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Manfredi E, Rocca MF, Zintgraff J, Irazu L, Miliwebsky E, Carbonari C, Deza N, Prieto M, Chinen I. Rapid and accurate detection of Shiga toxin-producing Escherichia coli (STEC) serotype O157 : H7 by mass spectrometry directly from the isolate, using 10 potential biomarker peaks and machine learning predictive models. J Med Microbiol 2023; 72. [PMID: 37130048 DOI: 10.1099/jmm.0.001675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Introduction. The different pathotypes of Escherichia coli can produce a large number of human diseases. Surveillance is complex since their differentiation is not easy. In particular, the detection of Shiga toxin-producing Escherichia coli (STEC) serotype O157 : H7 consists of stool culture of a diarrhoeal sample on enriched and/or selective media and identification of presumptive colonies and confirmation, which require a certain level of training and are time-consuming and expensive.Hypothesis. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a quick and easy way to obtain the protein spectrum of a microorganism, identify the genus and species, and detect potential biomarker peaks of certain characteristics.Aim. To verify the usefulness of MALDI-TOF MS to rapidly identify and differentiate STEC O157 : H7 from other E. coli pathotypes.Methodology. The direct method was employed, and the information obtained using Microflex LT platform-based analysis from 60 clinical isolates (training set) was used to detect differences between the peptide fingerprints of STEC O157 : H7 and other E. coli strains. The protein profiles detected laid the foundations for the development and evaluation of machine learning predictive models in this study.Results. The detection of potential biomarkers in combination with machine learning predictive models in a new set of 142 samples, called 'test set', achieved 99.3 % (141/142) correct classification, allowing us to distinguish between the isolates of STEC O157 : H7 and the other E. coli group. Great similarity was also observed with respect to this last group and the Shigella species when applying the potential biomarkers algorithm, allowing differentiation from STEC O157 : H7Conclusion. Given that STEC O157 : H7 is the main causal agent of haemolytic uremic syndrome, and based on the performance values obtained in the present study (sensitivity=98.5 % and specificity=100.0 %), the implementation of this technique provides a proof of principle for MALDI-TOF MS and machine learning to identify biomarkers to rapidly screen or confirm STEC O157 : H7 versus other diarrhoeagenic E. coli in the future.
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Affiliation(s)
- Eduardo Manfredi
- Servicio Fisiopatogenia, Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - María Florencia Rocca
- Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
- Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (RNEM Argentina), Buenos Aires, Argentina
| | - Jonathan Zintgraff
- Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
- Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (RNEM Argentina), Buenos Aires, Argentina
| | - Lucía Irazu
- Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - Elizabeth Miliwebsky
- Servicio Fisiopatogenia, Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - Carolina Carbonari
- Servicio Fisiopatogenia, Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - Natalia Deza
- Servicio Fisiopatogenia, Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - Monica Prieto
- Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
- Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (RNEM Argentina), Buenos Aires, Argentina
| | - Isabel Chinen
- Servicio Fisiopatogenia, Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
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Cuénod A, Aerni M, Bagutti C, Bayraktar B, Boz ES, Carneiro CB, Casanova C, Coste AT, Damborg P, van Dam DW, Demirci M, Drevinek P, Dubuis O, Fernandez J, Greub G, Hrabak J, Hürkal Yiğitler G, Hurych J, Jensen TG, Jost G, Kampinga GA, Kittl S, Lammens C, Lang C, Lienhard R, Logan J, Maffioli C, Mareković I, Marschal M, Moran-Gilad J, Nolte O, Oberle M, Pedersen M, Pflüger V, Pranghofer S, Reichl J, Rentenaar RJ, Riat A, Rodríguez-Sánchez B, Schilt C, Schlotterbeck AK, Schrenzel J, Troib S, Willems E, Wootton M, Ziegler D, Egli A. Quality of MALDI-TOF mass spectra in routine diagnostics: results from an international external quality assessment including 36 laboratories from 12 countries using 47 challenging bacterial strains. Clin Microbiol Infect 2023; 29:190-199. [PMID: 35623578 DOI: 10.1016/j.cmi.2022.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 05/11/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a widely used method for bacterial species identification. Incomplete databases and mass spectral quality (MSQ) still represent major challenges. Important proxies for MSQ are the number of detected marker masses, reproducibility, and measurement precision. We aimed to assess MSQs across diagnostic laboratories and the potential of simple workflow adaptations to improve it. METHODS For baseline MSQ assessment, 47 diverse bacterial strains, which are challenging to identify by MALDI-TOF MS, were routinely measured in 36 laboratories from 12 countries, and well-defined MSQ features were used. After an intervention consisting of detailed reported feedback and instructions on how to acquire MALDI-TOF mass spectra, measurements were repeated and MSQs were compared. RESULTS At baseline, we observed heterogeneous MSQ between the devices, considering the median number of marker masses detected (range = [2-25]), reproducibility between technical replicates (range = [55%-86%]), and measurement error (range = [147 parts per million (ppm)-588 ppm]). As a general trend, the spectral quality was improved after the intervention for devices, which yielded low MSQs in the baseline assessment as follows: for four out of five devices with a high measurement error, the measurement precision was improved (p-values <0.001, paired Wilcoxon test); for six out of ten devices, which detected a low number of marker masses, the number of detected marker masses increased (p-values <0.001, paired Wilcoxon test). DISCUSSION We have identified simple workflow adaptations, which, to some extent, improve MSQ of poorly performing devices and should be considered by laboratories yielding a low MSQ. Improving MALDI-TOF MSQ in routine diagnostics is essential for increasing the resolution of bacterial identification by MALDI-TOF MS, which is dependent on the reproducible detection of marker masses. The heterogeneity identified in this external quality assessment (EQA) requires further study.
