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Topić Popović N, Kazazić SP, Bojanić K, Strunjak-Perović I, Čož-Rakovac R. Sample preparation and culture condition effects on MALDI-TOF MS identification of bacteria: A review. MASS SPECTROMETRY REVIEWS 2021. [PMID: 34642960 DOI: 10.1002/mas.21739] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an excellent tool for bacterial identification. It allows high throughput, sensitive and specific applications in clinical diagnostics and environmental research. Currently, there is no optimal standardized protocol for sample preparation and culture conditions to profile bacteria. The performance of MALDI-TOF MS is affected by several variables, such as sample preparation, culture media and culture conditions, incubation time/growth stage, incubation temperature, high salt content, blood in the culture media, and others. This review thus aims to clarify why a uniformed protocol is not plausible, to assess the effects these factors have on MALDI-TOF MS identification score, and discuss possible optimizations for its methodology, in relation to specific bacterial representatives and strain requirements.
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Affiliation(s)
- Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Snježana P Kazazić
- Laboratory for Mass Spectrometry and Functional Proteomics, Ruđer Bošković Institute, Zagreb, Croatia
| | - Krunoslav Bojanić
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
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Pinar-Méndez A, Fernández S, Baquero D, Vilaró C, Galofré B, González S, Rodrigo-Torres L, Arahal DR, Macián MC, Ruvira MA, Aznar R, Caudet-Segarra L, Sala-Comorera L, Lucena F, Blanch AR, Garcia-Aljaro C. Rapid and improved identification of drinking water bacteria using the Drinking Water Library, a dedicated MALDI-TOF MS database. WATER RESEARCH 2021; 203:117543. [PMID: 34433109 DOI: 10.1016/j.watres.2021.117543] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/23/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
According to the European Directives (UE) 2020/2184 and 2009/54/EC, which establishes the sanitary criteria for water intended for human consumption in Europe, water suitable for human consumption must be free of the bacterial indicators Escherichia coli, Clostridium perfringens and Enterococcus spp. Drinking water is also monitored for heterotrophic bacteria, which are not a human health risk, but can serve as an index of bacteriological water quality. Therefore, a rapid, accurate, and cost-effective method for the identification of these colonies would improve our understanding of the culturable bacteria of drinking water and facilitate the task of water management by treatment facilities. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is potentially such a method, although most of the currently available mass spectral libraries have been developed in a clinical setting and have limited environmental applicability. In this work, a MALDI-TOF MS drinking water library (DWL) was defined and developed by targeting bacteria present in water intended for human consumption. This database, made up of 319 different bacterial strains, can contribute to the routine microbiological control of either treated drinking water or mineral bottled water carried out by water treatment and distribution operators, offering a faster identification rate compared to a clinical sample-based library. The DWL, made up of 96 bacterial genera, 44 of which are not represented in the MALDI-TOF MS bacterial Bruker Daltonics (BDAL) database, was found to significantly improve the identification of bacteria present in drinking water.
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Affiliation(s)
- Anna Pinar-Méndez
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain; Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain.
| | - Sonia Fernández
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - David Baquero
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - Carles Vilaró
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Belén Galofré
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Susana González
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - Lidia Rodrigo-Torres
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - David R Arahal
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - M Carmen Macián
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - María A Ruvira
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Rosa Aznar
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Laia Caudet-Segarra
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Laura Sala-Comorera
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Francisco Lucena
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Anicet R Blanch
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain.
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Manzulli V, Rondinone V, Buchicchio A, Serrecchia L, Cipolletta D, Fasanella A, Parisi A, Difato L, Iatarola M, Aceti A, Poppa E, Tolve F, Pace L, Petruzzi F, Rovere ID, Raele DA, Del Sambro L, Giangrossi L, Galante D. Discrimination of Bacillus cereus Group Members by MALDI-TOF Mass Spectrometry. Microorganisms 2021; 9:microorganisms9061202. [PMID: 34199368 PMCID: PMC8228078 DOI: 10.3390/microorganisms9061202] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/29/2021] [Accepted: 05/30/2021] [Indexed: 11/16/2022] Open
Abstract
Matrix-Assisted Laser Desorption/Ionization Time Of Flight Mass Spectrometry (MALDI-TOF MS) technology is currently increasingly used in diagnostic laboratories as a cost effective, rapid and reliable routine technique for the identification and typing of microorganisms. In this study, we used MALDI-TOF MS to analyze a collection of 160 strains belonging to the Bacillus cereus group (57 B. anthracis, 49 B. cereus, 1 B. mycoides, 18 B. wiedmannii, 27 B. thuringiensis, 7 B. toyonensis and 1 B. weihenstephanensis) and to detect specific biomarkers which would allow an unequivocal identification. The Main Spectra Profiles (MSPs) were added to an in-house reference library, expanding the current commercial library which does not include B. toyonensis and B. wiedmannii mass spectra. The obtained mass spectra were statistically compared by Principal Component Analysis (PCA) that revealed seven different clusters. Moreover, for the identification purpose, were generated dedicate algorithms for a rapid and automatic detection of characteristic ion peaks after the mass spectra acquisition. The presence of specific biomarkers can be used to differentiate strains within the B. cereus group and to make a reliable identification of Bacillus anthracis, etiologic agent of anthrax, which is the most pathogenic and feared bacterium of the group. This could offer a critical time advantage for the diagnosis and for the clinical management of human anthrax even in case of bioterror attacks.
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Affiliation(s)
- Viviana Manzulli
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Valeria Rondinone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
- Correspondence: ; Tel.: +39-0881-786330
| | - Alessandro Buchicchio
- Bruker Italia s.r.l., Daltonics Division, Strada Cluentina, 26/R, 62100 Macerata, Italy;
| | - Luigina Serrecchia
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Dora Cipolletta
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Antonio Fasanella
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Laura Difato
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Michela Iatarola
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Angela Aceti
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Elena Poppa
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Francesco Tolve
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Lorenzo Pace
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Fiorenza Petruzzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Ines Della Rovere
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Donato Antonio Raele
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Luigi Giangrossi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
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Farag MA, Mesak MA, Saied DB, Ezzelarab NM. Uncovering the dormant food hazards, a review of foodborne microbial spores' detection and inactivation methods with emphasis on their application in the food industry. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2020.10.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Novel Strategy for Rapidly and Safely Distinguishing Bacillus anthracis and Bacillus cereus by Use of Peptide Mass Fingerprints Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2020; 59:JCM.02358-20. [PMID: 33115846 DOI: 10.1128/jcm.02358-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 10/19/2020] [Indexed: 12/28/2022] Open
Abstract
The objective of this study was to construct a rapid, high-throughput, and biosafety-compatible screening method for Bacillus anthracis and Bacillus cereus based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). MALDI-TOF MS coupled to ClinProTools was used to discover MALDI-TOF MS biomarker peaks and generate a classification model based on a genetic algorithm (GA) to differentiate between different Bacillus anthracis and Bacillus cereus isolates. Thirty Bacillus anthracis and 19 Bacillus cereus strains were used to construct and analyze the model, and 40 Bacillus strains were used for validation. For the GA screening model, the cross-validation values, which reflect the ability of the model to handle variability among the test spectra, and the recognition capability values, which reflect the model's ability to correctly identify its component spectra, were all 100%. This model contained 10 biomarker peaks (m/z 3,339.9, 3,396.3, 3,682.4, 5,476.7, 6,610.6, 6,680.1, 7,365.3, 7,792.4, 9,475.8, and 10,934.1) used to correctly identify 28 Bacillus anthracis and 12 Bacillus cereus isolates from 40 Bacillus isolates, with a sensitivity and specificity of 100%. With the obvious advantages of being rapid, highly accurate, and highly sensitive and having a low cost and high throughput, MALDI-TOF MS ClinProTools is a powerful and reliable tool for screening Bacillus anthracis and Bacillus cereus strains.
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McEvoy B, Lynch M, Rowan NJ. Opportunities for the application of real-time bacterial cell analysis using flow cytometry for the advancement of sterilization microbiology. J Appl Microbiol 2020; 130:1794-1812. [PMID: 33155740 DOI: 10.1111/jam.14876] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/10/2020] [Accepted: 09/21/2020] [Indexed: 01/11/2023]
Abstract
Medical devices provide critical care and diagnostic applications through patient contact. Sterility assurance level (SAL) may be defined as the probability of a single viable micro-organism occurring on an item after a sterilization process. Sterilization microbiology often relies upon using an overkill validation method where a 12-log reduction in recalcitrant bacterial endospore population occurs during the process that exploits conventional laboratory-based culture media for enumeration. This timely review explores key assumptions underpinning use of conventional culture-based methods in sterilization microbiology. Consideration is given to how such methods may limit the ability to fully appreciate the inactivation kinetics of a sterilization process such as vaporized hydrogen peroxide (VH2O2) sterilization, and consequently design efficient sterilization processes. Specific use of the real-time flow cytometry (FCM) is described by way of elucidating the practical relevance of these limitation factors with implications and opportunities for the sterilization industry discussed. Application of FCM to address these culture-based limitation factors will inform real-time kinetic inactivation modelling and unlock potential to embrace emerging opportunities for pharma, medical device and sterilization industries including potentially disruptive applications that may involve reduced usage of sterilant.
