass range. For MALDI-TOF MS spectra analysis, ClinProTools software was applied, but our observed classification was also confirmed by Self Organizing Map. For verifying the wide applicability of the method, brains from invertebrate and vertebrate species were used in order to detect the species related markers from two mayflies and eight fish as well as sex-related markers within bleak. Seven Ephemera larvae and sixty-one fish species related markers were observed and nineteen sex-related markers were identified in bleak. Similar patterns were observed between the individuals within one species. In contrast, there were markedly diverse patterns between the different species and sexes visualized by SOMs. Two different Ephemera species and male or female fish were identified with 100% accuracy. The various fish species were classified into 8 species with a high level of accuracy (96.2%). Based on MS data, dendrogram was generated from different fish species by using ClinProTools software. This MS-based dendrogram shows relatively high correspondence with the phylogenetic relationships of both the studied species and orders. In summary, MALDI-TOF MS provides a cheap, reliable, sensitive and fast identification tool for researchers in the case of closely related species using mass spectra acquired in a low mass range to define specific molecular profiles. Moreover, we presented evidence for the first time for determination of sex within one fish species by using this method. We conclude that it is a powerful tool that can revolutionize ecological and environmental research.
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Affiliation(s)
- G Maasz
- MTA-ÖK BLI NAP_B Adaptive Neuroethology, Department of Experimental Zoology, Balaton Limnological Institute, MTA Centre for Ecological Research, 8237 Tihany, Hungary; Department of Analytical Biochemistry, Institute of Biochemistry and Medical Chemistry, University of Pecs, 7624 Pecs, Hungary.
| | - P Takács
- Department of Hydrozoology, Balaton Limnological Institute, MTA Centre for Ecological Research, 8237 Tihany, Hungary
| | - P Boda
- Department of Tisza River Research, MTA Centre for Ecological Research, 4032 Debrecen, Hungary
| | - G Varbiro
- Department of Tisza River Research, MTA Centre for Ecological Research, 4032 Debrecen, Hungary
| | - Z Pirger
- MTA-ÖK BLI NAP_B Adaptive Neuroethology, Department of Experimental Zoology, Balaton Limnological Institute, MTA Centre for Ecological Research, 8237 Tihany, Hungary
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Identification of Trypanosomatids by detecting Single Nucleotide Fingerprints using DNA analysis by dynamic chemistry with MALDI-ToF. Talanta 2017; 176:299-307. [PMID: 28917755 DOI: 10.1016/j.talanta.2017.07.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 01/09/2023]
Abstract
Protozoan parasites of the Trypanosomatidae family can cause devastating diseases in humans and animals, such as Human African Trypanosomiasis or Sleeping Sickness, Chagas disease and Leishmaniasis. Currently, there are molecular assays for detecting parasitic infections and their post-treatment monitoring based on nucleic acid amplification, but there are still certain limitations which limit the development of assays that can detect and discriminate between parasite infections with a single test. Here, we present the development of a novel molecular assay for the rapid identification of Trypanosomatids, integrating DNA analysis by dynamic chemistry in conjunction with Matrix-Assisted Laser Desorption Ionization - Time-of-Flight Mass Spectrometry (MALDI-ToF). Differentiation of Trypanosoma cruzi, Trypanosoma brucei and Leishmania spp. is now possible using a single reaction tube, and enables rapid identification of Trypanosomatids. The test is based on a singleplex PCR, using a specific primer pair that amplifies a 155 base pair segment of the 28S ribosomal RNA gene, within a conserved homology region of Trypanosomatidae species. Amplified fragments are analysed by dynamic chemistry using two abasic PNA probes and the four reactive nucleobases - containing an aldehyde functional group - with MALDI-ToF to identify unique molecular patterns created by each specie due to their single base differences (Single Nucleotide Fingerprint 'SNF') in this highly homologous region. This novel assay offers the possibility to expand routine diagnostic testing for Trypanosomatids, and monitoring of therapeutic responses to these infectious diseases.
