1
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Gant MS, Chamot-Rooke J. Present and future perspectives on mass spectrometry for clinical microbiology. Microbes Infect 2024; 26:105296. [PMID: 38199266 DOI: 10.1016/j.micinf.2024.105296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/01/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
In the last decade, MALDI-TOF Mass Spectrometry (MALDI-TOF MS) has been introduced and broadly accepted by clinical laboratory laboratories throughout the world as a powerful and efficient tool for rapid microbial identification. 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. Whilst MALDI-TOF MS is currently the gold-standard, it suffers from several shortcomings such as lack of direct information on antibiotic resistance, poor depth of analysis and insufficient discriminatory power for the distinction of closely related bacterial species or for reliably sub-differentiating isolates to the level of clones or strains. Thus, new approaches targeting proteins and allowing a better characterization of bacterial strains are strongly needed, if possible, on a very short time scale after sample collection in the hospital. Bottom-up proteomics (BUP) is a nice alternative to MALDI-TOF MS, offering the possibility for in-depth proteome analysis. Top-down proteomics (TDP) provides the highest molecular precision in proteomics, allowing the characterization of proteins at the proteoform level. A number of studies have already demonstrated the potential of these techniques in clinical microbiology. In this review, we will discuss the current state-of-the-art of MALDI-TOF MS for the rapid microbial identification and detection of resistance to antibiotics and describe emerging approaches, including bottom-up and top-down proteomics as well as ambient MS technologies.
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Affiliation(s)
- Megan S Gant
- Institut Pasteur, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology 75015 Paris, France
| | - Julia Chamot-Rooke
- Institut Pasteur, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology 75015 Paris, France.
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2
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Díaz-Grijuela E, Hernández A, Caballero C, Fernandez R, Urtasun R, Gulak M, Astigarraga E, Barajas M, Barreda-Gómez G. From Lipid Signatures to Cellular Responses: Unraveling the Complexity of Melanoma and Furthering Its Diagnosis and Treatment. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:1204. [PMID: 39202486 PMCID: PMC11356604 DOI: 10.3390/medicina60081204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 09/03/2024]
Abstract
Recent advancements in mass spectrometry have significantly enhanced our understanding of complex lipid profiles, opening new avenues for oncological diagnostics. This review highlights the importance of lipidomics in the comprehension of certain metabolic pathways and its potential for the detection and characterization of various cancers, in particular melanoma. Through detailed case studies, we demonstrate how lipidomic analysis has led to significant breakthroughs in the identification and understanding of cancer types and its potential for detecting unique biomarkers that are instrumental in its diagnosis. Additionally, this review addresses the technical challenges and future perspectives of these methodologies, including their potential expansion and refinement for clinical applications. The discussion underscores the critical role of lipidomic profiling in advancing cancer diagnostics, proposing a new paradigm in how we approach this devastating disease, with particular emphasis on its application in comparative oncology.
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Affiliation(s)
| | | | | | - Roberto Fernandez
- IMG Pharma Biotech, Research and Development Division, 48170 Zamudio, Spain;
| | - Raquel Urtasun
- Biochemistry Area, Department of Health Science, Universidad Pública de Navarra, 31006 Pamplona, Spain; (R.U.); (M.B.)
| | | | - Egoitz Astigarraga
- Betternostics SL, 31110 Noáin, Spain; (E.D.-G.); (A.H.); (C.C.)
- IMG Pharma Biotech, Research and Development Division, 48170 Zamudio, Spain;
| | - Miguel Barajas
- Biochemistry Area, Department of Health Science, Universidad Pública de Navarra, 31006 Pamplona, Spain; (R.U.); (M.B.)
| | - Gabriel Barreda-Gómez
- Betternostics SL, 31110 Noáin, Spain; (E.D.-G.); (A.H.); (C.C.)