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Affiliation(s)
- B McEvoy
- STERIS Applied Sterilization Technologies, IDA Business and Technology Park, Tullamore, Ireland
| | - M Lynch
- Centre for Disinfection, Sterilization and Biosecurity, Athlone Institute of Technology, Athlone, Ireland
| | - N J Rowan
- Centre for Disinfection, Sterilization and Biosecurity, Athlone Institute of Technology, Athlone, Ireland
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Doellinger J, Schneider A, Stark TD, Ehling-Schulz M, Lasch P. Evaluation of MALDI-ToF Mass Spectrometry for Rapid Detection of Cereulide From Bacillus cereus Cultures. Front Microbiol 2020; 11:511674. [PMID: 33329410 PMCID: PMC7709880 DOI: 10.3389/fmicb.2020.511674] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
Bacillus cereus plays an often unrecognized role in food borne diseases. Food poisoning caused by this pathogen is manifested by either diarrhea or emesis. Due to the relatively high prevalence of emetic toxin cereulide associated food poisoning, methods for simple and reliable detection of cereulide producing strains are of utmost importance. Recently, two different studies reported on the application of MALDI-ToF MS for either the differentiation of emetic and non-emetic strains of B. cereus or for direct detection of cereulide from bacterial colony smears. However, for implementation of cereulide detection using MALDI-ToF MS in routine microbiological diagnostics additional investigations on the sensitivity and specificity as well as on the fitting into common workflows for bacterial identification are needed. These aspects prompted us to investigate open issues and to test sample preparation methods, commonly used for microbial identification for their suitability to detect the emetic toxin from bacteria. Based on our experimental findings we propose a workflow that allows identification of B. cereus and sensitive detection of cereulide in parallel, using linear-mode MALDI-ToF MS equipment. The protocol was validated in a blinded study and is based on the well-established ethanol/formic acid extraction method. Cereulide is detected in the ethanol wash solution of samples identified as B. cereus as peaks at m/z 1175 and 1191. Peak position difference of 16 Th (Thomson) indicates detection of the sodium and potassium adducts of cereulide. This sample treatment offers possibilities for further characterization by more sophisticated LC-MS-based methods. In summary, the ease of use and the achieved level of analytical sensitivity as well as the wide-spread availability of MALDI-ToF MS equipment in clinical microbiological laboratories provides a promising tool to improve and to facilitate routine diagnostics of B. cereus associated food intoxications.
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Affiliation(s)
- Joerg Doellinger
- Proteomics and Spectroscopy Unit (ZBS 6), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Andy Schneider
- Proteomics and Spectroscopy Unit (ZBS 6), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Timo D Stark
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Munich, Germany
| | - Monika Ehling-Schulz
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Peter Lasch
- Proteomics and Spectroscopy Unit (ZBS 6), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
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Mülner P, Schwarz E, Dietel K, Junge H, Herfort S, Weydmann M, Lasch P, Cernava T, Berg G, Vater J. Profiling for Bioactive Peptides and Volatiles of Plant Growth Promoting Strains of the Bacillus subtilis Complex of Industrial Relevance. Front Microbiol 2020; 11:1432. [PMID: 32695084 PMCID: PMC7338577 DOI: 10.3389/fmicb.2020.01432] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
Plant growth promoting rhizobacteria attain increasing importance in agriculture as biofertilizers and biocontrol agents. These properties significantly depend on the formation of bioactive compounds produced by such organisms. In our work we investigated the biosynthetic potential of 13 industrially important strains of the Bacillus subtilis complex by mass spectrometric methodology. Typing of these organisms was performed with MALDI-TOF mass spectrometry followed by comprehensive profiling of their bioactive peptide products. Volatiles were determined by gas chromatography-mass spectrometry. Representative products of the members of the B. subtilis complex investigated in detail were: the surfactin familiy (surfactins, lichenysins, pumilacidins); the iturin family (iturins, mycosubtilins and bacillomycins); plantazolicin and the dual lantibiotics lichenicidins, as well as a wide spectrum of volatiles, such as hydrocarbons (alkanes/alkenes), alcohols, ketones, sulfur-containing compounds and pyrazines. The subcomplexes of the B. subtilis organizational unit; (a) B. subtilis/Bacillus atrophaeus; (b) B. amyloliquefaciens/B. velezensis; (c) B. licheniformis, and (d) B. pumilus are equipped with specific sets of these compounds which are the basis for the evaluation of their biotechnological and agricultural usage. The 13 test strains were evaluated in field trials for growth promotion of potato and maize plants. All of the implemented strains showed efficient growth stimulation of these plants. The highest effects were obtained with B. velezensis, B. subtilis, and B. atrophaeus strains.
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Affiliation(s)
- Pascal Mülner
- ABiTEP GmbH, Berlin, Germany
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | | | | | - Stefanie Herfort
- ZBS6: Proteomics and Spectroscopy, Robert Koch-Institut, Berlin, Germany
| | - Max Weydmann
- ZBS6: Proteomics and Spectroscopy, Robert Koch-Institut, Berlin, Germany
| | - Peter Lasch
- ZBS6: Proteomics and Spectroscopy, Robert Koch-Institut, Berlin, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Joachim Vater
- ABiTEP GmbH, Berlin, Germany
- ZBS6: Proteomics and Spectroscopy, Robert Koch-Institut, Berlin, Germany
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9
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Highly accurate classification of biological spores by culture medium for forensic attribution using multiple chemical signature types and machine learning. Anal Bioanal Chem 2020; 412:4287-4299. [PMID: 32328690 DOI: 10.1007/s00216-020-02660-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/01/2020] [Accepted: 04/14/2020] [Indexed: 01/29/2023]
Abstract
Future proliferation of biological expertise and new technology may increasingly lower the difficulty to produce biological organisms for misuse. Rapid attribution of a biological attack is needed to quickly identify the person or lab responsible and prevent additional attacks by enabling the apprehension of suspects. Here, triplicate batches of Bacillus anthracis Sterne strain (BaSt) spores were grown in a total of seven amateur and professional media. Multiple orthogonal analytical signatures (peptides, metabolites, lipids by fatty acid methyl ester (FAME) analysis, bulk organic profile, and trace elements) were collected from the BaSt spores. The proteomics and metabolomics analyses identified promising attribution signature compounds that are unique to each of the seven production methods. In addition, while each of the signature types showed varying degrees of value individually for attributing BaSt spores to the culture medium used to prepare them, fusing results from all five signatures types to increase sourcing robustness and using a random forest sourcing algorithm yielded 100% hold-one-batch-out cross-validation classification accuracy and an average relative source probability for the correct source 5.5× higher than the most probable incorrect source. These preliminary results provide a proof-of-concept for the development of forensic examinations that can attribute biological agents to production methods for use in future investigations.
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10
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Palombo EA. Ethanol treatment does not inactivate spore-forming bacteria - A cautionary note about the safe transport of bacteria prior to identification by MALDI-TOF MS. J Microbiol Methods 2020; 172:105893. [PMID: 32184160 DOI: 10.1016/j.mimet.2020.105893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 11/29/2022]
Abstract
Treatment with 70% ethanol has been proposed as a safe and effective way to inactive bacteria for transport between laboratories prior to identification by MALDI-TOF MS. Ethanol alone does not inactivate spore-forming bacteria and additional chemical or physical treatment is necessary to guarantee inactivation of bacterial spores.
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Affiliation(s)
- Enzo A Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia.
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11
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Sun X, Wu P, Zhao C, Zheng F, Hu C, Lu X, Xu G. Protein profiling analysis based on matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry and its application in typing Streptomyces isolates. Talanta 2020; 208:120439. [PMID: 31816710 DOI: 10.1016/j.talanta.2019.120439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/22/2019] [Accepted: 10/03/2019] [Indexed: 10/25/2022]
Abstract
Marine Streptomyces is a potential source of novel bioactive natural products in medicine and agriculture. The current discrimination and screening method of Streptomyces isolates is not accurate and time-consuming, and a novel method is necessary. In this study, a protein profiling method based on an ultrahigh resolution 15 T Matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICR MS) was established and applied for differentiation and bioactivity screening of marine Streptomyces isolates. To obtain robust protein profiling, the effects of the protein extraction method, the matrix-solvent, the sample deposition mode, and the culture time of isolates on protein profiling were thoroughly studied, the optimal conditions were obtained. To evaluate the performance of the developed MALDI-FTICR MS method, MALDI-time of flight (TOF) MS and 16S rRNA were applied in parallel to analyze 25 marine Streptomyces isolates. We found that the clustering result of MALDI-FTICR MS was more similar to that of 16S rRNA than MALDI-TOF MS. And MALDI-FTICR MS could effectively indicate the antibacterial activity of Streptomyces isolates against three plant pathogenic bacteria including Xanthomonas campestris, Xanthomonas oryzae and Erwinia carotovora. Furthermore, a differential protein/peptide was defined and successfully applied to predict antibacterial activity of blind samples. This study demonstrated that MALDI-FTICR MS has great potential to discriminate and screen complex microorganisms, especially those closely related strains.