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Fernández-Álvarez C, Torres-Corral Y, Saltos-Rosero N, Santos Y. MALDI-TOF mass spectrometry for rapid differentiation of Tenacibaculum species pathogenic for fish. Appl Microbiol Biotechnol 2017; 101:5377-5390. [DOI: 10.1007/s00253-017-8324-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/29/2017] [Accepted: 04/29/2017] [Indexed: 11/24/2022]
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Barreiro JR, Gonçalves JL, Braga PAC, Dibbern AG, Eberlin MN, Veiga dos Santos M. Non-culture-based identification of mastitis-causing bacteria by MALDI-TOF mass spectrometry. J Dairy Sci 2017; 100:2928-2934. [DOI: 10.3168/jds.2016-11741] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/22/2016] [Indexed: 11/19/2022]
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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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Abstract
SUMMARYMatrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is currently being used for rapid and reproducible identification of bacteria, viruses and fungi in clinical microbiological laboratories. However, some studies have also reported the use of MALDI-TOF MS for identification of parasites, likeLeishmania, Giardia, Cryptosporidium, Entamoeba, ticks and fleas. The present review collates all the information available on the use of this technique for parasites, in an effort to assess its applicability and the constraints for identification/diagnosis of parasites and diseases caused by them. Though MALDI-TOF MS-based identification of parasites is currently done by reference laboratories only, in future, this promising technology might surely replace/augment molecular methods in clinical parasitology laboratories.
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Matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for the identification of Neisseria gonorrhoeae. Clin Microbiol Infect 2016; 22:815.e5-815.e7. [PMID: 27371346 DOI: 10.1016/j.cmi.2016.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/15/2016] [Accepted: 06/18/2016] [Indexed: 11/20/2022]
Abstract
Matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared with the API NH biochemical method for the identification of Neisseria gonorrhoeae in routine clinical samples. A retrospective review of laboratory records for 1090 isolates for which both biochemical and MALDI-TOF MS identifications were available was performed. Cases of discrepant results were examined in detail for evidence supportive of a particular organism identification. Of 1090 isolates, 1082 were identified as N. gonorrhoeae by API NH. MALDI-TOF MS successfully identified 984 (91%) of these after one analysis, rising to 1081 (99.9%) after two analyses, with a positive predictive value of 99.3%. For those isolates requiring a repeat analysis, failure to generate an identifiable proteomic signature was the reason in 76% of cases, with alternative initial identifications accounting for the remaining 24%. MALDI-TOF MS identified eight isolates as N. gonorrhoeae that were not identified as such by API NH-examination of these discrepant results suggested that the MALDI-TOF MS identification may be the more reliable. MALDI-TOF MS is at least as accurate and reliable a method of identifying N. gonorrhoeae as API NH. We propose that MALDI-TOF MS could potentially be used as a single method for N. gonorrhoeae identification in routine cases by laboratories with access to this technology.
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Nori P, Szymczak W, Park C, Gialanella P, Munjal I, Chung P, Guo Y, Williamson J, Ostrowsky B, Levi M. Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry as a First-Line Diagnostic Modality in Bacterial Meningitis and Septicemia: a Report of Five Cases. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.clinmicnews.2016.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Suffredini AF, Sacks DB, Yu YK. Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:194-210. [PMID: 26510657 PMCID: PMC4723618 DOI: 10.1007/s13361-015-1271-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/04/2015] [Accepted: 09/05/2015] [Indexed: 05/13/2023]
Abstract
Correct and rapid identification of microorganisms is the key to the success of many important applications in health and safety, including, but not limited to, infection treatment, food safety, and biodefense. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is challenging correct microbial identification because of the large number of choices present. To properly disentangle candidate microbes, one needs to go beyond apparent morphology or simple 'fingerprinting'; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptidome profiles of microbes to better separate them and by designing an analysis method that yields accurate statistical significance. Here, we present an analysis pipeline that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using MS/MS data of 81 samples, each composed of a single known microorganism, that the proposed pipeline can correctly identify microorganisms at least at the genus and species levels. We have also shown that the proposed pipeline computes accurate statistical significances, i.e., E-values for identified peptides and unified E-values for identified microorganisms. The proposed analysis pipeline has been implemented in MiCId, a freely available software for Microorganism Classification and Identification. MiCId is available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html . Graphical Abstract ᅟ.