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Affiliation(s)
- Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.
| | | | | | - Banu Bayraktar
- University of Health Sciences, Sisli Hamidiye Etfal Teaching and Research Hospital, Istanbul, Turkey
| | - Efe Serkan Boz
- Department of Medical Microbiology, University of Health Sciences, Haydarpasa Numune Teaching and Research Hospital, Istanbul, Turkey
| | | | - Carlo Casanova
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Alix T Coste
- Institute of Microbiology, University Hospital Lausanne, Lausanne, Switzerland
| | - Peter Damborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Mehmet Demirci
- Department of Medical Microbiology, Kirklareli University, Kirklareli, Turkey
| | - Pavel Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | | | - José Fernandez
- Division of Laboratory Medicine, Laboratory of Bacteriology, University Hospital of Geneva, Geneva, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Lausanne, Lausanne, Switzerland
| | - Jaroslav Hrabak
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Plzen, Czech Republic
| | - Gülen Hürkal Yiğitler
- University of Health Sciences, Sisli Hamidiye Etfal Teaching and Research Hospital, Istanbul, Turkey
| | - Jakub Hurych
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Thøger Gorm Jensen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | | | - Greetje A Kampinga
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sonja Kittl
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | | | | | | | - Julie Logan
- Reference Services Division, UK Health Security Agency, London, United Kingdom
| | | | - Ivana Mareković
- Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Matthias Marschal
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Jacob Moran-Gilad
- School of Public Health, Ben Gurion University of the Negev and Soroka University Medical Center, Beer Sheva, Israel
| | - Oliver Nolte
- Center for Laboratory Medicine, St. Gallen, Switzerland
| | | | - Michael Pedersen
- Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark
| | | | | | - Julia Reichl
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | | | - Arnaud Riat
- Division of Laboratory Medicine, Laboratory of Bacteriology, University Hospital of Geneva, Geneva, Switzerland
| | | | | | | | - Jacques Schrenzel
- Division of Laboratory Medicine, Laboratory of Bacteriology, University Hospital of Geneva, Geneva, Switzerland
| | - Shani Troib
- School of Public Health, Ben Gurion University of the Negev and Soroka University Medical Center, Beer Sheva, Israel
| | - Elise Willems
- Clinical Laboratory AZNikolaas, Sint-Niklaas, Belgium
| | - Mandy Wootton
- University Hospital of Wales, Cardiff, United Kingdom
| | | | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
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Hleba L, Hlebova M, Kovacik A, Petrova J, Maskova Z, Cubon J, Massanyi P. Use of MALDI-TOF MS to Discriminate between Aflatoxin B1-Producing and Non-Producing Strains of Aspergillus flavus. Molecules 2022; 27:molecules27227861. [PMID: 36431961 PMCID: PMC9692738 DOI: 10.3390/molecules27227861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Aflatoxin B1 (AFB1) is one of the most toxic mycotoxins. One of the producers of AFB1 is Aspergillus flavus. Therefore, its rapid identification plays a key role in various sectors of the food and feed industry. MALDI-TOF mass spectrometry is one of the fastest and most accurate methods today. Therefore, the aim of this research was to develop the rapid identification of producing and non-producing strains of A. flavus based on the entire mass spectrum. To accomplish the main goal a different confirmatory MALDI-TOF MS and TLC procedures such as direct AFB1 identification by scraping from TLC plates, A. flavus mycelium, nutrient media around A. flavus growth, and finally direct AFB1 identification from infected wheat and barley grains had to be conducted. In this experiment, MALDI-TOF mass spectrometry with various modifications was the main supporting technology. All confirmatory methods confirmed the presence of AFB1 in the samples of aflatoxin-producing strains of A. flavus and vice versa; AFB1 was not detected in the case of non-producing strains. Entire mass spectra (from 2 to 20 kDa) of aflatoxin-producing and non-producing A. flavus strains were collected, statistically analyzed and clustered. An in-depth analysis of the obtained entire mass spectra showed differences between AFB1-producing and non-producing strains of A. flavus. Statistical and cluster analysis divided AFB1-producing and non-producing strains of A. flavus into two monasteries. The results indicate that it is possible to distinguish between AFB1 producers and non-producers by comparing the entire mass spectra using MALDI-TOF MS. Finally, we demonstrated that if there are established local AFB1-producing and non-producing strains of A. flavus, the entire mass spectrum database identification of aflatoxigenic A. flavus strains can be even faster and cheaper, without the need to identify the toxin itself.