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Affiliation(s)
- Xiaoshan Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peichun Wu
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Chunxia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Fujian Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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12
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Doellinger J, Schneider A, Hoeller M, Lasch P. Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction. Mol Cell Proteomics 2020; 19:209-222. [PMID: 31754045 PMCID: PMC6944244 DOI: 10.1074/mcp.tir119.001616] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/01/2019] [Indexed: 12/12/2022] Open
Abstract
The main challenge of bottom-up proteomic sample preparation is to extract proteomes in a manner that enables efficient protein digestion for subsequent mass spectrometric analysis. Today's sample preparation strategies are commonly conceptualized around the removal of detergents, which are essential for extraction but strongly interfere with digestion and LC-MS. These multi-step preparations contribute to a lack of reproducibility as they are prone to losses, biases and contaminations, while being time-consuming and labor-intensive. We report a detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which consists of three mandatory steps, acidification, neutralization and digestion. SPEED is a universal method for peptide generation from various sources and is easily applicable even for lysis-resistant sample types as pure trifluoroacetic acid (TFA) is used for highly efficient protein extraction by complete sample dissolution. The protocol is highly reproducible, virtually loss-less, enables very rapid sample processing and is superior to the detergent/chaotropic agent-based methods FASP, ISD-Urea and SP3 for quantitative proteomics. SPEED holds the potential to dramatically simplify and standardize sample preparation while improving the depth of proteome coverage especially for challenging samples.
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Affiliation(s)
- Joerg Doellinger
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany.
| | - Andy Schneider
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
| | - Marcell Hoeller
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
| | - Peter Lasch
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
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13
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Lemmer K, Pauli G, Howaldt S, Schwebke I, Mielke M, Grunow R. Decontamination of Personal Protective Equipment. Health Secur 2019; 17:200-212. [PMID: 31173501 DOI: 10.1089/hs.2019.0005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Exploratory field analyses of the inactivation capacity of disinfectants on contaminated personal protective equipment (PPE) are required to select a suitable surrogate for biohazardous agents like spores of Bacillus anthracis. The objectives of our study were (1) the determination of an appropriate surrogate for the inactivation of spores of B. anthracis with peracetic acid (PAA), and (2) application of optimized inactivation conditions for an effective decontamination of PPE with PAA under field conditions. For inactivation studies, B. anthracis spores from different strains and B. thuringiensis spores were fixed by air drying on carriers prepared from PPE fabric. Time and concentration studies with PAA-based disinfectants revealed that the spores of the B. thuringiensis strain DSM 350 showed an inactivation profile comparable to that of the spores of the B. anthracis strain with the highest stability, implying that B. thuringiensis can serve as an appropriate surrogate. Rapid (3 to 5 minutes) and effective surface decontamination was achieved with 2% PAA/0.2% surfactant. In field studies, PPE contaminated with spores of B. thuringiensis was treated with the disinfectant. Optimizing the decontamination technique revealed that spraying in combination with brushing was effective within 5 minutes of exposure.
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Affiliation(s)
- Karin Lemmer
- Dr. Karin Lemmer is a scientist in the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; Professor Georg Pauli is the former Head of the Centre for Biological Threats and Special Pathogens; Sabine Howaldt is a medical technical assistant in the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; Dr. Ingeborg Schwebke is Deputy Head of the Unit Hospital Hygiene, Infection Prevention and Control, Department of Infectious Diseases; Professor Martin Mielke is Head of the Department of Infectious Diseases; and Professor Roland Grunow is Head of the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; all at the Robert Koch Institute, Berlin, Germany
| | - Georg Pauli
- Dr. Karin Lemmer is a scientist in the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; Professor Georg Pauli is the former Head of the Centre for Biological Threats and Special Pathogens; Sabine Howaldt is a medical technical assistant in the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; Dr. Ingeborg Schwebke is Deputy Head of the Unit Hospital Hygiene, Infection Prevention and Control, Department of Infectious Diseases; Professor Martin Mielke is Head of the Department of Infectious Diseases; and Professor Roland Grunow is Head of the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; all at the Robert Koch Institute, Berlin, Germany
| | - Sabine Howaldt
- Dr. Karin Lemmer is a scientist in the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; Professor Georg Pauli is the former Head of the Centre for Biological Threats and Special Pathogens; Sabine Howaldt is a medical technical assistant in the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; Dr. Ingeborg Schwebke is Deputy Head of the Unit Hospital Hygiene, Infection Prevention and Control, Department of Infectious Diseases; Professor Martin Mielke is Head of the Department of Infectious Diseases; and Professor Roland Grunow is Head of the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; all at the Robert Koch Institute, Berlin, Germany
| | - Ingeborg Schwebke
- Dr. Karin Lemmer is a scientist in the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; Professor Georg Pauli is the former Head of the Centre for Biological Threats and Special Pathogens; Sabine Howaldt is a medical technical assistant in the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; Dr. Ingeborg Schwebke is Deputy Head of the Unit Hospital Hygiene, Infection Prevention and Control, Department of Infectious Diseases; Professor Martin Mielke is Head of the Department of Infectious Diseases; and Professor Roland Grunow is Head of the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; all at the Robert Koch Institute, Berlin, Germany
| | - Martin Mielke
- Dr. Karin Lemmer is a scientist in the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; Professor Georg Pauli is the former Head of the Centre for Biological Threats and Special Pathogens; Sabine Howaldt is a medical technical assistant in the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; Dr. Ingeborg Schwebke is Deputy Head of the Unit Hospital Hygiene, Infection Prevention and Control, Department of Infectious Diseases; Professor Martin Mielke is Head of the Department of Infectious Diseases; and Professor Roland Grunow is Head of the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; all at the Robert Koch Institute, Berlin, Germany
| | - Roland Grunow
- Dr. Karin Lemmer is a scientist in the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; Professor Georg Pauli is the former Head of the Centre for Biological Threats and Special Pathogens; Sabine Howaldt is a medical technical assistant in the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; Dr. Ingeborg Schwebke is Deputy Head of the Unit Hospital Hygiene, Infection Prevention and Control, Department of Infectious Diseases; Professor Martin Mielke is Head of the Department of Infectious Diseases; and Professor Roland Grunow is Head of the Unit Highly Pathogenic Microorganisms, Centre for Biological Threats and Special Pathogens; all at the Robert Koch Institute, Berlin, Germany
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14
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Rifflet A, Filali S, Chenau J, Simon S, Fenaille F, Junot C, Carniel E, Becher F. Quantification of low abundance Yersinia pestis markers in dried blood spots by immuno-capture and quantitative high-resolution targeted mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:268-277. [PMID: 31096787 DOI: 10.1177/1469066718795978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plague, caused by the bacterium Yersinia pestis, is still present in several countries worldwide. Besides, Y. pestis has been designated as Tier 1 agent, the highest rank of bioterrorism agents. In this context, reliable diagnostic methods are of great importance. Here, we have developed an original workflow based upon dried blood spot for simplified sampling of clinical specimens, and specific immuno-mass spectrometry monitoring of Y. pestis biomarkers. Targeted proteins were selectively enriched from dried blood spot extracts by multiplex immunocapture using antibody-coated magnetic beads. After accelerated on-beads digestion, proteotypic peptides were monitored by multiplex LC-MS/MS through the parallel reaction monitoring mode. The DBS-IC-MS assay was designed to quantify both F1 and LcrV antigens, although 10-fold lower sensitivity was observed with LcrV. The assay was successfully validated for F1 with a lower limit of quantification at 5 ng·mL-1 in spiked blood, corresponding to only 0.1 ng on spots. In vivo quantification of F1 in blood and organ samples was demonstrated in the mouse model of pneumonic plague. The new assay could help to simplify the laboratory confirmation of positive point of care F1 dipstick.
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Affiliation(s)
- Aline Rifflet
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - Sofia Filali
- 2 Yersinia Research Unit, Institut Pasteur, Paris, France
| | - Jérôme Chenau
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - Stéphanie Simon
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - François Fenaille
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - Christophe Junot
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | | | - François Becher
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
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15
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Capture and Analysis of Cell Surface N-Glycans by Hydrazide-Modified Magnetic Beads and CE-LIF. Chromatographia 2019. [DOI: 10.1007/s10337-019-03742-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Analysis of bacteria associated with honeys of different geographical and botanical origin using two different identification approaches: MALDI-TOF MS and 16S rDNA PCR technique. PLoS One 2019; 14:e0217078. [PMID: 31120945 PMCID: PMC6532876 DOI: 10.1371/journal.pone.0217078] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/05/2019] [Indexed: 12/14/2022] Open
Abstract
In the presented work identification of microorganisms isolated from various types of honeys was performed. Martix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequencing were applied to study environmental bacteria strains.With both approches, problematic spore-forming Bacillus spp, but also Staphylococcus spp., Lysinibacillus spp., Micrococcus spp. and Brevibacillus spp were identified. However, application of spectrometric technique allows for an unambiguous distinction between species/species groups e.g.B. subtilis or B. cereus groups. MALDI TOF MS and 16S rDNA sequencing allow for construction of phyloproteomic and phylogenetic trees of identified bacterial species. Furthermore, the correlation beetween physicochemical properties, geographical and botanical origin and the presence bacterial species in honey samples were investigated.
