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Wang H, Yin X, Zhang L, Wang X, Zhang J, Wen R, Cao J. Insight into the Relationship between the Causes of Off-Odour and Microorganism Communities in Xuanwei Ham. Foods 2024; 13:776. [PMID: 38472889 PMCID: PMC10930425 DOI: 10.3390/foods13050776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
To expound on the correlation between the microorganism communities and the formation of off-odour in Xuanwei ham, the microorganism communities and volatile compounds were investigated in the biceps femoris (BF) and semimembranosus (SM) of Xuanwei ham with different quality grades (normal ham and spoiled ham). The single molecule real-time sequencing showed that differential bacteria and fungi were more varied in normal hams than in spoiled hams. Headspace solid-phase microextraction-gas chromatography (HS-SPME-GC-MS) results indicated that aldehydes and alcohols were significantly higher in spoiled hams than those in normal hams (p < 0.05). The off-odour of spoiled hams was dominated by ichthyic, malodourous, sweaty, putrid, sour, and unpleasant odours produced by compounds such as trimethylamine (SM: 13.05 μg/kg), hexanal (BF: 206.46 μg/kg), octanal (BF: 59.52 μg/kg), methanethiol (SM: 12.85 μg/kg), and valeric acid (BF: 15.08 μg/kg), which are positively correlated with Bacillus cereus, Bacillus subtilis, Bacillus licheniformis, Pseudomonas sp., Aspergillus ruber, and Moraxella osloensis. Furthermore, the physicochemical property and quality characteristics results showed that high moisture (BF: 56.32 g/100 g), pH (BF: 6.63), thiobarbituric acid reactive substances (TBARS) (SM: 1.98 MDA/kg), and low NaCl content (SM: 6.31%) were also responsible for the spoilage of hams with off-odour. This study provided a deep insight into the off-odour of Xuanwei ham from the perspective of microorganism communities and a theoretical basis for improving the flavour and overall quality of Xuanwei hams.
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Affiliation(s)
- Haoyi Wang
- College of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (H.W.); (X.Y.); (L.Z.); (X.W.); (J.Z.)
| | - Xiaoyu Yin
- College of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (H.W.); (X.Y.); (L.Z.); (X.W.); (J.Z.)
| | - Lu Zhang
- College of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (H.W.); (X.Y.); (L.Z.); (X.W.); (J.Z.)
| | - Xuejiao Wang
- College of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (H.W.); (X.Y.); (L.Z.); (X.W.); (J.Z.)
| | - Jiliang Zhang
- College of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (H.W.); (X.Y.); (L.Z.); (X.W.); (J.Z.)
| | - Rongxin Wen
- College of Life Sciences, Yantai University, Yantai 264005, China;
| | - Jianxin Cao
- College of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (H.W.); (X.Y.); (L.Z.); (X.W.); (J.Z.)
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Xu Z, Luo Y, Mao Y, Peng R, Chen J, Soteyome T, Bai C, Chen L, Liang Y, Su J, Wang K, Liu J, Kjellerup BV. Spoilage Lactic Acid Bacteria in the Brewing Industry. J Microbiol Biotechnol 2020; 30:955-961. [PMID: 31986245 PMCID: PMC9728350 DOI: 10.4014/jmb.1908.08069] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/06/2020] [Indexed: 02/05/2023]
Abstract
Lactic acid bacteria (LAB) have caused many microbiological incidents in the brewing industry, resulting in severe economic loss. Meanwhile, traditional culturing method for detecting LAB are time-consuming for brewers. The present review introduces LAB as spoilage microbes in daily life, with focus on LAB in the brewing industry, targeting at the spoilage mechanism of LAB in brewing industry including the special metabolisms, the exist of the viable but nonculturable (VBNC) state and the hop resistance. At the same time, this review compares the traditional and novel rapid detection methods for these microorganisms which may provide innovative control and detection strategies for preventing alcoholic beverage spoilage, such as improvement of microbiological quality control using advanced culture media or different isothermal amplification methods.
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Affiliation(s)
- Zhenbo Xu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, P.R. China
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD 21201, USA
| | - Yuting Luo
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, P.R. China
| | - Yuzhu Mao
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, P.R. China
| | - Ruixin Peng
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, P.R. China
| | - Jinxuan Chen
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, P.R. China
| | - Thanapop Soteyome
- Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand
| | - Caiying Bai
- Guangdong Women and Children Hospital, Guangzhou 510010, P.R. China
| | - Ling Chen
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, P.R. China
| | - Yi Liang
- Guangdong Zhongqing Font Biochemical Science and Technology Co. Ltd., Maoming, Guangdong 525427, P.R. China
| | - Jianyu Su
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, P.R. China
| | - Kan Wang
- Research Center of Translational Medicine, Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Corresponding authors J.L. Phone: +86-20-87113252 Fax: +86-20-87113252 E-mail:
| | - Junyan Liu
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD 20742, USA
- Corresponding authors J.L. Phone: +86-20-87113252 Fax: +86-20-87113252 E-mail:
| | - Birthe V. Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD 20742, USA
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3
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Malik YS, Verma A, Kumar N, Deol P, Kumar D, Ghosh S, Dhama K. Biotechnological innovations in farm and pet animal disease diagnosis. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7150312 DOI: 10.1016/b978-0-12-816352-8.00013-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The application of innovative diagnostic technologies for the detection of animal pathogens at an early stage is essential in restricting the economic loss incurred due to emerging infectious animal diseases. The desirable characteristics of such diagnostic methods are easy to use, cost-effective, highly sensitive, and specific, coupled with the high-throughput detection capabilities. The enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) are still the most common assays used for the detection of animal pathogens across the globe. However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Furthermore, animal disease diagnostics need to be updated regularly to capture new, emerging and divergent infectious pathogens, and biotechnological innovations are helpful in fulfilling the rising demand for such diagnostics for the welfare of the society. Therefore, this chapter primarily describes and discusses in detail the serological, molecular, novel high-throughput, and POC assays to detect pathogens affecting farm and companion animals.
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Velichko NV, Pinevich AV. Classification and Identification Tasks in Microbiology: Mass Spectrometric Methods Coming to the Aid. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719050151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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5
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Zhang Y, Hu A, Andini N, Yang S. A 'culture' shift: Application of molecular techniques for diagnosing polymicrobial infections. Biotechnol Adv 2019; 37:476-490. [PMID: 30797092 PMCID: PMC6447436 DOI: 10.1016/j.biotechadv.2019.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/04/2019] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
With the advancement of microbiological discovery, it is evident that many infections, particularly bloodstream infections, are polymicrobial in nature. Consequently, new challenges have emerged in identifying the numerous etiologic organisms in an accurate and timely manner using the current diagnostic standard. Various molecular diagnostic methods have been utilized as an effort to provide a fast and reliable identification in lieu or parallel to the conventional culture-based methods. These technologies are mostly based on nucleic acid, proteins, or physical properties of the pathogens with differing advantages and limitations. This review evaluates the different molecular methods and technologies currently available to diagnose polymicrobial infections, which will help determine the most appropriate option for future diagnosis.
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Affiliation(s)
- Yi Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore.
| | - Anne Hu
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Nadya Andini
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Samuel Yang
- Emergency Medicine, Stanford University, Stanford, California 94305, USA.