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Affiliation(s)
- Lukas Hleba
- Faculty of Biotechnology and Food Sciences, Institute of Biotechnology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
- Correspondence:
| | - Miroslava Hlebova
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 917 01 Trnava, Slovakia
| | - Anton Kovacik
- Faculty of Biotechnology and Food Sciences, Institute of Applied Biology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Jana Petrova
- Faculty of Biotechnology and Food Sciences, Institute of Biotechnology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Zuzana Maskova
- Faculty of Biotechnology and Food Sciences, Institute of Biotechnology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Juraj Cubon
- Faculty of Biotechnology and Food Sciences, Institute of Food Sciences, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Peter Massanyi
- Faculty of Biotechnology and Food Sciences, Institute of Applied Biology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
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Discrimination and Characterization of Escherichia coli Originating from Clinical Cases of Femoral Head Necrosis in Broilers by MALDI-TOF Mass Spectrometry Confirms Great Heterogeneity of Isolates. Microorganisms 2022; 10:microorganisms10071472. [PMID: 35889191 PMCID: PMC9323188 DOI: 10.3390/microorganisms10071472] [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: 06/17/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023] Open
Abstract
Escherichia coli, a major pathogen in poultry production, is involved in femoral head necrosis (FHN) in broiler birds. So far, the characterization and relationship of isolates in context with this disease are mainly based on phenotypic and genotypic characteristics. Previously, an involvement of diverse E. coli isolates was reported. MALDI-TOF MS has been successfully applied investigating the clonality of different bacteria. Therefore, its application to characterize a well-defined selection of E. coli isolates beyond the species level was tested. The isolates were derived from clinical cases of FHN as well as from healthy birds. Reproducibility studies to perform a standardized protocol were done, and LB agar as well as the usage of fresh bacterial cultures proved most appropriate. No distinct clustering in context with the origin of isolates, association with lesions, serotype, or PFGE profile was found. Most of the isolates belonging to phylogroup B2 revealed a characteristic peak shift at 9716 m/z and could be attributed to the same MALDI-TOF MS cluster. The present study confirmed the previously found pheno- and genotypic heterogeneity of E. coli involved in FHN on the proteomic level. The study also highlights the need for standardized protocols when using MALDI-TOF MS for bacterial typing, especially beyond species level.
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Differentiation of Bacillus cereus and Bacillus thuringiensis Using Genome-Guided MALDI-TOF MS Based on Variations in Ribosomal Proteins. Microorganisms 2022; 10:microorganisms10050918. [PMID: 35630362 PMCID: PMC9146703 DOI: 10.3390/microorganisms10050918] [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: 03/16/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 12/10/2022] Open
Abstract
Bacillus cereus and B. thuringiensis are closely related species that are relevant to foodborne diseases and biopesticides, respectively. Unambiguous differentiation of these two species is crucial for bacterial taxonomy. As genome analysis offers an objective but time-consuming classification of B. cereus and B. thuringiensis, in the present study, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was used to accelerate this process. By combining in silico genome analysis and MALDI-TOF MS measurements, four species-specific peaks of B. cereus and B. thuringiensis were screened and identified. The species-specific peaks of B. cereus were m/z 3211, 6427, 9188, and 9214, and the species-specific peaks of B. thuringiensis were m/z 3218, 6441, 9160, and 9229. All the above peaks represent ribosomal proteins, which are conserved and consistent with the phylogenetic relationship between B. cereus and B. thuringiensis. The specificity of the peaks was robustly verified using common foodborne pathogens. Thus, we concluded that genome-guided MALDI-TOF MS allows high-throughput differentiation of B. cereus and B. thuringiensis and provides a framework for differentiating other closely related species.
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Cuénod A, Wüthrich D, Seth-Smith HMB, Ott C, Gehringer C, Foucault F, Mouchet R, Kassim A, Revathi G, Vogt DR, von Felten S, Bassetti S, Tschudin-Sutter S, Hettich T, Schlotterbeck G, Homberger C, Casanova C, Moran-Gilad J, Sagi O, Rodríguez-Sánchez B, Müller F, Aerni M, Gaia V, van Dessel H, Kampinga GA, Müller C, Daubenberger C, Pflüger V, Egli A. Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study. Genome Med 2021; 13:150. [PMID: 34517886 PMCID: PMC8438989 DOI: 10.1186/s13073-021-00960-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Klebsiella spp. are opportunistic pathogens which can cause severe infections, are often multi-drug resistant and are a common cause of hospital-acquired infections. Multiple new Klebsiella species have recently been described, yet their clinical impact and antibiotic resistance profiles are largely unknown. We aimed to explore Klebsiella group- and species-specific clinical impact, antimicrobial resistance (AMR) and virulence. METHODS We analysed whole-genome sequence data of a diverse selection of Klebsiella spp. isolates and identified resistance and virulence factors. Using the genomes of 3594 Klebsiella isolates, we predicted the masses of 56 ribosomal subunit proteins and identified species-specific marker masses. We then re-analysed over 22,000 Matrix-Assisted Laser Desorption Ionization - Time Of Flight (MALDI-TOF) mass spectra routinely acquired at eight healthcare institutions in four countries looking for these species-specific markers. Analyses of clinical and microbiological endpoints from a subset of 957 patients with infections from Klebsiella species were performed using generalized linear mixed-effects models. RESULTS Our comparative genomic analysis shows group- and species-specific trends in accessory genome composition. With the identified species-specific marker masses, eight Klebsiella species can be distinguished using MALDI-TOF MS. We identified K. pneumoniae (71.2%; n = 12,523), K. quasipneumoniae (3.3%; n = 575), K. variicola (9.8%; n = 1717), "K. quasivariicola" (0.3%; n = 52), K. oxytoca (8.2%; n = 1445), K. michiganensis (4.8%; n = 836), K. grimontii (2.4%; n = 425) and K. huaxensis (0.1%; n = 12). Isolates belonging to the K. oxytoca group, which includes the species K. oxytoca, K. michiganensis and K. grimontii, were less often resistant to 4th-generation cephalosporins than isolates of the K. pneumoniae group, which includes the species K. pneumoniae, K. quasipneumoniae, K. variicola and "K. quasivariicola" (odds ratio = 0.17, p < 0.001, 95% confidence interval [0.09,0.28]). Within the K. pneumoniae group, isolates identified as K. pneumoniae were more often resistant to 4th-generation cephalosporins than K. variicola isolates (odds ratio = 2.61, p = 0.003, 95% confidence interval [1.38,5.06]). K. oxytoca group isolates were found to be more likely associated with invasive infection to primary sterile sites than K. pneumoniae group isolates (odds ratio = 2.39, p = 0.0044, 95% confidence interval [1.05,5.53]). CONCLUSIONS Currently misdiagnosed Klebsiella spp. can be distinguished using a ribosomal marker-based approach for MALDI-TOF MS. Klebsiella groups and species differed in AMR profiles, and in their association with invasive infection, highlighting the importance for species identification to enable effective treatment options.
