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Ahrens D. Species Diagnosis and DNA Taxonomy. Methods Mol Biol 2024; 2744:33-52. [PMID: 38683310 DOI: 10.1007/978-1-0716-3581-0_2] [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] [Indexed: 05/01/2024]
Abstract
The use of DNA has helped to improve and speed up species identification and delimitation. However, it also provides new challenges to taxonomists. Incongruence of outcome from various markers and delimitation methods, bias from sampling and skewed species distribution, implemented models, and the choice of methods/priors may mislead results and also may, in conclusion, increase elements of subjectivity in species taxonomy. The lack of direct diagnostic outcome from most contemporary molecular delimitation approaches and the need for a reference to existing and best sampled trait reference systems reveal the need for refining the criteria of species diagnosis and diagnosability in the current framework of nomenclature codes and good practices to avoid nomenclatorial instability, parallel taxonomies, and consequently more and new taxonomic impediment.
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Affiliation(s)
- Dirk Ahrens
- Museum A. Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany.
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2
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Stauning MA, Jensen CS, Staalsøe T, Kurtzhals JAL. Detection and quantification of Plasmodium falciparum in human blood by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a proof of concept study. Malar J 2023; 22:285. [PMID: 37752504 PMCID: PMC10523782 DOI: 10.1186/s12936-023-04719-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/13/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) has revolutionized identification of bacteria and is becoming available in an increasing number of laboratories in malaria-endemic countries. The purpose of this proof-of-concept study was to explore the potential of MALDI-TOF as a diagnostic tool for direct detection and quantification of Plasmodium falciparum in human blood. METHODS Three different P. falciparum strains (3D7, HB3 and IT4) were cultured and synchronized following standard protocols. Ring-stages were diluted in fresh blood group 0 blood drawn in EDTA from healthy subjects to mimic clinical samples. Samples were treated with saponin and washed in PBS to concentrate protein material. Samples were analysed using a Microflex LT MALDI-TOF and resulting mass spectra were compared using FlexAnalysis software. RESULTS More than 10 peaks specific for P. falciparum were identified. The identified peaks were consistent among the three genetically unrelated strains. Identification was possible in clinically relevant concentrations of 0.1% infected red blood cells, and a close relationship between peak intensity and the percentage of infected red blood cells was seen. CONCLUSION The findings indicate that the method has the potential to detect and quantify P. falciparum at clinically relevant infection intensities and provides proof-of-concept for MALDI-TOF-based diagnosis of human malaria. Further research is needed to include other Plasmodium spp., wildtype parasite isolates and to increase sensitivity. MALDI-TOF may be a useful tool for mass-screening purposes and for diagnosis of malaria in settings where it is readily available.
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Affiliation(s)
- Marius Ahm Stauning
- Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark.
| | - Christian Salgård Jensen
- Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Trine Staalsøe
- Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen A L Kurtzhals
- Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
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Razuvaeva AV, Ulyanova EG, Skolotneva ES, Andreeva IV. Species identification of spider mites (Tetranychidae: Tetranychinae): a review of methods. Vavilovskii Zhurnal Genet Selektsii 2023; 27:240-249. [PMID: 37293445 PMCID: PMC10244583 DOI: 10.18699/vjgb-23-30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/25/2022] [Accepted: 01/07/2022] [Indexed: 06/10/2023] Open
Abstract
Spider mites (Acari: Tetranychidae) are dangerous pests of agricultural and ornamental crops, the most economically significant of them belonging to the genera Tetranychus, Eutetranychus, Oligonychus and Panonychus. The expansion of the distribution areas, the increased harmfulness and dangerous status of certain species in the family Tetranychidae and their invasion of new regions pose a serious threat to the phytosanitary status of agro- and biocenoses. Various approaches to acarofauna species diagnosis determine a rather diverse range of currently existing methods generally described in this review. Identification of spider mites by morphological traits, which is currently considered the main method, is complicated due to the complexity of preparing biomaterials for diagnosis and a limited number of diagnostic signs. In this regard, biochemical and molecular genetic methods such as allozyme analysis, DNA barcoding, restriction fragment length polymorphism (PCR-RFLP), selection of species-specific primers and real-time PCR are becoming important. In the review, close attention is paid to the successful use of these methods for species discrimination in the mites of the subfamily Tetranychinae. For some species, e. g., the two-spotted spider mite (Tetranychus urticae), a range of identification methods has been developed - from allozyme analysis to loop isothermal amplification (LAMP), while for many other species a much smaller variety of approaches is available. The greatest accuracy in the identification of spider mites can be achieved using a combination of several methods, e. g., examination of morphological features and one of the molecular approaches (DNA barcoding, PCR-RFLP, etc.). This review may be useful to specialists who are in search of an effective system for spider mite species identification as well as when developing new test systems relevant to specific plant crops or a specific region.
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Affiliation(s)
- A V Razuvaeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E G Ulyanova
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk, Novosibirsk Region, Russia
| | - E S Skolotneva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I V Andreeva
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk, Novosibirsk Region, Russia
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He X, Sun Y, Yang F, Zheng G, Li R, Liu M, Li W, Zhou DH, Zheng Y. Heat shock protein 60 in parasitic helminths: A role in immune responses and therapeutic applications. Mol Biochem Parasitol 2023; 253:111544. [PMID: 36641059 DOI: 10.1016/j.molbiopara.2023.111544] [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: 12/07/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Heat shock protein 60 (HSP60) is an unique member of the heat shock protein family, being involved in parasite infections. To cope with harsh environments where parasites live, HSP60s are indispensable and involved in a variety of biological processes. HSP60s have relative low similarity among parasites, but their ATPase /Mg2+ active sites are highly conserved. The interactions of HSP60s with signaling pathway regulators in immune cells suggest a crucial role in immune responses, rendering them a potential therapeutic target. This paper reviews the current understandings of HSP60s in parasitic helminths in aspects of molecular characteristics, immunoregulatory responses and HSP60-based therapeutics.
