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Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, Saegeman V, Franceschetti L, Novati S, Fernández-Rodríguez A, Verzeletti A, Farina C, Bandi C. Forensic Microbiology: When, Where and How. Microorganisms 2024; 12:988. [PMID: 38792818 PMCID: PMC11123702 DOI: 10.3390/microorganisms12050988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.
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Affiliation(s)
- Riccardo Nodari
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Milena Arghittu
- Analysis Laboratory, ASST Melegnano e Martesana, 20077 Vizzolo Predabissi, Italy
| | - Paolo Bailo
- Section of Legal Medicine, School of Law, University of Camerino, 62032 Camerino, Italy
| | - Cristina Cattaneo
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Roberta Creti
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesco D’Aleo
- Microbiology and Virology Laboratory, GOM—Grande Ospedale Metropolitano, 89124 Reggio Calabria, Italy
| | - Veroniek Saegeman
- Microbiology and Infection Control, Vitaz Hospital, 9100 Sint-Niklaas, Belgium
| | - Lorenzo Franceschetti
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Stefano Novati
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy
| | - Amparo Fernández-Rodríguez
- Microbiology Department, Biology Service, Instituto Nacional de Toxicología y Ciencias Forenses, 41009 Madrid, Spain
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, 25123 Brescia, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Claudio Bandi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, 20133 Milan, Italy
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Balvers M, Gordijn IF, Voskamp-Visser IA, Schelling MF, Schuurman R, Heikens E, Braakman R, Stingl C, van Leeuwen HC, Luider TM, Dekker LJ, Levin E, Paauw A. Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification. JOURNAL OF CLINICAL VIROLOGY PLUS 2023. [DOI: 10.1016/j.jcvp.2023.100147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
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Paauw A, Scholz HC, Mars-Groenendijk RH, Dekker LJM, Luider TM, van Leeuwen HC. Expression of virulence and antimicrobial related proteins in Burkholderia mallei and Burkholderia pseudomallei. PLoS Negl Trop Dis 2023; 17:e0011006. [PMID: 36607891 PMCID: PMC9821509 DOI: 10.1371/journal.pntd.0011006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/06/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Burkholderia mallei and Burkholderia pseudomallei are both potential biological threat agents. Melioidosis caused by B. pseudomallei is endemic in Southeast Asia and Northern Australia, while glanders caused by B. mallei infections are rare. Here we studied the proteomes of different B. mallei and B. pseudomallei isolates to determine species specific characteristics. METHODS The expressed proteins of 5 B. mallei and 6 B. pseudomallei strains were characterized using liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS). Subsequently, expression of potential resistance and virulence related characteristics were analyzed and compared. RESULTS Proteome analysis can be used for the identification of B. mallei and B. pseudomallei. Both species were identified based on >60 discriminative peptides. Expression of proteins potentially involved in antimicrobial resistance, AmrAB-OprA, BpeAB-OprB, BpeEF-OprC, PenA as well as several other efflux pump related proteins and putative β-lactamases was demonstrated. Despite, the fact that efflux pump BpeAB-OprB was expressed in all isolates, no clear correlation with an antimicrobial phenotype and the efflux-pump could be established. Also consistent with the phenotypes, no amino acid mutations in PenA known to result in β-lactam resistance could be identified. In all studied isolates, the expression of virulence (related) factors Capsule-1 and T2SS was demonstrated. The expression of T6SS-1 was demonstrated in all 6 B. pseudomallei isolates and in 2 of the 5 B. mallei isolates. In all, except one B. pseudomallei isolate, poly-beta-1,6 N-acetyl-D-glucosamine export porin (Pga), important for biofilm formation, was detected, which were absent in the proteomes of B. mallei. Siderophores, iron binding proteins, malleobactin and malleilactone are possibly expressed in both species under standard laboratory growth conditions. Expression of multiple proteins from both the malleobactin and malleilactone polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) clusters was demonstrated in both species. All B. pseudomallei expressed at least seven of the nine proteins of the bactobolin synthase cluster (bactobolin, is a ribosome targeting antibiotic), while only in one B. mallei isolate expression of two proteins of this synthase cluster was identified. CONCLUSIONS Analyzing the expressed proteomes revealed differences between B. mallei and B. pseudomallei but also between isolates from the same species. Proteome analysis can be used not only to identify B. mallei and B. pseudomallei but also to characterize the presence of important factors that putatively contribute to the pathogenesis of B. mallei and B. pseudomallei.