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Affiliation(s)
- Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland.
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland.
| | - Daniel Wüthrich
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
- Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Helena M B Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
- Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Chantal Ott
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Christian Gehringer
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
- Division of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | | | | | - Ali Kassim
- Aga Khan University Hospital, Nairobi, Kenya
| | | | - Deborah R Vogt
- Department of Clinical Research, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Stefanie von Felten
- Department of Clinical Research, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biostatistics, Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Stefano Bassetti
- Division of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Sarah Tschudin-Sutter
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Timm Hettich
- Division of Instrumental Analytics, School of Applied Sciences (FHNW), Muttenz, Switzerland
| | - Götz Schlotterbeck
- Division of Instrumental Analytics, School of Applied Sciences (FHNW), Muttenz, Switzerland
| | - Christina Homberger
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Carlo Casanova
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Jacob Moran-Gilad
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Soroka University Medical Center, Beer Sheva, Israel
| | - Orli Sagi
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Soroka University Medical Center, Beer Sheva, Israel
| | - Belén Rodríguez-Sánchez
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | | | - Valeria Gaia
- Servizio di microbiologia EOLAB, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Helke van Dessel
- Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Greetje A Kampinga
- Department of Medical Microbiology & Infection prevention, University of Groningen, Groningen, the Netherlands
- University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | | | - Claudia Daubenberger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Department of Sciences, University of Basel, Basel, Switzerland
| | | | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland.
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland.
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Kubo Y, Ueda O, Nagamitsu S, Yamanishi H, Nakamura A, Komatsu M. Novel strategy of rapid typing of Shiga toxin-producing Escherichia coli using MALDI Biotyper and ClinProTools analysis. J Infect Chemother 2021; 27:1137-1142. [PMID: 33745812 DOI: 10.1016/j.jiac.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/14/2021] [Accepted: 03/01/2021] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Rapid detection of Shiga toxin-producing Escherichia coli (STEC) is essential. Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) allows rapid, accurate, and low-cost microbial identification. We aimed to examine the discrimination ability of MALDI Biotyper (Bruker Daltonics) between STEC and non-STEC. METHODS In total, 234 strains (79 STEC strains and 155 non-STEC strains) isolated from stool between 2009 and 2014 were measured by MALDI Biotyper and mass spectra of 2000-20,000 m/z were analyzed with ClinProTools (Bruker Daltonics). Eighty-three strains were randomly extracted to produce STEC detection models using 3 algorithms, and 151 strains were used as validation samples to verify STEC detection performance and discrimination performance of Shiga toxins with the STEC detection models. RESULTS The STEC detection model with Quick Classifier (QC) algorithm was the most sensitive: sensitivity, 84.1% (37/44); specificity, 94.4% (101/107). Discrimination between STEC and non-STEC was excellent, but individual discrimination of Shiga toxins was not possible. CONCLUSION MALDI Biotyper may be a useful rapid diagnostic method for STEC infection.
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Affiliation(s)
- Yumi Kubo
- FALCO Biosystems K. K., Tokai Central Laboratory, Test Group Microbiology, Aichi, Japan.
| | | | - Sawa Nagamitsu
- FALCO Biosystems K. K., Okayama Laboratory, Test Group Microbiology, Okayama, Japan.
| | - Hachiro Yamanishi
- Department of Clinical Laboratory Science, Faculty of Health Care, Tenri Health Care University, Japan.
| | - Akihiro Nakamura
- Department of Clinical Laboratory Science, Faculty of Health Care, Tenri Health Care University, Japan.
| | - Masaru Komatsu
- Department of Clinical Laboratory Science, Faculty of Health Care, Tenri Health Care University, Japan.