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Shen J, Hu R, Zhou T, Wang Z, Zhang Y, Li S, Gui C, Jiang M, Qin A, Tang BZ. Fluorescent Sensor Array for Highly Efficient Microbial Lysate Identification through Competitive Interactions. ACS Sens 2018; 3:2218-2222. [PMID: 30350949 DOI: 10.1021/acssensors.8b00650] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Optical cross-reactive sensor arrays have recently been proven to be a powerful tool for high-throughput bioanalytes identification. Nevertheless, identification and classification of microbes, especially using microbial lysates as the analytes, still is a great challenge due to their complex composition. Herein, we achieve this goal by using luminogens featuring aggregation-induced emission characteristics (AIEgens) and graphene oxide (GO) to construct a microbial lysate responsive fluorescent sensor array. The combination of AIEgen with GO not only reduces the background signal but also induces the competition interactions among AIEgen, microbial lysates, and GO, which highly improves the discrimination ability of the sensor array. As a result, six microbes, including two fungi, two Gram-positive bacteria, and two Gram-negative bacteria are precisely identified. Thus, this work provides a new way to design safer and simpler sensor arrays for the discrimination of complex analytes.
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Affiliation(s)
- Jianlei Shen
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Rong Hu
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Taotao Zhou
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Zhiming Wang
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Yiru Zhang
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Shiwu Li
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Chen Gui
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Meijuan Jiang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Anjun Qin
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Ben Zhong Tang
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
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7
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Li B, Dunham SJB, Ellis JF, Lange JD, Smith JR, Yang N, King TL, Amaya KR, Arnett CM, Sweedler JV. A Versatile Strategy for Characterization and Imaging of Drip Flow Microbial Biofilms. Anal Chem 2018; 90:6725-6734. [PMID: 29723465 DOI: 10.1021/acs.analchem.8b00560] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The inherent architectural and chemical complexities of microbial biofilms mask our understanding of how these communities form, survive, propagate, and influence their surrounding environment. Here we describe a simple and versatile workflow for the cultivation and characterization of model flow-cell-based microbial ecosystems. A customized low-shear drip flow reactor was designed and employed to cultivate single and coculture flow-cell biofilms at the air-liquid interface of several metal surfaces. Pseudomonas putida F1 and Shewanella oneidensis MR-1 were selected as model organisms for this study. The utility and versatility of this platform was demonstrated via the application of several chemical and morphological imaging techniques-including matrix-assisted laser desorption/ionization mass spectrometry imaging, secondary ion mass spectrometry imaging, and scanning electron microscopy-and through the examination of model systems grown on iron substrates of varying compositions. Implementation of these techniques in combination with tandem mass spectrometry and a two-step imaging principal component analysis strategy resulted in the identification and characterization of 23 lipids and 3 oligosaccharides in P. putida F1 biofilms, the discovery of interaction-specific analytes, and the observation of several variations in cell and substrate morphology present during microbially influenced corrosion. The presented workflow is well-suited for examination of both single and multispecies drip flow biofilms and offers a platform for fundamental inquiries into biofilm formation, microbe-microbe interactions, and microbially influenced corrosion.
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Affiliation(s)
- Bin Li
- Department of Chemistry and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Sage J B Dunham
- Department of Chemistry and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Joanna F Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Justin D Lange
- Engineer Research and Development Center-Construction Engineering Research Laboratory (ERDC-CERL) , Champaign , Illinois 61822 , United States
| | - Justin R Smith
- Engineer Research and Development Center-Construction Engineering Research Laboratory (ERDC-CERL) , Champaign , Illinois 61822 , United States
| | - Ning Yang
- Department of Chemistry and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Travis L King
- Engineer Research and Development Center-Construction Engineering Research Laboratory (ERDC-CERL) , Champaign , Illinois 61822 , United States
| | - Kensey R Amaya
- Engineer Research and Development Center-Construction Engineering Research Laboratory (ERDC-CERL) , Champaign , Illinois 61822 , United States
| | - Clint M Arnett
- Engineer Research and Development Center-Construction Engineering Research Laboratory (ERDC-CERL) , Champaign , Illinois 61822 , United States
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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8
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Quéro L, Girard V, Pawtowski A, Tréguer S, Weill A, Arend S, Cellière B, Polsinelli S, Monnin V, van Belkum A, Vasseur V, Nodet P, Mounier J. Development and application of MALDI-TOF MS for identification of food spoilage fungi. Food Microbiol 2018; 81:76-88. [PMID: 30910090 DOI: 10.1016/j.fm.2018.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/30/2018] [Accepted: 05/01/2018] [Indexed: 01/20/2023]
Abstract
Filamentous fungi are frequently involved in food spoilage and cause important food losses and substantial economic damage. Their rapid and accurate identification is a key step to better manage food safety and quality. In recent years, MALDI-TOF MS has emerged as a powerful tool to identify microorganisms and has successfully been applied to the identification of filamentous fungi especially in the clinical context. The aim of this study was to implement a spectral database representative of food spoilage molds. To this end, after application of a standardized extraction protocol, 6477 spectra were acquired from 618 fungal strains belonging to 136 species and integrated in the VITEK MS database. The performances of this database were then evaluated by cross-validation and ∼95% of correct identification to the species level was achieved, independently of the cultivation medium and incubation time. The database was also challenged with external isolates belonging to 52 species claimed in the database and 90% were correctly identified to the species level. To our best knowledge, this is the most comprehensive database of food-relevant filamentous fungi developed to date. This study demonstrates that MALDI-TOF MS could be an alternative to conventional techniques for the rapid and reliable identification of spoilage fungi in food and industrial environments.
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Affiliation(s)
- Laura Quéro
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France; BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Victoria Girard
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Audrey Pawtowski
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Sylvie Tréguer
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Amélie Weill
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France; Université de Bretagne Occidentale Culture Collection, Université de Brest, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Sandrine Arend
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Béatrice Cellière
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Sophie Polsinelli
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Valérie Monnin
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Alex van Belkum
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390 La Balme les Grottes, France.
| | - Valérie Vasseur
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Patrice Nodet
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Jérôme Mounier
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
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Pulliam CJ, Wei P, Snyder DT, Wang X, Ouyang Z, Pielak RM, Graham Cooks R. Rapid discrimination of bacteria using a miniature mass spectrometer. Analyst 2017; 141:1633-6. [PMID: 26844973 DOI: 10.1039/c5an02575c] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Bacteria colonies were analyzed using paper spray ionization coupled with a portable mass spectrometer. The spectra were averaged and processed using multivariate analysis to discriminate between different species of bacteria based on their unique phospholipid profiles. Full scan mass spectra and product ion MS/MS data were compared to those recorded using a benchtop linear ion trap mass spectrometer.
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Affiliation(s)
| | - Pu Wei
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - Dalton T Snyder
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiao Wang
- Department of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Zheng Ouyang
- Department of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Rafal M Pielak
- L'Oreal California Research Center, San Francisco, CA, USA
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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Calderaro A, Arcangeletti MC, Rodighiero I, Buttrini M, Montecchini S, Vasile Simone R, Medici MC, Chezzi C, De Conto F. Identification of different respiratory viruses, after a cell culture step, by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Sci Rep 2016; 6:36082. [PMID: 27786297 PMCID: PMC5081539 DOI: 10.1038/srep36082] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023] Open
Abstract
In this study matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), a reliable identification method for the diagnosis of bacterial and fungal infections, is presented as an innovative tool to investigate the protein profile of cell cultures infected by the most common viruses causing respiratory tract infections in humans. MALDI-TOF MS was applied to the identification of influenza A and B viruses, adenovirus C species, parainfluenza virus types 1, 2 and 3, respiratory syncytial virus, echovirus, cytomegalovirus and metapneumovirus. In this study MALDI-TOF MS was proposed as a model to be applied to the identification of cultivable respiratory viruses using cell culture as a viral proteins enrichment method to the proteome profiling of virus infected and uninfected cell cultures. The reference virus strains and 58 viruses identified from respiratory samples of subjects with respiratory diseases positive for one of the above mentioned viral agents by cell culture were used for the in vitro infection of suitable cell cultures. The isolated viral particles, concentrated by ultracentrifugation, were used for subsequent protein extraction and their spectra profiles were generated by MALDI-TOF MS analysis. The newly created library allowed us to discriminate between uninfected and respiratory virus infected cell cultures.