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Affiliation(s)
- Gelio Alves
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Guanghui Wang
- Proteomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Steven K Drake
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marjan Gucek
- Proteomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anthony F Suffredini
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David B Sacks
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yi-Kuo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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Identification of Neisseria gonorrhoeae by the Bruker Biotyper Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry System Is Improved by a Database Extension. J Clin Microbiol 2016; 54:1130-2. [PMID: 26763972 DOI: 10.1128/jcm.00016-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 12/11/2022] Open
Abstract
Identification ofNeisseria gonorrhoeaeby the Bruker matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system may be affected by "B consistency categorization." A supplementary database of 17N. gonorrhoeaemain spectra was constructed. Twelve of 64N. gonorrhoeaeidentifications were categorized with B consistency, which disappeared using the supplementary database. Database extension did not result in misidentification ofNeisseria meningitidis.
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Evaluation of the Bruker MALDI Biotyper for Identification of Fastidious Gram-Negative Rods. J Clin Microbiol 2015; 54:543-8. [PMID: 26659214 DOI: 10.1128/jcm.03107-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 11/29/2015] [Indexed: 12/21/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has entered clinical laboratories, facilitating identification of bacteria. Here, we evaluated the MALDI Biotyper (Bruker Daltonics) for the identification of fastidious Gram-negative rods (GNR). Three sample preparation methods, direct colony transfer, direct transfer plus on-target formic acid preparation, and ethanol-formic acid extraction, were analyzed for 151 clinical isolates. Direct colony transfer applied with the manufacturer's interpretation criteria resulted in overall species and genus identification rates of 43.0% and 32.5%, respectively; 23.2% of the isolates were not identified, and two misidentifications (1.3%) were observed. The species identification rates increased to 46.4% and 53.7% for direct transfer plus formic acid preparation and ethanol-formic acid extraction, respectively. In addition, we evaluated score value cutoff alterations. The identification rates hardly increased by reducing the genus cutoff, while reducing the 2.0 species cutoff to 1.9 and to 1.8 increased the identification rates to up to 66.2% without increasing the rate of misidentifications. This study shows that fastidious GNR can reliably be identified using the MALDI Biotyper. However, the identification rates do not reach those of nonfastidious GNR such as the Enterobacteriaceae. In addition, two approaches optimizing the identification of fastidious GNR by the MALDI Biotyper were demonstrated: formic acid-based on-target sample treatment and reductions in cutoff scores to increase the species identification rates.
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Meningitis and Bacteremia Due to Neisseria cinerea following a Percutaneous Rhizotomy of the Trigeminal Ganglion. J Clin Microbiol 2015; 54:233-5. [PMID: 26511743 DOI: 10.1128/jcm.02041-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/26/2015] [Indexed: 11/20/2022] Open
Abstract
Neisseria cinerea is a human commensal. The first known case of meningitis and bacteremia due to Neisseria cinerea following percutaneous glycerol instillation of the trigeminal ganglion is reported. Conventional phenotypic methods and complete 16S RNA gene sequencing accurately identified the pathogen. Difficulties in differentiation from pathogenic neisseriae are discussed.
