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Liu J, Deng S, Chang W, Yu D, Wang H. Development of a Multiplex PCR Assay for the Detection of Tomato Wilt Caused by Coinfection of Fusarium brachygibbosum, Fusarium oxysporum, and Ralstonia solanacearum Based on Comparative Genomics. PLANT DISEASE 2024; 108:1128-1138. [PMID: 37953228 DOI: 10.1094/pdis-05-23-0962-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Tomato is consumed worldwide as fresh or processed food products. However, soilborne diseases of tomato plants caused by coinfection of various pathogens result in great economic losses to the tomato industry. It is difficult to accurately identify and diagnose soilborne diseases of tomato plants caused by pathogen complexes. In this study, we investigated field diseases of tomato plants by pathogen isolation and molecular identification and found that tomato wilt was caused by coinfection of Fusarium brachygibbosum, F. oxysporum, and Ralstonia solanacearum. Therefore, developing a method for simultaneous detection of DNA from F. brachygibbosum, F. oxysporum, and R. solanacearum is of great importance to efficiently and accurately monitor disease development at different growth stages of tomato plants. In this study, we performed a comparative genomic analysis of F. brachygibbosum, F. oxysporum, and R. solanacearum and determined the primer sets for simultaneous detection of DNA from these target pathogens. Then, we tested the reagent and condition parameters of multiplex PCR, including primers, dNTP and Mg2+ concentrations, and annealing temperatures, to determine the optimal parameters of a multiplex PCR system. We evaluated the specificity, sensitivity, and stability of the multiplex PCR system based on the optimized reaction conditions. The multiplex PCR system can specifically identify 13 target pathogens from 57 different fungal and bacterial pathogens, at the lower detection limit of the three target pathogens at concentrations of 100 pg/μl. In addition, we can accurately identify the three pathogens in tomato plants using the optimized multiplex PCR method. These results demonstrated that the multiplex PCR method developed in this study can simultaneously detect DNA from F. brachygibbosum, F. oxysporum, and R. solanacearum in a single PCR system to accurately identify and diagnose the pathogen causing tomato wilt.
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Affiliation(s)
- Jun Liu
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
| | - Siyi Deng
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
| | - Wei Chang
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
| | - Dazhao Yu
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
| | - Hua Wang
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
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Lamoth F, Kontoyiannis DP. PCR diagnostic platforms for non- Aspergillus mold infections: ready for routine implementation in the clinic? Expert Rev Mol Diagn 2024; 24:273-282. [PMID: 38501431 DOI: 10.1080/14737159.2024.2326474] [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: 11/02/2023] [Accepted: 02/29/2024] [Indexed: 03/20/2024]
Abstract
INTRODUCTION While Aspergillus spp. remain the predominant cause of invasive mold infections, non-Aspergillus molds, such as the Mucorales or Fusarium spp., account for an increasing proportion of cases. The diagnosis of non-Aspergillus invasive mold infections (NAIMI) is challenging because of the low sensitivity and delay of conventional microbiological tests. Therefore, there is a particular interest to develop molecular tools for their early detection in blood or other clinical samples. AREAS COVERED This extensive review of the literature discusses the performance of Mucorales-specific PCR and other genus-specific or broad-range fungal PCR that can be used for the diagnosis of NAIMI in diverse clinical samples, with a focus on novel technologies. EXPERT OPINION PCR currently represents the most promising approach, combining good sensitivity/specificity and ability to detect NAIMI in clinical samples before diagnosis by conventional cultures and histopathology. Several PCR assays have been designed for the detection of Mucorales in particular, but also Fusarium spp. or Scedosporium/Lomentospora spp. Some commercial Mucorales PCRs are now available. While efforts are still needed for standardized protocols and the development of more rapid and simpler techniques, PCR is on the way to becoming an essential test for the early diagnosis of mucormycosis and possibly other NAIMIs.
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Affiliation(s)
- Frederic Lamoth
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Institute of Microbiology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dimitrios P Kontoyiannis
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Deng S, Liu Q, Chang W, Liu J, Wang H. First specific detection and validation of tomato wilt caused by Fusarium brachygibbosum using a PCR assay. PeerJ 2023; 11:e16473. [PMID: 38047027 PMCID: PMC10693239 DOI: 10.7717/peerj.16473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/25/2023] [Indexed: 12/05/2023] Open
Abstract
Tomato wilt is a widespread soilborne disease of tomato that has caused significant yield losses in many tomato growing regions of the world. Previously, it was reported that tomato wilt can be caused by many pathogens, such as Fusarium oxysporum, Ralstonia solanacearum, Ralstonia pseudosolanacearum, Fusarium acuminatum, and Plectosphaerella cucumerina. In addition, we have already reported that Fusarium brachygibbosum caused symptomatic disease of tomato wilt for the first time in China. The symptoms of tomato wilt caused by these pathogens are similar, making it difficult to distinguish them in the field. However, F. brachygibbosum specific identification method has not been reported. Therefore, it is of great importance to develop a rapid and reliable diagnostic method for Fusarium brachygibbosum to establish a more effective plan to control the disease. In this study, we designed F. brachygibbosum-specific forward primers and reverse primers with a fragment size of 283bp located in the gene encoding carbamoyl phosphate synthase arginine-specific large chain by whole genome sequence comparison analysis of the genomes of eight Fusarium spp.. We then tested different dNTP, Mg2+ concentrations, and annealing temperatures to determine the optimal parameters for the PCR system. We evaluated the specificity, sensitivity and stability of the PCR system based on the optimized reaction system and conditions. The PCR system can specifically identify the target pathogens from different fungal pathogens, and the lower detection limit of the target pathogens is at concentrations of 10 pg/uL. In addition, we can accurately identify F. brachygibbosum in tomato samples using the optimized PCR method. These results prove that the PCR method developed in this study can accurately identify and diagnose F. brachygibbosum.