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Affiliation(s)
- Armand Paauw
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Rijswijk, The Netherlands
- * E-mail:
| | - Holger C. Scholz
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Roos H. Mars-Groenendijk
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Rijswijk, The Netherlands
| | | | - Theo M. Luider
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - Hans C. van Leeuwen
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Rijswijk, The Netherlands
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Recent Studies on Advance Spectroscopic Techniques for the Identification of Microorganisms: A Review. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Moses S, Aftalion M, Mamroud E, Rotem S, Steinberger-Levy I. Reporter-Phage-Based Detection and Antibiotic Susceptibility Testing of Yersinia pestis for a Rapid Plague Outbreak Response. Microorganisms 2021; 9:1278. [PMID: 34208306 PMCID: PMC8231171 DOI: 10.3390/microorganisms9061278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Pneumonic plague is a lethal infectious disease caused by Yersinia pestis, a Tier-1 biothreat agent. Antibiotic treatment can save infected patients; however, therapy should begin within 24 h of symptom onset. As some Y. pestis strains showed an antibiotic resistance phenotype, an antibiotic susceptibility test (AST) must be performed. Performing the Clinical and Laboratory Standards Institute (CLSI)-recommended standard process, which includes bacterial isolation, enumeration and microdilution testing, lasts several days. Thus, rapid AST must be developed. As previously published, the Y. pestis-specific reporter phage ϕA1122::luxAB can serve for rapid identification and AST (ID-AST). Herein, we demonstrate the ability to use ϕA1122::luxAB to determine minimal inhibitory concentration (MIC) values and antibiotic susceptibility categories for various Y. pestis therapeutic antibiotics. We confirmed the assay by testing several nonvirulent Y. pestis isolates with reduced susceptibility to doxycycline or ciprofloxacin. Moreover, the assay can be performed directly on positive human blood cultures. Furthermore, as Y. pestis may naturally or deliberately be spread in the environment, we demonstrate the compatibility of this direct method for this scenario. This direct phage-based ID-AST shortens the time needed for standard AST to less than a day, enabling rapid and correct treatment, which may also prevent the spread of the disease.
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Affiliation(s)
| | | | | | | | - Ida Steinberger-Levy
- Department of Biochemistry and Molecular Genetics, The Israel Institute for Biological Research, Ness-Ziona 74100, Israel; (S.M.); (M.A.); (E.M.); (S.R.)
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Lasch P, Schneider A, Blumenscheit C, Doellinger J. Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS 1) and in Silico Peptide Mass Libraries. Mol Cell Proteomics 2020; 19:2125-2139. [PMID: 32998977 PMCID: PMC7710138 DOI: 10.1074/mcp.tir120.002061] [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: 03/26/2020] [Revised: 09/21/2020] [Indexed: 01/03/2023] Open
Abstract
Over the past decade, modern methods of MS (MS) have emerged that allow reliable, fast and cost-effective identification of pathogenic microorganisms. Although MALDI-TOF MS has already revolutionized the way microorganisms are identified, recent years have witnessed also substantial progress in the development of liquid chromatography (LC)-MS based proteomics for microbiological applications. For example, LC-tandem MS (LC-MS2) has been proposed for microbial characterization by means of multiple discriminative peptides that enable identification at the species, or sometimes at the strain level. However, such investigations can be laborious and time-consuming, especially if the experimental LC-MS2 data are tested against sequence databases covering a broad panel of different microbiological taxa. In this proof of concept study, we present an alternative bottom-up proteomics method for microbial identification. The proposed approach involves efficient extraction of proteins from cultivated microbial cells, digestion by trypsin and LC-MS measurements. Peptide masses are then extracted from MS1 data and systematically tested against an in silico library of all possible peptide mass data compiled in-house. The library has been computed from the UniProt Knowledgebase covering Swiss-Prot and TrEMBL databases and comprises more than 12,000 strain-specific in silico profiles, each containing tens of thousands of peptide mass entries. Identification analysis involves computation of score values derived from correlation coefficients between experimental and strain-specific in silico peptide mass profiles and compilation of score ranking lists. The taxonomic positions of the microbial samples are then determined by using the best-matching database entries. The suggested method is computationally efficient - less than 2 mins per sample - and has been successfully tested by a test set of 39 LC-MS1 peak lists obtained from 19 different microbial pathogens. The proposed method is rapid, simple and automatable and we foresee wide application potential for future microbiological applications.