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Affiliation(s)
- Adriana Calderaro
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Maria Cristina Arcangeletti
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Isabella Rodighiero
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Mirko Buttrini
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Sara Montecchini
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Rosita Vasile Simone
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Maria Cristina Medici
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Carlo Chezzi
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Flora De Conto
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
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11
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Bacteria in the apical root canals of teeth with apical periodontitis. J Formos Med Assoc 2016; 116:448-456. [PMID: 27745799 DOI: 10.1016/j.jfma.2016.08.010] [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: 07/04/2016] [Revised: 08/09/2016] [Accepted: 08/15/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND/PURPOSE Bacteria in the tooth root canal may cause apical periodontitis. This study examined the bacterial species present in the apical root canal of teeth with apical periodontitis. Antibiotic sensitivity tests were performed to evaluate whether these identified bacterial species were susceptible to specific kinds of antibiotics. METHODS Selective media plating and biochemical tests were used first to detect the bacterial species in samples taken from the apical portion of root canals of 62 teeth with apical periodontitis. The isolated bacterial species were further confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry. RESULTS We found concomitant presence of two (32 teeth) or three species (18 teeth) of bacteria in 50 (80.6%) out of 62 tested teeth. However, only 34 bacterial species were identified. Of a total of 118 bacterial isolates (83 anaerobes and 35 aerobes), Prophyromonas endodontalis was detected in 10; Bacteroides, Dialister invisus or Fusobacterium nucleatum in 9; Treponema denticola or Enterococcus faecalis in 8; Peptostreptococcus or Olsenella uli in 6; and Veillonella in 5 teeth. The other 25 bacterial species were detected in fewer than five teeth. Approximately 80-95% of bacterial isolates of anaerobes were sensitive to ampicillin/sulbactam (Unasyn), amoxicillin/clavulanate (Augmentin), cefoxitin, and clindamycin. For E. faecalis, 85-90% of bacterial isolates were sensitive to gentamicin and linezolid. CONCLUSION Root canal infections are usually caused by a mixture of two or three species of bacteria. Specific kinds of antibiotic can be selected to control these bacterial infections after antibiotic sensitivity testing.
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12
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Bolt F, Cameron SJS, Karancsi T, Simon D, Schaffer R, Rickards T, Hardiman K, Burke A, Bodai Z, Perdones-Montero A, Rebec M, Balog J, Takats Z. Automated High-Throughput Identification and Characterization of Clinically Important Bacteria and Fungi using Rapid Evaporative Ionization Mass Spectrometry. Anal Chem 2016; 88:9419-9426. [DOI: 10.1021/acs.analchem.6b01016] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Frances Bolt
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Simon J. S. Cameron
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Tamas Karancsi
- Waters Research
Centre, 7 Zahony Street, Budapest, 1031, Hungary
| | - Daniel Simon
- Waters Research
Centre, 7 Zahony Street, Budapest, 1031, Hungary
| | - Richard Schaffer
- Waters Research
Centre, 7 Zahony Street, Budapest, 1031, Hungary
| | - Tony Rickards
- Department
of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross
Hospital, London W6 8RF, United Kingdom
| | - Kate Hardiman
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Adam Burke
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Zsolt Bodai
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Alvaro Perdones-Montero
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Monica Rebec
- Department
of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross
Hospital, London W6 8RF, United Kingdom
| | - Julia Balog
- Waters Research
Centre, 7 Zahony Street, Budapest, 1031, Hungary
| | - Zoltan Takats
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
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13
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Bulaev AG, Sukhacheva MV, Kuznetsov BB. Typing of the closely related strains of euryarchaeal genus Acidiplasma (Thermoplasmatales) using REP-PCR DNA fingerprinting. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716020041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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14
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In Vitro Efficacy of Nonantibiotic Treatments on Biofilm Disruption of Gram-Negative Pathogens and an In Vivo Model of Infectious Endometritis Utilizing Isolates from the Equine Uterus. J Clin Microbiol 2015; 54:631-9. [PMID: 26719448 DOI: 10.1128/jcm.02861-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/21/2015] [Indexed: 12/21/2022] Open
Abstract
In this study, we evaluated the ability of the equine clinical treatments N-acetylcysteine, EDTA, and hydrogen peroxide to disrupt in vitro biofilms and kill equine reproductive pathogens (Escherichia coli, Pseudomonas aeruginosa, or Klebsiella pneumoniae) isolated from clinical cases. N-acetylcysteine (3.3%) decreased biofilm biomass and killed bacteria within the biofilms of E. coli isolates. The CFU of recoverable P. aeruginosa and K. pneumoniae isolates were decreased, but the biofilm biomass was unchanged. Exposure to hydrogen peroxide (1%) decreased the biofilm biomass and reduced the CFU of E. coli isolates, K. pneumoniae isolates were observed to have a reduction in CFU, and minimal effects were observed for P. aeruginosa isolates. Chelating agents (EDTA formulations) reduced E. coli CFU but were ineffective at disrupting preformed biofilms or decreasing the CFU of P. aeruginosa and K. pneumoniae within a biofilm. No single nonantibiotic treatment commonly used in equine veterinary practice was able to reduce the CFU and biofilm biomass of all three Gram-negative species of bacteria evaluated. An in vivo equine model of infectious endometritis was also developed to monitor biofilm formation, utilizing bioluminescence imaging with equine P. aeruginosa isolates from this study. Following infection, the endometrial surface contained focal areas of bacterial growth encased in a strongly adherent "biofilm-like" matrix, suggesting that biofilms are present during clinical cases of infectious equine endometritis. Our results indicate that Gram-negative bacteria isolated from the equine uterus are capable of producing a biofilm in vitro, and P. aeruginosa is capable of producing biofilm-like material in vivo.