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Affiliation(s)
- Siyi Deng
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, Hubei, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, Hubei, China
| | - Quanke Liu
- General Plant Protection Station of Hubei Province, Wuhan, Hubei, China
| | - Wei Chang
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, Hubei, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, Hubei, China
| | - Jun Liu
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, Hubei, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, Hubei, China
| | - Hua Wang
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, Hubei, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, Hubei, China
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Dellière S, Guitard J, Sabou M, Angebault C, Moniot M, Cornu M, Hamane S, Bougnoux ME, Imbert S, Pasquier G, Botterel F, Garcia-Hermoso D, Alanio A. Detection of circulating DNA for the diagnosis of invasive fusariosis: retrospective analysis of 15 proven cases. Med Mycol 2022; 60:6679565. [PMID: 36044994 DOI: 10.1093/mmy/myac049] [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: 05/10/2022] [Revised: 06/23/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022] Open
Abstract
Fusarium spp. are plant pathogens and opportunistic pathogens in severely immunocompromised (hematological malignancy, neutropenia, solid organ transplantation, …) and severely burned patients. Invasive fusariosis often disseminates and mortality remains high partly due to delayed diagnosis in the absence of a positive culture. The aim of our study is to design a qPCR assay and evaluate the detection of Fusarium spp. DNA for early diagnosis of invasive infection. A qPCR assay was designed and optimized to identify all Fusarium species complex and secondarily evaluated on patient samples. A total of 81 blood samples from 15 patients diagnosed with proven invasive fusariosis from 9 centers in France were retrospectively tested. Circulating DNA was detected in 14 patients out of 15 (sensitivity of 93% [IC95, 70.1-99.7]). Detection was possible up to 18 days (median 6 days) before the diagnosis was confirmed by positive blood culture or biopsy. By comparison serum galactomannan and ß-D-glucan were positive in 7.1 and 58.3% of patients respectively. qPCR was negative for all patients with other invasive fungal diseases (IFD) tested (n = 12) and IFD-free control patients (n = 40). No cross-reactions were detected using DNA extracted from 81 other opportunistic fungi. We developed and validated a pan-Fusarium qPCR assay in serum/plasma with high sensitivity, specificity and reproducibility that could facilitates early diagnosis and treatment monitoring of invasive fusariosis.
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Affiliation(s)
- Sarah Dellière
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, F-75010 Paris, France.,Institut Pasteur, Université de Paris Cité, CNRS, Unité de Mycologie Moléculaire, UMR2000, F-75015 Paris, France
| | - Juliette Guitard
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint-Antoine, Service de Parasitologie-Mycologie, F-75012 Paris, France
| | - Marcela Sabou
- Laboratoire de Parasitologie et de Mycologie Médicale, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Parasitologie et de Pathologie Tropicale, UR7292 Dynamique des interactions hôte pathogène, Fédération de Médecine Translationnelle, Université de Strasbourg, Strasbourg, France
| | - Cécile Angebault
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpitaux Universitaires Henri Mondor, UR Dynamyc UPEC, EnVA, ANSES, F-94010 Créteil, France
| | - Maxime Moniot
- Service de parasitologie-mycologie, CHU Clermont-Ferrand, 3IHP, France
| | - Marjorie Cornu
- Inserm U1285, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Univ. Lille, F-59000, Lille, France ; CHU Lille, Laboratoire de Parasitologie-Mycologie, F-59000 Lille, France
| | - Samia Hamane
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, F-75010 Paris, France
| | | | - Sébastien Imbert
- Laboratoire de parasitologie-mycologie, Bordeaux University Hospital, F-33000 Bordeaux, France
| | - Grégoire Pasquier
- University of Montpellier, CNRS, IRD, Academic Hospital (CHU) of Montpellier, MiVEGEC, Montpellier, France
| | - Françoise Botterel
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpitaux Universitaires Henri Mondor, UR Dynamyc UPEC, EnVA, ANSES, F-94010 Créteil, France
| | - Dea Garcia-Hermoso
- Institut Pasteur, Université de Paris Cité, CNRS, Unité de Mycologie Moléculaire, UMR2000, F-75015 Paris, France.,Institut Pasteur, Centre National de Référence Mycologie et Antifongiques, F-75015 Paris, France
| | - Alexandre Alanio
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, F-75010 Paris, France.,Institut Pasteur, Université de Paris Cité, CNRS, Unité de Mycologie Moléculaire, UMR2000, F-75015 Paris, France.,Institut Pasteur, Centre National de Référence Mycologie et Antifongiques, F-75015 Paris, France
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Chen L, Li L, Xie X, Chai A, Shi Y, Fan T, Xie J, Li B. An Improved Method for Quantification of Viable Fusarium Cells in Infected Soil Products by Propidium Monoazide Coupled with Real-Time PCR. Microorganisms 2022; 10:microorganisms10051037. [PMID: 35630479 PMCID: PMC9143521 DOI: 10.3390/microorganisms10051037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 11/30/2022] Open
Abstract
Fusarium is a soil-borne pathogen that causes root rot disease in cucumber. To date, quantitative real-time PCR (qPCR) is a common tool to detect the content of Fusarium in soil. However, qPCR cannot distinguish between viable and nonviable cells. The aim of this study was to develop a detection technique to pretreat tissue fluid with propidium monoazide (PMA) followed by extract DNA, and then to quantify viable Fusarium cells in contaminated soil. In this work, the specific primer pair F8-1/F8-2 was designed based on the translation elongation factor (EF) gene and a PMA-qPCR assay was established to amplify and quantify soils of viable Fusarium cells. The PMA pretreatment test was optimized, which indicated that the optimal PMA concentration and light exposure time were 50 mmol L−1 and 15 min, respectively. The lowest limit of viable cells in suspension detected and soil by PMA-qPCR were 82 spore mL−1 and 91.24 spore g−1, respectively. For naturally contaminated soil, viable Fusarium cells were detected in eight of the 18 samples, and the Fusarium amount ranged from 104 to 106 spore g−1. In conclusion, the PMA-qPCR method has the characteristics of high sensitivity, efficiency, and time saving, which could support nursery plants to avoid Fusarium infection and agro-industry losses.
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Affiliation(s)
- Lida Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China;
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (X.X.); (A.C.); (Y.S.); (T.F.)
| | - Lei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (X.X.); (A.C.); (Y.S.); (T.F.)
| | - Xuewen Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (X.X.); (A.C.); (Y.S.); (T.F.)
- Shouguang R&D Center of Vegetables, Chinese Academy of Agricultural Sciences, Weifang 262700, China
| | - Ali Chai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (X.X.); (A.C.); (Y.S.); (T.F.)
| | - Yanxia Shi
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (X.X.); (A.C.); (Y.S.); (T.F.)
| | - Tengfei Fan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (X.X.); (A.C.); (Y.S.); (T.F.)
| | - Jianming Xie
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China;
- Correspondence: (J.X.); (B.L.)
| | - Baoju Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.); (X.X.); (A.C.); (Y.S.); (T.F.)