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17
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Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) shows adaptation of grass pollen composition. Sci Rep 2018; 8:16591. [PMID: 30409982 PMCID: PMC6224550 DOI: 10.1038/s41598-018-34800-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/22/2018] [Indexed: 11/22/2022] Open
Abstract
MALDI time-of-flight mass spectrometry (MALDI-TOF MS) has become a widely used tool for the classification of biological samples. The complex chemical composition of pollen grains leads to highly specific, fingerprint-like mass spectra, with respect to the pollen species. Beyond the species-specific composition, the variances in pollen chemistry can be hierarchically structured, including the level of different populations, of environmental conditions or different genotypes. We demonstrate here the sensitivity of MALDI-TOF MS regarding the adaption of the chemical composition of three Poaceae (grass) pollen for different populations of parent plants by analyzing the mass spectra with partial least squares discriminant analysis (PLS-DA) and principal component analysis (PCA). Thereby, variances in species, population and specific growth conditions of the plants were observed simultaneously. In particular, the chemical pattern revealed by the MALDI spectra enabled discrimination of the different populations of one species. Specifically, the role of environmental changes and their effect on the pollen chemistry of three different grass species is discussed. Analysis of the group formation within the respective populations showed a varying influence of plant genotype on the classification, depending on the species, and permits conclusions regarding the respective rigidity or plasticity towards environmental changes.
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18
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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19
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Chong YK, Ho CC, Leung SY, Lau SK, Woo PC. Clinical Mass Spectrometry in the Bioinformatics Era: A Hitchhiker's Guide. Comput Struct Biotechnol J 2018; 16:316-334. [PMID: 30237866 PMCID: PMC6138949 DOI: 10.1016/j.csbj.2018.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 02/06/2023] Open
Abstract
Mass spectrometry (MS) is a sensitive, specific and versatile analytical technique in the clinical laboratory that has recently undergone rapid development. From initial use in metabolic profiling, it has matured into applications including clinical toxicology assays, target hormone and metabolite quantitation, and more recently, rapid microbial identification and antimicrobial resistance detection by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In this mini-review, we first succinctly outline the basics of clinical mass spectrometry. Examples of hard ionization (electron ionization) and soft ionization (electrospray ionization, MALDI) are presented to demonstrate their clinical applications. Next, a conceptual discourse on mass selection and determination is presented: quadrupole mass filter, time-of-flight mass spectrometer and the Orbitrap; and MS/MS (tandem-in-space, tandem-in-time and data acquisition), illustrated with clinical examples. Current applications in (1) bacterial and fungal identification, antimicrobial susceptibility testing and phylogenetic classification, (2) general unknown urine toxicology screening and expanded new-born metabolic screening and (3) clinical metabolic profiling by gas chromatography are outlined. Finally, major limitations of MS-based techniques, including the technical challenges of matrix effect and isobaric interference; and novel challenges in the post-genomic era, such as protein molecular variants, are critically discussed from the perspective of service laboratories. Computer technology and structural biology have played important roles in the maturation of this field. MS-based techniques have the potential to replace current analytical techniques, and existing expertise and instrument will undergo rapid evolution. Significant automation and adaptation to regulatory requirements are underway. Mass spectrometry is unleashing its potentials in clinical laboratories.
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Affiliation(s)
- Yeow-Kuan Chong
- Hospital Authority Toxicology Reference Laboratory, Department of Pathology, Princess Margaret Hospital (PMH), Kowloon, Hong Kong
- Chemical Pathology and Medical Genetics, Department of Pathology, Princess Margaret Hospital (PMH), Kowloon, Hong Kong
| | - Chi-Chun Ho
- Division of Chemical Pathology, Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital (PYNEH), Hong Kong
- Division of Clinical Biochemistry, Department of Pathology, Queen Mary Hospital (QMH), Hong Kong
- Centre for Genomic Sciences, The University of Hong Kong, Hong Kong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Shui-Yee Leung
- Department of Ocean Science, School of Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Susanna K.P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Patrick C.Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
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20
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van Belkum A, Welker M, Pincus D, Charrier JP, Girard V. Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry in Clinical Microbiology: What Are the Current Issues? Ann Lab Med 2018; 37:475-483. [PMID: 28840984 PMCID: PMC5587819 DOI: 10.3343/alm.2017.37.6.475] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 06/20/2017] [Accepted: 07/25/2017] [Indexed: 12/12/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microbial species in clinical microbiology laboratories. MALDI-TOF-MS has swiftly become the new gold-standard method owing to its key advantages of simplicity and robustness. However, as with all new methods, adoption of the MALDI-TOF MS approach is still not widespread. Optimal sample preparation has not yet been achieved for several applications, and there are continuing discussions on the need for improved database quality and the inclusion of additional microbial species. New applications such as in the field of antimicrobial susceptibility testing have been proposed but not yet translated to the level of ease and reproducibility that one should expect in routine diagnostic systems. Finally, during routine identification testing, unexpected results are regularly obtained, and the best methods for transmitting these results into clinical care are still evolving. We here discuss the success of MALDI-TOF MS in clinical microbiology and highlight fields of application that are still amenable to improvement.
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Affiliation(s)
- Alex van Belkum
- Scientific Office, bioMérieux, La Balme Les Grottes, France.
| | - Martin Welker
- Scientific Office, bioMérieux, La Balme Les Grottes, France
| | - David Pincus
- Scientific Office, bioMérieux, La Balme Les Grottes, France
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21
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Improved Discrimination of Bacillus anthracis from Closely Related Species in the Bacillus cereus Sensu Lato Group Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2018. [PMID: 29514939 DOI: 10.1128/jcm.01900-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Discrimination of highly pathogenic bacteria, such as Bacillus anthracis, from closely related species based on molecular biological methods is challenging. We applied matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to a collection of B. anthracis strains and close relatives in order to significantly improve the statistical confidence of identification results for this group of bacteria. Protein mass spectra of 189 verified and diverse Bacillus strains of the Bacillus cereus sensu lato group were generated using MALDI-TOF MS and subsequently analyzed with supervised and unsupervised statistical methods, such as shrinkage discriminant analysis (SDA) and principal-component analysis (PCA). We aimed at identifying specific biomarkers in the protein spectra of B. anthracis not present in closely related Bacillus species. We could identify 7, 10, 18, and 14 B. anthracis-specific biomarker candidates that were absent in B. cereus, B. mycoides, B. thuringiensis, and B. weihenstephanensis strains, respectively. Main spectra (MSP) of a defined collection of Bacillus strains were compiled using the Bruker Biotyper software and added to an in-house reference library. Reevaluation of this library with 15 hitherto untested strains of B. anthracis and B. cereus yielded improved score values. The B. anthracis strains were identified with score values between 2.33 and 2.55 using the in-house database, while the same strains were identified with scores between 1.94 and 2.37 using the commercial database, and no false-positive identifications occurred using the in-house database.
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Dieckmann R, Hammerl JA, Hahmann H, Wicke A, Kleta S, Dabrowski PW, Nitsche A, Stämmler M, Al Dahouk S, Lasch P. Rapid characterisation of Klebsiella oxytoca isolates from contaminated liquid hand soap using mass spectrometry, FTIR and Raman spectroscopy. Faraday Discuss 2018; 187:353-75. [PMID: 27053001 DOI: 10.1039/c5fd00165j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Microbiological monitoring of consumer products and the efficiency of early warning systems and outbreak investigations depend on the rapid identification and strain characterisation of pathogens posing risks to the health and safety of consumers. This study evaluates the potential of three rapid analytical techniques for identification and subtyping of bacterial isolates obtained from a liquid hand soap product, which has been recalled and reported through the EU RAPEX system due to its severe bacterial contamination. Ten isolates recovered from two bottles of the product were identified as Klebsiella oxytoca and subtyped using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI TOF MS), near-infrared Fourier transform (NIR FT) Raman spectroscopy and Fourier transform infrared (FTIR) spectroscopy. Comparison of the classification results obtained by these phenotype-based techniques with outcomes of the DNA-based methods pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis of whole-genome sequencing (WGS) data revealed a high level of concordance. In conclusion, a set of analytical techniques might be useful for rapid, reliable and cost-effective microbial typing to ensure safe consumer products and allow source tracking.