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Biotyping of IRE/CTVM19 tick cell line infected by tick-borne encephalitis virus. Ticks Tick Borne Dis 2020; 11:101420. [DOI: 10.1016/j.ttbdis.2020.101420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/26/2020] [Accepted: 03/20/2020] [Indexed: 01/24/2023]
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9
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Determination of methicillin-resistant Staphylococcus aureus and Staphylococcus epidermidis by MALDI-TOF MS in clinical isolates from Latvia. CLINICAL MASS SPECTROMETRY 2020; 16:33-39. [DOI: 10.1016/j.clinms.2020.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/12/2020] [Accepted: 03/21/2020] [Indexed: 12/12/2022]
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10
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Fukuyama Y, Ojima-Kato T, Nagai S, Shima K, Funatsu S, Yamada Y, Tamura H, Nomura S, Ogata K, Sekiya S, Iwamoto S, Tanaka K. Improved MALDI-MS method for the highly sensitive and reproducible detection of biomarker peaks for the proteotyping of Salmonella serotypes. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:966-975. [PMID: 31697871 DOI: 10.1002/jms.4469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
The rapid identification and classification of pathogenic microorganisms, including Salmonella enterica, is important for the surveillance and prevention of foodborne diseases. Matrix-assisted laser desorption\ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been shown to be an effective tool for the rapid identification of microorganisms. In a previous report, a mass database consisting of 12 biomarker proteins, S8, L15, L17, L21, L25, S7, superoxide dismutase (SodA), peptidylprolyl cis-trans isomerase C, Gns, YibT, YaiA, and YciF, was introduced for the serotyping of S. enterica via MALDI-MS (Applied Microbiology and Biotechnology, 2017, 101, 8557-8569). However, the reproducibility of peak detection of biomarkers such as SodA at m\z 23 000 was poor. We report here an optimized MALDI-MS method for detecting these biomarkers with high sensitivity and reproducibility. The issue was solved by controlling the bacterial concentration at 1 × 10 to 1 × 102 MFU (3 × 106 to 3 × 107 CFU\μL, as calculated from the MFU), using the colony suspension supernatant obtained by centrifugation, and using matrix additives such as methylenediphosphonic acid and N-decyl-β-D-maltopyranoside. We propose that the method including the above steps is one of the best for detecting biomarkers with high sensitivity and reproducibility.
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Affiliation(s)
- Yuko Fukuyama
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Teruyo Ojima-Kato
- School of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-0073, Japan
| | - Satomi Nagai
- School of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-0073, Japan
| | - Keisuke Shima
- Analytical and Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Shinji Funatsu
- Analytical and Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Yoshihiro Yamada
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Hiroto Tamura
- School of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-0073, Japan
| | - Shizuo Nomura
- Analytical and Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Koretsugu Ogata
- Analytical and Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Sadanori Sekiya
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
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11
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Response to Questions Posed by the Food and Drug Administration Regarding Virulence Factors and Attributes that Define Foodborne Shiga Toxin-Producing Escherichia coli (STEC) as Severe Human Pathogens †. J Food Prot 2019; 82:724-767. [PMID: 30969806 DOI: 10.4315/0362-028x.jfp-18-479] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
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- NACMCF Executive Secretariat, * U.S. Department of Agriculture, Food Safety and Inspection Service, Office of Public Health Science, PP3, 9-178, 1400 Independence Avenue S.W., Washington, D.C. 20250-3700, USA
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12
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Månsson V, Gilsdorf JR, Kahlmeter G, Kilian M, Kroll JS, Riesbeck K, Resman F. Capsule Typing of Haemophilus influenzae by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Emerg Infect Dis 2019; 24:443-452. [PMID: 29460728 PMCID: PMC5823330 DOI: 10.3201/eid2403.170459] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Encapsulated Haemophilus influenzae strains belong to type-specific genetic lineages. Reliable capsule typing requires PCR, but a more efficient method would be useful. We evaluated capsule typing by using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Isolates of all capsule types (a−f and nontypeable; n = 258) and isogenic capsule transformants (types a−d) were investigated. Principal component and biomarker analyses of mass spectra showed clustering, and mass peaks correlated with capsule type-specific genetic lineages. We used 31 selected isolates to construct a capsule typing database. Validation with the remaining isolates (n = 227) showed 100% sensitivity and 92.2% specificity for encapsulated strains (a−f; n = 61). Blinded validation of a supplemented database (n = 50) using clinical isolates (n = 126) showed 100% sensitivity and 100% specificity for encapsulated strains (b, e, and f; n = 28). MALDI-TOF mass spectrometry is an accurate method for capsule typing of H. influenzae.
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13
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Li P, Xin W, Xia S, Luo Y, Chen Z, Jin D, Gao S, Yang H, Ji B, Wang H, Yan Y, Kang L, Wang J. MALDI-TOF mass spectrometry-based serotyping of V. parahaemolyticus isolated from the Zhejiang province of China. BMC Microbiol 2018; 18:185. [PMID: 30424744 PMCID: PMC6234682 DOI: 10.1186/s12866-018-1328-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/29/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is as an important food-borne pathogen circulating in China. Since 1996, the core serotype has become O3:K6, which has specific genetic markers. This serotype causes the majority of outbreaks worldwide. Until now, nearly 21 serotypes were considered as serovariants of O3:K6. Among these, O4:K68, O1:K25 and O1:KUT have caused pandemic outbreaks. O4:K8, a serovariant of O3:K6, has become the second most dominant serotype circulating in China after O3:K6. In this study, we report the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze and characterize 146 V. parahaemolyticus isolates belonging to 23 serotypes. RESULTS Upon mass spectral analysis, isolates belonging to O4:K8 formed a distinct group among the five main pandemic groups (O3:K6, O4:K8, O4:K68, O1:K25 and O1:KUT). Two major protein peaks (m/z 4383 and 4397) were significantly different between serotype O4:K8 and the four other pandemic strains. Both of these peaks were present in 32 out of 36 O4:K8 isolates, but were absent in 105 out of 110 non-O4:K8 isolates. These peaks were also absent in all 74 pandemic serotypes (O3:K6, O4:K68, O1:K25 and O1:KUT). CONCLUSION Our results highlight the threat of O4:K8 forming a distinct group, which differs significantly from pandemic serotypes on the proteomic level. The use of MALDI-TOF MS has not been reported before in a study of this nature. Mass spectrum peaks at m/z 4383 and 4397 may be specific for O4:K8. However, we cannot conclude that MALDI-TOF MS can be used to serotype V. parahaemolyticus.