- Correspondence: (J.X.); (B.L.)
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Banfalvi G. Janus-Faced Molecules against Plant Pathogenic Fungi. Int J Mol Sci 2021; 22:12323. [PMID: 34830204 PMCID: PMC8623416 DOI: 10.3390/ijms222212323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Abstract
The high cytotoxicity of the secondary metabolites of mycotoxins is capable of killing microbes and tumour cells alike, similarly to the genotoxic effect characteristic of Janus-faced molecules. The "double-edged sword" effect of several cytotoxins is known, and these agents have, therefore, been utilized only reluctantly against fungal infections. In this review, consideration was given to (a) toxins that could be used against plant and human pathogens, (b) animal models that measure the effect of antifungal agents, (c) known antifungal agents that have been described and efficiently prevent the growth of fungal cells, and (d) the chemical interactions that are characteristic of antifungal agents. The utilization of apoptotic effects against tumour growth by agents that, at the same time, induce mutations may raise ethical issues. Nevertheless, it deserves consideration despite the mutagenic impact of Janus-faced molecules for those patients who suffer from plant pathogenic fungal infections and are older than their fertility age, in the same way that the short-term cytotoxicity of cancer treatment is favoured over the long-term mutagenic effect.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 1 Egyetem Square, 4010 Debrecen, Hungary
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Brackin AP, Hemmings SJ, Fisher MC, Rhodes J. Fungal Genomics in Respiratory Medicine: What, How and When? Mycopathologia 2021; 186:589-608. [PMID: 34490551 PMCID: PMC8421194 DOI: 10.1007/s11046-021-00573-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/14/2021] [Indexed: 12/20/2022]
Abstract
Respiratory infections caused by fungal pathogens present a growing global health concern and are a major cause of death in immunocompromised patients. Worryingly, coronavirus disease-19 (COVID-19) resulting in acute respiratory distress syndrome has been shown to predispose some patients to airborne fungal co-infections. These include secondary pulmonary aspergillosis and mucormycosis. Aspergillosis is most commonly caused by the fungal pathogen Aspergillus fumigatus and primarily treated using the triazole drug group, however in recent years, this fungus has been rapidly gaining resistance against these antifungals. This is of serious clinical concern as multi-azole resistant forms of aspergillosis have a higher risk of mortality when compared against azole-susceptible infections. With the increasing numbers of COVID-19 and other classes of immunocompromised patients, early diagnosis of fungal infections is critical to ensuring patient survival. However, time-limited diagnosis is difficult to achieve with current culture-based methods. Advances within fungal genomics have enabled molecular diagnostic methods to become a fast, reproducible, and cost-effective alternative for diagnosis of respiratory fungal pathogens and detection of antifungal resistance. Here, we describe what techniques are currently available within molecular diagnostics, how they work and when they have been used.
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Affiliation(s)
- Amelie P Brackin
- MRC Centre for Global Disease Analysis, Imperial College London, London, UK
| | - Sam J Hemmings
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Johanna Rhodes
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
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Lopes LG, Csonka LA, Castellane JAS, Oliveira AW, de Almeida-Júnior S, Furtado RA, Tararam C, Levy LO, Crivellenti LZ, Moretti ML, Giannini MJSM, Pires RH. Disinfectants in a Hemodialysis Setting: Antifungal Activity Against Aspergillus and Fusarium Planktonic and Biofilm Cells and the Effect of Commercial Peracetic Acid Residual in Mice. Front Cell Infect Microbiol 2021; 11:663741. [PMID: 33996634 PMCID: PMC8116949 DOI: 10.3389/fcimb.2021.663741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/04/2021] [Indexed: 11/17/2022] Open
Abstract
Aspergillus and Fusarium cause a broad spectrum of infections in humans, mainly in immunocompromised patients. Among these, patients undergoing hemodialysis are highly susceptible to infections, requiring a constant and adequate environmental disinfection program. Nevertheless, monitoring the residual disinfectants can contribute to the morbidity and mortality reduction in these patients. Here, we evaluated the susceptibility of Aspergillus spp. (n=19) and Fusarium spp. (n=13) environmental isolates against disinfectants (acetic acid, citric acid, peracetic acid, sodium hypochlorite, and sodium metabisulphite) at different concentrations and time exposures. Also, we investigated the in vivo toxicity of the peracetic acid residual concentration in mice. Fusarium isolates were identified by F. equiseti, F. oxysporum and F. solani while Aspergillus presented clinically relevant species (A. fumigatus, A. niger and A. terreus) and environmental ones. Against planktonic cells, only two disinfectants (acetic acid and sodium hypochlorite) showed a fungicidal effect on Fusarium spp., while only one (sodium hypochlorite) was effective against Aspergillus spp. Both fungi formed robust in vitro biofilms with large amounts of the extracellular matrix, as evidenced by electron micrographs. Exposure of fungal biofilms to disinfectants showed sensitivity to three (acetic, citric, and peracetic acids), although the concentrations and times of exposure varied according to the fungal genus. Mice exposure to the residual dose of peracetic acid during 60 weeks showed anatomopathological, hematological, and biochemical changes. The implementation of news control measures and those that already exist can help reduce infections, the second cause of death and morbidity in these patients, besides providing safety and well-being to them, a priority of any quality health program.