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Affiliation(s)
- Ralf Dieckmann
- Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
| | - Jens Andre Hammerl
- Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
| | - Hartmut Hahmann
- Landesamt für Verbraucherschutz Sachsen-Anhalt, Fachbereich Lebensmittelsicherheit, Freiimfelder Str. 68, D-06112 Halle, Germany
| | - Amal Wicke
- Landesamt für Verbraucherschutz Sachsen-Anhalt, Fachbereich Lebensmittelsicherheit, Freiimfelder Str. 68, D-06112 Halle, Germany
| | - Sylvia Kleta
- Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
| | | | - Andreas Nitsche
- Robert Koch-Institut, ZBS 1 - Highly Pathogenic Viruses, Seestraße 10, D-13353 Berlin, Germany
| | - Maren Stämmler
- Robert Koch-Institut, ZBS 6 - Proteomics and Spectroscopy, Seestraße 10, D-13353 Berlin, Germany
| | - Sascha Al Dahouk
- Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
| | - Peter Lasch
- Robert Koch-Institut, ZBS 6 - Proteomics and Spectroscopy, Seestraße 10, D-13353 Berlin, Germany
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Tracz DM, Tober AD, Antonation KS, Corbett CR. MALDI-TOF mass spectrometry and high-consequence bacteria: safety and stability of biothreat bacterial sample testing in clinical diagnostic laboratories. J Med Microbiol 2018; 67:341-346. [PMID: 29458687 DOI: 10.1099/jmm.0.000695] [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: 01/05/2023] Open
Abstract
We considered the application of MALDI-TOF mass spectrometry for BSL-3 bacterial diagnostics, with a focus on the biosafety of live-culture direct-colony testing and the stability of stored extracts. Biosafety level 2 (BSL-2) bacterial species were used as surrogates for BSL-3 high-consequence pathogens in all live-culture MALDI-TOF experiments. Viable BSL-2 bacteria were isolated from MALDI-TOF mass spectrometry target plates after 'direct-colony' and 'on-plate' extraction testing, suggesting that the matrix chemicals alone cannot be considered sufficient to inactivate bacterial culture and spores in all samples. Sampling of the instrument interior after direct-colony analysis did not recover viable organisms, suggesting that any potential risks to the laboratory technician are associated with preparation of the MALDI-TOF target plate before or after testing. Secondly, a long-term stability study (3 years) of stored MALDI-TOF extracts showed that match scores can decrease below the threshold for reliable species identification (<1.7), which has implications for proficiency test panel item storage and distribution.
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Affiliation(s)
- Dobryan M Tracz
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Ashley D Tober
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Kym S Antonation
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Cindi R Corbett
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
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Rudrik JT, Soehnlen MK, Perry MJ, Sullivan MM, Reiter-Kintz W, Lee PA, Pettit D, Tran A, Swaney E. Safety and Accuracy of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Highly Pathogenic Organisms. J Clin Microbiol 2017; 55:3513-3529. [PMID: 29021156 PMCID: PMC5703816 DOI: 10.1128/jcm.01023-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/01/2017] [Indexed: 11/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) sample preparation methods, including the direct, on-plate formic acid, and ethanol/formic acid tube extraction methods, were evaluated for their ability to render highly pathogenic organisms nonviable and safe for handling in a biosafety level 2 laboratory. Of these, the tube extraction procedure was the most successful, with none of the tested strains surviving this sample preparation method. Tube extracts from several agents of bioterrorism and their near neighbors were analyzed in an eight-laboratory study to examine the utility of the Bruker Biotyper and Vitek MS MALDI-TOF MS systems and their in vitro diagnostic (IVD), research-use-only, and Security-Relevant databases, as applicable, to accurately identify these agents. Forty-six distinct strains of Bacillus anthracis, Yersinia pestis, Francisella tularensis, Burkholderia mallei, Burkholderia pseudomallei, Clostridium botulinum, Brucella melitensis, Brucella abortus, Brucella suis, and Brucella canis were extracted and distributed to participating laboratories for analysis. A total of 35 near-neighbor isolates were also analyzed.
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Affiliation(s)
- James T Rudrik
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, Michigan, USA
| | - Marty K Soehnlen
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, Michigan, USA
| | - Michael J Perry
- Biodefense Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Maureen M Sullivan
- Public Health Laboratory, Minnesota Department of Health, St. Paul, Minnesota, USA
| | - Wanda Reiter-Kintz
- State Hygienic Laboratory at the University of Iowa, Coralville, Iowa, USA
| | - Philip A Lee
- Bureau of Public Health Laboratories, Florida Department of Health, Jacksonville, Florida, USA
| | - Denise Pettit
- North Carolina State Laboratory of Public Health, North Carolina Department of Health and Human Services, Raleigh, North Carolina, USA
| | - Anthony Tran
- Bureau of the Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York City, New York, USA
| | - Erin Swaney
- Texas Department of State Health Services Laboratory, Austin, Texas, USA
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25
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Shu LJ, Yang YL. Bacillus Classification Based on Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry-Effects of Culture Conditions. Sci Rep 2017; 7:15546. [PMID: 29138467 PMCID: PMC5686160 DOI: 10.1038/s41598-017-15808-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 11/02/2017] [Indexed: 12/15/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a reliable and rapid technique applied widely in the identification and classification of microbes. MALDI-TOF MS has been used to identify many endospore-forming Bacillus species; however, endospores affect the identification accuracy when using MALDI-TOF MS because they change the protein composition of samples. Since culture conditions directly influence endospore formation and Bacillus growth, in this study we clarified how culture conditions influence the classification of Bacillus species by using MALDI-TOF MS. We analyzed members of the Bacillus subtilis group and Bacillus cereus group using different incubation periods, temperatures and media. Incubation period was found to affect mass spectra due to endospores which were observed mixing with vegetative cells after 24 hours. Culture temperature also resulted in different mass spectra profiles depending on the temperature best suited growth and sporulation. Conversely, the four common media for Bacillus incubation, Luria-Bertani agar, nutrient agar, plate count agar and brain-heart infusion agar did not result in any significant differences in mass spectra profiles. Profiles in the range m/z 1000-3000 were found to provide additional data to the standard ribosomal peptide/protein region m/z 3000-15000 profiles to enable easier differentiation of some highly similar species and the identification of new strains under fresh culture conditions. In summary, control of culture conditions is vital for Bacillus identification and classification by MALDI-TOF MS.
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Affiliation(s)
- Lin-Jie Shu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan.
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26
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Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Use with Positive Blood Cultures: Methodology, Performance, and Optimization. J Clin Microbiol 2017; 55:3328-3338. [PMID: 28855303 DOI: 10.1128/jcm.00868-17] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Early initiation of effective antibiotics for septic patients is essential for patient survival. Matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has revolutionized clinical microbiology for isolate identification and has the possibility to impact how blood culture testing is performed. This review discusses the various uses of MALDI-TOF MS for the identification and susceptibility testing of positive blood cultures, the performance of these methods, and the outcomes involved with its implementation.
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27
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Wine yeasts identification by MALDI-TOF MS: Optimization of the preanalytical steps and development of an extensible open-source platform for processing and analysis of an in-house MS database. Int J Food Microbiol 2017; 254:1-10. [DOI: 10.1016/j.ijfoodmicro.2017.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/07/2017] [Accepted: 05/05/2017] [Indexed: 11/19/2022]
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28
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Turvey ME, Weiland F, Keller EJ, Hoffmann P. The changing face of microbial quality control practices in the brewing industry: Introducing mass spectrometry proteomic fingerprinting for microbial identification. JOURNAL OF THE INSTITUTE OF BREWING 2017. [DOI: 10.1002/jib.428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- M. E. Turvey
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
- Singapore-MIT Alliance for Research and Technology Centre; Singapore
| | - F. Weiland
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
| | - E. J. Keller
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
| | - P. Hoffmann
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
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29
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High stringency evaluation of the inactivation / exclusion efficacy of a MALDI-TOF MS chemical extraction method, with filtration of extract through 0.1 µm filters, on Bacillus anthracis Vollum vegetative cells and spores. PLoS One 2017; 12:e0177294. [PMID: 28481931 PMCID: PMC5421796 DOI: 10.1371/journal.pone.0177294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/25/2017] [Indexed: 11/19/2022] Open
Abstract
A previous report indicated that a formic acid chemical extraction method for the preparation of protein extracts for matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) identification, with filtration of extracts through 0.2 μm regenerated cellulose (RC) filters, would not reliably inactivate or exclude Bacillus anthracis Vollum cells or spores when tested under high stringency conditions. B. anthracis was recovered from 13/36 extracts (3/18 from vegetative cell extracts and 10/18 from bacterial spore extracts). In this paper we report the repetition of this study but with the substitution of the 0.2 μm, regenerated cellulose, filters with 0.1 μm polyvinylidene fluoride (PVDF) filters. Experiments were conducted under the same high stringency post-treatment viability test methods (100% of resulting protein content; 7 days Luria (L)-broth and a further 7 days L-agar plate incubation; or 7 days L-agar plate only incubation). B. anthracis was not recovered from any of 18 replicates generated from high concentrations of vegetative cells (107 to 108 cfu), but a single B. anthracis colony was recovered from one of 18 replicates generated from high concentrations of bacterial spores (108 cfu), using a post-treatment viability culture method of 7 days on L-agar plate only. We discuss our results in the context of other similar studies and also a requirement to develop standardised post-treatment viability test methods.