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Affiliation(s)
- Ping Li
- Graduate College, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, Anhui, China.,Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Nanhu district, Jiaxing, 314050, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Wenwen Xin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Susu Xia
- Graduate College, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, Anhui, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Yun Luo
- Department of Microbiology, Zhejiang Province Center for Disease Control and Prevention, No.3399 Binsheng Road, Hangzhou, 310000, China
| | - Zhongwen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Nanhu district, Jiaxing, 314050, China
| | - Dazhi Jin
- Department of Microbiology, Zhejiang Province Center for Disease Control and Prevention, No.3399 Binsheng Road, Hangzhou, 310000, China
| | - Shan Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Hao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Bin Ji
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Henghui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Nanhu district, Jiaxing, 314050, China
| | - Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Nanhu district, Jiaxing, 314050, China
| | - Lin Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China.
| | - Jinglin Wang
- Graduate College, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, Anhui, China. .,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China.
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14
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Rapid and robust analytical protocol for E. coli STEC bacteria subspecies differentiation using whole cell MALDI mass spectrometry. Talanta 2018; 182:164-170. [PMID: 29501136 DOI: 10.1016/j.talanta.2018.01.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/17/2018] [Accepted: 01/20/2018] [Indexed: 12/30/2022]
Abstract
Whole cell MALDI is regularly used for the identification of bacteria to species level in clinical Microbiology laboratories. However, there remains a need to rapidly characterize and differentiate isolates below the species level to support outbreak management. We describe the implementation of a modified preparative approach for MALDI-MS combined with a custom analytical computational pipeline as a rapid procedure for subtyping Shigatoxigenic E. coli (STEC) and accurately identifying strain-specifying biomarkers. The technique was able to differentiate E. coli O157:H7 from other STEC. Within O157 serotype O157:H7 isolates were readily distinguishable from Sorbitol Fermenting O157 isolates. Overall, nine homogeneous groups of isolates were distinguished, each exhibiting distinct profiles of defining mass spectra features. This offers a robust analytical tool useable in reference/diagnostic public health scenarios.
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15
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Application of proteotyping Strain Solution™ ver. 2 software and theoretically calculated mass database in MALDI-TOF MS typing of Salmonella serotype. Appl Microbiol Biotechnol 2017; 101:8557-8569. [PMID: 29032472 DOI: 10.1007/s00253-017-8563-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 10/18/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based microbial identification is a popular analytical method. Strain Solution proteotyping software available for MALDI-TOF MS has great potential for the precise and detailed discrimination of microorganisms at serotype- or strain-level, beyond the conventional mass fingerprinting approaches. Here, we constructed a theoretically calculated mass database of Salmonella enterica subspecies enterica consisting of 12 biomarker proteins: ribosomal proteins S8, L15, L17, L21, L25, and S7, Mn-cofactor-containing superoxide dismutase (SodA), peptidyl-prolyl cis-trans isomerase C (PPIase C), and protein Gns, and uncharacterized proteins YibT, YaiA, and YciF, that can allow serotyping of Salmonella. Strain Solution ver. 2 software with the novel database constructed in this study demonstrated that 109 strains (94%), including the major outbreak-associated serotypes, Enteritidis, Typhimurium, and Infantis, could be correctly identified from others by colony-directed MALDI-TOF MS using 116 strains belonging to 23 kinds of typed and untyped serotypes of S. enterica from culture collections, patients, and foods. We conclude that Strain Solution ver. 2 software integrated with the accurate mass database will be useful for the bacterial proteotyping by MALDI-TOF MS-based microbial classification in the clinical and food safety fields.
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16
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Sato J, Nakayama M, Tomita A, Sonoda T, Hasumi M, Miyamoto T. Evaluation of repetitive-PCR and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid strain typing of Bacillus coagulans. PLoS One 2017; 12:e0186327. [PMID: 29020109 PMCID: PMC5636150 DOI: 10.1371/journal.pone.0186327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 09/20/2017] [Indexed: 11/17/2022] Open
Abstract
In order to establish rapid and accurate typing method for Bacillus coagulans strains which is important for controlling in some canned foods and tea-based beverages manufacturing because of the high-heat resistance of the spores and high tolerance of the vegetative cells to catechins and chemicals, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and repetitive-PCR (rep-PCR) were evaluated. For this purpose, 28 strains of B. coagulans obtained from various culture collections were tested. DNA sequence analyses of the genes encoding 16S rRNA and DNA gyrase classified the test strains into two and three groups, respectively, regardless of their phenotypes. Both MALDI-TOF MS and rep-PCR methods classified the test strains in great detail. Strains classified in each group showed similar phenotypes, such as carbohydrate utilization determined using API 50CH. In particular, the respective two pairs of strains which showed the same metabolic characteristic were classified into the same group by both MALDI-TOF MS and rep-PCR methods separating from the other strains. On the other hand, the other strains which have the different profiles of carbohydrate utilization were separated into different groups by these methods. These results suggested that the combination of MALDI-TOF MS and rep-PCR analyses was advantageous for the rapid and detailed typing of bacterial strains in respect to both phenotype and genotype.