- IMG Pharma Biotech, Research and Development Division, 48170 Zamudio, Spain;
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3
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Sasiene ZJ, LeBrun ES, Velappan N, Anderson AR, Patterson NH, Dufresne M, Farrow MA, Norris JL, Caprioli RM, Mach PM, McBride EM, Glaros TG. Multidimensional mass profiles increase confidence in bacterial identification when using low-resolution mass spectrometers. Analyst 2024; 149:3564-3574. [PMID: 38717518 DOI: 10.1039/d4an00325j] [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: 06/25/2024]
Abstract
Field-forward analytical technologies, such as portable mass spectrometry (MS), enable essential capabilities for real-time monitoring and point-of-care diagnostic applications. Significant and recent investments improving the features of miniaturized mass spectrometers enable various new applications outside of small molecule detection. Most notably, the addition of tandem mass spectrometry scans (MS/MS) allows the instrument to isolate and fragment ions and increase the analytical specificity by measuring unique chemical signatures for ions of interest. Notwithstanding these technological advancements, low-cost, portable systems still struggle to confidently identify clinically significant organisms of interest, such as bacteria, viruses, and proteinaceous toxins, due to the limitations in resolving power. To overcome these limitations, we developed a novel multidimensional mass fingerprinting technique that uses tandem mass spectrometry to increase the chemical specificity for low-resolution mass spectral profiles. We demonstrated the method's capabilities for differentiating four different bacteria, including attentuated strains of Yersinia pestis. This approach allowed for the accurate (>92%) identification of each organism at the strain level using de-resolved matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data to mimic the performance characteristics of miniaturized mass spectrometers. This work demonstrates that low-resolution mass spectrometers, equipped with tandem MS acquisition modes, can accurately identify clinically relevant bacteria. These findings support the future application of these technologies for field-forward and point-of-care applications where high-performance mass spectrometers would be cost-prohibitive or otherwise impractical.
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Affiliation(s)
- Zachary J Sasiene
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Erick S LeBrun
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Nileena Velappan
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Austin R Anderson
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Nathan H Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Melissa A Farrow
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Jeremy L Norris
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Phillip M Mach
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Ethan M McBride
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Trevor G Glaros
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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4
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Sibińska E, Arendowski A, Fijałkowski P, Gabryś D, Pomastowski P. Comparison of the Bruker Microflex LT and Zybio EXS2600 MALDI TOF MS systems for the identification of clinical microorganisms. Diagn Microbiol Infect Dis 2024; 108:116150. [PMID: 38035652 DOI: 10.1016/j.diagmicrobio.2023.116150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]
Abstract
The emergence of Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI TOF MS) technology has expanded the capabilities for identifying microorganisms in clinical labs, replacing traditional biochemical testing with a proteomic approach. In the present study, we compared results between the two commercial MALDI TOF MS systems, Bruker Microflex LT Biotyper and Zybio EXS2600 Ex-Accuspec, for the identification of 1979 urinary isolates by direct extraction method. Current study found that both systems identified a high percentage of isolates to at least the genus level - Bruker 95.6 % of isolates, Zybio 92.4 %. In the case of 89.5 % of all analyzed spectra, the identification results were consistent between the used devices. The highest score values and the highest percentage of spectra identified to species were obtained for gram-negative bacteria. The results show that both systems are equally good choices in terms of analytical performance for routine microbiological diagnostic procedures.
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Affiliation(s)
- Ewelina Sibińska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland
| | - Adrian Arendowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland.
| | - Piotr Fijałkowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland
| | - Dorota Gabryś
- Radiotherapy Department, Maria Sklodowska-Curie National Research Institute of Oncology, Wybrzeże Armii Krajowej 15 Str., Gliwice 44-102, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland
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5
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Raslan MA, Raslan SA, Shehata EM, Mahmoud AS, Viana MVC, Aburjaile F, Barh D, Sabri NA, Azevedo V. Mass Spectrometry Applications to Study Human Microbiome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:87-101. [PMID: 38409417 DOI: 10.1007/978-3-031-50624-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbiotas are an adaptable component of ecosystems, including human ecology. Microorganisms influence the chemistry of their specialized niche, such as the human gut, as well as the chemistry of distant surroundings, such as other areas of the body. Metabolomics based on mass spectrometry (MS) is one of the primary methods for detecting and identifying small compounds generated by the human microbiota, as well as understanding the functional significance of these microbial metabolites. This book chapter gives basic knowledge on the kinds of untargeted mass spectrometry as well as the data types that may be generated in the context of microbiome study. While data analysis remains a barrier, the emphasis is on data analysis methodologies and integrative analysis, particularly the integration of microbiome sequencing data. Mass spectrometry (MS)-based techniques have resurrected culture methods for studying the human gut microbiota, filling in the gaps left by high-throughput sequencing methods in terms of culturing minor populations.