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Affiliation(s)
- Leonardo G. Lopes
- Postgraduate Program in Health Promotion, University of Franca, Franca, Brazil
| | - Larissa A. Csonka
- Postgraduate Program in Health Promotion, University of Franca, Franca, Brazil
| | | | | | | | | | - Cibele Tararam
- Faculty of Medical Sciences, University of Campinas, Campinas, Brazil
| | | | | | | | | | - Regina H. Pires
- Postgraduate Program in Health Promotion, University of Franca, Franca, Brazil
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Zaniol E, Daprà V, Filomena R, Alliaudi C, Calvi C, Montanari P, Galliano I, Bergallo M. Real time qPCR TaqMan method for detection of Fusarium solani. MINERVA BIOTECNOL 2020. [DOI: 10.23736/s1120-4826.20.02621-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Hino Y, Muraosa Y, Oguchi M, Yahiro M, Yarita K, Watanabe A, Sakaida E, Yokote K, Kamei K. Drain outlets in patient rooms as sources for invasive fusariosis: an analysis of patients with haematological disorders. J Hosp Infect 2020; 105:S0195-6701(20)30204-8. [PMID: 32360338 DOI: 10.1016/j.jhin.2020.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/21/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND Invasive fusariosis (IF) is a frequently fatal disease as there are few antifungals to treat it, making the prevention of IF crucial. However, fusarium infections have not been as thoroughly studied as other common pathogenic fungi such as Aspergillus or Candida. AIM To investigate the epidemiology of IF in patients with haematological diseases in Japan and to elucidate the infectious route of fusarium infection. METHODS We retrospectively analysed 29 IF cases in patients with haematological diseases from 2009 to 2019 in Japan. To discover the infectious source of IF, we performed an indoor environment survey targeted at indoor air and drain outlets in medical institutions and residences using culture-based and metagenomic methods. Finally, we performed aerosol- and droplet-mediated dispersion studies. FINDINGS The epidemiological study showed that the primary pathogen of IF was Fusarium solani species complex (FSSC), and the most common species was Fusarium petroliphilum. Most patients were likely to develop IF during hospitalization. A fusarium culture was positive in 26 of 72 drain samples. Few fusarium were detected from air samples; by contrast, 29 of 108 isolates from the drain outlets were identified as fusarium. Furthermore, similar results were obtained in the metagenomic analysis. Interestingly, species belonging to FSSC were isolated from indoor drain outlets, which was similar to those of the IF patients. In the droplet-mediated dispersion study, eight to 17 colonies of fusarium were isolated. CONCLUSION Our study indicates that causative Fusarium spp. could inhabit drain outlets in hospitals or residences, and droplet-mediated fusarium dispersion is a potential cause of IF.
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Affiliation(s)
- Y Hino
- Medical Mycology Research Center, Chiba University, Chiba, Japan; Department of Haematology, Chiba University Hospital, Chiba, Japan; Department of Endocrinology, Haematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Y Muraosa
- Medical Mycology Research Center, Chiba University, Chiba, Japan.
| | - M Oguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - M Yahiro
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - K Yarita
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - A Watanabe
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - E Sakaida
- Department of Haematology, Chiba University Hospital, Chiba, Japan; Department of Endocrinology, Haematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - K Yokote
- Department of Endocrinology, Haematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - K Kamei
- Medical Mycology Research Center, Chiba University, Chiba, Japan
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Shen Y, Nie J, Kuang L, Zhang J, Li H. DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microb Biotechnol 2020; 14:323-362. [PMID: 32207561 PMCID: PMC7936329 DOI: 10.1111/1751-7915.13560] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.
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Affiliation(s)
- Youming Shen
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jiyun Nie
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China.,College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lixue Kuang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jianyi Zhang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Haifei Li
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
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Haarith D, Bushley KE, Chen S. Fungal communities associated with Heterodera glycines and their potential in biological control: a current update. J Nematol 2020; 52:1-17. [PMID: 32180383 PMCID: PMC7266048 DOI: 10.21307/jofnem-2020-022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Indexed: 11/11/2022] Open
Abstract
The soybean cyst nematode (SCN) is the most important pest on soybean, a major crop worldwide. The SCN is considered both parasitic and pathogenic as it derives nutrition from the host and manipulates host physiology to do so. Currently, there are no commercially available chemicals that are specific, environmentally safe and cost effective to control SCN levels. Crop rotation, use of host resistance and other cultural practices remain the main management strategies. The need for bioprospecting other methods of controlling SCN is paramount, and fungi show promise in that respect. Several studies have evaluated fungi and fungal products as biocontrol options against plant-parasitic nematodes. This review discusses fungal genera isolated from the SCN with potential for use as biocontrol agents and the effects of their secondary metabolites on various stages of SCN development. The review also summarizes efforts to control SCN using soil amendments that could potentially impact fungal communities in the soil. The soybean cyst nematode (SCN) is the most important pest on soybean, a major crop worldwide. The SCN is considered both parasitic and pathogenic as it derives nutrition from the host and manipulates host physiology to do so. Currently, there are no commercially available chemicals that are specific, environmentally safe and cost effective to control SCN levels. Crop rotation, use of host resistance and other cultural practices remain the main management strategies. The need for bioprospecting other methods of controlling SCN is paramount, and fungi show promise in that respect. Several studies have evaluated fungi and fungal products as biocontrol options against plant-parasitic nematodes. This review discusses fungal genera isolated from the SCN with potential for use as biocontrol agents and the effects of their secondary metabolites on various stages of SCN development. The review also summarizes efforts to control SCN using soil amendments that could potentially impact fungal communities in the soil.
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Affiliation(s)
- Deepak Haarith
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Kathryn E. Bushley
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108
| | - Senyu Chen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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Thornton CR. Detection of the 'Big Five' mold killers of humans: Aspergillus, Fusarium, Lomentospora, Scedosporium and Mucormycetes. ADVANCES IN APPLIED MICROBIOLOGY 2019; 110:1-61. [PMID: 32386603 DOI: 10.1016/bs.aambs.2019.10.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fungi are an important but frequently overlooked cause of morbidity and mortality in humans. Life-threatening fungal infections mainly occur in immunocompromised patients, and are typically caused by environmental opportunists that take advantage of a weakened immune system. The filamentous fungus Aspergillus fumigatus is the most important and well-documented mold pathogen of humans, causing a number of complex respiratory diseases, including invasive pulmonary aspergillosis, an often fatal disease in patients with acute leukemia or in immunosuppressed bone marrow or solid organ transplant recipients. However, non-Aspergillus molds are increasingly reported as agents of disseminated diseases, with Fusarium, Scedosporium, Lomentospora and mucormycete species now firmly established as pathogens of immunosuppressed and immunocompetent individuals. Despite well-documented risk factors for invasive fungal diseases, and increased awareness of the risk factors for life-threatening infections, the number of deaths attributable to molds is likely to be severely underestimated driven, to a large extent, by the lack of readily accessible, cheap, and accurate tests that allow detection and differentiation of infecting species. Early diagnosis is critical to patient survival but, unlike Aspergillus diseases, where a number of CE-marked or FDA-approved biomarker tests are now available for clinical diagnosis, similar tests for fusariosis, scedosporiosis and mucormycosis remain experimental, with detection reliant on insensitive and slow culture of pathogens from invasive bronchoalveolar lavage fluid, tissue biopsy, or from blood. This review examines the ecology, epidemiology, and contemporary methods of detection of these mold pathogens, and the obstacles to diagnostic test development and translation of novel biomarkers to the clinical setting.