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Baarda BI, Sikora AE. Proteomics of Neisseria gonorrhoeae: the treasure hunt for countermeasures against an old disease. Front Microbiol 2015; 6:1190. [PMID: 26579097 PMCID: PMC4620152 DOI: 10.3389/fmicb.2015.01190] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/12/2015] [Indexed: 01/26/2023] Open
Abstract
Neisseria gonorrhoeae is an exquisitely adapted, strictly human pathogen and the causative agent of the sexually transmitted infection gonorrhea. This ancient human disease remains a serious problem, occurring at high incidence globally and having a major impact on reproductive and neonatal health. N. gonorrhoeae is rapidly evolving into a superbug and no effective vaccine exists to prevent gonococcal infections. Untreated or inadequately treated gonorrhea can lead to severe sequelae, including pelvic inflammatory disease and infertility in women, epididymitis in men, and sight-threatening conjunctivitis in infants born to infected mothers. Therefore, there is an immediate need for accelerated research toward the identification of molecular targets for development of drugs with new mechanisms of action and preventive vaccine(s). Global proteomic approaches are ideally suited to guide these studies. Recent quantitative proteomics (SILAC, iTRAQ, and ICAT) have illuminated the pathways utilized by N. gonorrhoeae to adapt to different lifestyles and micro-ecological niches within the host, while comparative 2D SDS-PAGE analysis has been used to elucidate spectinomycin resistance mechanisms. Further, high-throughput examinations of cell envelopes and naturally released membrane vesicles have unveiled the ubiquitous and differentially expressed proteins between temporally and geographically diverse N. gonorrhoeae isolates. This review will focus on these different approaches, emphasizing the role of proteomics in the search for vaccine candidates. Although our knowledge of N. gonorrhoeae has been expanded, still far less is known about this bacterium than the closely related N. meningitidis, where genomics- and proteomics-driven studies have led to the successful development of vaccines.
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Affiliation(s)
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
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Kim SW, Jang HB, Lee JS, Im SP, Lazarte JMS, Seo JP, Lee WJ, Kim JS, Jung TS. Comparison of proteome typing and serotyping of Streptococcus parauberis isolates from olive flounder (Paralichthys olivaceus). J Microbiol Methods 2015; 118:168-72. [PMID: 26423006 DOI: 10.1016/j.mimet.2015.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/24/2015] [Accepted: 09/24/2015] [Indexed: 01/21/2023]
Abstract
The olive flounder (Paralichthys olivaceus) is a cultivated marine species that is economically important in Korea and Japan. Several bacterial pathogens have caused severe mortalities in farmed olive flounder, especially Streptococcus parauberis. We collected 145 S. parauberis isolates from diseased olive flounders from 2003 to 2008 in Jeju Island, South Korea and characterized them by Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS) and by serology. The serological analysis divided the isolates into serotype I (62.1%) and serotype II (36.6%) and the proteome analysis divided the isolates into cluster 1 (43.4%) and cluster 2 (56.6%). All cluster 1 isolates had serotype I, but cluster 2 consisted of serotype I (32.9%), serotype II (64.6%), and others (2.5%). Further detailed analysis of the mass spectra led to identification of several specific m/z peaks that enabled discrimination between cluster 1 and 2 and between serotype I and II within cluster 2. Our results suggest that MALDI TOF MS analysis has potential as an alternative method for the rapid and reliable identification of the fish pathogen S. parauberis.
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Affiliation(s)
- Si Won Kim
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Ho Bin Jang
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jung Seok Lee
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Se Pyeong Im
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jassy Mary S Lazarte
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jong Pyo Seo
- Korea Fish Breeding Research Institute, 866, Haemajihaean-ro, Gujwa, Jeju-si, Jeju-do, Korea
| | - Woo Jai Lee
- BluGen Korea, Mangmibeonyeong-ro 38beon-gil, Suyeong-gu, Busan, Korea
| | - Jae Sung Kim
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Tae Sung Jung
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Republic of Korea.
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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: 781] [Impact Index Per Article: 86.8] [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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The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 2015; 28:237-64. [PMID: 25567229 DOI: 10.1128/cmr.00014-14] [Citation(s) in RCA: 522] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.