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Affiliation(s)
- Xuedong He
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology&College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Yue Sun
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology&College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Fang Yang
- Zhejiang Kangjia Gene Technology Limited Liability Company, Hangzhou 310022, China
| | - Guanghui Zheng
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology&College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Rui Li
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology&College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Mengqi Liu
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology&College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Wanjing Li
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology&College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Dong-Hui Zhou
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yadong Zheng
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology&College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China.
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Recent Advances and Potential Future Applications of MALDI-TOF Mass Spectrometry for Identification of Helminths. Diagnostics (Basel) 2022; 12:diagnostics12123035. [PMID: 36553043 PMCID: PMC9777230 DOI: 10.3390/diagnostics12123035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Helminth infections caused by nematodes, trematodes, and cestodes are major neglected tropical diseases and of great medical and veterinary relevance. At present, diagnosis of helminthic diseases is mainly based on microscopic observation of different parasite stages, but microscopy is associated with limited diagnostic accuracy. Against this background, recent studies described matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry as a potential, innovative tool for helminth identification and differentiation. MALDI-TOF mass spectrometry is based on the analysis of spectra profiles generated from protein extracts of a given pathogen. It requires an available spectra database containing reference spectra, also called main spectra profiles (MSPs), which are generated from well characterized specimens. At present, however, there are no commercially available databases for helminth identification using this approach. In this narrative review, we summarize recent developments and published studies between January 2019 and September 2022 that report on the use of MALDI-TOF mass spectrometry for helminths. Current challenges and future research needs are identified and briefly discussed.
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Where Have All the Diagnostic Morphological Parasitologists Gone? J Clin Microbiol 2022; 60:e0098622. [PMID: 36314793 PMCID: PMC9667774 DOI: 10.1128/jcm.00986-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Advances in laboratory techniques have revolutionized parasitology diagnostics over the past several decades. Widespread implementation of rapid antigen detection tests has greatly expanded access to tests for global parasitic threats such as malaria, while next-generation amplification and sequencing methods allow for sensitive and specific detection of human and animal parasites in complex specimen matrices.
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Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: An effective method for identification and phylogenetic analysis of Leishmania species. Exp Parasitol 2022; 240:108278. [PMID: 35764122 DOI: 10.1016/j.exppara.2022.108278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid and reproducible method that has been widely applied for the identification of bacteria and fungi. However, this technique has not yet been applied in clinical laboratories for parasitology, such as for the study of the protozoan Leishmania. METHODOLOGY By using MALDI-TOF MS, mass spectra database entries (MSPs) were created with 7 World Health Organization reference strains in order to establish a rapid method for Leishmania species identification. Furthermore, cluster analysis was performed with 18 Chinese Leishmania isolates. PRINCIPAL FINDINGS The MSPs of Leishmania corresponded well with our past identification results, and the dendrogram analysis result was more or less similar to that of the phylogenetic analysis performed by multi-locus sequence typing. CONCLUSIONS/SIGNIFICANCE MALDI-TOF MS is a promising method that offers both rapidity and efficiency for the identification and dendrogram analysis of Leishmania species.
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Artificial Intelligence and Malaria. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ruenchit P. State-of-the-Art Techniques for Diagnosis of Medical Parasites and Arthropods. Diagnostics (Basel) 2021; 11:diagnostics11091545. [PMID: 34573887 PMCID: PMC8470585 DOI: 10.3390/diagnostics11091545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/29/2022] Open
Abstract
Conventional methods such as microscopy have been used to diagnose parasitic diseases and medical conditions related to arthropods for many years. Some techniques are considered gold standard methods. However, their limited sensitivity, specificity, and accuracy, and the need for costly reagents and high-skilled technicians are critical problems. New tools are therefore continually being developed to reduce pitfalls. Recently, three state-of-the-art techniques have emerged: DNA barcoding, geometric morphometrics, and artificial intelligence. Here, data related to the three approaches are reviewed. DNA barcoding involves an analysis of a barcode sequence. It was used to diagnose medical parasites and arthropods with 95.0% accuracy. However, this technique still requires costly reagents and equipment. Geometric morphometric analysis is the statistical analysis of the patterns of shape change of an anatomical structure. Its accuracy is approximately 94.0-100.0%, and unlike DNA barcoding, costly reagents and equipment are not required. Artificial intelligence technology involves the analysis of pictures using well-trained algorithms. It showed 98.8-99.0% precision. All three approaches use computer programs instead of human interpretation. They also have the potential to be high-throughput technologies since many samples can be analyzed at once. However, the limitation of using these techniques in real settings is species coverage.
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Affiliation(s)
- Pichet Ruenchit
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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Sevestre J, Diarra AZ, Oumarou HA, Durant J, Delaunay P, Parola P. Detection of emerging tick-borne disease agents in the Alpes-Maritimes region, southeastern France. Ticks Tick Borne Dis 2021; 12:101800. [PMID: 34352531 DOI: 10.1016/j.ttbdis.2021.101800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/13/2021] [Accepted: 07/17/2021] [Indexed: 11/19/2022]
Abstract
Lyme borreliosis is a zoonotic tick-borne infection representing the most frequent vector-borne disease in the northern hemisphere. The Mediterranean rim is generally described as unsuitable for the European vector, Ixodes ricinus. We conducted an epidemiological study to assess whether I. ricinus was present and study its infection status for tick-borne bacteria. Ticks originating from southeastern France were obtained from flagging sampling and removed from animals and tick-bitten patients. Species level identification used morphological keys and MALDI-TOF MS. Quantitative PCR and sequencing assays were used to detect and identify tick-associated bacteria (Borrelia, Rickettsia, Anaplasmataceae, Bartonella, Coxiella burnetii) in each specimen. A total of 1232 ticks were collected in several localities. Among these, 863 were identified as I. ricinus (70%). Bacterial screening allowed identification of Lyme group Borrelia among I. ricinus ticks originating from various regional areas. Other emerging tick-borne pathogens like Borrelia miyamotoi and Rickettsia species were also detected. The Alpes-Maritimes region, part of the French Riviera, harbours I. ricinus ticks infected with Lyme group Borrelia and several other tick-borne bacterial agents. Clinicians and outdoor activity participants should be aware of the local Lyme borreliosis transmission risk.