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Affiliation(s)
| | | | | | - Amr S Mahmoud
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Marcus Vinicius Canário Viana
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávia Aburjaile
- Preventive Veterinary Medicine Departament, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Debmalya Barh
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India
| | - Nagwa A Sabri
- Department of Clinical Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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6
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Zhu Y. Plasma/Serum Proteomics based on Mass Spectrometry. Protein Pept Lett 2024; 31:192-208. [PMID: 38869039 PMCID: PMC11165715 DOI: 10.2174/0109298665286952240212053723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 06/14/2024]
Abstract
Human blood is a window of physiology and disease. Examination of biomarkers in blood is a common clinical procedure, which can be informative in diagnosis and prognosis of diseases, and in evaluating treatment effectiveness. There is still a huge demand on new blood biomarkers and assays for precision medicine nowadays, therefore plasma/serum proteomics has attracted increasing attention in recent years. How to effectively proceed with the biomarker discovery and clinical diagnostic assay development is a question raised to researchers who are interested in this area. In this review, we comprehensively introduce the background and advancement of technologies for blood proteomics, with a focus on mass spectrometry (MS). Analyzing existing blood biomarkers and newly-built diagnostic assays based on MS can shed light on developing new biomarkers and analytical methods. We summarize various protein analytes in plasma/serum which include total proteome, protein post-translational modifications, and extracellular vesicles, focusing on their corresponding sample preparation methods for MS analysis. We propose screening multiple protein analytes in the same set of blood samples in order to increase success rate for biomarker discovery. We also review the trends of MS techniques for blood tests including sample preparation automation, and further provide our perspectives on their future directions.
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Affiliation(s)
- Yiying Zhu
- Department of Chemistry, Tsinghua University, Beijing, China
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7
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Zhang H, Yang Y, Jiang Y, Zhang M, Xu Z, Wang X, Jiang J. Mass Spectrometry Analysis for Clinical Applications: A Review. Crit Rev Anal Chem 2023:1-20. [PMID: 37910438 DOI: 10.1080/10408347.2023.2274039] [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: 11/03/2023]
Abstract
Mass spectrometry (MS) has become an attractive analytical method in clinical analysis due to its comprehensive advantages of high sensitivity, high specificity and high throughput. Separation techniques coupled MS detection (e.g., LC-MS/MS) have shown unique advantages over immunoassay and have developed as golden criterion for many clinical applications. This review summarizes the characteristics and applications of MS, and emphasizes the high efficiency of MS in clinical research. In addition, this review also put forward further prospects for the future of mass spectrometry technology, including the introduction of miniature MS instruments, point-of-care detection and high-throughput analysis, to achieve better development of MS technology in various fields of clinical application. Moreover, as ambient ionization mass spectrometry (AIMS) requires little or no sample pretreatment and improves the flux of MS, this review also summarizes its potential applications in clinic.
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Affiliation(s)
- Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
| | - Yali Yang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| | - Yanxiao Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
| | - Meng Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| | - Zhilong Xu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| | - Xiaofei Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
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8
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Kaushal S, Priyadarshi N, Garg P, Singhal NK, Lim DK. Nano-Biotechnology for Bacteria Identification and Potent Anti-bacterial Properties: A Review of Current State of the Art. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2529. [PMID: 37764558 PMCID: PMC10536455 DOI: 10.3390/nano13182529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/26/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]
Abstract
Sepsis is a critical disease caused by the abrupt increase of bacteria in human blood, which subsequently causes a cytokine storm. Early identification of bacteria is critical to treating a patient with proper antibiotics to avoid sepsis. However, conventional culture-based identification takes a long time. Polymerase chain reaction (PCR) is not so successful because of the complexity and similarity in the genome sequence of some bacterial species, making it difficult to design primers and thus less suitable for rapid bacterial identification. To address these issues, several new technologies have been developed. Recent advances in nanotechnology have shown great potential for fast and accurate bacterial identification. The most promising strategy in nanotechnology involves the use of nanoparticles, which has led to the advancement of highly specific and sensitive biosensors capable of detecting and identifying bacteria even at low concentrations in very little time. The primary drawback of conventional antibiotics is the potential for antimicrobial resistance, which can lead to the development of superbacteria, making them difficult to treat. The incorporation of diverse nanomaterials and designs of nanomaterials has been utilized to kill bacteria efficiently. Nanomaterials with distinct physicochemical properties, such as optical and magnetic properties, including plasmonic and magnetic nanoparticles, have been extensively studied for their potential to efficiently kill bacteria. In this review, we are emphasizing the recent advances in nano-biotechnologies for bacterial identification and anti-bacterial properties. The basic principles of new technologies, as well as their future challenges, have been discussed.