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Mehta A, Silva LP. MALDI-TOF MS profiling approach: how much can we get from it? FRONTIERS IN PLANT SCIENCE 2015; 6:184. [PMID: 25852729 PMCID: PMC4369652 DOI: 10.3389/fpls.2015.00184] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/06/2015] [Indexed: 05/25/2023]
Affiliation(s)
- Angela Mehta
- *Correspondence: Angela Mehta and Luciano P. Silva, ;
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41
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Xiao D, Ye C, Zhang H, Kan B, Lu J, Xu J, Jiang X, Zhao F, You Y, Yan X, Wang D, Hu Y, Zhang M, Zhang J. The construction and evaluation of reference spectra for the identification of human pathogenic microorganisms by MALDI-TOF MS. PLoS One 2014; 9:e106312. [PMID: 25181391 PMCID: PMC4152241 DOI: 10.1371/journal.pone.0106312] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/30/2014] [Indexed: 11/18/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an emerging technique for the rapid and high-throughput identification of microorganisms. There remains a dearth of studies in which a large number of pathogenic microorganisms from a particular country or region are utilized for systematic analyses. In this study, peptide mass reference spectra (PMRS) were constructed and evaluated from numerous human pathogens (a total of 1019 strains from 94 species), including enteric (46 species), respiratory (21 species), zoonotic (17 species), and nosocomial pathogens (10 species), using a MALDI-TOF MS Biotyper system (MBS). The PMRS for 380 strains of 52 species were new contributions to the original reference database (ORD). Compared with the ORD, the new reference database (NRD) allowed for 28.2% (from 71.5% to 99.7%) and 42.3% (from 51.3% to 93.6%) improvements in identification at the genus and species levels, respectively. Misidentification rates were 91.7% and 57.1% lower with the NRD than with the ORD for genus and species identification, respectively. Eight genera and 25 species were misidentified. For genera and species that are challenging to accurately identify, identification results must be manually determined and adjusted in accordance with the database parameters. Through augmentation, the MBS demonstrated a high identification accuracy and specificity for human pathogenic microorganisms. This study sought to provide theoretical guidance for using PMRS databases in various fields, such as clinical diagnosis and treatment, disease control, quality assurance, and food safety inspection.
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Affiliation(s)
- Di Xiao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Huifang Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jingxing Lu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiugao Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Fei Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yuanhai You
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiaomei Yan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Duochun Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yuan Hu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Maojun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jianzhong Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
- * E-mail:
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Zhang Y, Liu Y, Ma Q, Song Y, Zhang Q, Wang X, Chen F. Identification of Lactobacillus from the saliva of adult patients with caries using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. PLoS One 2014; 9:e106185. [PMID: 25166027 PMCID: PMC4148440 DOI: 10.1371/journal.pone.0106185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/28/2014] [Indexed: 11/18/2022] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has been presented as a superior method for the detection of microorganisms in body fluid samples (e.g., blood, saliva, pus, etc.) However, the performance of MALDI-TOF MS in routine identification of caries-related Lactobacillus isolates from saliva of adult patients with caries has not been determined. In the present study, we introduced a new MALDI-TOF MS system for identification of lactobacilli. Saliva samples were collected from 120 subjects with caries. Bacteria were isolated and cultured, and each isolate was identified by both 16S rRNA sequencing and MALDI-TOF MS. The identification results obtained by MALDI-TOF MS were concordant at the genus level with those of conventional 16S rRNA-based sequencing for 88.6% of lactobacilli (62/70) and 95.5% of non-lactobacilli (21/22). Up to 96 results could be obtained in parallel on a single MALDI target, suggesting that this is a reliable high-throughput approach for routine identification of lactobacilli. However, additional reference strains are necessary to increase the sensitivity and specificity of species-level identification.