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Chenau J, Fenaille F, Simon S, Filali S, Volland H, Junot C, Carniel E, Becher F. Detection of Yersinia pestis in Complex Matrices by Intact Cell Immunocapture and Targeted Mass Spectrometry. Methods Mol Biol 2017; 1600:69-83. [PMID: 28478558 DOI: 10.1007/978-1-4939-6958-6_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We describe an immunoaffinity-liquid chromatography-tandem mass spectrometry (immuno-LC-MS/MS) protocol for the direct (i.e., without prior culture), sensitive and specific detection of Yersinia pestis in complex matrices. Immunoaffinity enables isolation and concentration of intact bacterial cells from food and environmental samples. After protein extraction and digestion, suitable proteotypic peptides corresponding to three Y. pestis-specific protein markers (murine toxine, plasminogen activator and pesticin) are monitored by targeted LC-MS/MS using the selected reaction monitoring (SRM) mode. This immuno-LC-MS/MS assay has a limit of detection of 2 × 104 CFU/mL in milk or tap water, and 4.5 × 105 CFU in 10 mg of soil.
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Affiliation(s)
- Jérôme Chenau
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, Bât. 136, 91191, Gif-sur-Yvette, France
| | - François Fenaille
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, Bât. 136, 91191, Gif-sur-Yvette, France
| | - Stéphanie Simon
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, Bât. 136, 91191, Gif-sur-Yvette, France
| | - Sofia Filali
- Institut Pasteur, Unité de Recherche Yersinia, Paris, France
| | - Hervé Volland
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, Bât. 136, 91191, Gif-sur-Yvette, France
| | - Christophe Junot
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, Bât. 136, 91191, Gif-sur-Yvette, France
| | | | - François Becher
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, Bât. 136, 91191, Gif-sur-Yvette, France.
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31
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Lasch P, Grunow R, Antonation K, Weller SA, Jacob D. Inactivation techniques for MALDI-TOF MS analysis of highly pathogenic bacteria – A critical review. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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32
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Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) for the identification of highly pathogenic bacteria. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.04.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Karger A. Current developments to use linear MALDI-TOF spectra for the identification and typing of bacteria and the characterization of other cells/organisms related to infectious diseases. Proteomics Clin Appl 2016; 10:982-993. [PMID: 27400768 DOI: 10.1002/prca.201600038] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/30/2016] [Accepted: 07/07/2016] [Indexed: 12/21/2022]
Abstract
Within the past few years identification of bacteria by MALDI-TOF MS has become a standard technique in bacteriological laboratories for good reasons. MALDI-TOF MS identification is rapid, robust, automatable, and the per-sample costs are low. Yet, the spectra are very informative and the reliable identification of bacterial species is usually possible. Recently, new MS-based approaches for the identification of bacteria are emerging that are based on the detailed analysis of the bacterial proteome by high-resolution MS. These "proteotyping" approaches are highly discriminative and outperform MALDI-TOF MS-based identification in terms of specificity, but require a laborious proteomic workflow and far more expertise and sophisticated instrumentation than identification on basis of MALDI-TOF MS spectra, which can be obtained with relative simple and uncostly linear MALDI-TOF mass spectrometers. Thus MALDI-TOF MS identification of bacteria remains an attractive option for routine diagnostics. Additionally, MALDI-TOF MS identification protocols have been extended and improved in many respects making linear MALDI-TOF MS a versatile tool that can be useful beyond the identification of a bacterial species, e.g. for the characterization of leucocytes and arthropod vectors of infectious diseases. This review focuses on such improvements and extensions of the typical MALDI-TOF MS workflow in the field of infectious diseases.
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Affiliation(s)
- Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, , Federal Research Institute for Animal Health Südufer, Greifswald-Insel Riems, Germany.
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Schneider EL, Henise J, Reid R, Ashley GW, Santi DV. Hydrogel Drug Delivery System Using Self-Cleaving Covalent Linkers for Once-a-Week Administration of Exenatide. Bioconjug Chem 2016; 27:1210-5. [DOI: 10.1021/acs.bioconjchem.5b00690] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eric L. Schneider
- ProLynx, 455 Mission Bay Boulevard South, Suite 145, San Francisco, California 94158, United States
| | - Jeff Henise
- ProLynx, 455 Mission Bay Boulevard South, Suite 145, San Francisco, California 94158, United States
| | - Ralph Reid
- ProLynx, 455 Mission Bay Boulevard South, Suite 145, San Francisco, California 94158, United States
| | - Gary W. Ashley
- ProLynx, 455 Mission Bay Boulevard South, Suite 145, San Francisco, California 94158, United States
| | - Daniel V. Santi
- ProLynx, 455 Mission Bay Boulevard South, Suite 145, San Francisco, California 94158, United States
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Weller SA, Stokes MGM, Lukaszewski RA. Observations on the Inactivation Efficacy of a MALDI-TOF MS Chemical Extraction Method on Bacillus anthracis Vegetative Cells and Spores. PLoS One 2015; 10:e0143870. [PMID: 26633884 PMCID: PMC4669126 DOI: 10.1371/journal.pone.0143870] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/10/2015] [Indexed: 11/19/2022] Open
Abstract
A chemical (ethanol; formic acid; acetonitrile) protein extraction method for the preparation of bacterial samples for matrix assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) identification was evaluated for its ability to inactivate bacterial species. Initial viability tests (with and without double filtration of the extract through 0.2 μM filters), indicated that the method could inactivate Escherichia coli MRE 162 and Klebsiella pneumoniae ATCC 35657, with or without filtration, but that filtration was required to exclude viable, avirulent, Bacillus anthracis UM23CL2 from extracts. Multiple, high stringency, viability experiments were then carried out on entire filtered extracts prepared from virulent B. anthracis Vollum vegetative cells and spores ranging in concentration from 106-108cfu per extract. B. anthracis was recovered in 3/18 vegetative cell extracts and 10/18 spore extracts. From vegetative cell extracts B. anthracis was only recovered from extracts that had undergone prolonged Luria (L)-broth (7 day) and L-agar plate (a further 7 days) incubations. We hypothesise that the recovery of B. anthracis in vegetative cell extracts is due to the escape of individual sub-lethally injured cells. We discuss our results in view of working practises in clinical laboratories and in the context of recent inadvertent releases of viable B. anthracis.
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Affiliation(s)
- Simon A. Weller
- CBR Division, Defence Science and Technology Laboratory, Ministry of Defence, Porton Down, Salisbury, United Kingdom
- * E-mail:
| | - Margaret G. M. Stokes
- CBR Division, Defence Science and Technology Laboratory, Ministry of Defence, Porton Down, Salisbury, United Kingdom
| | - Roman A. Lukaszewski
- CBR Division, Defence Science and Technology Laboratory, Ministry of Defence, Porton Down, Salisbury, United Kingdom
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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: 795] [Impact Index Per Article: 88.3] [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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Evaluation of MALDI-ToF as a method for the identification of bacteria in the veterinary diagnostic laboratory. Res Vet Sci 2015; 101:42-9. [DOI: 10.1016/j.rvsc.2015.05.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/30/2015] [Accepted: 05/30/2015] [Indexed: 11/23/2022]
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Seifert S, Weidner SM, Panne U, Kneipp J. Taxonomic relationships of pollens from matrix-assisted laser desorption/ionization time-of-flight mass spectrometry data using multivariate statistics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1145-54. [PMID: 25981545 DOI: 10.1002/rcm.7207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/01/2015] [Accepted: 04/01/2015] [Indexed: 05/09/2023]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been suggested as a promising tool for the investigation of pollen, but the usefulness of this approach for classification and identification of pollen species has to be proven by an application to samples of varying taxonomic relations. METHOD MALDI-MS in combination with hierarchical cluster analysis (HCA) and principal component analysis (PCA) was used to delineate taxonomic relations between plants based on pollen biochemistry. To assess the robustness of the approach, pollen of 74 species of the plant orders Fagales and Coniferales were probed. RESULTS Discrimination at the levels of plant order and genus were achieved using the whole spectral range. In many cases, different species of the same genus could be distinguished. The sources of the spectral/chemical differences at the genus level can be understood using PCA. Specifically, typical mass regions for exact genus detection were identified. CONCLUSIONS Our results indicate that the chemical information represented by MALDI-TOFMS data is useful for reconstructing taxonomic relationships and is complementary to other chemical information on pollen from other spectroscopic data.