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Affiliation(s)
- Shimayali Kaushal
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea;
| | - Nitesh Priyadarshi
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, India; (N.P.); (P.G.)
| | - Priyanka Garg
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, India; (N.P.); (P.G.)
| | - Nitin Kumar Singhal
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, India; (N.P.); (P.G.)
| | - Dong-Kwon Lim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea;
- Department of Integrative Energy Engineering, College of Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Brain Science Institute, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
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9
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Farhat TM, Al Disi ZA, Ashfaq MY, Zouari N. Study of diversity of mineral-forming bacteria in sabkha mats and sediments of mangrove forest in Qatar. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2023; 39:e00811. [PMID: 37663542 PMCID: PMC10470404 DOI: 10.1016/j.btre.2023.e00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/13/2023] [Accepted: 08/20/2023] [Indexed: 09/05/2023]
Abstract
The involvement of microorganisms in carbonate minerals and modern dolomite formation in evaporitic environments occupied with microbial mats (i.e., sabkha) and in mangrove forests is evidenced, while its potential diversity requires further elucidation. Microorganisms can create supersaturated microenvironments facilitating the formation of various carbonate minerals through specific metabolic pathways. This is particularly important in arid environments, where deposition and sedimentary structures can occur. This study investigated the biodiversity of halophilic, heterotrophic, and aerobic mineral-forming bacteria in mangrove forests and living and decaying mats of Qatari sabkha. The diversity study was performed at the protein level using MALDI-TOF mass spectrometry protein profiles combined with principal component analysis (PCA), which revealed a high diversity of isolated strains at the taxonomy and protein profile levels. The diversity of the minerals formed in pure cultures was evidenced by SEM/EDS and XRD analysis. Different types of carbonate minerals (calcium carbonate, magnesium carbonates, and high-magnesium calcites) were formed in pure cultures of the studied strains, which might explain their occurrence in the bulk composition of the sediments from where the strains were isolated. These results illuminate the diversity of biological mineral-formation processes in the extreme environments of Qatari sabkhas and mangroves, explaining the high diversity of minerals in these environments.
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Affiliation(s)
- Toka Mahmoud Farhat
- Environmental Sciences Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O.B 2713, Doha Qatar
| | - Zulfa Ali Al Disi
- Environmental Sciences Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O.B 2713, Doha Qatar
- Environmental Science Center, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammad Yousaf Ashfaq
- Environmental Sciences Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O.B 2713, Doha Qatar
| | - Nabil Zouari
- Environmental Sciences Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O.B 2713, Doha Qatar
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10
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Wang X, Wu G, Han S, Yang J, He X, Li H. Differentiation and Identification of Endophytic Bacteria from Populus Based on Mass Fingerprints and Gene Sequences. Int J Mol Sci 2023; 24:13449. [PMID: 37686254 PMCID: PMC10487577 DOI: 10.3390/ijms241713449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Plant endophytic bacteria play important roles in plants' growth and resistance to stress. It is important to characterize endophytic bacteria to be able to understand their benefits. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a powerful technique for bacterial identification due to its high throughput and simple procedures. In this study, the endophytic bacteria separated from Populus (the leaves, roots and stems of Populus tomentosa Carrière; stems of Populus nigra Linn. var. nigra; and stems of Populus canadensis Moench) were identified and classified based on MALDI-TOF MS data and 16S rRNA gene sequencing. The sampling and preparation of bacteria were optimized to obtain meaningful protein mass fingerprints. The composite correlation index (CCI) values of the inter-genera and inter-species protein mass fingerprints demonstrated sufficient differences between the strains. In the CCI value matrix for ten species in the same genus, all the CCI values were less than 0.5. Among the species, 95.6% of all the CCI values were less than 0.5. After data processing, the classification capacity of the protein mass fingerprints was verified using inter-specific and inter-generic PCoA. To compare different methods' potential for differentiation and phylogenetic analysis, a dendrogram of the MS profiles and a phylogenetic tree based on the 16S rRNA gene sequences were constructed using 61 endophytic bacteria found in Populus. The clustering and grouping results show that the phylogenetic analysis based on MALDI-TOF MS is similar to that based on 16S rRNA gene sequencing. This study provides a valuable reference for differentiating and identifying endophytic bacteria according to their protein mass fingerprints.