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Affiliation(s)
- Jacques Sevestre
- Service de Parasitologie, Centre Hospitalier Universitaire de Nice, Nice, France; Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13385 Cedex 05, France; Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Adama Zan Diarra
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13385 Cedex 05, France; Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | | | - Jacques Durant
- Service d'Infectiologie, Centre Hospitalier Universitaire de Nice, Nice, France
| | - Pascal Delaunay
- Service de Parasitologie, Centre Hospitalier Universitaire de Nice, Nice, France; MIVEGEC, Université de Montpellier, Montpellier, France
| | - Philippe Parola
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13385 Cedex 05, France; Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
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MALDI-TOF Mass Spectroscopy Applications in Clinical Microbiology. Adv Pharmacol Pharm Sci 2021; 2021:9928238. [PMID: 34041492 PMCID: PMC8121603 DOI: 10.1155/2021/9928238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
There is a range of proteomics methods to spot and analyze bacterial protein contents such as liquid chromatography-mass spectrometry (LC-MS), two-dimensional gel electrophoresis, and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS), which give comprehensive information about the microorganisms that may be helpful within the diagnosis and coverings of infections. Microorganism identification by mass spectrometry is predicted on identifying a characteristic spectrum of every species so matched with an outsized database within the instrument. MALDI-TOF MS is one of the diagnostic methods, which is a straightforward, quick, and precise technique, and is employed in microbial diagnostic laboratories these days and may replace other diagnostic methods. This method identifies various microorganisms such as bacteria, fungi, parasites, and viruses, which supply comprehensive information. One of the MALDI-TOF MS's crucial applications is bacteriology, which helps identify bacterial species, identify toxins, and study bacterial antibiotic resistance. By knowing these cases, we will act more effectively against bacterial infections.
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Sevestre J, Diarra AZ, Laroche M, Almeras L, Parola P. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: an emerging tool for studying the vectors of human infectious diseases. Future Microbiol 2021; 16:323-340. [PMID: 33733821 DOI: 10.2217/fmb-2020-0145] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Arthropod vectors have historically been identified morphologically, and more recently using molecular biology methods. However, both of these methods are time-consuming and require specific expertise and equipment. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, which has revolutionized the routine identification of microorganisms in clinical microbiology laboratories, was recently successfully applied to the identification of arthropod vectors. Since then, the robustness of this identification technique has been confirmed, extended to a large panel of arthropod vectors, and assessed for detecting blood feeding behavior and identifying the infection status in regard to certain pathogenic agents. In this study, we summarize the state-of-the-art of matrix-assisted laser desorption ionization time-of-flight mass spectrometry applied to the identification of arthropod vectors (ticks, mosquitoes, phlebotomine sand-flies, fleas, triatomines, lice and Culicoides), their trophic preferences and their ability to discriminate between infection statuses.
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Affiliation(s)
- Jacques Sevestre
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Adama Z Diarra
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Maureen Laroche
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Lionel Almeras
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,Département Microbiologie et Maladies Infectieuses, Unité Parasitologie et Entomologie, Institut de Recherche Biomédicale des Armées, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Philippe Parola
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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New assessment of Anopheles vector species identification using MALDI-TOF MS. Malar J 2021; 20:33. [PMID: 33422056 PMCID: PMC7796594 DOI: 10.1186/s12936-020-03557-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 12/18/2020] [Indexed: 11/24/2022] Open
Abstract
Background Anopheles species identification is essential for an effective malaria vector control programme. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has been developed to identify adult Anopheles species, using the legs or the cephalothorax. The protein repertoire from arthropods can vary according to compartment, but there is no general consensus regarding the anatomic part to be used. Methods To determine the body part of the Anopheles mosquitoes best suited for the identification of field specimens, a mass spectral library was generated with head, thorax with wings and legs of Anopheles gambiae, Anopheles arabiensis and Anopheles funestus obtained from reference centres. The MSL was evaluated using two independent panels of 52 and 40 An. gambiae field-collected in Mali and Guinea, respectively. Geographic variability was also tested using the panel from Mali and several databases containing added specimens from Mali and Senegal. Results Using the head and a database without specimens from the same field collection, the proportion of interpretable and correct identifications was significantly higher than using the other body parts at a threshold value of 1.7 (p < 0.0001). The thorax of engorged specimens was negatively impacted by the blood meal after frozen storage. The addition of specimens from Mali into the database significantly improved the results of Mali panel (p < 0.0001), which became comparable between head and legs. With higher identification scores, the using of the head will allow to decrease the number of technical replicates of protein extract per specimen, which represents a significant improvement for routine use of MALDI-TOF MS. Conclusions The using of the head of Anopheles may improve the performance of MALDI-TOF MS. Region-specific mass spectrum databases will have to be produced. Further research is needed to improve the standardization in order to share online spectral databases.
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Gittens RA, Almanza A, Bennett KL, Mejía LC, Sanchez-Galan JE, Merchan F, Kern J, Miller MJ, Esser HJ, Hwang R, Dong M, De León LF, Álvarez E, Loaiza JR. Proteomic fingerprinting of Neotropical hard tick species (Acari: Ixodidae) using a self-curated mass spectra reference library. PLoS Negl Trop Dis 2020; 14:e0008849. [PMID: 33108372 PMCID: PMC7647123 DOI: 10.1371/journal.pntd.0008849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/06/2020] [Accepted: 10/02/2020] [Indexed: 02/01/2023] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry is an analytical method that detects macromolecules that can be used for proteomic fingerprinting and taxonomic identification in arthropods. The conventional MALDI approach uses fresh laboratory-reared arthropod specimens to build a reference mass spectra library with high-quality standards required to achieve reliable identification. However, this may not be possible to accomplish in some arthropod groups that are difficult to rear under laboratory conditions, or for which only alcohol preserved samples are available. Here, we generated MALDI mass spectra of highly abundant proteins from the legs of 18 Neotropical species of adult field-collected hard ticks, several of which had not been analyzed by mass spectrometry before. We then used their mass spectra as fingerprints to identify each tick species by applying machine learning and pattern recognition algorithms that combined unsupervised and supervised clustering approaches. Both Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) classification algorithms were able to identify spectra from different tick species, with LDA achieving the best performance when applied to field-collected specimens that did have an existing entry in a reference library of arthropod protein spectra. These findings contribute to the growing literature that ascertains mass spectrometry as a rapid and effective method to complement other well-established techniques for taxonomic identification of disease vectors, which is the first step to predict and manage arthropod-borne pathogens.