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Affiliation(s)
- Yifei Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, P.R. China
| | - Yingyi Liu
- Department of Cariology and Endodontology, Peking University School and Hospital of Stomatology, Beijing, P.R. China
| | - Qingwei Ma
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yeqing Song
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, P.R. China
| | - Qian Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, P.R. China
| | - Xiaoyan Wang
- Department of Cariology and Endodontology, Peking University School and Hospital of Stomatology, Beijing, P.R. China
| | - Feng Chen
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, P.R. China
- * E-mail:
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Bennett JS, Watkins ER, Jolley KA, Harrison OB, Maiden MCJ. Identifying Neisseria species by use of the 50S ribosomal protein L6 (rplF) gene. J Clin Microbiol 2014; 52:1375-81. [PMID: 24523465 PMCID: PMC3993661 DOI: 10.1128/jcm.03529-13] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/03/2014] [Indexed: 02/05/2023] Open
Abstract
The comparison of 16S rRNA gene sequences is widely used to differentiate bacteria; however, this gene can lack resolution among closely related but distinct members of the same genus. This is a problem in clinical situations in those genera, such as Neisseria, where some species are associated with disease while others are not. Here, we identified and validated an alternative genetic target common to all Neisseria species which can be readily sequenced to provide an assay that rapidly and accurately discriminates among members of the genus. Ribosomal multilocus sequence typing (rMLST) using ribosomal protein genes has been shown to unambiguously identify these bacteria. The PubMLST Neisseria database (http://pubmlst.org/neisseria/) was queried to extract the 53 ribosomal protein gene sequences from 44 genomes from diverse species. Phylogenies reconstructed from these genes were examined, and a single 413-bp fragment of the 50S ribosomal protein L6 (rplF) gene was identified which produced a phylogeny that was congruent with the phylogeny reconstructed from concatenated ribosomal protein genes. Primers that enabled the amplification and direct sequencing of the rplF gene fragment were designed to validate the assay in vitro and in silico. Allele sequences were defined for the gene fragment, associated with particular species names, and stored on the PubMLST Neisseria database, providing a curated electronic resource. This approach provides an alternative to 16S rRNA gene sequencing, which can be readily replicated for other organisms for which more resolution is required, and it has potential applications in high-resolution metagenomic studies.
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Affiliation(s)
- Julia S Bennett
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Arpornsuwan T, Buasakul B, Jaresitthikunchai J, Roytrakul S. Potent and rapid antigonococcal activity of the venom peptide BmKn2 and its derivatives against different Maldi biotype of multidrug-resistant Neisseria gonorrhoeae. Peptides 2014; 53:315-20. [PMID: 24184420 DOI: 10.1016/j.peptides.2013.10.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 10/18/2013] [Accepted: 10/18/2013] [Indexed: 11/27/2022]
Abstract
The emergence of multidrug-resistant strains of Neisseria gonorrhoeae constitutes a serious threat to public health and necessitates the discovery of new types of antimicrobial agents. Among the 18 clinical isolates of N. gonorrhoeae with susceptible to spectinomycin, ceftriaxone and cefixime, 14 isolates were resistance to penicillin, tetracycline and ciprofloxacin, while 2 isolates were susceptible to tetracycline and another was penicillin intermediate isolate. Significant differences between laboratory strain and multidrug resistant strains were revealed by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling and bioinformatics examination using the MALDI BioTyper software. However, Maldi Biotyper was not successfully separated ciprofloxacin-penicillin resistance and ciprofloxacin-tetracycline resistance from ciprofloxacin-penicillin-tetracycline resistant N. gonorrhoeae isolates. BmKn2 is a basic, alpha-helical peptide with no disulfide-bridge venom peptides that was first isolated from Buthus martensii Kasch. A panel of BmKn2 scorpion venom peptide and its derivatives of varying length and characteristics were synthesized chemically and evaluated for their ability to inhibit the growth of clinical N. gonorrhoeae isolates. Synthetic BmKn2 displayed potent activity against 18 clinical isolates of N. gonorrhoeae with MIC50 values of 6.9-27.6 μM. BmKn2 exerted its antibacterial activity via a bactericidal mechanism. Cyclic BmKn1 did not show antigonococcal activity. Decreasing the cationicity and helix percentage at the C-terminus of BmKn2 reduced the potency against N. gonorrhoeae. Taken together, the BmKn1 peptide can be developed as a topical therapeutic agent for treating multidrug-resistant strains of N. gonorrhoeae infections.