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Affiliation(s)
- Stephan Seifert
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Straße 2, 12489, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Steffen M Weidner
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Ulrich Panne
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Straße 2, 12489, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Janina Kneipp
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Straße 2, 12489, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
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39
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Identification of Highly Pathogenic Microorganisms by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry: Results of an Interlaboratory Ring Trial. J Clin Microbiol 2015; 53:2632-40. [PMID: 26063856 DOI: 10.1128/jcm.00813-15] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/01/2015] [Indexed: 02/02/2023] Open
Abstract
In the case of a release of highly pathogenic bacteria (HPB), there is an urgent need for rapid, accurate, and reliable diagnostics. MALDI-TOF mass spectrometry is a rapid, accurate, and relatively inexpensive technique that is becoming increasingly important in microbiological diagnostics to complement classical microbiology, PCR, and genotyping of HPB. In the present study, the results of a joint exercise with 11 partner institutions from nine European countries are presented. In this exercise, 10 distinct microbial samples, among them five HPB, Bacillus anthracis, Brucella canis, Burkholderia mallei, Burkholderia pseudomallei, and Yersinia pestis, were characterized under blinded conditions. Microbial strains were inactivated by high-dose gamma irradiation before shipment. Preparatory investigations ensured that this type of inactivation induced only subtle spectral changes with negligible influence on the quality of the diagnosis. Furthermore, pilot tests on nonpathogenic strains were systematically conducted to ensure the suitability of sample preparation and to optimize and standardize the workflow for microbial identification. The analysis of the microbial mass spectra was carried out by the individual laboratories on the basis of spectral libraries available on site. All mass spectra were also tested against an in-house HPB library at the Robert Koch Institute (RKI). The averaged identification accuracy was 77% in the first case and improved to >93% when the spectral diagnoses were obtained on the basis of the RKI library. The compilation of complete and comprehensive databases with spectra from a broad strain collection is therefore considered of paramount importance for accurate microbial identification.
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40
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Kryazhevskikh NA, Loiko NG, Demkina EV, Mulyukin AL, Lebedev AT, Gaponov AM, Tutel’yan AV, Nikolaev YA, El’-Registan GI. Applicability of MALDI mass spectrometry for diagnostics of phase variants in bacterial populations. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715030121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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41
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Lin A, Merkley ED, Clowers BH, Hutchison JR, Kreuzer HW. Effects of bacterial inactivation methods on downstream proteomic analysis. J Microbiol Methods 2015; 112:3-10. [PMID: 25620019 DOI: 10.1016/j.mimet.2015.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/19/2015] [Accepted: 01/19/2015] [Indexed: 11/18/2022]
Abstract
Inactivation of pathogenic microbial samples is often necessary for the protection of researchers and to comply with local and federal regulations. By its nature, biological inactivation causes changes to microbial samples, potentially affecting observed experimental results. While inactivation-induced damage to materials such as DNA has been evaluated, the effect of various inactivation strategies on proteomic data, to our knowledge, has not been discussed. To this end, we inactivated samples of Yersinia pestis and Escherichia coli by autoclave, ethanol, or irradiation treatment to determine how inactivation changes liquid chromatography-tandem mass spectrometry data quality as well as apparent protein content of cells. Proteomic datasets obtained from aliquots of samples inactivated by different methods were highly similar, with Pearson correlation coefficients ranging from 0.822 to 0.985 and 0.816 to 0.985 for E. coli and Y. pestis, respectively, suggesting that inactivation had only slight impacts on the set of proteins identified. In addition, spectral quality metrics such as distributions of various database search algorithm scores remained constant across inactivation methods, indicating that inactivation does not appreciably degrade spectral quality. Though overall changes resulting from inactivation were small, there were detectable trends. For example, one-sided Fischer exact tests determined that periplasmic proteins decrease in observed abundance after sample inactivation by autoclaving (α=1.71×10(-2) for E. coli, α=4.97×10(-4) for Y. pestis) and irradiation (α=9.43×10(-7) for E. coli, α=1.21×10(-5) for Y. pestis) when compared to controls that were not inactivated. Based on our data, if sample inactivation is necessary, we recommend inactivation with ethanol treatment with secondary preference given to irradiation.
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Affiliation(s)
- Andy Lin
- Signatures Sciences & Technology Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Eric D Merkley
- Signatures Sciences & Technology Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Brian H Clowers
- Signatures Sciences & Technology Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States; Department of Chemistry, Washington State University, Pullman, WA 99164, United States
| | - Janine R Hutchison
- Signatures Sciences & Technology Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Helen W Kreuzer
- Signatures Sciences & Technology Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States.
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42
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Zhang L, Vranckx K, Janssens K, Sandrin TR. Use of MALDI-TOF mass spectrometry and a custom database to characterize bacteria indigenous to a unique cave environment (Kartchner Caverns, AZ, USA). J Vis Exp 2015:e52064. [PMID: 25590854 DOI: 10.3791/52064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
MALDI-TOF mass spectrometry has been shown to be a rapid and reliable tool for identification of bacteria at the genus and species, and in some cases, strain levels. Commercially available and open source software tools have been developed to facilitate identification; however, no universal/standardized data analysis pipeline has been described in the literature. Here, we provide a comprehensive and detailed demonstration of bacterial identification procedures using a MALDI-TOF mass spectrometer. Mass spectra were collected from 15 diverse bacteria isolated from Kartchner Caverns, AZ, USA, and identified by 16S rDNA sequencing. Databases were constructed in BioNumerics 7.1. Follow-up analyses of mass spectra were performed, including cluster analyses, peak matching, and statistical analyses. Identification was performed using blind-coded samples randomly selected from these 15 bacteria. Two identification methods are presented: similarity coefficient-based and biomarker-based methods. Results show that both identification methods can identify the bacteria to the species level.
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Affiliation(s)
- Lin Zhang
- School of Mathematical and Natural Sciences, Arizona State University
| | | | | | - Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University;
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43
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Branquinho R, Sousa C, Osório H, Meirinhos-Soares L, Lopes J, Carriço JA, Busse HJ, Abdulmawjood A, Klein G, Kämpfer P, Pintado ME, Peixe LV. Bacillus invictae sp. nov., isolated from a health product. Int J Syst Evol Microbiol 2014; 64:3867-3876. [DOI: 10.1099/ijs.0.067850-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, rod-shaped, endospore-forming
Bacillus
isolate, Bi.FFUP1
T, recovered in Portugal from a health product was subjected to a polyphasic study and compared with the type strains of
Bacillus pumilus
,
Bacillus safensis
,
Bacillus altitudinis
and
Bacillus xiamenensis
, the phenotypically and genotypically most closely related species. Acid production from cellobiose, d-glucose and d-mannose and absence of acid production from d-arabinose, erythritol, inositol, maltose, mannitol, raffinose, rhamnose, sorbitol, starch and l-tryptophan discriminated this new isolate from the type strains of the most closely related species. Additionally, a significant different protein and carbohydrate signature was evidenced by spectroscopic techniques, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and Fourier transform IR spectroscopy with attenuated total reflectance. Using a chemometric approach, the score plot generated by principal component analysis clearly delineated the isolate as a separate cluster. The quinone system for strain Bi.FFUP1
T comprised predominantly menaquinone MK-7 and major polar lipids were diphosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. Strain Bi.FFUP1
T showed ≥99 % 16S rRNA gene sequence similarity to
B. safensis
FO-036bT,
B. pumilus
(7061T and SAFR-032),
B. altitudinis
41KF2bT and
B. xiamenensis
HYC-10T. Differences in strain Bi.FFUP1
T
gyrB and rpoB sequences in comparison with the most closely related species and DNA–DNA hybridization experiments with Bi.FFUP1
T and
B. pumilus
ATCC 7061T,
B. safensis
FO-036bT,
B. altitudinis
41KF2bT and
B. xiamenensis
HYC-10T gave relatedness values of 39.6 % (reciprocal 38.0 %), 49.9 % (reciprocal 42.9 %), 61.9 % (reciprocal 52.2 %) and 61.7 % (reciprocal 49.2 %), respectively, supported the delineation of strain Bi.FFUP1
T as a representative of a novel species of the genus
Bacillus
, for which the name
Bacillus
invictae sp. nov. is proposed, with strain Bi.FFUP1
T ( = DSM 26896T = CCUG 64113T) as the type strain.