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Affiliation(s)
- Rolando A. Gittens
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
- Centro de Neurociencias, INDICASAT AIP, Panama, Republic of Panama
| | - Alejandro Almanza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
| | - Kelly L. Bennett
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
| | - Luis C. Mejía
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
| | - Javier E. Sanchez-Galan
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
- Grupo de Investigación en Biotecnología, Bioinformática y Biología de Sistemas, Facultad de Ingeniería de Sistemas Computacionales, Universidad Tecnológica de Panamá, Panama, Republic of Panama
| | - Fernando Merchan
- Grupo de Investigación en Sistemas de Comunicaciones Digitales Avanzados, Facultad de Ingeniería Eléctrica, Universidad Tecnológica de Panamá, Panama, Republic of Panama
| | - Jonathan Kern
- Grupo de Investigación en Sistemas de Comunicaciones Digitales Avanzados, Facultad de Ingeniería Eléctrica, Universidad Tecnológica de Panamá, Panama, Republic of Panama
- ENSEIRB-MATMECA–Bordeaux INP, France
| | - Matthew J. Miller
- Department of Anthropology, Pennsylvania State University, University Park, PA, United States of America
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, United States of America
| | - Helen J. Esser
- Department of Environmental Sciences, Wageningen University, Wageningen, the Netherlands
| | - Robert Hwang
- Department of Biology, Swarthmore College, Swarthmore, PA, United States of America
| | - May Dong
- Department of Biology, Swarthmore College, Swarthmore, PA, United States of America
| | - Luis F. De León
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
- Department of Biology, University of Massachusetts Boston, Boston, MA, United States of America
| | - Eric Álvarez
- Programa Centroamericano de Maestría en Entomología, Universidad de Panamá, Panama, Republic of Panama
| | - Jose R. Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Programa Centroamericano de Maestría en Entomología, Universidad de Panamá, Panama, Republic of Panama
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15
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Accuracy of matrix-assisted LASER desorption ionization-time of flight mass spectrometry for identification of Candida. Biosci Rep 2020; 39:BSR20190859. [PMID: 31537628 PMCID: PMC6822510 DOI: 10.1042/bsr20190859] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/29/2019] [Accepted: 09/06/2019] [Indexed: 01/23/2023] Open
Abstract
Background: Candida is a fungus that causes various types of candidemia, which is the fourth major infectious disease of the blood system. MALDI-TOF-MS is a simple and rapid detection instrument. The aim of the present study was to verify the accuracy of MALDI-TOF-MS in detecting Candida. Method: A pooled analysis of articles on MALDI-TOF-MS for diagnosis of candidemia was performed. The quality of original research was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) guidelines. Stata 12.0 software was used to merge the correct identification rates of Candida and Candida subspecies and obtain pooled sensitivity and specificity of the diagnostic methods. Heterogeneity was found in the subgroup analysis of the included articles. Hence, we explored the factors causing the heterogeneity and its impact on the overall situation. Sensitivity analysis was used to examine the effect of Candida level on total response. Egger’s test was used to evaluate the publication bias of the included articles. Results: A total of 16 articles in Pubmed, 79 articles in Embase, 1 article in Cochrane Library, 30 articles in Web of Science and 3 from other sources were identified, of which 10 articles were included based on the inclusion and exclusion criteria. The overall identification accuracy was 100%. Conclusion: The accuracy of MALDI-TOF-MS for the identification of Candida was 100%. Further research is necessary to determine whether MALDI-TOF-MS can be used as a clinical diagnostic standard for the identification of Candida.
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Prediction of malaria transmission drivers in Anopheles mosquitoes using artificial intelligence coupled to MALDI-TOF mass spectrometry. Sci Rep 2020; 10:11379. [PMID: 32647135 PMCID: PMC7347643 DOI: 10.1038/s41598-020-68272-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/16/2020] [Indexed: 11/21/2022] Open
Abstract
Vector control programmes are a strategic priority in the fight against malaria. However, vector control interventions require rigorous monitoring. Entomological tools for characterizing malaria transmission drivers are limited and are difficult to establish in the field. To predict Anopheles drivers of malaria transmission, such as mosquito age, blood feeding and Plasmodium infection, we evaluated artificial neural networks (ANNs) coupled to matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) and analysed the impact on the proteome of laboratory-reared Anopheles stephensi mosquitoes. ANNs were sensitive to Anopheles proteome changes and specifically recognized spectral patterns associated with mosquito age (0–10 days, 11–20 days and 21–28 days), blood feeding and P. berghei infection, with best prediction accuracies of 73%, 89% and 78%, respectively. This study illustrates that MALDI-TOF MS coupled to ANNs can be used to predict entomological drivers of malaria transmission, providing potential new tools for vector control. Future studies must assess the field validity of this new approach in wild-caught adult Anopheles. A similar approach could be envisaged for the identification of blood meal source and the detection of insecticide resistance in Anopheles and to other arthropods and pathogens.
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Mass Spectrometry Based-Proteomic Analysis of Anisakis spp.: A Preliminary Study towards a New Diagnostic Tool. Genes (Basel) 2020; 11:genes11060693. [PMID: 32599802 PMCID: PMC7349252 DOI: 10.3390/genes11060693] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/15/2022] Open
Abstract
Anisakiasis is nowadays a well-known infection, mainly caused by the accidental ingestion of Anisakis larvae, following the consumption of raw or undercooked fishes and cephalopods. Due to the similarity of symptoms with those of common gastrointestinal disorders, this infection is often underestimated, and the need for new specific diagnostic tools is becoming crucial. Given the remarkable impact that MALDI–TOF MS biotyping had in the last decade in clinical routine practice for the recognition of bacterial and fungi strains, a similar scenario could be foreseen for the identification of parasites, such as nematodes. In this work, a MALDI–TOF MS profiling of Anisakis proteome was pursued with a view to constructing a first spectral library for the diagnosis of Anisakis infections. At the same time, a shotgun proteomics approach by LC–ESI–MS/MS was performed on the two main fractions obtained from protein extraction, to evaluate the protein species enriched by the protocol. A set of MALDI–TOF MS signals associated with proteins originating in the ribosomal fraction of the nematode extract was selected as a potential diagnostic tool for the identification of Anisakis spp.