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Affiliation(s)
- Teerakul Arpornsuwan
- Department of Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand.
| | - Brisana Buasakul
- Sexually Transmitted Infection Cluster, Bureau of AIDS TB and STIs, Department of Disease Control, Ministry of Public Health, Sathon, Bangkok, Thailand
| | - Janthima Jaresitthikunchai
- Genome Institute, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Klong Luang, Pathumthani, Thailand
| | - Sittiruk Roytrakul
- Genome Institute, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Klong Luang, Pathumthani, Thailand
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 2014; 26:547-603. [PMID: 23824373 DOI: 10.1128/cmr.00072-12] [Citation(s) in RCA: 514] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.
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La Scola B. Intact cell MALDI-TOF mass spectrometry-based approaches for the diagnosis of bloodstream infections. Expert Rev Mol Diagn 2014; 11:287-98. [DOI: 10.1586/erm.11.12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bernard La Scola
- URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
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A new approach to bacterial colony morphotyping by matrix-assisted laser desorption ionization time of flight-based mass spectrometry. Talanta 2013; 116:100-7. [DOI: 10.1016/j.talanta.2013.04.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 04/21/2013] [Accepted: 04/24/2013] [Indexed: 01/14/2023]
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Ribosomal proteins as biomarkers for bacterial identification by mass spectrometry in the clinical microbiology laboratory. J Microbiol Methods 2013; 94:390-6. [PMID: 23916798 DOI: 10.1016/j.mimet.2013.07.021] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/19/2013] [Accepted: 07/23/2013] [Indexed: 11/22/2022]
Abstract
Whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a rapid method for identification of microorganisms that is increasingly used in microbiology laboratories. This identification is based on the comparison of the tested isolate mass spectrum with reference databases. Using Neisseria meningitidis as a model organism, we showed that in one of the available databases, the Andromas database, 10 of the 13 species-specific biomarkers correspond to ribosomal proteins. Remarkably, one biomarker, ribosomal protein L32, was subject to inter-strain variability. The analysis of the ribosomal protein patterns of 100 isolates for which whole genome sequences were available, confirmed the presence of inter-strain variability in the molecular weight of 29 ribosomal proteins, thus establishing a correlation between the sequence type (ST) and/or clonal complex (CC) of each strain and its ribosomal protein pattern. Since the molecular weight of three of the variable ribosomal proteins (L30, L31 and L32) was included in the spectral window observed by MALDI-TOF MS in clinical microbiology, i.e., 3640-12000 m/z, we were able by analyzing the molecular weight of these three ribosomal proteins to classify each strain in one of six subgroups, each of these subgroups corresponding to specific STs and/or CCs. Their detection by MALDI-TOF allows therefore a quick typing of N. meningitidis isolates.