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Detection of Fusarium Species in Clinical Specimens by Probe-Based Real-Time PCR. J Fungi (Basel) 2019; 5:jof5040105. [PMID: 31726656 PMCID: PMC6958410 DOI: 10.3390/jof5040105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/28/2022] Open
Abstract
The mold Fusarium is a ubiquitous fungus causing plant, animal and human infections. In humans, Fusarium spp. are the major cause of eye infections in patients wearing contact lenses or after local trauma. Systemic infections by Fusarium spp. mainly occur in immunosuppressed patients and can disseminate throughout the human body. Due to high levels of resistance to antifungals a fast identification of the causative agent is an urgent need. By using a probe-based real-time PCR assay specific for the genus Fusarium we analysed several different clinical specimens detecting Fusarium spp. commonly found in clinical samples in Germany. Also, a large collection of lung fluid samples of haematological patients was analysed (n = 243). In these, two samples (0.8%) were reproducibly positive, but only one could be confirmed by sequencing. For this case of probable invasive fungal disease (IFD) culture was positive for Fusarium species. Here we describe a rapid, probe-based real-time PCR assay to specifically detect DNA from a broad range of Fusarium species and its application to clinically relevant specimens.
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Koo SH, Teoh YL, Koh WL, Ochi H, Tan SK, Sim DMF, Jiang B, Tan AL, Tan TY, Lim SPR. Development and validation of a real-time multiplex PCR assay for the detection of dermatophytes and Fusarium spp. J Med Microbiol 2019; 68:1641-1648. [PMID: 31526456 DOI: 10.1099/jmm.0.001082] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Introduction: Onychomycosis is a debilitating, difficult-to-treat nail fungal infection with increasing prevalence worldwide. The main etiological agents are dermatophytes, which are common causative pathogens in superficial fungal mycoses. Conventional detection methods such as fungal culture have low sensitivity and specificity and are time-consuming.Aim: The main objective of this study was to design, develop and validate a real-time probe-based multiplex qPCR assay for the detection of dermatophytes and Fusarium species.Methodology: The performance characteristics of the qPCR assays were evaluated. The multiplex qPCR assays targeted four genes (assay 1: pan-dermatophytes/Fusarium spp.; assay 2: Trichophyton rubrum/Microsporum spp.). Analytical validation was accomplished using 150 fungal isolates and clinical validation was done on 204 nail specimens. The performance parameters were compared against the gold standard (fungal culture) and expanded gold standard (culture in conjunction with sequencing).Results: Both the single-plex and multiplex qPCR assays performed well especially when compared against the expanded gold standard. Among the 204 tested nail specimens, the culture method showed that 125 (61.3 %) were infected with at least one organism, of which 40 yielded positive results for dermatophytes and Fusarium spp. These target organisms detected include 20 dermatophytes and 22 Fusarium spp. The developed qPCR assays demonstrated excellent limit of detection, efficiency, coefficient of determination, analytical and clinical sensitivity and specificity.Conclusion: The multiplex qPCR assays were reliable for the diagnosis of onychomycosis, with shorter turn-around time as compared to culture method. This aids in the planning of treatment strategies to achieve optimal therapeutic outcome.
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Affiliation(s)
- Seok Hwee Koo
- Clinical Trials and Research Unit, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Yee Leng Teoh
- Department of Dermatology, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Wei Liang Koh
- Department of Dermatology, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Harumi Ochi
- Department of Dermatology, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Sher Kye Tan
- School of Chemical and Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Singapore
| | - Diana Miao Fang Sim
- Department of Laboratory Medicine, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Boran Jiang
- Department of Laboratory Medicine, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Ai Ling Tan
- Department of Microbiology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Thean Yen Tan
- Department of Laboratory Medicine, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Su Ping Regina Lim
- Department of Dermatology, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
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Niu L, Liu X, Ma Z, Yin Y, Sun L, Yang L, Zheng Y. Fungal keratitis: Pathogenesis, diagnosis and prevention. Microb Pathog 2019; 138:103802. [PMID: 31626916 DOI: 10.1016/j.micpath.2019.103802] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/12/2019] [Accepted: 10/12/2019] [Indexed: 02/08/2023]
Abstract
As a kind of serious, potentially sight-threatening corneal infections with poor prognosis, fungal keratitis can bring a heavy economic burden to patients and seriously affect the quality of life, especially those in developing countries where fungal keratitis is more prevalent. Typical clinical features include immune rings, satellite lesions, pseudopods, hypha moss, hypopyon and endothelial plaques. The ideal therapeutic effects could not be achieved by current treatments for many reasons. Therefore, under the current status, understanding the pathogenesis, early diagnosis and prevention strategies might be of great importance. Here, in this review, we discuss the recent progresses that may advance our understanding of pathogenesis, early diagnosis and prevention of fungal keratitis.
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Affiliation(s)
- Lingzhi Niu
- Eye Center, The Second Hospital of Jilin University, Changchun 130041, China
| | - Xin Liu
- Eye Center, The Second Hospital of Jilin University, Changchun 130041, China
| | - Zhiming Ma
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun 130041, China
| | - Yuan Yin
- Eye Center, The Second Hospital of Jilin University, Changchun 130041, China
| | - Lixia Sun
- Department of Ophthalmology, Yanbian University Affiliated Hospital, Yanbian University, Yanji, 133000, China
| | - Longfei Yang
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetics, The Second Hospital of Jilin University, Changchun 130041, China.
| | - Yajuan Zheng
- Eye Center, The Second Hospital of Jilin University, Changchun 130041, China.
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Villarino M, De la Lastra E, Basallote-Ureba MJ, Capote N, Larena I, Melgarejo P, De Cal A. Characterization of Fusarium solani Populations Associated with Spanish Strawberry Crops. PLANT DISEASE 2019; 103:1974-1982. [PMID: 31210598 DOI: 10.1094/pdis-02-19-0342-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fusarium solani is an emerging pathogen reported on Spanish strawberry crops both in nurseries and in fruit production fields, causing wilt and root rot. Pathogenicity, morphocultural characteristics, and sensitivity to biocides of 103 F. solani isolates recovered from symptomatic strawberry plants and soils from both Spanish strawberry areas were determined. The differences of isolates within and between nurseries and field crops in relation to these parameters were analyzed. Considerable variability in morphological and pathogenic characteristics was observed among the isolates in both areas. The majority of isolates were not pathogenic (62%), and only 38 F. solani isolates (37.62%) caused disease on strawberry plants under controlled conditions; 52.63% of pathogenic isolates induced low severity symptoms. Almost 70% of pathogenic isolates caused stunting on plants. The morphological characters that best explain the F. solani variability (86.85%) were colony color and the presence of macroconidia on culture medium. The sensitivity to the fumigants tested was similar between the isolates from nurseries and fruit production fields, showing greater sensitivity to the field doses of dazomet and chloropicrin. However, the isolates were less sensitive to metam sodium and poorly sensitive to 1,3-dichloropropene. This work can contribute to the advancement of sustainable production of strawberry.