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18
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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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19
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Bredtmann CM, Krücken J, Murugaiyan J, Balard A, Hofer H, Kuzmina TA, von Samson-Himmelstjerna G. Concurrent Proteomic Fingerprinting and Molecular Analysis of Cyathostomins. Proteomics 2020; 19:e1800290. [PMID: 30786147 DOI: 10.1002/pmic.201800290] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/07/2018] [Indexed: 12/24/2022]
Abstract
Rapid, cost-effective, efficient, and reliable helminth species identification is of considerable importance to understand host-parasite interactions, clinical disease, and drug resistance. Cyathostomins (Nematoda: Strongylidae) are considered to be the most important equine parasites, yet research on this group is hampered by the large number of 50 morphologically differentiated species, their occurrence in mixed infections with often more than 10 species and the difficulties associated with conventional identification methods. Here, MALDI-TOF MS, previously successfully applied to identify numerous organisms, is evaluated and compared with conventional and molecular genetic approaches. A simple and robust protocol for protein extraction and subsequent DNA isolation allowing molecular confirmation of proteomic findings is developed, showing that MALDI-TOF MS can discriminate adult stages of the two closely related cyathostomin species Cylicostephanus longibursatus and Cylicostephanus minutus. Intraspecific variability of proteomic profiles within morphospecies demonstrated an identification of morphospecies with an accuracy of close to 100%. In contrast, three genospecies within C. minutus and sex-specific profiles within both morphospecies could not be reliably discriminated using MALDI-TOF MS. In conclusion, MALDI-TOF MS complemented by the molecular protocol is a reliable and efficient approach for cyathostomin species identification.
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Affiliation(s)
- Christina Maria Bredtmann
- Institute for Parasitology and Tropical Veterinary Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Jayaseelan Murugaiyan
- Institute for Animal Hygiene and Environmental Health, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany.,Department of Biotechnology, SRM University AP, 522502, Amaravati, India
| | - Alice Balard
- Ecology and Evolution of Molecular Parasite Host Interactions, Molecular Parasitology, Institute for Biology, Humboldt University Berlin, 10115, Berlin, Germany.,Ecology and Evolution of Molecular Parasite Host Interactions, Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany
| | - Heribert Hofer
- Institute for Parasitology and Tropical Veterinary Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany.,Department of Ecological Dynamics, Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany.,Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195, Berlin, Germany
| | - Tetiana A Kuzmina
- Department of Parasitology, I. I. Schmalhausen Institute of Zoology, 01030, Kiev, Ukraine
| | - Georg von Samson-Himmelstjerna
- Institute for Parasitology and Tropical Veterinary Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
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20
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Baumeister TUH, Vallet M, Kaftan F, Guillou L, Svatoš A, Pohnert G. Identification to species level of live single microalgal cells from plankton samples with matrix-free laser/desorption ionization mass spectrometry. Metabolomics 2020; 16:28. [PMID: 32090296 PMCID: PMC7036359 DOI: 10.1007/s11306-020-1646-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/27/2020] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Marine planktonic communities are complex microbial consortia often dominated by microscopic algae. The taxonomic identification of individual phytoplankton cells usually relies on their morphology and demands expert knowledge. Recently, a live single-cell mass spectrometry (LSC-MS) pipeline was developed to generate metabolic profiles of microalgae. OBJECTIVE Taxonomic identification of diverse microalgal single cells from collection strains and plankton samples based on the metabolic fingerprints analyzed with matrix-free laser desorption/ionization high-resolution mass spectrometry. METHODS Matrix-free atmospheric pressure laser-desorption ionization mass spectrometry was performed to acquire single-cell mass spectra from collection strains and prior identified environmental isolates. The computational identification of microalgal species was performed by spectral pattern matching (SPM). Three similarity scores and a bootstrap-derived confidence score were evaluated in terms of their classification performance. The effects of high and low-mass resolutions on the classification success were evaluated. RESULTS Several hundred single-cell mass spectra from nine genera and nine species of marine microalgae were obtained. SPM enabled the identification of single cells at the genus and species level with high accuracies. The receiver operating characteristic (ROC) curves indicated a good performance of the similarity measures but were outperformed by the bootstrap-derived confidence scores. CONCLUSION This is the first study to solve taxonomic identification of microalgae based on the metabolic fingerprints of the individual cell using an SPM approach.
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Affiliation(s)
- Tim U H Baumeister
- Max Planck Institute for Chemical Ecology, Max Planck Fellow Group On Plankton Community Interaction, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Marine Vallet
- Max Planck Institute for Chemical Ecology, Max Planck Fellow Group On Plankton Community Interaction, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Filip Kaftan
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Laure Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation Et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany.
| | - Georg Pohnert
- Max Planck Institute for Chemical Ecology, Max Planck Fellow Group On Plankton Community Interaction, Hans-Knöll-Str. 8, 07745, Jena, Germany.
- Department of Bioorganic Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany.
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21
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dos Santos Souza É, Fernandes RP, Guedes WN, dos Santos FN, Eberlin MN, Lopes NP, Padovani VD, da Rosa JA. Rhodnius spp. are differentiated based on the peptide/protein profile by matrix-assisted laser desorption/ionization mass spectrometry and chemometric tools. Anal Bioanal Chem 2020; 412:1431-1439. [DOI: 10.1007/s00216-019-02376-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/22/2019] [Accepted: 12/23/2019] [Indexed: 10/25/2022]
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Naseem MT, Ashfaq M, Khan AM, Rasool A, Asif M, Hebert PDN. BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae). PLoS One 2019; 14:e0220426. [PMID: 31821347 PMCID: PMC6903727 DOI: 10.1371/journal.pone.0220426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/24/2019] [Indexed: 11/25/2022] Open
Abstract
DNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these species with conspecific populations from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from a range of plant species at sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. Sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance. These species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 49% of the species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.