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15
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Liang M, Shu J, Zhang P, Li Y, Sun W. Online Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry with In situMixing. ANAL LETT 2015. [DOI: 10.1080/00032719.2015.1043666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Baarda BI, Sikora AE. Proteomics of Neisseria gonorrhoeae: the treasure hunt for countermeasures against an old disease. Front Microbiol 2015; 6:1190. [PMID: 26579097 PMCID: PMC4620152 DOI: 10.3389/fmicb.2015.01190] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/12/2015] [Indexed: 01/26/2023] Open
Abstract
Neisseria gonorrhoeae is an exquisitely adapted, strictly human pathogen and the causative agent of the sexually transmitted infection gonorrhea. This ancient human disease remains a serious problem, occurring at high incidence globally and having a major impact on reproductive and neonatal health. N. gonorrhoeae is rapidly evolving into a superbug and no effective vaccine exists to prevent gonococcal infections. Untreated or inadequately treated gonorrhea can lead to severe sequelae, including pelvic inflammatory disease and infertility in women, epididymitis in men, and sight-threatening conjunctivitis in infants born to infected mothers. Therefore, there is an immediate need for accelerated research toward the identification of molecular targets for development of drugs with new mechanisms of action and preventive vaccine(s). Global proteomic approaches are ideally suited to guide these studies. Recent quantitative proteomics (SILAC, iTRAQ, and ICAT) have illuminated the pathways utilized by N. gonorrhoeae to adapt to different lifestyles and micro-ecological niches within the host, while comparative 2D SDS-PAGE analysis has been used to elucidate spectinomycin resistance mechanisms. Further, high-throughput examinations of cell envelopes and naturally released membrane vesicles have unveiled the ubiquitous and differentially expressed proteins between temporally and geographically diverse N. gonorrhoeae isolates. This review will focus on these different approaches, emphasizing the role of proteomics in the search for vaccine candidates. Although our knowledge of N. gonorrhoeae has been expanded, still far less is known about this bacterium than the closely related N. meningitidis, where genomics- and proteomics-driven studies have led to the successful development of vaccines.
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Affiliation(s)
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
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17
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Singhal N, Kumar M, Kanaujia PK, Virdi JS. MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 2015; 6:791. [PMID: 26300860 PMCID: PMC4525378 DOI: 10.3389/fmicb.2015.00791] [Citation(s) in RCA: 778] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/21/2015] [Indexed: 01/13/2023] Open
Abstract
Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.
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Affiliation(s)
- Neelja Singhal
- Department of Microbiology, University of Delhi New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi New Delhi, India
| | - Pawan K Kanaujia
- Department of Microbiology, University of Delhi New Delhi, India
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18
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Proteotyping: Proteomic characterization, classification and identification of microorganisms--A prospectus. Syst Appl Microbiol 2015; 38:246-57. [PMID: 25933927 DOI: 10.1016/j.syapm.2015.03.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 03/23/2015] [Indexed: 12/13/2022]
Abstract
Modern microbial systematics requires a range of methodologies for the comprehensive characterization, classification and identification of microorganisms. While whole-genome sequences provide the ultimate reference for defining microbial phylogeny and taxonomy, selected biomarker-based strategies continue to provide the means for the bulk of microbial systematic studies. Proteomics, the study of the expression of genes, as well as the structure and function of the resulting proteins, offers indirect measures of genome sequence data. Recent developments in applications of proteomics for analyzing microorganisms have paralleled the growing microbial genome sequence database, as well as the evolution of mass spectrometry (MS) instrumentation and bioinformatics. MALDI-TOF MS, which generates proteomic mass patterns for 'fingerprint'-based characterizations, has provided a marked breakthrough for microbial identification. However, MALDI-TOF MS is limited in the number of targets that can be detected for strain characterization. Advanced methods of tandem mass spectrometry, in which proteins and peptides generated from proteins, are characterized and identified, using LC-MS/MS, provide the ability to detect hundreds or thousands of expressed microbial strain markers for high-resolution characterizations and identifications. Model studies demonstrate the application of proteomics-based analyses for bacterial species- and strain-level detection and identification and for characterization of environmentally relevant, metabolically diverse bacteria. Proteomics-based approaches represent an emerging complement to traditional methods of characterizing microorganisms, enabling the elucidation of the expressed biomarkers of genome sequence information, which can be applied to 'proteotyping' applications of microorganisms at all taxonomic levels.
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Vladimirova ES, Alekseechkina OA, Menshikov DD, Titova GP, Popova IE. [Features of severe surgical infections of soft tissues]. Khirurgiia (Mosk) 2015:25-34. [PMID: 26978620 DOI: 10.17116/hirurgia20151125-34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
AIM To analyze clinical and microbiological examinations in severe soft tissues infections and their significance in predictors of outcomes. MATERIAL AND METHODS Treatment of 19 patients with severe suppurative infection and suspected non-clostridial anaerobic flora with different causes of soft tissues infection was analyzed. All patients were treated in N.V. Sklifosovskiy Research Institute of Emergency Care for the period 2010-2012. Diagnosis was based on X-ray survey, sonography and CT data. Multicomponent management included surgery, intensive therapy, proteinic and water-electrolyte balance correction, deintoxication, nutritive support and immune therapy.Microbiological diagnosis was performed using Bactec-9050, Multiscan and WalkAway-40 analyzers. Culture mediums and microanaerostats to detect aerobic and obligately-anaerobic pathogens certified in Russia were used. Of 19 patients bacteriological examination was performed in 11 patients. So 107 specimens from wounds predominantly and blood were studied. 91 strains were revealed and identified. RESULTS 8 of 11 patients in group 1 were operated. Three patients were inoperable due to severe condition and endotoxic shock. Despite complex treatment inflammation progressed in 5 of 8 patients followed by death. The second group consisted of 8 survivors. Staphylococcus aureus played leading role. There were no significant differences related to obligately-anaerobic pathogens. Mixed populations of aerobic and facultative anaerobic pathogens were diagnosed in 45% of specimens sampled from deads that is significantly greater than from survivors (8.7%). Leading pathogens of severe suppurative infections of soft tissues were more frequent revealed in mono-culture. Early diagnosis of tissue infections caused by nonsporeforming microorganisms should be based on clinical instrumental data, microbiological and morphological examinations.
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Affiliation(s)
- E S Vladimirova
- N.V. Sklifosovsky Research Institute of Emergency Care, Moscow,Russia
| | - O A Alekseechkina
- N.V. Sklifosovsky Research Institute of Emergency Care, Moscow,Russia
| | - D D Menshikov
- N.V. Sklifosovsky Research Institute of Emergency Care, Moscow,Russia
| | - G P Titova
- N.V. Sklifosovsky Research Institute of Emergency Care, Moscow,Russia
| | - I E Popova
- N.V. Sklifosovsky Research Institute of Emergency Care, Moscow,Russia
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20
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Moura H, Izquierdo F, Woolfitt AR, Wagner G, Pinto T, del Aguila C, Barr JR. Detection of biomarkers of pathogenic Naegleria fowleri through mass spectrometry and proteomics. J Eukaryot Microbiol 2014; 62:12-20. [PMID: 25231600 DOI: 10.1111/jeu.12178] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/21/2014] [Accepted: 08/14/2014] [Indexed: 11/28/2022]
Abstract
Emerging methods based on mass spectrometry (MS) can be used in the rapid identification of microorganisms. Thus far, these practical and rapidly evolving methods have mainly been applied to characterize prokaryotes. We applied matrix-assisted laser-desorption-ionization-time-of-flight mass spectrometry MALDI-TOF MS in the analysis of whole cells of 18 N. fowleri isolates belonging to three genotypes. Fourteen originated from the cerebrospinal fluid or brain tissue of primary amoebic meningoencephalitis patients and four originated from water samples of hot springs, rivers, lakes or municipal water supplies. Whole Naegleria trophozoites grown in axenic cultures were washed and mixed with MALDI matrix. Mass spectra were acquired with a 4700 TOF-TOF instrument. MALDI-TOF MS yielded consistent patterns for all isolates examined. Using a combination of novel data processing methods for visual peak comparison, statistical analysis and proteomics database searching we were able to detect several biomarkers that can differentiate all species and isolates studied, along with common biomarkers for all N. fowleri isolates. Naegleria fowleri could be easily separated from other species within the genus Naegleria. A number of peaks detected were tentatively identified. MALDI-TOF MS fingerprinting is a rapid, reproducible, high-throughput alternative method for identifying Naegleria isolates. This method has potential for studying eukaryotic agents.