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Affiliation(s)
- Xia Wang
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (X.W.); (G.W.); (S.H.); (J.Y.)
- Department of Chemistry, MOE (Ministry of Education) Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Guanqi Wu
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (X.W.); (G.W.); (S.H.); (J.Y.)
- Department of Chemistry, MOE (Ministry of Education) Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Shuo Han
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (X.W.); (G.W.); (S.H.); (J.Y.)
| | - Jingjing Yang
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (X.W.); (G.W.); (S.H.); (J.Y.)
| | - Xiangwei He
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (X.W.); (G.W.); (S.H.); (J.Y.)
| | - Haifang Li
- Department of Chemistry, MOE (Ministry of Education) Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
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11
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Buszewski B, Błońska D, Kłodzińska E, Konop M, Kubesová A, Šalplachta J. Determination of Pathogens by Electrophoretic and Spectrometric Techniques. Crit Rev Anal Chem 2023:1-24. [PMID: 37326587 DOI: 10.1080/10408347.2023.2219748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In modern medical diagnostics, where analytical chemistry plays a key role, fast and accurate identification of pathogens is becoming increasingly important. Infectious diseases pose a growing threat to public health due to population growth, international air travel, bacterial resistance to antibiotics, and other factors. For instance, the detection of SARS-CoV-2 in patient samples is a key tool to monitor the spread of the disease. While there are several techniques for identifying pathogens by their genetic code, most of these methods are too expensive or slow to effectively analyze clinical and environmental samples that may contain hundreds or even thousands of different microbes. Standard approaches (e.g., culture media and biochemical assays) are known to be very time- and labor-intensive. The purpose of this review paper is to highlight the problems associated with the analysis and identification of pathogens that cause many serious infections. Special attention was paid to the description of mechanisms and the explanation of the phenomena and processes occurring on the surface of pathogens as biocolloids (charge distribution). This review also highlights the importance of electromigration techniques and demonstrates their potential for pathogen pre-separation and fractionation and demonstrates the use of spectrometric methods, such as MALDI-TOF MS, for their detection and identification.
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Affiliation(s)
- Bogusław Buszewski
- Prof. Jan Czochralski Kuyavian-Pomeranian Research & Development Centre, Torun, Poland
- Department of Environmental Chemistry and Bioanalytics, Nicolaus Copernicus University in Toruń, Torun, Poland
| | - Dominika Błońska
- Department of Environmental Chemistry and Bioanalytics, Nicolaus Copernicus University in Toruń, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Torun, Poland
| | - Ewa Kłodzińska
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Marek Konop
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Anna Kubesová
- Institute of Analytical Chemistry of the CAS, Brno, Czech Republic
| | - Jiří Šalplachta
- Institute of Analytical Chemistry of the CAS, Brno, Czech Republic
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12
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Fast Track Diagnostic Tools for Clinical Management of Sepsis: Paradigm Shift from Conventional to Advanced Methods. Diagnostics (Basel) 2023; 13:diagnostics13020277. [PMID: 36673087 PMCID: PMC9857847 DOI: 10.3390/diagnostics13020277] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/24/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Sepsis is one of the deadliest disorders in the new century due to specific limitations in early and differential diagnosis. Moreover, antimicrobial resistance (AMR) is becoming the dominant threat to human health globally. The only way to encounter the spread and emergence of AMR is through the active detection and identification of the pathogen along with the quantification of resistance. For better management of such disease, there is an essential requirement to approach many suitable diagnostic techniques for the proper administration of antibiotics and elimination of these infectious diseases. The current method employed for the diagnosis of sepsis relies on the conventional culture of blood suspected infection. However, this method is more time consuming and generates results that are false negative in the case of antibiotic pretreated samples as well as slow-growing microbes. In comparison to the conventional method, modern methods are capable of analyzing blood samples, obtaining accurate results from the suspicious patient of sepsis, and giving all the necessary information to identify the pathogens as well as AMR in a short period. The present review is intended to highlight the culture shift from conventional to modern and advanced technologies including their limitations for the proper and prompt diagnosing of bloodstream infections and AMR detection.