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Affiliation(s)
- Jun Sato
- Safety Science Research, R&D, Kao Corporation, Ichikai, Tochigi, Japan.,Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Hakozaki, Higashi-ku, Fukuoka, Japan
| | - Motokazu Nakayama
- Health Care Food Research, R&D, Kao Corporation, Sumida, Tokyo, Japan
| | - Ayumi Tomita
- Safety Science Research, R&D, Kao Corporation, Ichikai, Tochigi, Japan
| | - Takumi Sonoda
- Safety Science Research, R&D, Kao Corporation, Ichikai, Tochigi, Japan
| | - Motomitsu Hasumi
- Safety Science Research, R&D, Kao Corporation, Ichikai, Tochigi, Japan
| | - Takahisa Miyamoto
- Division of Food Science & Biotechnology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki, Higashi-ku, Fukuoka, Japan
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17
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Andjelković U, Šrajer Gajdošik M, Gašo-Sokač D, Martinović T, Josić D. Foodomics and Food Safety: Where We Are. Food Technol Biotechnol 2017; 55:290-307. [PMID: 29089845 PMCID: PMC5654429 DOI: 10.17113/ftb.55.03.17.5044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 05/31/2017] [Indexed: 12/21/2022] Open
Abstract
The power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identification, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special attention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is influenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affinity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affinity-based methods, are the cross-reactivity between similar molecules and the influence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identification and quantification, and for corresponding modeling.
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Affiliation(s)
- Uroš Andjelković
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, RS-11000 Belgrade, Serbia
| | - Martina Šrajer Gajdošik
- Department of Chemistry, J. J. Strossmayer University of Osijek, Cara Hadrijana 8/A, HR-31000 Osijek, Croatia
| | - Dajana Gašo-Sokač
- Faculty of Food Technology, J. J. Strossmayer University of Osijek, Franje Kuhača 20, HR-31000 Osijek, Croatia
| | - Tamara Martinović
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
| | - Djuro Josić
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Warren Alpert Medical School, Brown University, 222 Richmond St, Providence, RI 02903, USA
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18
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Nirujogi RS, Muthusamy B, Kim MS, Sathe GJ, Lakshmi PTV, Kovbasnjuk ON, Prasad TSK, Wade M, Jabbour RE. Secretome analysis of diarrhea-inducing strains of Escherichia coli. Proteomics 2017; 17. [PMID: 28070933 DOI: 10.1002/pmic.201600299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 12/19/2016] [Accepted: 01/05/2017] [Indexed: 01/05/2023]
Abstract
Secreted proteins constitute a major part of virulence factors that are responsible for pathogenesis caused by Gram-negative bacteria. Enterohemorrhagic Escherichia coli, O157:H7, is the major pathogen often causing outbreaks. However, studies have reported that the significant outbreaks caused by non-O157:H7 E. coli strains, also known as "Big-Six" serogroup strains, are increasing. There is no systematic study describing differential secreted proteins from these non-O157:H7 E. coli strains. In this study, we carried out MS-based differential secretome analysis using tandem mass tags labeling strategy of non-O157:H7 E. coli strains, O103, O111, O121, O145, O26, and O45. We identified 1241 proteins, of which 565 proteins were predicted to be secreted. We also found that 68 proteins were enriched in type III secretion system and several of them were differentially expressed across the strains. Additionally, we identified several strain-specific secreted proteins that could be used for developing potential markers for the identification and strain-level differentiation. To our knowledge, this study is the first comparative proteomic study on secretome of E. coli Big-Six serogroup and the several of these strain-specific secreted proteins can be further studied to develop potential markers for identification and strain-level differentiation. Moreover, the results of this study can be utilized in several applications, including food safety, diagnostics of E. coli outbreaks, and detection and identification of bio threats in biodefense.
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Affiliation(s)
- Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Centre for Bioinformatics, Pondicherry University, Puducherry, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, South Korea
| | - Gajanan J Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal University, Madhav Nagar, Manipal, India
| | - P T V Lakshmi
- Centre for Bioinformatics, Pondicherry University, Puducherry, India
| | - Olga N Kovbasnjuk
- Division of Gastroenterology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Centre for Bioinformatics, Pondicherry University, Puducherry, India.,Manipal University, Madhav Nagar, Manipal, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | - Mary Wade
- Research and Technology Directorate, US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Rabih E Jabbour
- Research and Technology Directorate, US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, USA
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19
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Beinhauer J, Lenobel R, Loginov D, Chamrád I, Řehulka P, Sedlářová M, Marchetti-Deschmann M, Allmaier G, Šebela M. Identification ofBremia lactucaeandOidium neolycopersiciproteins extracted for intact spore MALDI mass spectrometric biotyping. Electrophoresis 2016; 37:2940-2952. [DOI: 10.1002/elps.201600144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/19/2016] [Accepted: 08/17/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Jana Beinhauer
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - René Lenobel
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Dmitry Loginov
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Ivo Chamrád
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Pavel Řehulka
- Institute of Molecular Pathology, Faculty of Military Health Sciences; University of Defence; Hradec Králové Czech Republic
| | - Michaela Sedlářová
- Department of Botany, Faculty of Science; Palacký University; Olomouc Czech Republic
| | | | - Günter Allmaier