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Affiliation(s)
- Hercules Moura
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, M.S. F-50, 4770 Buford Hwy NE, Atlanta, Georgia, 30341, USA
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21
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Calvano CD, Italiano F, Catucci L, Agostiano A, Cataldi TRI, Palmisano F, Trotta M. The lipidome of the photosynthetic bacterium Rhodobacter sphaeroides R26 is affected by cobalt and chromate ions stress. Biometals 2013; 27:65-73. [PMID: 24249151 DOI: 10.1007/s10534-013-9687-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/10/2013] [Indexed: 02/07/2023]
Abstract
A detailed characterization of membrane lipids of the photosynthetic bacterium Rhodobacter (R.) sphaeroides was accomplished by thin-layer chromatography coupled with matrix-assisted laser desorption ionization mass spectrometry. Such an approach allowed the identification of the main membrane lipids belonging to different classes, namely cardiolipins (CLs), phosphatidylethanolamines, phosphatidylglycerols (PGs), phosphatidylcholines, and sulfoquinovosyldiacylglycerols (SQDGs). Thus, the lipidomic profile of R. sphaeroides R26 grown in abiotic stressed conditions by exposure to bivalent cobalt cation and chromate oxyanion, was investigated. Compared to bacteria grown under control conditions, significant lipid alterations take place under both stress conditions; cobalt exposure stress results in the relative content increase of CLs and SQDGs, most likely compensating the decrease in PGs content, whereas chromate stress conditions result in the relative content decrease of both PGs and SQDGs, leaving CLs unaltered. For the first time, the response of R. sphaeroides to heavy metals as Co(2+) and CrO4 (2-) is reported and changes in membrane lipid profiles were rationalised.
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Affiliation(s)
- Cosima Damiana Calvano
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
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22
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Han-Jen RE, Wai-Fong Y, Kok-Gan C. Pandoraea sp. RB-44, a novel quorum sensing soil bacterium. SENSORS 2013; 13:14121-32. [PMID: 24145919 PMCID: PMC3859112 DOI: 10.3390/s131014121] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 09/20/2013] [Accepted: 09/30/2013] [Indexed: 11/16/2022]
Abstract
Proteobacteria are known to communicate via signaling molecules and this process is known as quorum sensing. The most commonly studied quorum sensing molecules are N-acylhomoserine lactones (AHLs) that consists of a homoserine lactone moiety and an N-acyl side chain with various chain lengths and degrees of saturation at the C-3 position. We have isolated a bacterium, RB-44, from a site which was formally a landfill dumping ground. Using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry analysis, this isolate was identified as a Pandoraea sp.which was then screened for AHL production using biosensors which indicated its quorum sensing properties. To identify the AHL profile of Pandoraea sp. RB-44, we used high resolution tandem mass spectrometry confirming that this isolate produced N-octanoylhomoserine lactone (C8-HSL). To the best of our knowledge, this is the first report that showed quorum sensing activity exhibited by Pandoraea sp. Our data add Pandoraea sp. to the growing number of bacteria that possess QS systems.
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Affiliation(s)
- Robson Ee Han-Jen
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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23
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Fernández-No I, Böhme K, Díaz-Bao M, Cepeda A, Barros-Velázquez J, Calo-Mata P. Characterisation and profiling of Bacillus subtilis, Bacillus cereus and Bacillus licheniformis by MALDI-TOF mass fingerprinting. Food Microbiol 2013. [DOI: 10.1016/j.fm.2012.09.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Kilár A, Dörnyei Á, Kocsis B. Structural characterization of bacterial lipopolysaccharides with mass spectrometry and on- and off-line separation techniques. MASS SPECTROMETRY REVIEWS 2013; 32:90-117. [PMID: 23165926 DOI: 10.1002/mas.21352] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 03/27/2012] [Accepted: 03/27/2012] [Indexed: 06/01/2023]
Abstract
The focus of this review is the application of mass spectrometry to the structural characterization of bacterial lipopolysaccharides (LPSs), also referred to as "endotoxins," because they elicit the strong immune response in infected organisms. Recently, a wide variety of MS-based applications have been implemented to the structure elucidation of LPS. Methodological improvements, as well as on- and off-line separation procedures, proved the versatility of mass spectrometry to study complex LPS mixtures. Special attention is given in the review to the tandem mass spectrometric methods and protocols for the analyses of lipid A, the endotoxic principle of LPS. We compare and evaluate the different ionization techniques (MALDI, ESI) in view of their use in intact R- and S-type LPS and lipid A studies. Methods for sample preparation of LPS prior to mass spectrometric analysis are also described. The direct identification of intrinsic heterogeneities of most intact LPS and lipid A preparations is a particular challenge, for which separation techniques (e.g., TLC, slab-PAGE, CE, GC, HPLC) combined with mass spectrometry are often necessary. A brief summary of these combined methodologies to profile LPS molecular species is provided.
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Affiliation(s)
- Anikó Kilár
- Department of Analytical and Environmental Chemistry, Institute of Chemistry, Faculty of Sciences, University of Pécs, Pécs, Hungary.
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25
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Gopal J, Abdelhamid HN, Hua PY, Wu HF. Chitosan nanomagnets for effective extraction and sensitive mass spectrometric detection of pathogenic bacterial endotoxin from human urine. J Mater Chem B 2013; 1:2463-2475. [DOI: 10.1039/c3tb20079e] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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von Bergen M, Eidner A, Schmidt F, Murugaiyan J, Wirth H, Binder H, Maier T, Roesler U. Identification of harmless and pathogenic algae of the genus Prototheca by MALDI-MS. Proteomics Clin Appl 2012; 3:774-84. [PMID: 21136986 DOI: 10.1002/prca.200780138] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The only plants infectious for mammals, green algae from the genus Prototheca, are often overseen or mistaken for yeast in clinical diagnosis. To improve this diagnostical gap, a method was developed for fast and reliable identification of Prototheca. A collection of all currently recognized Prototheca species, most represented by several strains, were submitted to a simple extraction by 70% formic acid and ACN; the extracts were analyzed by means of MALDI-MS. Most of the peaks were found in the range from 4 to 20 kDa and showed a high reproducibility, not in absolute intensities, but in their peak pattern. The selection of measured peaks is mostly due to the technique of ionization in MALDI-MS, because proteins in the range up to 200 kDa were detected using gel electrophoresis. Some of the proteins were identified by peptide mass fingerprinting and MS(2) analysis and turned out to be ribosomal proteins or other highly abundant proteins such as ubiquitin. For the preparation of a heatmap, the intensities of the peaks were plotted and a cluster analysis was performed. From the peak-lists, a principal component analysis was conducted and a dendrogram was built. This dendrogram, based on MALDI spectra, was in fairly good agreement with a dendrogram based on sequence information from 18S DNA. As a result, pathogenic and nonpathogenic species from the genus Prototheca can be identified, with possible consequences for clinical diagnostics by MALDI-typing.
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Affiliation(s)
- Martin von Bergen
- Department of Proteomics, UFZ - Helmholtz-Centre for Environmental Research, Leipzig, Germany.