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Sandrin TR, Goldstein JE, Schumaker S. MALDI TOF MS profiling of bacteria at the strain level: a review. MASS SPECTROMETRY REVIEWS 2013; 32:188-217. [PMID: 22996584 DOI: 10.1002/mas.21359] [Citation(s) in RCA: 198] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 06/18/2012] [Accepted: 06/18/2012] [Indexed: 05/16/2023]
Abstract
Since the advent of the use of matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF MS) as a tool for microbial characterization, efforts to increase the taxonomic resolution of the approach have been made. The rapidity and efficacy of the approach have suggested applications in counter-bioterrorism, prevention of food contamination, and monitoring the spread of antibiotic-resistant bacteria. Strain-level resolution has been reported with diverse bacteria, using library-based and bioinformatics-enabled approaches. Three types of characterization at the strain level have been reported: strain categorization, strain differentiation, and strain identification. Efforts to enhance the library-based approach have involved sample pre-treatment and data reduction strategies. Bioinformatics approaches have leveraged the ever-increasing amount of publicly available genomic and proteomic data to attain strain-level characterization. Bioinformatics-enabled strategies have facilitated strain characterization via intact biomarker identification, bottom-up, and top-down approaches. Rigorous quantitative and advanced statistical analyses have fostered success at the strain level with both approaches. Library-based approaches can be limited by effects of sample preparation and culture conditions on reproducibility, whereas bioinformatics-enabled approaches are typically limited to bacteria, for which genetic and/or proteomic data are available. Biological molecules other than proteins produced in strain-specific manners, including lipids and lipopeptides, might represent other avenues by which strain-level resolution might be attained. Immunological and lectin-based chemistries have shown promise to enhance sensitivity and specificity. Whereas the limits of the taxonomic resolution of MALDI TOF MS profiling of bacteria appears bacterium-specific, recent data suggest that these limits might not yet have been reached.
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Affiliation(s)
- Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona 85069, USA.
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50
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Berrazeg M, Diene SM, Drissi M, Kempf M, Richet H, Landraud L, Rolain JM. Biotyping of multidrug-resistant Klebsiella pneumoniae clinical isolates from France and Algeria using MALDI-TOF MS. PLoS One 2013; 8:e61428. [PMID: 23620754 PMCID: PMC3631213 DOI: 10.1371/journal.pone.0061428] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 03/09/2013] [Indexed: 11/18/2022] Open
Abstract
Background Klebsiella pneumoniae is one of the most important pathogens responsible for nosocomial outbreaks worldwide. Epidemiological analyses are useful in determining the extent of an outbreak and in elucidating the sources and the spread of infections. The aim of this study was to investigate the epidemiological spread of K. pneumoniae strains using a MALDI-TOF MS approach. Methods Five hundred and thirty-five strains of K. pneumoniae were collected between January 2008 and March 2011 from hospitals in France and Algeria and were identified using MALDI-TOF. Antibiotic resistance patterns were investigated. Clinical and epidemiological data were recorded in an Excel file, including clustering obtained from the MSP dendrogram, and were analyzed using PASW Statistics software. Results Antibiotic susceptibility and phenotypic tests of the 535 isolates showed the presence of six resistance profiles distributed unequally between the two countries. The MSP dendrogram revealed five distinct clusters according to an arbitrary cut-off at the distance level of 500. Data mining analysis of the five clusters showed that K. pneumoniae strains isolated in Algerian hospitals were significantly associated with respiratory infections and the ESBL phenotype, whereas those from French hospitals were significantly associated with urinary tract infections and the wild-type phenotype. Conclusions MALDI-TOF was found to be a promising tool to identify and differentiate between K. pneumoniae strains according to their phenotypic properties and their epidemiological distribution. This is the first time that MALDI-TOF has been used as a rapid tool for typing K. pneumoniae clinical isolates.
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Affiliation(s)
- Meryem Berrazeg
- Aix-Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France
- Laboratoire Antibiotiques, Antifongiques: Physico-Chimie, Synthèse et Activité Biologiques, Faculté des Sciences de la Nature, de la Vie, de la Terre et de l’Univers, Université Abou Bekr Belkaid, Tlemcen, Algérie
| | - Seydina M. Diene
- Aix-Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Mourad Drissi
- Laboratoire Antibiotiques, Antifongiques: Physico-Chimie, Synthèse et Activité Biologiques, Faculté des Sciences de la Nature, de la Vie, de la Terre et de l’Univers, Université Abou Bekr Belkaid, Tlemcen, Algérie
| | - Marie Kempf
- Aix-Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France
- Laboratoire de Bactériologie, Institut de Biologie en santé – PBH, CHU, Angers, France
| | - Hervé Richet
- Aix-Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Luce Landraud
- Laboratoire de Bactériologie, Institut de Biologie en santé – PBH, CHU, Angers, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France
- * E-mail:
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