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Affiliation(s)
- M Villarino
- 1Department of Plant Protection, INIA, Carretera de La Coruña Km 7,5. 28040 Madrid, Spain
| | - E De la Lastra
- 2IFAPA Centro Las Torres, Apdo. Oficial, 41200 Alcalá del Rio, Sevilla, Spain
| | - M J Basallote-Ureba
- 2IFAPA Centro Las Torres, Apdo. Oficial, 41200 Alcalá del Rio, Sevilla, Spain
| | - N Capote
- 2IFAPA Centro Las Torres, Apdo. Oficial, 41200 Alcalá del Rio, Sevilla, Spain
| | - I Larena
- 1Department of Plant Protection, INIA, Carretera de La Coruña Km 7,5. 28040 Madrid, Spain
| | - P Melgarejo
- 1Department of Plant Protection, INIA, Carretera de La Coruña Km 7,5. 28040 Madrid, Spain
| | - A De Cal
- 1Department of Plant Protection, INIA, Carretera de La Coruña Km 7,5. 28040 Madrid, Spain
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Nikitin M, Deych K, Grevtseva I, Girsova N, Kuznetsova M, Pridannikov M, Dzhavakhiya V, Statsyuk N, Golikov A. Preserved Microarrays for Simultaneous Detection and Identification of Six Fungal Potato Pathogens with the Use of Real-Time PCR in Matrix Format. BIOSENSORS 2018; 8:E129. [PMID: 30551630 PMCID: PMC6316111 DOI: 10.3390/bios8040129] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/08/2018] [Accepted: 12/11/2018] [Indexed: 01/11/2023]
Abstract
Fungal diseases of plants are of great economic importance causing 70⁻80% of crop losses associated with microbial plant pathogens. Advanced on-site disease diagnostics is very important to maximize crop productivity. In this study, diagnostic systems have been developed for simultaneous detection and identification of six fungal pathogens using 48-well microarrays (micromatrices) for qPCR. All oligonucleotide sets were tested for their specificity using 59 strains of target and non-target species. Detection limit of the developed test systems varied from 0.6 to 43.5 pg of DNA depending on target species with reproducibility within 0.3-0.7% (standard deviation). Diagnostic efficiency of test systems with stabilized and freeze-dried PCR master-mixes did not significantly differ from that of freshly prepared microarrays, though detection limit increased. Validation of test systems on 30 field samples of potato plants showed perfect correspondence with the results of morphological identification of pathogens. Due to the simplicity of the analysis and the automated data interpretation, the developed microarrays have good potential for on-site use by technician-level personnel, as well as for high-throughput monitoring of fungal potato pathogens.
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Affiliation(s)
- Maksim Nikitin
- GenBit LLC, Nauchny pr., 20, Bld. 4, Moscow 117246, Russia.
| | - Ksenia Deych
- GenBit LLC, Nauchny pr., 20, Bld. 4, Moscow 117246, Russia.
| | | | - Natalya Girsova
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
| | - Maria Kuznetsova
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
| | - Mikhail Pridannikov
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
- Centre of Parasitology, Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii Prospect 33, Moscow 119071, Russia.
| | - Vitaly Dzhavakhiya
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
| | - Natalia Statsyuk
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
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Moretti ML, Busso-Lopes AF, Tararam CA, Moraes R, Muraosa Y, Mikami Y, Gonoi T, Taguchi H, Lyra L, Reichert-Lima F, Trabasso P, de Hoog GS, Al-Hatmi AMS, Schreiber AZ, Kamei K. Airborne transmission of invasive fusariosis in patients with hematologic malignancies. PLoS One 2018; 13:e0196426. [PMID: 29698435 PMCID: PMC5919535 DOI: 10.1371/journal.pone.0196426] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/12/2018] [Indexed: 01/01/2023] Open
Abstract
From 2006 to 2013, an increasing incidence of fusariosis was observed in the hematologic patients of our University Hospital. We suspected of an environmental source, and the indoor hospital air was investigated as a potential source of the fungemia. Air samplings were performed in the hematology and bone marrow transplant (BMT) wards using an air sampler with pre-defined air volumes. To study the molecular relationship among environmental and clinical isolates, 18 Fusarium spp. recovered from blood cultures were included in the study. DNA sequencing of a partial portion of TEF1α gene was performed for molecular identification. Molecular typing was carried out by multi-locus sequence typing (MLST) using a four-gene scheme: TEF1α, rDNA, RPB1 and RPB2. One hundred four isolates were recovered from the air of the hematology (n = 76) and the BMT (n = 28) wards. Fusarium isolates from the air were from five species complexes: Fusarium fujikuroi (FFSC, n = 56), Fusarium incarnatum-equiseti (FIESC, n = 24), Fusarium solani (FSSC, n = 13), Fusarium chlamydosporum (FCSC, n = 10), and Fusarium oxysporum (FOSC, n = 1). Fifteen Fusarium isolates recovered from blood belonged to FSSC, and three to FFSC. MLST identified the same sequence type (ST) in clinical and environmental isolates. ST1 was found in 5 isolates from blood and in 7 from the air, both identified as FSSC (Fusarium petroliphilum). STn1 was found in one isolate from blood and in one from the air, both identified as FFSC (Fusarium napiforme). F. napiforme was isolated from the air of the hospital room of the patient with fungemia due to F. napiforme. These findings suggested a possible clonal origin of the Fusarium spp. recovered from air and bloodcultures. In conclusion, our study found a diversity of Fusarium species in the air of our hospital, and a possible role of the air as source of systemic fusariosis in our immunocompromised patients.