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Abstract
INTRODUCTION Current management of sepsis relies on the early detection and early administration of antimicrobials. This requires detection of pathogens earlier than conventional blood cultures and recognition of the immune status of the host earlier than the conventional biomarkers. This can be achieved by molecular techniques. AREAS COVERED Molecular diagnosis of pathogens is based on either rapid detection of pathogens grown in blood cultures or direct use of whole blood and blood products. Molecular diagnosis of the constellation of activations and inhibitions of pathways implicated in cellular processes can be achieved by gene profiling of a large array of genes. EXPERT OPINION Molecular microbial diagnosis enables rapid identification and precedes results obtained by conventional culture methods. Its role can be proved more useful in sepsis caused by specific microorganisms such as fungi performed by PMA-FISH and MALDI-TOF MS. Molecular techniques using blood aim for rapid pathogen identification. However, the provided information regarding the antimicrobial susceptibility of the pathogen is limited. Gene profiling in sepsis provides individualized information for the activation or inhibition of pathways of a variety of cellular processes. The transcriptome information is difficult to interpret in everyday clinical practice particularly on how information translates to patient needs.
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Affiliation(s)
- Antigone Kotsaki
- University of Athens, Medical School, 4th Department of Internal Medicine , Athens , Greece
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Pavlovic M, Konrad R, Iwobi AN, Sing A, Busch U, Huber I. A dual approach employing MALDI-TOF MS and real-time PCR for fast species identification within the Enterobacter cloacae complex. FEMS Microbiol Lett 2012; 328:46-53. [DOI: 10.1111/j.1574-6968.2011.02479.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 11/05/2011] [Accepted: 12/02/2011] [Indexed: 11/27/2022] Open
Affiliation(s)
- Melanie Pavlovic
- Bavarian Health and Food Safety Authority; Oberschleißheim; Germany
| | - Regina Konrad
- Bavarian Health and Food Safety Authority; Oberschleißheim; Germany
| | - Azuka N. Iwobi
- Bavarian Health and Food Safety Authority; Oberschleißheim; Germany
| | - Andreas Sing
- Bavarian Health and Food Safety Authority; Oberschleißheim; Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority; Oberschleißheim; Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority; Oberschleißheim; Germany
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29
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Parsiegla G, Shrestha B, Carrière F, Vertes A. Direct Analysis of Phycobilisomal Antenna Proteins and Metabolites in Small Cyanobacterial Populations by Laser Ablation Electrospray Ionization Mass Spectrometry. Anal Chem 2011; 84:34-8. [DOI: 10.1021/ac202831w] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Goetz Parsiegla
- CNRS, Aix-Marseille Université, Enzymologie Interfaciale et Physiologie
de la Lipolyse, UPR 9025, Marseille, France
| | - Bindesh Shrestha
- Department of Chemistry, W. M.
Keck Institute for Proteomics Technology and Applications, George Washington University, Washington, D.C. 20052,
United States
| | - Frédéric Carrière
- CNRS, Aix-Marseille Université, Enzymologie Interfaciale et Physiologie
de la Lipolyse, UPR 9025, Marseille, France
| | - Akos Vertes
- Department of Chemistry, W. M.
Keck Institute for Proteomics Technology and Applications, George Washington University, Washington, D.C. 20052,
United States
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Characterisation of histamine-producing bacteria from farmed blackspot seabream (Pagellus bogaraveo) and turbot (Psetta maxima). Int J Food Microbiol 2011; 151:182-9. [DOI: 10.1016/j.ijfoodmicro.2011.08.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 07/27/2011] [Accepted: 08/24/2011] [Indexed: 11/18/2022]
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31
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Šedo O, Sedláček I, Zdráhal Z. Sample preparation methods for MALDI-MS profiling of bacteria. MASS SPECTROMETRY REVIEWS 2011; 30:417-434. [PMID: 21500244 DOI: 10.1002/mas.20287] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 11/15/2009] [Accepted: 11/15/2009] [Indexed: 05/30/2023]
Abstract
Direct matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) bacterial cell or lysate analysis appears to meet all the criteria required for a rapid and reliable analytical microorganism identification and taxonomical classification tool. Few-minute analytical procedure providing information extending up to sub-species level underlines the potential of the MALDI-MS profiling in comparison with other methods employed in the field. However, the quality of MALDI-MS profiles and consequently the performance of the method are influenced by numerous factors, which involve particular steps of the sample preparation procedure. This review is aimed at advances in development and optimization of the MALDI-MS profiling methodology. Approaches improving the quality of the MALDI-MS profiles and universal feasibility of the method are discussed.
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Affiliation(s)
- Ondrej Šedo
- Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
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32
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Venkatesh M, Flores A, Luna RA, Versalovic J. Molecular microbiological methods in the diagnosis of neonatal sepsis. Expert Rev Anti Infect Ther 2011; 8:1037-48. [PMID: 20818947 DOI: 10.1586/eri.10.89] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Neonatal sepsis is a major cause of neonatal mortality and morbidity. The current gold standard for diagnosis of sepsis, namely blood culture, suffers from low sensitivity and a reporting delay of approximately 48-72 h. Rapid detection of sepsis and institution of antimicrobial therapy may improve patient outcomes. Rapid and sensitive tests that can inform clinicians regarding the institution or optimization of antimicrobial therapy are urgently needed. The ideal diagnostic test should have adequate specificity and negative predictive value to reliably exclude sepsis and avoid unnecessary antibiotic therapy. We comprehensively searched for neonatal studies that evaluated molecular methods for diagnosis of sepsis. We identified 19 studies that were assessed with respect to assay methodology and diagnostic characteristics. In addition, we also reviewed newer molecular microbiological assays of relevance that have not been fully evaluated in neonates. Molecular methods offer distinct advantages over blood cultures, including increased sensitivity and rapid diagnosis. However, diagnostic accuracy and cost-effectiveness should be established before implementation in clinical practice.
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Affiliation(s)
- Mohan Venkatesh
- Section of Neonatology, Department of Pediatrics, Texas Children's Hospital & Baylor College of Medicine, 6621 Fannin St, Houston, TX 77030, USA.
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Pierce CL, Rees JC, Fernández FM, Barr JR. Detection of Staphylococcus aureus using 15N-labeled bacteriophage amplification coupled with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Anal Chem 2011; 83:2286-93. [PMID: 21341703 DOI: 10.1021/ac103024m] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel approach to rapid bacterial detection using an isotopically labeled (15)N bacteriophage and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is introduced. Current phage amplification detection (PAD) via mass spectrometric analysis is limited because host bacteria must be inoculated with low phage titers in such a way that initial infecting phage concentrations must be below the detection limit of the instrument, thus lengthening incubation times. Additionally, PAD techniques cannot distinguish inoculate input phage from output phage which can increase the possibility of false positive results. Here, we report a rapid and accurate PAD approach for identification of Staphylococcus aureus via detection of bacteriophage capsid proteins. This approach uses both a wild-type (14)N and a (15)N-isotopically labeled S. aureus-specific bacteriophage. High (15)N phage titers, above our instrument's detection limits, were used to inoculate S. aureus. MALDI-TOF MS detection of the (14)N progeny capsid proteins in the phage-amplified culture indicated the presence of the host bacteria. Successful phage amplification was observed after 90 min of incubation. The amplification was observed by both MALDI-TOF MS analysis and by standard plaque assay measurements. This method overcomes current limitations by improving analysis times while increasing selectivity when compared to previously reported PAD methodologies.