- Institute of Chemical Technologies and Analytics; Vienna University of Technology (TU Wien); Vienna Austria
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
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20
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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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Pinu FR. Early detection of food pathogens and food spoilage microorganisms: Application of metabolomics. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.05.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Ojima-Kato T, Yamamoto N, Takahashi H, Tamura H. Matrix-assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Can Precisely Discriminate the Lineages of Listeria monocytogenes and Species of Listeria. PLoS One 2016; 11:e0159730. [PMID: 27442502 PMCID: PMC4956195 DOI: 10.1371/journal.pone.0159730] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/07/2016] [Indexed: 12/11/2022] Open
Abstract
The genetic lineages of Listeria monocytogenes and other species of the genus Listeria are correlated with pathogenesis in humans. Although matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a prevailing tool for rapid and reliable microbial identification, the precise discrimination of Listeria species and lineages remains a crucial issue in clinical settings and for food safety. In this study, we constructed an accurate and reliable MS database to discriminate the lineages of L. monocytogenes and the species of Listeria (L. monocytogenes, L. innocua, L. welshimeri, L. seeligeri, L. ivanovii, L. grayi, and L. rocourtiae) based on the S10-spc-alpha operon gene encoded ribosomal protein mass spectrum (S10-GERMS) proteotyping method, which relies on both genetic information (genomics) and observed MS peaks in MALDI-TOF MS (proteomics). The specific set of eight biomarkers (ribosomal proteins L24, L6, L18, L15, S11, S9, L31 type B, and S16) yielded characteristic MS patterns for the lineages of L. monocytogenes and the different species of Listeria, and led to the construction of a MS database that was successful in discriminating between these organisms in MALDI-TOF MS fingerprinting analysis followed by advanced proteotyping software Strain Solution analysis. We also confirmed the constructed database on the proteotyping software Strain Solution by using 23 Listeria strains collected from natural sources.
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Affiliation(s)
- Teruyo Ojima-Kato
- Knowledge Hub Aichi, Aichi Science and Technology Foundation, Yakusa, Toyota, Aichi 470-0356, Japan
- School of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-0073, Japan
- * E-mail: (TOK); (HT)
| | - Naomi Yamamoto
- School of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-0073, Japan
| | - Hajime Takahashi
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo, 108-8477 Japan
| | - Hiroto Tamura
- Knowledge Hub Aichi, Aichi Science and Technology Foundation, Yakusa, Toyota, Aichi 470-0356, Japan
- School of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-0073, Japan
- * E-mail: (TOK); (HT)
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Fiedoruk K, Daniluk T, Fiodor A, Drewicka E, Buczynska K, Leszczynska K, Bideshi DK, Swiecicka I. MALDI-TOF MS portrait of emetic and non-emetic Bacillus cereus group members. Electrophoresis 2016; 37:2235-47. [PMID: 27196540 DOI: 10.1002/elps.201500308] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 04/25/2016] [Accepted: 05/09/2016] [Indexed: 11/09/2022]
Abstract
The number of foodborne intoxications caused by emetic Bacillus cereus isolates has increased significantly. As such, rapid and reliable methods to identify emetic strains appear to be clinically relevant. In this study, intact cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to differentiate emetic and non-emetic bacilli. The phyloproteomic clustering of 34 B. cereus emetic and 88 non-emetic isolates classified as B. cereus, Bacillus thuringiensis, Bacillus weihenstephanensis, and Bacillus mycoides, showed (i) a clear separation of both groups at a similarity level of 43%, and (ii) a high relatedness among the emetic isolates (similarity of 78%). Specifically, 83 mass peak classes were recognized in the spectral window range between m/z 4000 and 12 000 that were tentatively assigned to 41 protein variants based on a bioinformatic approach. Mass variation between the emetic and the non-emetic subsets was recorded for 27 of them, including ten ribosomal subunit proteins, for which inter-strain polymorphism was confirmed by gene sequencing. Additional peaks were assigned to other proteins such as small acid soluble proteins, cold shock proteins and hypothetical proteins, e.g., carbohydrate kinase. Moreover, the results were supported by in silico analysis of the biomarkers in 259 members of B. cereus group, including Bacillus anthracis, based on their whole-genome sequences. In conclusion, the proteomic profiling by MALDI-TOF MS is a promising and rapid method for pre-screening B. cereus to identify medically relevant isolates and for epidemiologic purposes.
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Affiliation(s)
- Krzysztof Fiedoruk
- Department of Microbiology, Medical University of Bialystok, Bialystok, Poland
| | - Tamara Daniluk
- Department of Microbiology, Medical University of Bialystok, Bialystok, Poland
| | - Angelika Fiodor
- Department of Microbiology, University of Bialystok, Bialystok, Poland
| | - Ewa Drewicka
- Department of Microbiology, University of Bialystok, Bialystok, Poland
| | | | | | - Dennis Ken Bideshi
- Department of Natural and Mathematical Science, California Baptist University, Riverside, USA.,Department of Entomology, University of California, Riverside, USA
| | - Izabela Swiecicka
- Department of Microbiology, University of Bialystok, Bialystok, Poland.,Laboratory of Applied Microbiology, University of Bialystok, Bialystok, Poland
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Ojima-Kato T, Yamamoto N, Iijima Y, Tamura H. Assessing the performance of novel software Strain Solution on automated discrimination of Escherichia coli serotypes and their mixtures using matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Microbiol Methods 2015; 119:233-8. [DOI: 10.1016/j.mimet.2015.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/05/2015] [Accepted: 11/07/2015] [Indexed: 11/26/2022]
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