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A novel time-lapse imaging method for studying developing bacterial biofilms. Sci Rep 2022; 12:21120. [PMID: 36476631 PMCID: PMC9729682 DOI: 10.1038/s41598-022-24431-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
In nature, bacteria prevailingly reside in the form of biofilms. These elaborately organized surface-bound assemblages of bacterial cells show numerous features of multicellular organization. We recently showed that biofilm growth is a true developmental process, which resembles developmental processes in multicellular eukaryotes. To study the biofilm growth in a fashion of eukaryotic ontogeny, it is essential to define dynamics and critical transitional phases of this process. The first step in this endeavor is to record the gross morphological changes of biofilm ontogeny under standardized conditions. This visual information is instrumental in guiding the sampling strategy for the later omics analyses of biofilm ontogeny. However, none of the currently available visualizations methods is specifically tailored for recording gross morphology across the whole biofilm development. To address this void, here we present an affordable Arduino-based approach for time-lapse visualization of complete biofilm ontogeny using bright field stereomicroscopy with episcopic illumination. The major challenge in recording biofilm development on the air-solid interphase is water condensation, which compromises filming directly through the lid of a Petri dish. To overcome these trade-offs, we developed an Arduino microcontroller setup which synchronizes a robotic arm, responsible for opening and closing the Petri dish lid, with the activity of a stereomicroscope-mounted camera and lighting conditions. We placed this setup into a microbiological incubator that maintains temperature and humidity during the biofilm growth. As a proof-of-principle, we recorded biofilm development of five Bacillus subtilis strains that show different morphological and developmental dynamics.
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Elbehiry A, Aldubaib M, Abalkhail A, Marzouk E, ALbeloushi A, Moussa I, Ibrahem M, Albazie H, Alqarni A, Anagreyyah S, Alghamdi S, Rawway M. How MALDI-TOF Mass Spectrometry Technology Contributes to Microbial Infection Control in Healthcare Settings. Vaccines (Basel) 2022; 10:1881. [PMID: 36366389 PMCID: PMC9699604 DOI: 10.3390/vaccines10111881] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 08/01/2023] Open
Abstract
Healthcare settings have been utilizing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) since 2010. MALDI-TOF MS has various benefits over the conventional method of biochemical identification, including ease of use, speed, accuracy, and low cost. This approach can solve many of the obstacles to identifying bacteria, fungi and viruses. As technology advanced, more and more databases kept track of spectra, allowing species with similar morphological, genotypic, and biochemical traits to be identified. Using MALDI-TOF MS for identification has become more accurate and quicker due to advances in sample preparation and database enrichment. Rapid sample detection and colony identification using MALDI-TOF MS have produced promising results. A key application of MALDI-TOF MS is quickly identifying highly virulent and drug-resistant diseases. Here, we present a review of the scientific literature assessing the effectiveness of MALDI-TOF MS for locating clinically relevant pathogenic bacteria, fungi, and viruses. MALDI-TOF MS is a useful strategy for locating clinical pathogens, however, it also has some drawbacks. A small number of spectra in the database and inherent similarities among organisms can make it difficult to distinguish between different species, which can result in misidentifications. The majority of the time additional testing may correct these problems, which happen very seldom. In conclusion, infectious illness diagnosis and clinical care are being revolutionized by the use of MALDI-TOF MS in the clinical microbiology laboratory.
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Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32511, Egypt
| | - Musaad Aldubaib
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Eman Marzouk
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Ahmad ALbeloushi
- Al Bukayriyah General Hospital, Qassim, Al Bukayriyah 52725, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mai Ibrahem
- Department of Public Health, College of Applied Medical Science, King Khalid University, Abha 61421, Saudi Arabia
- Department of Aquatic Animal Medicine and Management, Faculty of Veterinary Medicine, Cairo University, Cairo 12211, Egypt
| | - Hamad Albazie
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Abdullah Alqarni
- Department of Support Service, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Sulaiman Anagreyyah
- Department of Preventive Medicine, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Saleh Alghamdi
- Department of Biomedical Engineering, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Mohammed Rawway
- Biology Department, College of Science, Jouf University, Sakaka 42421, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, AL-Azhar University, Assiut 71524, Egypt