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Affiliation(s)
- Carrie L Pierce
- National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, MS F-50, Atlanta, Georgia 30341, United States
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Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning. Syst Appl Microbiol 2011; 34:20-9. [DOI: 10.1016/j.syapm.2010.11.003] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 11/17/2010] [Accepted: 11/19/2010] [Indexed: 11/19/2022]
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35
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Zhang JI, Costa AB, Tao WA, Cooks RG. Direct detection of fatty acid ethyl esters using low temperature plasma (LTP) ambient ionization mass spectrometry for rapid bacterial differentiation. Analyst 2011; 136:3091-7. [DOI: 10.1039/c0an00940g] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Böhme K, Fernández-No IC, Barros-Velázquez J, Gallardo JM, Calo-Mata P, Cañas B. Species differentiation of seafood spoilage and pathogenic gram-negative bacteria by MALDI-TOF mass fingerprinting. J Proteome Res 2010; 9:3169-83. [PMID: 20408567 DOI: 10.1021/pr100047q] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Species differentiation is important for the early detection and identification of pathogenic and food-spoilage microorganisms that may be present in fish and seafood products. The main 26 species of seafood spoilage and pathogenic Gram-negative bacteria, including Aeromonas hydrophila, Acinetobacter baumanii, Pseudomonas spp., and Enterobacter spp. among others, were characterized by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) of low molecular weight proteins extracted from intact bacterial cells by a fast procedure. From the acquired spectra, a library of specific mass spectral fingerprints was constructed. To analyze spectral fingerprints, peaks in the mass range of 2000-10 000 Da were considered and representative mass lists of 10-35 peak masses were compiled. At least one unique biomarker peak was observed for each species, and various genus-specific peaks were detected for genera Proteus, Providencia, Pseudomonas, Serratia, Shewanella, and Vibrio. Phyloproteomic relationships based on these data were compared to phylogenetic analysis based on the 16S rRNA gene, and a similar clustering was found. The method was also successfully applied for the identification of three bacterial strains isolated from seafood by comparing the spectral fingerprints with the created library of reference fingerprints. Thus, the proteomic approach demonstrated to be a competent tool for species identification.
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Affiliation(s)
- Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
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Böhme K, Fernández-No IC, Gallardo JM, Cañas B, Calo-Mata P. Safety Assessment of Fresh and Processed Seafood Products by MALDI-TOF Mass Fingerprinting. FOOD BIOPROCESS TECH 2010. [DOI: 10.1007/s11947-010-0441-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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38
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Kitayeva NV, Frigo NV, Rotanov SV, Khairulin RF. Prospects of using proteome technologies in the diagnostics of sexually transmitted infections and skin diseases. VESTNIK DERMATOLOGII I VENEROLOGII 2010. [DOI: 10.25208/vdv876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The article presents data from the literature describing up-to-date syphilis diagnostics methods used in the Russian Federation. It
also describes main proteome techniques and gives the results of applying proteome technologies in the diagnostics of diseases
including infectious ones, and prospects and opportunities for using direct proteome profiling to develop a new method for syphilis
diagnostics are analyzed.
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Abstract
BACKGROUND Mass spectrometry (MS) is a suitable technology for microorganism identification and characterization. CONTENT This review summarizes the MS-based methods currently used for the analyses of pathogens. Direct analysis of whole pathogenic microbial cells using MS without sample fractionation reveals specific biomarkers for taxonomy and provides rapid and high-throughput capabilities. MS coupled with various chromatography- and affinity-based techniques simplifies the complexity of the signals of the microbial biomarkers and provides more accurate results. Affinity-based methods, including those employing nanotechnology, can be used to concentrate traces of target microorganisms from sample solutions and, thereby, improve detection limits. Approaches combining amplification of nucleic acid targets from pathogens with MS-based detection are alternatives to biomarker analyses. Many data analysis methods, including multivariate analysis and bioinformatics approaches, have been developed for microbial identification. The review concludes with some current clinical applications of MS in the identification and typing of infectious microorganisms, as well as some perspectives. SUMMARY Advances in instrumentation (separation and mass analysis), ionization techniques, and biological methodologies will all enhance the capabilities of MS for the analysis of pathogens.
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Affiliation(s)
- Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan.
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The era of molecular and other non-culture-based methods in diagnosis of sepsis. Clin Microbiol Rev 2010; 23:235-51. [PMID: 20065332 DOI: 10.1128/cmr.00043-09] [Citation(s) in RCA: 256] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Sepsis, a leading cause of morbidity and mortality throughout the world, is a clinical syndrome with signs and symptoms relating to an infectious event and the consequent important inflammatory response. From a clinical point of view, sepsis is a continuous process ranging from systemic inflammatory response syndrome (SIRS) to multiple-organ-dysfunction syndrome (MODS). Blood cultures are the current "gold standard" for diagnosis, and they are based on the detection of viable microorganisms present in blood. However, on some occasions, blood cultures have intrinsic limitations in terms of sensitivity and rapidity, and it is not expected that these drawbacks will be overcome by significant improvements in the near future. For these principal reasons, other approaches are therefore needed in association with blood culture to improve the overall diagnostic yield for septic patients. These considerations have represented the rationale for the development of highly sensitive and fast laboratory methods. This review addresses non-culture-based techniques for the diagnosis of sepsis, including molecular and other non-culture-based methods. In particular, the potential clinical role for the sensitive and rapid detection of bacterial and fungal DNA in the development of new diagnostic algorithms is discussed.
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Sariyar-Akbulut B. Rapid differentiation of new isolates with MALDI-TOF mass spectrometry via discriminant function analysis based on principal components. KOREAN J CHEM ENG 2010. [DOI: 10.1007/s11814-009-0243-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Fernández-No IC, Böhme K, Gallardo JM, Barros-Velázquez J, Cañas B, Calo-Mata P. Differential characterization of biogenic amine-producing bacteria involved in food poisoning using MALDI-TOF mass fingerprinting. Electrophoresis 2010; 31:1116-27. [DOI: 10.1002/elps.200900591] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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43
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Mamone G, Picariello G, Caira S, Addeo F, Ferranti P. Analysis of food proteins and peptides by mass spectrometry-based techniques. J Chromatogr A 2009; 1216:7130-42. [DOI: 10.1016/j.chroma.2009.07.052] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 06/19/2009] [Accepted: 07/24/2009] [Indexed: 10/20/2022]
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44
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Phylogenetic analysis of Rhodococcus erythropolis based on the variation of ribosomal proteins as observed by matrix-assisted laser desorption ionization-mass spectrometry without using genome information. J Biosci Bioeng 2009; 108:348-53. [DOI: 10.1016/j.jbiosc.2009.04.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2009] [Revised: 04/09/2009] [Accepted: 04/13/2009] [Indexed: 11/24/2022]
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45
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Vater J, Wilde C, Kell H. In situ detection of the intermediates in the biosynthesis of surfactin, a lipoheptapeptide from Bacillus subtilis OKB 105, by whole-cell cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in combination with mutant analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:1493-1498. [PMID: 19350532 DOI: 10.1002/rcm.4031] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
An innovative technique to investigate the intermediates involved in the biosynthesis of the lipoheptapeptide surfactin from Bacillus subtilis OKB105 combining whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) with targeted generation of knock-out mutants was demonstrated. This method allows efficient, sensitive detection of biosynthetic intermediates in a minimum of time directly at the outer surface of microbial cells picked from agar plates or in surface extracts prepared thereof. Biosynthesis of surfactin is encoded by the srf-operon which is organized into four open reading frames which have been attributed to three multifunctional NRPS enzymes (SrfA-C) and a thioesterase/acyltransferase enzyme SrfD. For the wild-type strain OKB 105 only the end product surfactin was found mass spectrometrically. For the detection of lipopeptide intermediates three plasmid- and transposon-insertion mutants were generated interrupting the surfactin assembly line at defined positions. Strain LAB 327 was mutated in the spacer region between enzymes SrfA and B. Here only SrfA was active with the lipotripeptide beta-OH-acyl-L-Glu-L-Leu-D-Leu as the end product. Mutant OKB 120 bears a transposon mutation in SrfB between the first and second amino acid activating modules SrfB1 and SrfB2. It showed all intermediates from the lipodi- until to the lipotetrapeptide beta-OH-acyl-L-Glu-L-Leu-D-Leu-L-Val. In LAB 223 SrfC was knocked out by a transposon mutation. It produced the lipohexapeptide beta-OH-acyl-L-Glu-L-Leu-D-Leu-L-Val-L-Asp-D-Leu. Our work highlights the applicability and the potential of whole-cell MALDI-TOFMS as an innovative efficient tool for the analysis of intermediate steps of biosynthetic pathways.