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Affiliation(s)
- Peter Lasch
- Robert Koch-Institute, ZBS6, Proteomics and Spectroscopy, Berlin, Germany.
| | - Andy Schneider
- Robert Koch-Institute, ZBS6, Proteomics and Spectroscopy, Berlin, Germany
| | | | - Joerg Doellinger
- Robert Koch-Institute, ZBS6, Proteomics and Spectroscopy, Berlin, Germany
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Armengaud J. The proteomics contribution to the counter-bioterrorism toolbox in the post-COVID-19 era. Expert Rev Proteomics 2020; 17:507-511. [PMID: 32907407 DOI: 10.1080/14789450.2020.1822745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jean Armengaud
- CEA, INRAE, Département Médicaments et Technologies Pour la Santé (DMTS), SPI, Université Paris-Saclay , Bagnols-sur-Cèze, France
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High-throughput proteotyping of bacterial isolates by double barrel chromatography-tandem mass spectrometry based on microplate paramagnetic beads and phylopeptidomics. J Proteomics 2020; 226:103887. [PMID: 32619772 DOI: 10.1016/j.jprot.2020.103887] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 12/18/2022]
Abstract
Tandem mass spectrometry-based proteotyping of microorganisms presents several advantages over whole-cell MALDI-TOF mass spectrometry: because a larger number of signals are recorded with better accuracy and precision, the approach allows for the identification of microorganisms at more resolved taxonomic levels, and can easily manage complex samples. Additionally, the use of SP3 paramagnetic beads for cell lysis and protein cleanup simplifies sample preparation for proteotyping. Based on these features, we have developed and tested a 96-well plate platform for high-throughput proteotyping of a large variety of bacteria. We evaluated the performance of the platform in terms of bacterial load and found no cross-contamination between wells. Likewise, phylopeptidomics analysis revealed no alteration in the relative quantifications of microorganisms. Finally, we applied this new format for rapid proteotyping of a large set of dental isolates using double-barrel chromatography coupled to tandem mass spectrometry, which maximizes the number of spectra per unit of time. The procedure allowed us to establish whether these isolates were pure strains or mixtures of strains and to identify the microorganisms at the most resolved taxonomic level. SIGNIFICANCE: The rapid and accurate identification of microorganisms is a clinical priority in medical diagnostics; however, specimens containing mixtures of microorganisms are difficult to analyze and the procedure is time-consuming. Tandem mass spectrometry proteotyping allows the fast identification of complex mixtures of microorganisms, known or unknown, and can also establish the biomass ratio of each component. We describe here a new workflow for preparing microbial samples in a 96-well-plate format for tandem mass spectrometry proteotyping and document its advantages and limitations. We demonstrate that this new format coupled to a highly efficient double-barrel LC-MS/MS system allows proteotyping of 96 isolates in 55 h.