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Affiliation(s)
- Maria Luiza Moretti
- Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, Sao Paulo, Brazil
- * E-mail:
| | | | - Cibele Aparecida Tararam
- Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, Sao Paulo, Brazil
| | - Renato Moraes
- Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, Sao Paulo, Brazil
| | - Yasunori Muraosa
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Yuzuru Mikami
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Tohru Gonoi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Hideaki Taguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Luzia Lyra
- Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Campinas, Sao Paulo, Brazil
| | - Franqueline Reichert-Lima
- Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Campinas, Sao Paulo, Brazil
| | - Plínio Trabasso
- Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, Sao Paulo, Brazil
| | - Gerrit Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Institutes of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Basic Pathology Department, Federal University of Paraná State, Curitiba, Paraná, Brazil
- Biology Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdullah Mohammed Said Al-Hatmi
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Institutes of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Directorate General of Health Services, Ibri Hospital, Ministry of Health, Muscat, Oman
| | - Angelica Zaninelli Schreiber
- Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Campinas, Sao Paulo, Brazil
| | - Katsuhiko Kamei
- Medical Mycology Research Center, Chiba University, Chiba, Japan
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Visible DNA Microarray System as an Adjunctive Molecular Test in Identification of Pathogenic Fungi Directly from a Blood Culture Bottle. J Clin Microbiol 2018. [PMID: 29514940 DOI: 10.1128/jcm.01908-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A DNA microarray platform, based on the nucleotide sequences of the internal transcribed spacer regions (ITS1 and ITS2) of the rRNA gene, was developed to identify 32 fungal pathogens at the species level. The probe sequences were spotted onto polycarbonate slides with a mini-microarray printer, and after the hybridization, the results were visible with the naked eye. The performance of the microarray platform was evaluated against the commercial automated systems (Vitek 2 and BD Phoenix systems) and DNA sequencing (gold standard). A total of 461 blood culture bottles were tested: 127 positive for fungi, 302 positive for bacteria, and 32 that were negative. Once the microorganisms were identified by automated systems, fungal DNA was extracted directly from the blood culture bottles. The DNA products were tested using the microarray platform, and DNA sequencing was performed. The results of the microarray and DNA sequencing were concordant in 96.7% of cases, and the results from the automated systems and DNA sequencing were concordant in 98.4%. Of all the nucleotide sequences contained in the microarray platform, the microarray failed to identify four fungal isolates (one Candida parapsilosis, two Candida tropicalis, and one Cryptococcus neoformans). Of note, the microarray detected Candida krusei DNA in two blood cultures from the same patient, whereas the automated system was only positive for Enterococcus faecium Our microarray system provided reliable and fast fungal identification compared to that from DNA sequencing and the automated systems. The simplicity of reading the results by the naked eye made this DNA platform a suitable method for fungal molecular diagnosis.
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Disseminated fusariosis emerged from prolonged local genital infection after cord blood transplantation. J Infect Chemother 2018; 24:660-663. [PMID: 29373264 DOI: 10.1016/j.jiac.2017.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 12/14/2017] [Accepted: 12/21/2017] [Indexed: 11/23/2022]
Abstract
Disseminated fusariosis (DF) is a rare life threatening fungal infection in immunocompromised hosts. We herein report a case of a fatal DF mimicking varicella zoster virus (VZV) infection that was emerged from a localized genital infection during cord blood transplantation (CBT) in a patient with severe aplastic anemia (SAA). The patient developed an ulcer following small painful vesicles mimics herpes simplex virus infection (HSV) on the glans penis before CBT, but a Fusarium species was identified. Despite administration of voriconazole, liposomal amphotericin B and granulocyte transfusion, the lesion was extended to extensive skin looked like VZV infection and the patients died after CBT. Massive fusarium infiltration was detected in multiple organs at autopsy. A genetic analysis of the mold identified Fusarium solani after his death. It should be noted that in patients with fusarium infection, localized and disseminated lesions of fusarium infection sometimes mimic HSV and VZV infections, which hampers an early diagnosis.
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López LF, Muñoz CO, Cáceres DH, Tobón ÁM, Loparev V, Clay O, Chiller T, Litvintseva A, Gade L, González Á, Gómez BL. Standardization and validation of real time PCR assays for the diagnosis of histoplasmosis using three molecular targets in an animal model. PLoS One 2017; 12:e0190311. [PMID: 29287097 PMCID: PMC5747470 DOI: 10.1371/journal.pone.0190311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/12/2017] [Indexed: 12/04/2022] Open
Abstract
Histoplasmosis is considered one of the most important endemic and systemic mycoses worldwide. Until now few molecular techniques have been developed for its diagnosis. The aim of this study was to develop and evaluate three real time PCR (qPCR) protocols for different protein-coding genes (100-kDa, H and M antigens) using an animal model. Fresh and formalin-fixed and paraffin-embedded (FFPE) lung tissues from BALB/c mice inoculated i.n. with 2.5x106Histoplasma capsulatum yeast or PBS were obtained at 1, 2, 3, 4, 8, 12 and 16 weeks post-infection. A collection of DNA from cultures representing different clades of H. capsulatum (30 strains) and other medically relevant pathogens (36 strains of related fungi and Mycobacterium tuberculosis) were used to analyze sensitivity and specificity. Analytical sensitivity and specificity were 100% when DNAs from the different strains were tested. The highest fungal burden occurred at first week post-infection and complete fungal clearance was observed after the third week; similar results were obtained when the presence of H. capsulatum yeast cells was demonstrated in histopathological analysis. In the first week post-infection, all fresh and FFPE lung tissues from H. capsulatum-infected animals were positive for the qPCR protocols tested except for the M antigen protocol, which gave variable results when fresh lung tissue samples were analyzed. In the second week, all qPCR protocols showed variable results for both fresh and FFPE tissues. Samples from the infected mice at the remaining times post-infection and uninfected mice (controls) were negative for all protocols. Good agreement was observed between CFUs, histopathological analysis and qPCR results for the 100-kDa and H antigen protocols. We successfully standardized and validated three qPCR assays for detecting H. capsulatum DNA in fresh and FFPE tissues, and conclude that the 100-kDa and H antigen molecular assays are promising tests for diagnosing this mycosis.