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Affiliation(s)
- Muhammad Tayyib Naseem
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Muhammad Ashfaq
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
- * E-mail:
| | - Arif Muhammad Khan
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Akhtar Rasool
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Zoology, University of Swat, Swat, Pakistan
| | - Muhammad Asif
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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23
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Diarra AZ, Laroche M, Berger F, Parola P. Use of MALDI-TOF MS for the Identification of Chad Mosquitoes and the Origin of Their Blood Meal. Am J Trop Med Hyg 2019; 100:47-53. [PMID: 30526738 DOI: 10.4269/ajtmh.18-0657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Matrix-assisted desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a clinical microbiology tool for the systematic identification of microorganisms. It has recently been presented as an innovative tool for the rapid and accurate identification of mosquitoes and their blood meal. To evaluate the capacity of this tool to identify mosquitoes collected in a tropical environment and preserved with silica gel, we analyzed 188 mosquitoes of different species collected in Chad, which were preserved with silica gel for 2 months. The MALDI-TOF MS analysis correctly identified 96% of the mosquitoes and 37.5% of their blood meals. Using MALDI-TOF MS and molecular biology, eight mosquito species were identified, including Anopheles gambiae s.l., Anopheles rufipes, Culex quinquefasciatus, Culex neavei, Culex pipiens, Culex perexiguus, Culex rima, and Culex watti. Blood meal identification revealed that mosquitoes fed mainly on humans, birds, and cows. Matrix-assisted desorption/ionization time-of-flight mass spectrometry appears to be a promising, fast, and reliable tool to identify mosquitoes and the origin of their blood meal for samples stored with silica gel.
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Affiliation(s)
- Adama Zan Diarra
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France.,Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Maureen Laroche
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France
| | - Franck Berger
- Aix Marseille Univ, Inserm, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l'Information Médicale, Marseille, France.,SSA, CESPA, Marseille, France
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France
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24
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Su J, Jin C, Wu H, Fei J, Li N, Guo Y, Feng Y, Xiao L. Differential Expression of Three Cryptosporidium Species-Specific MEDLE Proteins. Front Microbiol 2019; 10:1177. [PMID: 31191495 PMCID: PMC6549896 DOI: 10.3389/fmicb.2019.01177] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/08/2019] [Indexed: 01/23/2023] Open
Abstract
Cryptosporidium parvum and Cryptosporidium hominis share highly similar proteomes, with merely ~3% divergence in overall nucleotide sequences. Cryptosporidium-specific MEDLE family is one of the major differences in gene content between the two species. Comparative genomic analysis indicated that MEDLE family may contribute to differences in host range among Cryptosporidium spp. Previous studies have suggested that CpMEDLE-1 encoded by cgd5_4580 and CpMEDLE-2 encoded by cgd5_4590 are potentially involved in the invasion of C. parvum. In this study, we expressed in Escherichia coli, the C. hominis-specific member of the MEDLE protein family, ChMEDLE-1 encoded by chro.50507, and two C. parvum-specific members, CpMEDLE-3 encoded by cgd5_4600 and CpMEDLE-5 encoded by cgd6_5480. Quantitative PCR, immunofluorescence staining and in vitro neutralization assay were conducted to assess their biologic characteristics. The expression of the cgd5_4600 gene was high during 12–48 h of the in vitro culture, while the expression of cgd6_5480 was the highest at 2 h. ChMEDLE-1 and CpMEDLE-3 proteins were mostly located in the anterior and mid-anterior region of sporozoites and merozoites, whereas CpMEDLE-5 was expressed over the entire surface of these invasive stages. Polyclonal antibodies against MEDLE proteins had different neutralization efficiency, reaching approximately 50% for ChMEDLE-1 and 60% for CpMEDLE-3, but only 20% for CpMEDLE-5. The differences in protein and gene expression and neutralizing capacity indicated the MEDLE proteins may have different roles during Cryptosporidium invasion and growth.
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Affiliation(s)
- Jiayuan Su
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Chanchan Jin
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Haizhen Wu
- School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jilan Fei
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Na Li
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yaqiong Guo
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yaoyu Feng
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China.,Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lihua Xiao
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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Bennett KL, Gómez Martínez C, Almanza A, Rovira JR, McMillan WO, Enriquez V, Barraza E, Diaz M, Sanchez-Galan JE, Whiteman A, Gittens RA, Loaiza JR. High infestation of invasive Aedes mosquitoes in used tires along the local transport network of Panama. Parasit Vectors 2019; 12:264. [PMID: 31133041 PMCID: PMC6537307 DOI: 10.1186/s13071-019-3522-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/20/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The long-distance dispersal of the invasive disease vectors Aedes aegypti and Aedes albopictus has introduced arthropod-borne viruses into new geographical regions, causing a significant medical and economic burden. The used-tire industry is an effective means of Aedes dispersal, yet studies to determine Aedes occurrence and the factors influencing their distribution along local transport networks are lacking. To assess infestation along the primary transport network of Panama we documented all existing garages that trade used tires on the highway and surveyed a subset for Ae. aegypti and Ae. albopictus. We also assess the ability of a mass spectrometry approach to classify mosquito eggs by comparing our findings to those based on traditional larval surveillance. RESULTS Both Aedes species had a high infestation rate in garages trading used tires along the highways, providing a conduit for rapid dispersal across Panama. However, generalized linear models revealed that the presence of Ae. aegypti is associated with an increase in road density by a log-odds of 0.44 (0.73 ± 0.16; P = 0.002), while the presence of Ae. albopictus is associated with a decrease in road density by a log-odds of 0.36 (0.09 ± 0.63; P = 0.008). Identification of mosquito eggs by mass spectrometry depicted similar occurrence patterns for both Aedes species as that obtained with traditional rearing methods. CONCLUSIONS Garages trading used tires along highways should be targeted for the surveillance and control of Aedes-mosquitoes and the diseases they transmit. The identification of mosquito eggs using mass spectrometry allows for the rapid evaluation of Aedes presence, affording time and cost advantages over traditional vector surveillance; this is of importance for disease risk assessment.