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Affiliation(s)
- Raquel Branquinho
- REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Clara Sousa
- REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Hugo Osório
- Faculdade de Medicina, Universidade do Porto, Porto, Portugal
- IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | | | - João Lopes
- Departamento de Farmácia Galénica e Tecnologia Farmacutica, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- REQUIMTE, Laboratório de Química Aplicada, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - João A. Carriço
- Faculdade de Medicina de Lisboa, Instituto de Microbiologia, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Hans-Jürgen Busse
- Microbiology and Genetics Institute, University of Wien, Vienna, Austria
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Günter Klein
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Manuela E. Pintado
- CBQF, Centro de Biotecnologia e Química Fina, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Luísa V. Peixe
- REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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44
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Branquinho R, Sousa C, Lopes J, Pintado ME, Peixe LV, Osório H. Differentiation of Bacillus pumilus and Bacillus safensis using MALDI-TOF-MS. PLoS One 2014; 9:e110127. [PMID: 25314655 PMCID: PMC4196992 DOI: 10.1371/journal.pone.0110127] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 09/17/2014] [Indexed: 11/29/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) despite being increasingly used as a method for microbial identification, still present limitations in which concerns the differentiation of closely related species. Bacillus pumillus and Bacillus safensis, are species of biotechnological and pharmaceutical significance, difficult to differentiate by conventional methodologies. In this study, using a well-characterized collection of B. pumillus and B. safensis isolates, we demonstrated the suitability of MALDI-TOF-MS combined with chemometrics to accurately and rapidly identify them. Moreover, characteristic species-specific ion masses were tentatively assigned, using UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases and primary literature. Delineation of B. pumilus (ions at m/z 5271 and 6122) and B. safensis (ions at m/z 5288, 5568 and 6413) species were supported by a congruent characteristic protein pattern. Moreover, using a chemometric approach, the score plot created by partial least square discriminant analysis (PLSDA) of mass spectra demonstrated the presence of two individualized clusters, each one enclosing isolates belonging to a species-specific spectral group. The generated pool of species-specific proteins comprised mostly ribosomal and SASPs proteins. Therefore, in B. pumilus the specific ion at m/z 5271 was associated with a small acid-soluble spore protein (SASP O) or with 50S protein L35, whereas in B. safensis specific ions at m/z 5288 and 5568 were associated with SASP J and P, respectively, and an ion at m/z 6413 with 50S protein L32. Thus, the resulting unique protein profile combined with chemometric analysis, proved to be valuable tools for B. pumilus and B. safensis discrimination, allowing their reliable, reproducible and rapid identification.
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Affiliation(s)
- Raquel Branquinho
- REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Clara Sousa
- REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- CEB, Centro de Engenharia Biológica, Universidade do Minho, Braga, Portugal
| | - João Lopes
- REQUIMTE, Laboratório de Química Aplicada, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- CBQF, Centro de Biotecnologia e Química Fina, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Manuela E. Pintado
- Departmento de Tecnologia Farmacêutica, Faculdade Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Luísa V. Peixe
- REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Hugo Osório
- IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
- Faculdade de Medicina, Universidade do Porto, Porto, Portugal
- * E-mail:
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45
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Emerging mass spectrometry techniques for the direct analysis of microbial colonies. Curr Opin Microbiol 2014; 19:120-129. [PMID: 25064218 DOI: 10.1016/j.mib.2014.06.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 06/30/2014] [Accepted: 06/30/2014] [Indexed: 12/22/2022]
Abstract
One of the emerging areas in microbiology is detecting specialized metabolites produced by microbial colonies and communities with mass spectrometry. In this review/perspective, we illustrate the emerging mass spectrometry methodologies that enable the interrogation of specialized metabolites directly from microbial colonies. Mass spectrometry techniques such as imaging mass spectrometry and real-time mass spectrometry allow two and three-dimensional visualization of the distribution of metabolites, often with minimal sample pretreatment. The speed in which molecules are captured using these methods requires the development of new molecular visualization tools such as molecular networking. Together, these tools are beginning to provide unprecedented insight into the chemical world that microbes experience.
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46
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AlMasoud N, Xu Y, Nicolaou N, Goodacre R. Optimization of matrix assisted desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) for the characterization of Bacillus and Brevibacillus species. Anal Chim Acta 2014; 840:49-57. [PMID: 25086893 PMCID: PMC4223412 DOI: 10.1016/j.aca.2014.06.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 06/16/2014] [Accepted: 06/19/2014] [Indexed: 11/23/2022]
Abstract
Optimization of MALDI-TOF-MS for characterizing Bacillus and Brevibacillus species. Development of a suitable chemometric workflow for processing raw MALDI-TOF-MS data. Classification of 7 species from bacteria achieved high accuracy (∼90%). Allowed to dry at room temperature (ca. 22 °C) for 1 h.
Over the past few decades there has been an increased interest in using various analytical techniques for detecting and identifying microorganisms. More recently there has been an explosion in the application of matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) for bacterial characterization, and here we optimize this approach in order to generate reproducible MS data from bacteria belonging to the genera Bacillus and Brevibacillus. Unfortunately MALDI-TOF-MS generates large amounts of data and is prone to instrumental drift. To overcome these challenges we have developed a preprocessing pipeline that includes baseline correction, peak alignment followed by peak picking that in combination significantly reduces the dimensionality of the MS spectra and corrects for instrument drift. Following this two different prediction models were used which are based on support vector machines and these generated satisfactory prediction accuracies of approximately 90%.
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Affiliation(s)
- Najla AlMasoud
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yun Xu
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nicoletta Nicolaou
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Royston Goodacre
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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47
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Chenau J, Fenaille F, Simon S, Filali S, Volland H, Junot C, Carniel E, Becher F. Detection of Yersinia pestis in environmental and food samples by intact cell immunocapture and liquid chromatography-tandem mass spectrometry. Anal Chem 2014; 86:6144-52. [PMID: 24847944 DOI: 10.1021/ac501371r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Yersinia pestis is the causative agent of bubonic and pneumonic plague, an acute and often fatal disease in humans. In addition to the risk of natural exposure to plague, there is also the threat of a bioterrorist act, leading to the deliberate spread of the bacteria in the environment or food. We report here an immuno-liquid chromatography-tandem mass spectrometry (immuno-LC-MS/MS) method for the direct (i.e., without prior culture), sensitive, and specific detection of Y. pestis in such complex samples. In the first step, a bottom-up proteomics approach highlighted three relevant protein markers encoded by the Y. pestis-specific plasmids pFra (murine toxin) and pPla (plasminogen activator and pesticin). Suitable proteotypic peptides were thoroughly selected to monitor the three protein markers by targeted MS using the selected reaction monitoring (SRM) mode. Immunocapture conditions were optimized for the isolation and concentration of intact bacterial cells from complex samples. The immuno-LC-SRM assay has a limit of detection of 2 × 10(4) CFU/mL in milk or tap water, which compares well with those of state-of-the-art immunoassays. Moreover, we report the first direct detection of Y. pestis in soil, which could be extremely useful in confirming Y. pestis persistence in the ground.
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Affiliation(s)
- Jérôme Chenau
- Service de Pharmacologie et d'Immunoanalyse, Institut de Biologie et de Technologies de Saclay (iBiTec-S), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA) , 91191 Gif-sur-Yvette, France
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48
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Insufficient discriminatory power of MALDI-TOF mass spectrometry for typing of Enterococcus faecium and Staphylococcus aureus isolates. J Microbiol Methods 2014; 100:58-69. [DOI: 10.1016/j.mimet.2014.02.015] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/24/2014] [Accepted: 02/24/2014] [Indexed: 12/15/2022]
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49
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Hartmann EM, Durighello E, Pible O, Nogales B, Beltrametti F, Bosch R, Christie-Oleza JA, Armengaud J. Proteomics meets blue biotechnology: a wealth of novelties and opportunities. Mar Genomics 2014; 17:35-42. [PMID: 24780860 DOI: 10.1016/j.margen.2014.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/11/2014] [Accepted: 04/12/2014] [Indexed: 10/25/2022]
Abstract
Blue biotechnology, in which aquatic environments provide the inspiration for various products such as food additives, aquaculture, biosensors, green chemistry, bioenergy, and pharmaceuticals, holds enormous promise. Large-scale efforts to sequence aquatic genomes and metagenomes, as well as campaigns to isolate new organisms and culture-based screenings, are helping to push the boundaries of known organisms. Mass spectrometry-based proteomics can complement 16S gene sequencing in the effort to discover new organisms of potential relevance to blue biotechnology by facilitating the rapid screening of microbial isolates and by providing in depth profiles of the proteomes and metaproteomes of marine organisms, both model cultivable isolates and, more recently, exotic non-cultivable species and communities. Proteomics has already contributed to blue biotechnology by identifying aquatic proteins with potential applications to food fermentation, the textile industry, and biomedical drug development. In this review, we discuss historical developments in blue biotechnology, the current limitations to the known marine biosphere, and the ways in which mass spectrometry can expand that knowledge. We further speculate about directions that research in blue biotechnology will take given current and near-future technological advancements in mass spectrometry.
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Affiliation(s)
- Erica M Hartmann
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Emie Durighello
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Olivier Pible
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Balbina Nogales
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | | | - Rafael Bosch
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV47AL, United Kingdom
| | - Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
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50
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Intact cell/intact spore mass spectrometry (IC/ISMS) on polymer-based, nano-coated disposable targets. Mol Cell Probes 2014; 28:99-105. [DOI: 10.1016/j.mcp.2013.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/29/2013] [Accepted: 11/02/2013] [Indexed: 11/21/2022]
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