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Affiliation(s)
- Joachim Vater
- Institut für Chemie, Arbeitsgruppe Biochemie und Molekulare Biologie, Technische Universität Berlin, Franklinstr. 29, D-10587 Berlin, Germany.
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Hu C, van der Heijden R, Wang M, van der Greef J, Hankemeier T, Xu G. Analytical strategies in lipidomics and applications in disease biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:2836-46. [PMID: 19233743 DOI: 10.1016/j.jchromb.2009.01.038] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2008] [Revised: 01/24/2009] [Accepted: 01/27/2009] [Indexed: 11/25/2022]
Abstract
Lipidomics is a lipid-targeted metabolomics approach aiming at comprehensive analysis of lipids in biological systems. Recently, lipid profiling, or so-called lipidomics research, has captured increased attention due to the well-recognized roles of lipids in numerous human diseases to which lipid-associated disorders contribute, such as diabetes, obesity, atherosclerosis and Alzheimer's disease. Investigating lipid biochemistry using a lipidomics approach will not only provide insights into the specific roles of lipid molecular species in health and disease, but will also assist in identifying potential biomarkers for establishing preventive or therapeutic approaches for human health. Recent technological advancements in mass spectrometry and rapid improvements in chromatographic techniques have led to the rapid expansion of the lipidomics research field. In this review, emphasis is given to the recent advances in lipidomics technologies and their applications in disease biomarker discovery.
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Affiliation(s)
- Chunxiu Hu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, the Chinese Academy of Sciences, 457 Zhongshan Road, 116023 Dalian, China
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Demirev PA, Fenselau C. Mass spectrometry in biodefense. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:1441-57. [PMID: 18720458 DOI: 10.1002/jms.1474] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Potential agents for biological attacks include both microorganisms and toxins. In mass spectrometry (MS), rapid identification of potential bioagents is achieved by detecting the masses of unique biomarkers, correlated to each agent. Currently, proteins are the most reliable biomarkers for detection and characterization of both microorganisms and toxins, and MS-based proteomics is particularly well suited for biodefense applications. Confident identification of an organism can be achieved by top-down proteomics following identification of individual protein biomarkers from their tandem mass spectra. In bottom-up proteomics, rapid digestion of intact protein biomarkers is again followed by MS/MS to provide unambiguous bioagent identification and characterization. Bioinformatics obviates the need for culturing and rigorous control of experimental variables to create and use MS fingerprint libraries for various classes of bioweapons. For specific applications, MS methods, instruments and algorithms have also been developed for identification based on biomarkers other than proteins and peptides.
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Affiliation(s)
- Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD 20723, USA.
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Abstract
Direct detection technologies for pathogenic microorganisms are emerging to be applied in the diagnosis of serious bloodstream infections and infections at sterile body sites, as well as for quality control measures prior to the release of sterile blood products and to ascertain microbial safety of food. Standard blood cultures as the current gold standard for detection of bacteraemia/sepsis and other culture-based microbiological identification procedures are comparatively slow and have limited sensitivity for fastidious or slow-growing microorganisms. Rapid nucleic acid-based technologies with PCR amplification or hybridisation probes for specific pathogens, broad-range bacterial or fungal assays, flow cytometry, as well as protein-based characterisation by mass spectrometry, aim at identification of pathogenic microorganisms within minutes to hours. Interpretation of direct detection of panbacterial or panfungal nucleic acids instead of living microorganisms in blood is complex, given the risk of contamination, the ubiquitous presence of bacterial and fungal DNA, and the lack of a gold standard. Since many of the infections at sterile sites, particularly sepsis, are medical emergencies requiring immediate therapeutic responses, rapid technologies could contribute to reduction of morbidity, mortality, and of the economic burden. This review summarises the currently available data on rapid non-culture-based technologies and outlines the potential clinical usefulness in infectious disease diagnosis.
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Affiliation(s)
- Mariam Klouche
- Bremer Zentrum für Laboratoriumsmedizin GmbH and LADR GmbH Medizinisches Versorgungszentrum Bremen, Bremen, Germany.
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John CM, Liu M, Jarvis GA. Profiles of structural heterogeneity in native lipooligosaccharides of Neisseria and cytokine induction. J Lipid Res 2008; 50:424-438. [PMID: 18832773 DOI: 10.1194/jlr.m800184-jlr200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fine differences in the phosphorylation and acylation of lipooligosaccharide (LOS) from Neisseria species are thought to profoundly influence the virulence of the organisms and the innate immune responses of the host, such as signaling through toll-like receptor 4 (TLR4) and triggering receptor expressed on myeloid cells (TREM). MALDI time-of-flight (TOF) mass spectrometry was used to characterize heterogeneity in the native LOS from Neisseria gonorrheae and N. meningitidis. A sample preparation methodology previously reported for Escherichia coli lipopolysaccharide (LPS) employing deposition of untreated LOS on a thin layer of a film composed of 2,4,6-trihydroxyacetophenone and nitrocellulose was used. Prominent peaks were observed corresponding to molecular ions and to fragment ions primarily formed by cleavage between the 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) and the lipid A (LA). Analyses of these data and comparison with spectra of the corresponding O-deacylated or hydrogen fluoride-treated LOS enabled the detection of novel species that apparently differed by the expression of up to three phosphates with one or more phosphoethanolamine (PEA) groups on the LA. We found that the heterogeneity profile of acylation and phosphorylation correlates with the induction of proinflammatory cytokines in THP-1 monocytic cells. This methodology enabled us to rapidly profile components of structural variants of native LOS that are of importance biologically.
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Affiliation(s)
- Constance M John
- Center for Immunochemistry, Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, CA, 94121
| | - Mingfeng Liu
- Center for Immunochemistry, Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, CA, 94121
| | - Gary A Jarvis
- Center for Immunochemistry, Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, CA, 94121; Department of Laboratory Medicine, University of California, San Francisco, CA 94143.
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50
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Dugas AJ, Murray KK. On-target digestion of collected bacteria for MALDI mass spectrometry. Anal Chim Acta 2008; 627:154-61. [DOI: 10.1016/j.aca.2008.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 07/07/2008] [Accepted: 07/14/2008] [Indexed: 12/13/2022]
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