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Affiliation(s)
- Kelly L Bennett
- Smithsonian Tropical Research Institute, Balboa Ancón, Republic of Panama
| | | | - Alejandro Almanza
- Smithsonian Tropical Research Institute, Balboa Ancón, Republic of Panama
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panamá, Republic of Panama
| | - Jose R Rovira
- Smithsonian Tropical Research Institute, Balboa Ancón, Republic of Panama
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panamá, Republic of Panama
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Balboa Ancón, Republic of Panama
| | | | | | | | | | - Ari Whiteman
- Smithsonian Tropical Research Institute, Balboa Ancón, Republic of Panama
- University of North Carolina, Charlotte, NC, USA
| | - Rolando A Gittens
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panamá, Republic of Panama.
| | - Jose R Loaiza
- Smithsonian Tropical Research Institute, Balboa Ancón, Republic of Panama.
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panamá, Republic of Panama.
- Universidad de Panamá, Panamá, Republic of Panama.
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Kumsa B, Abiy Y, Abunna F. Ectoparasites infesting dogs and cats in Bishoftu, central Oromia, Ethiopia. VETERINARY PARASITOLOGY- REGIONAL STUDIES AND REPORTS 2019; 15:100263. [PMID: 30929940 DOI: 10.1016/j.vprsr.2019.100263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 12/24/2018] [Accepted: 01/08/2019] [Indexed: 11/16/2022]
Abstract
A total of 200 dogs and 137 cats were examined for the presence of fleas, ticks and lice in Bishoftu, central Oromia, Ethiopia from September 2009 through April 2010. At least one ectoparasite species was found on 97% (194/200) of the dogs and 90.5% (124/137) of the cats. On dogs, fleas (Ctenocephalides felis (95%), Pulex irritans (20.5%), Echidnophaga gallinacea (9%) and Xenopsylla cheopis (0.5%)), ticks (Haemaphysalis leachi (17.5%), Amblyomma variegatum (8.5%), Rhipicephalus sanguineus (8%), Rhipicephalus pulchellus (5.5%) and Rhipicephalus (Boophilus) decoloratus (2.5%)) and lice (Heterodoxus spiniger (5%), Linognathus setosus (1.5%) and Trichodectes canis (0.5%)) were identified. On cats, fleas (C. felis (61.7%), E. gallinacea (24.1%), P. irritans (1.5%) and X. cheopis (0.7%)) and ticks (Ha. leachi (10.9%), Am. variegatum (1.5%) and Rh. sanguineus (0.7%)) were identified. C. felis was identified as the predominant ectoparasite on both dogs and cats. The overall frequency and count of ectoparasites was higher on dogs than on cats. Significantly higher overall frequency of fleas on young versus adult cats (p = .01) was recorded. However, ticks were significantly higher on adult cats than on young cats (p = .01). In conclusion, this study demonstrated great species diversity and high frequency of ectoparasites on dogs and cats in the study area. Further studies are required to investigate the role of these ectoparasites in transmission of zoonotic pathogens to humans and animals in Ethiopia.
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Affiliation(s)
- Bersissa Kumsa
- Department of Parasitology, College of Veterinary Medicine and Agriculture, Addis Ababa University, PO Box 34, Bishoftu, Ethiopia.
| | - Yonas Abiy
- Veterinary Drug and Animal Feed Administration and Control Authority, Addis Ababa, Ethiopia
| | - Fufa Abunna
- Department of Clinical Studies, College of Veterinary Medicine and Agriculture, Addis Ababa University, PO Box 34, Bishoftu, Ethiopia
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Reeve MA, Buddie AG, Pollard KM, Varia S, Seier MK, Offord LC, Cock MJW. A highly-simplified and inexpensive MALDI-TOF mass spectrometry sample-preparation method with broad applicability to microorganisms, plants, and insects. J Biol Methods 2018; 5:e103. [PMID: 31453253 PMCID: PMC6706156 DOI: 10.14440/jbm.2018.261] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 11/26/2022] Open
Abstract
Matrix-assisted laser-desorption and ionization time-of-flight mass spectrometry prepares proteins intact in the gas phase with predominantly a single positive charge. The times-of-flight of charged proteins along a tube held at high vacuum after acceleration in an electrical field are proportional to the square root of the mass-over-charge ratios for the proteins, thereby allowing a mass spectrum to be generated, which can then be used to characterize or identify a protein-containing sample. Several sample-preparation methods are currently available but not all of these are applicable to some forms of fungal biomass and few of these are well suited to the analysis of plant or insect material. We have therefore developed a simplified method that: lyses cells, selectively solubilizes basic proteins, dissolves matrix to a suitable concentration, generates spectra with good intensity and peak richness, costs no more (and generally less) than current methods, and is not constrained in terms of throughput by the availability of centrifuges. Using this method, and a reagent formulation comprising α-cyano-4-hydroxycinnamic acid matrix close to saturation in 60%–65% (v/v) acetonitrile in water containing 2.5% (v/v) trifluoroacetic acid, we have been able to differentiate between strains for a representative subset of aflatoxin-producing and aflatoxin-non-producing strains of Aspergillus fungi, to differentiate between Indian and Pakistani strains of Himalayan balsam rust, to differentiate between closely-related Crassula spp. and regional biotypes of Crassula helmsii, and to differentiate between rubbervine introduced into Australia and Brazil. We have also analyzed fall armyworm and stem-borer samples stored in 70% (v/v) ethanol and old dried insect specimens.