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Antimicrobial and Methicillin Resistance Pattern of Potential Mastitis-Inducing Staphylococcus aureus and Coagulase-Negative Staphylococci Isolates from the Mammary Secretion of Dairy Goats. BIOLOGY 2022; 11:biology11111591. [PMID: 36358292 PMCID: PMC9687969 DOI: 10.3390/biology11111591] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 01/24/2023]
Abstract
Staphylococcus spp. is an important mastitis-inducing zoonotic pathogen in goats and is associated with antimicrobial resistance (AMR). The objectives of this study were to determine the prevalence and composition of staphylococci in individual mammary secretion (MS) samples of clinically healthy goats and to evaluate the phenotypic AMR pattern and the presence of methicillin resistance in the Staphylococcus spp. strains. Staphylococcus spp. isolates (n = 101) from the MS samples (n = 220) were identified to species level using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The antimicrobial susceptibility testing included a disk diffusion assay and the determination of the minimum inhibitory concentrations (MIC) of resistant strains (n = 46). Presumptive methicillin-resistant strains (n = 9) were assessed for the presence of mecA, mecC and SCCmec/orfx genes. Staphylococcus spp. isolates were recovered from 45.9% of the MS samples, of which, 72.3% was identified as coagulase-negative staphylococci (CoNS), with the remaining being Staphylococcus aureus. CoNS and S. aureus were most commonly resistant to ampicillin (56.2% and 57.1%, respectively), penicillin (26.0% and 39.3%, respectively), amoxicillin (26 % and 25 %, respectively) and cephalexin (12.3% and 25%, respectively) in the disk diffusion method. CoNS exhibited a broader AMR pattern and a higher percentage of resistant strains than S. aureus in the disk diffusion and MIC methods. Of the nine oxacillin- and cefoxitin-resistant strains, three S. aureus and five CoNS strains carried the mecA gene and, thus, were identified as methicillin-resistant. The mecC gene was not found in any of the studied strains. The presence of AMR and methicillin resistance in caprine S. aureus and CoNS poses a concern for animal and public health.
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Capitoli G, Piga I, L’Imperio V, Clerici F, Leni D, Garancini M, Casati G, Galimberti S, Magni F, Pagni F. Cytomolecular Classification of Thyroid Nodules Using Fine-Needle Washes Aspiration Biopsies. Int J Mol Sci 2022; 23:ijms23084156. [PMID: 35456973 PMCID: PMC9028391 DOI: 10.3390/ijms23084156] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 12/13/2022] Open
Abstract
Fine-needle aspiration biopsies (FNA) represent the gold standard to exclude the malignant nature of thyroid nodules. After cytomorphology, 20–30% of cases are deemed “indeterminate for malignancy” and undergo surgery. However, after thyroidectomy, 70–80% of these nodules are benign. The identification of tools for improving FNA’s diagnostic performances is explored by matrix-assisted laser-desorption ionization mass spectrometry imaging (MALDI-MSI). A clinical study was conducted in order to build a classification model for the characterization of thyroid nodules on a large cohort of 240 samples, showing that MALDI-MSI can be effective in separating areas with benign/malignant cells. The model had optimal performances in the internal validation set (n = 70), with 100.0% (95% CI = 83.2–100.0%) sensitivity and 96.0% (95% CI = 86.3–99.5%) specificity. The external validation (n = 170) showed a specificity of 82.9% (95% CI = 74.3–89.5%) and a sensitivity of 43.1% (95% CI = 30.9–56.0%). The performance of the model was hampered in the presence of poor and/or noisy spectra. Consequently, restricting the evaluation to the subset of FNAs with adequate cellularity, sensitivity improved up to 76.5% (95% CI = 58.8–89.3). Results also suggest the putative role of MALDI-MSI in routine clinical triage, with a three levels diagnostic classification that accounts for an indeterminate gray zone of nodules requiring a strict follow-up.
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Affiliation(s)
- Giulia Capitoli
- Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (G.C.); (S.G.)
| | - Isabella Piga
- Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (I.P.); (F.C.); (F.M.)
| | - Vincenzo L’Imperio
- Department of Medicine and Surgery, Pathology, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Francesca Clerici
- Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (I.P.); (F.C.); (F.M.)
| | - Davide Leni
- Department of Radiology, San Gerardo Hospital, ASST Monza, 20900 Monza, Italy;
| | - Mattia Garancini
- Department of Surgery, San Gerardo Hospital, ASST Monza, 20900 Monza, Italy;
| | - Gabriele Casati
- Department of Clinical Pathology, San Gerardo Hospital, ASST Monza, 20900 Monza, Italy;
| | - Stefania Galimberti
- Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (G.C.); (S.G.)
| | - Fulvio Magni
- Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (I.P.); (F.C.); (F.M.)
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, University of Milano-Bicocca, 20900 Monza, Italy;
- Correspondence: ; Tel.: +39-03-9233-2090
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