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Wareth G, Pletz MW, Neubauer H, Murugaiyan J. Proteomics of Brucella: Technologies and Their Applications for Basic Research and Medical Microbiology. Microorganisms 2020; 8:microorganisms8050766. [PMID: 32443785 PMCID: PMC7285364 DOI: 10.3390/microorganisms8050766] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/26/2022] Open
Abstract
Brucellosis is a global zoonosis caused by Gram-negative, facultative intracellular bacteria of the genus Brucella (B.). Proteomics has been used to investigate a few B. melitensis and B. abortus strains, but data for other species and biovars are limited. Hence, a comprehensive analysis of proteomes will significantly contribute to understanding the enigmatic biology of brucellae. For direct identification and typing of Brucella, matrix-assisted laser desorption ionization - time of flight mass spectrometry (MALDI - TOF MS) has become a reliable tool for routine diagnosis due to its ease of handling, price and sensitivity highlighting the potential of proteome-based techniques. Proteome analysis will also help to overcome the historic but still notorious Brucella obstacles of infection medicine, the lack of safe and protective vaccines and sensitive serologic diagnostic tools by identifying the most efficient protein antigens. This perspective summarizes past and recent developments in Brucella proteomics with a focus on species identification and serodiagnosis. Future applications of proteomics in these fields are discussed.
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Affiliation(s)
- Gamal Wareth
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany;
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
- Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, Egypt
- Correspondence: ; Tel.: +49-364-1804-2296
| | - Mathias W. Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany;
| | - Jayaseelan Murugaiyan
- Institute of Animal Hygiene and Environmental Health, Centre for Infectious Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany;
- Department of Biotechnology, SRM University AP, Neerukonda, Mangalagiri, Andhra Pradesh 522502, India
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Nomura F, Tsuchida S, Murata S, Satoh M, Matsushita K. Mass spectrometry-based microbiological testing for blood stream infection. Clin Proteomics 2020; 17:14. [PMID: 32435163 PMCID: PMC7222329 DOI: 10.1186/s12014-020-09278-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The most successful application of mass spectrometry (MS) in laboratory medicine is identification (ID) of microorganisms using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in blood stream infection. We describe MALDI-TOF MS-based bacterial ID with particular emphasis on the methods so far developed to directly identify microorganisms from positive blood culture bottles with MALDI-TOF MS including our own protocols. We touch upon the increasing roles of Liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) as well. MAIN BODY Because blood culture bottles contain a variety of nonbacterial proteins that may interfere with analysis and interpretation, appropriate pretreatments are prerequisites for successful ID. Pretreatments include purification of bacterial pellets and short-term subcultures to form microcolonies prior to MALDI-TOF MS analysis. Three commercial protocols are currently available: the Sepsityper® kit (Bruker Daltonics), the Vitek MS blood culture kit (bioMerieux, Inc.), and the rapid BACpro® II kit (Nittobo Medical Co., Tokyo). Because these commercially available kits are costly and bacterial ID rates using these kits are not satisfactory, particularly for Gram-positive bacteria, various home-brew protocols have been developed: 1. Stepwise differential sedimentation of blood cells and microorganisms, 2. Combination of centrifugation and lysis procedures, 3. Lysis-vacuum filtration, and 4. Centrifugation and membrane filtration technique (CMFT). We prospectively evaluated the performance of this CMFT protocol compared with that of Sepsityper® using 170 monomicrobial positive blood cultures. Although preliminary, the performance of the CMFT was significantly better than that of Sepsityper®, particularly for Gram-positive isolates. MALDI-TOF MS-based testing of polymicrobial blood specimens, however, is still challenging. Also, its contribution to assessment of susceptibility and resistance to antibiotics is still limited. For this purpose, liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) should be more useful because this approach can identify as many as several thousand peptide sequences. CONCLUSION MALDI-TOF MS is now an essential tool for rapid bacterial ID of pathogens that cause blood stream infection. For the purpose of assessment of susceptibility and resistance to antibiotics of the pathogens, the roles of liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) will increase in the future.
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Affiliation(s)
- Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Syota Murata
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
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