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Affiliation(s)
| | | | | | - Sonal Varia
- CABI, Bakeham Lane, Egham, Surrey, TW20 9 TY, UK
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Halada P, Hlavackova K, Risueño J, Berriatua E, Volf P, Dvorak V. Effect of trapping method on species identification of phlebotomine sandflies by MALDI-TOF MS protein profiling. MEDICAL AND VETERINARY ENTOMOLOGY 2018; 32:388-392. [PMID: 29774958 DOI: 10.1111/mve.12305] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/19/2018] [Accepted: 04/15/2018] [Indexed: 06/08/2023]
Abstract
Sandflies (Diptera: Psychodidae) (Newstead, 1911) are blood-feeding insects that transmit human pathogens including Leishmania (Trypanosomatida: Trypanosomatidae) parasites, causative agents of the leishmaniases. To elucidate Leishmania transmission cycles, conclusive identification of vector species is essential. Molecular approaches including matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) protein profiling have recently emerged to complement morphological identification. The aim of this study was to evaluate the effect of the trap type used to collect sandflies, specifically Centers for Disease Control (CDC) light or sticky traps, the two most commonly used in sandfly surveys, on subsequent MALDI-TOF MS protein profiling. Specimens of five species (Phlebotomus ariasi, Phlebotomus papatasi, Phlebotomus perniciosus, Phlebotomus sergenti, Sergentomyia minuta) collected in periurban and agricultural habitats in southeast Spain were subjected to protein profiling. Acquired protein spectra were queried against an in-house reference database and their quality assessed to evaluate the trap type effect. The results indicate that trap choice can substantially affect the quality of protein spectra in collected sandflies. Whereas specimens retrieved from light traps produced intense and reproducible spectra that allowed reliable species determination, profiles of specimens from sticky traps were compromised and often did not enable correct identification. Sticky traps should therefore not be used in surveys that deploy MALDI-TOF MS protein profiling for species identification.
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Affiliation(s)
- P Halada
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - K Hlavackova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - J Risueño
- Department of Animal Health, Faculty of Veterinary Science, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, Murcia, Spain
| | - E Berriatua
- Department of Animal Health, Faculty of Veterinary Science, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, Murcia, Spain
| | - P Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - V Dvorak
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
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Kriegsmann J, Casadonte R, Kriegsmann K, Longuespée R, Kriegsmann M. Mass spectrometry in pathology - Vision for a future workflow. Pathol Res Pract 2018; 214:1057-1063. [PMID: 29910062 DOI: 10.1016/j.prp.2018.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 04/23/2018] [Accepted: 05/11/2018] [Indexed: 02/09/2023]
Abstract
Mass spectrometric (MS) techniques are applied in various areas of medical diagnostics. For the detection of microbiological germs and genetic mutations, MS is a method used in routine. Since MS also allows the analysis of proteins and peptides, it seems an ideal candidate to supplement histopatholological diagnostics. Matrix-assisted laser desorption/ionization time-of-flight Imaging MS links molecular analysis of numerous analytes with morphological information about their spatial distribution in cells or tissues. Herein, we review principle MS techniques as well as potential applications in pathology and discuss our vision for a future workflow.
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Affiliation(s)
- Jörg Kriegsmann
- MVZ for Histology, Cytology and Molecular Diagnostics Trier, Trier, Germany; Proteopath GmbH, Trier, Germany
| | | | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Rémi Longuespée
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mark Kriegsmann
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
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Boucheikhchoukh M, Laroche M, Aouadi A, Dib L, Benakhla A, Raoult D, Parola P. MALDI-TOF MS identification of ticks of domestic and wild animals in Algeria and molecular detection of associated microorganisms. Comp Immunol Microbiol Infect Dis 2018; 57:39-49. [PMID: 30017077 DOI: 10.1016/j.cimid.2018.05.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 02/04/2018] [Accepted: 05/09/2018] [Indexed: 11/26/2022]
Abstract
Recent studies have reported the reliability of MALDI-TOF MS for arthropod identification, including fresh or alcohol-preserved ticks based on leg-derived mass spectra. The aim of this study was to evaluate the performance of MALDI-TOF MS for the identification of alcohol-preserved Algerian ticks collected from different domestic and wild hosts. Secondly, we conducted a molecular survey to detect the presence of bacterial DNA in all ticks that were previously subjected to MALDI-TOF MS. A total of 2635 ixodid and 1401 argasid ticks belonging to 9 distinct species were collected in nine different regions of northeastern Algeria. The legs of 230 specimens were subjected to MALDI-TOF MS assays. Spectral analysis revealed intra-species similarity and inter-species specificity for the MS spectra, which was consistent with the morphological identification. Blind tests against the in-lab database revealed that 93.48% of the tested specimens were correctly identified. The accuracy of the morphological and MALDI-TOF MS identifications was validated by sequencing the 12S ribosomal RNA gene (rRNA) for 33 specimens and all the ticks were correctly identified. The quantitative PCR screening showed that for 219 tested ticks, 15 were positive for Rickettsia spp., 8 for Borrelia spp. and 17 for Anaplasmataceae. The PCR tests were negative for Coxiella burnetii and Bartonella spp. This study supports MALDI-TOF MS being a reliable tool for the identification of arthropods and brings new data that sheds light on tick species diversity and tick-borne diseases in Algeria.
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Affiliation(s)
- Mehdi Boucheikhchoukh
- Université Chadli Bendjdid, Département des Sciences Vétérinaires, El Tarf, 36000, Algeria.
| | - Maureen Laroche
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.
| | - Atef Aouadi
- Université Chadli Bendjdid, Département des Sciences Vétérinaires, El Tarf, 36000, Algeria; Université Cherif Messaadia, Département des Sciences Vétérinaires, Souk Ahras, 41000, Algeria.
| | - Loubna Dib
- Université Chadli Bendjdid, Département des Sciences Vétérinaires, El Tarf, 36000, Algeria.
| | - Ahmed Benakhla
- Université Chadli Bendjdid, Département des Sciences Vétérinaires, El Tarf, 36000, Algeria.
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France.
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.
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Evers DL, Frye FA, Weina PJ. A simple empirical algorithm to distinguish among Leishmania braziliensis , major , and tropica species by MALDI-TOF mass spectrometry. J Microbiol Methods 2018; 148:46-48. [DOI: 10.1016/j.mimet.2017.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 10/18/2022]
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32
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An Introduction to Current Trends in Foodborne Pathogens and Diseases. CURRENT CLINICAL MICROBIOLOGY REPORTS 2018. [DOI: 10.1007/s40588-018-0093-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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