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Affiliation(s)
- Luisa F. López
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
| | - César O. Muñoz
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
| | - Diego H. Cáceres
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Ángela M. Tobón
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
| | - Vladimir Loparev
- Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Oliver Clay
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
- Cell and Molecular Biology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
| | - Tom Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Anastasia Litvintseva
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Ángel González
- Basic and Applied Microbiology Research Group (MICROBA), School of Microbiology, Universidad de Antioquia, Medellín, Colombia
| | - Beatriz L. Gómez
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
- * E-mail:
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Muraosa Y, Oguchi M, Yahiro M, Watanabe A, Yaguchi T, Kamei K. Epidemiological Study of Fusarium Species Causing Invasive and Superficial Fusariosis in Japan. Med Mycol J 2017; 58:E5-E13. [PMID: 28250364 DOI: 10.3314/mmj.16-00024] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In Japan, Fusarium species are known etiological agents of human fungal infection; however, there has been no report of a large-scale epidemiological study on the etiological agents of fusariosis. A total of 73 Fusarium isolates from patients with invasive fusariosis (IF, n= 36) or superficial fusariosis (SF, n= 37), which were obtained at hospitals located in 28 prefectures in Japan between 1998 and 2015, were used for this study. Fusarium isolates were identified using Fusarium- and Fusarium solani species complex (FSSC) -specific real-time PCR and partial DNA sequences of the elongation factor-1 alpha (EF-1α) gene and the nuclear ribosomal internal transcribed spacer (ITS) region. FSSC was predominately isolated from both patients with IF and SF (IF, 77.8% and SF, 67.6%). Distribution of the phylogenetic species of FSSC isolates from patients with IF and SF exhibited different spectra; specifically, F. keratoplasticum (FSSC 2) (25.0%) was the most frequent isolate from patients with IF, whereas F. falciforme (FSSC 3+4) (32.4%) was the most frequent isolate from patients with SF. Fusarium sp. (FSSC 5) was the second most frequent isolate from both patients with IF and SF (IF, 22.2% and SF, 24.3%). Notably, F. petroliphilum (FSSC 1) was isolated only from patients with IF. Each species was isolated from a broad geographic area, and an epidemic was not observed. This is the first epidemiological study of Fusarium species causing IF and SF in Japan.
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Comparison of DNA Microarray, Loop-Mediated Isothermal Amplification (LAMP) and Real-Time PCR with DNA Sequencing for Identification of Fusarium spp. Obtained from Patients with Hematologic Malignancies. Mycopathologia 2017; 182:625-632. [PMID: 28324245 DOI: 10.1007/s11046-017-0129-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 02/24/2017] [Indexed: 01/17/2023]
Abstract
The performance of three molecular biology techniques, i.e., DNA microarray, loop-mediated isothermal amplification (LAMP), and real-time PCR were compared with DNA sequencing for properly identification of 20 isolates of Fusarium spp. obtained from blood stream as etiologic agent of invasive infections in patients with hematologic malignancies. DNA microarray, LAMP and real-time PCR identified 16 (80%) out of 20 samples as Fusarium solani species complex (FSSC) and four (20%) as Fusarium spp. The agreement among the techniques was 100%. LAMP exhibited 100% specificity, while DNA microarray, LAMP and real-time PCR showed 100% sensitivity. The three techniques had 100% agreement with DNA sequencing. Sixteen isolates were identified as FSSC by sequencing, being five Fusarium keratoplasticum, nine Fusarium petroliphilum and two Fusarium solani. On the other hand, sequencing identified four isolates as Fusarium non-solani species complex (FNSSC), being three isolates as Fusarium napiforme and one isolate as Fusarium oxysporum. Finally, LAMP proved to be faster and more accessible than DNA microarray and real-time PCR, since it does not require a thermocycler. Therefore, LAMP signalizes as emerging and promising methodology to be used in routine identification of Fusarium spp. among cases of invasive fungal infections.
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Real-Time Polymerase Chain Reaction (PCR) Based Identification and Detection of Fungi Belongs to Genus Fusarium. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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New Panfungal Real-Time PCR Assay for Diagnosis of Invasive Fungal Infections. J Clin Microbiol 2016; 54:2910-2918. [PMID: 27629898 DOI: 10.1128/jcm.01580-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/08/2016] [Indexed: 11/20/2022] Open
Abstract
The diagnosis of invasive fungal infections (IFIs) is usually based on the isolation of the fungus in culture and histopathological techniques. However, these methods have many limitations often delaying the definitive diagnosis. In recent years, molecular diagnostics methods have emerged as a suitable alternative for IFI diagnosis. When there is not a clear suspicion of the fungus involved in the IFI, panfungal real-time PCR assays have been used, allowing amplification of any fungal DNA. However, this approach requires subsequent amplicon sequencing to identify the fungal species involved, increasing response time. In this work, a new panfungal real-time PCR assay using the combination of an intercalating dye and sequence-specific probes was developed. After DNA amplification, a melting curve analysis was also performed. The technique was standardized by using 11 different fungal species and validated in 60 clinical samples from patients with proven and probable IFI. A melting curve database was constructed by collecting those melting curves obtained from fungal species included in the standardization assay. Results showed high reproducibility (coefficient of variation [CV] < 5%; r > 0.95) and specificity (100%). The overall sensitivity of the technique was 83.3%, with the group of fungi involved in the infection detected in 77.8% of the positive samples with IFIs covered by molecular beacon probes. Moreover, sequencing was avoided in 67.8% of these "probe-positive" results, enabling report of a positive result in 24 h. This technique is fast, sensitive, and specific and promises to be useful for improving early diagnosis of IFIs.
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Graça MG, van der Heijden IM, Perdigão L, Taira C, Costa SF, Levin AS. Evaluation of two methods for direct detection of Fusarium spp. in water. J Microbiol Methods 2016; 123:39-43. [PMID: 26844885 DOI: 10.1016/j.mimet.2016.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 01/28/2016] [Accepted: 01/29/2016] [Indexed: 12/14/2022]
Abstract
Fusarium is a waterborne fungus that causes severe infections especially in patients with prolonged neutropenia. Traditionally, the detection of Fusarium in water is done by culturing which is difficult and time consuming. A faster method is necessary to prevent exposure of susceptible patients to contaminated water. The objective of this study was to develop a molecular technique for direct detection of Fusarium in water. A direct DNA extraction method from water was developed and coupled to a genus-specific PCR, to detect 3 species of Fusarium (verticillioides, oxysporum and solani). The detection limits were 10 cells/L and 1 cell/L for the molecular and culture methods, respectively. To our knowledge, this is the first method developed to detect Fusarium directly from water.
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Affiliation(s)
- Mariana G Graça
- Department of Infectious Diseases, Faculty of Medicine, University of São Paulo, Brazil; LIM 54, Institute of Tropical Medicine of the University of São Paulo, Brazil.
| | | | - Lauro Perdigão
- Department of Infectious Diseases, Faculty of Medicine, University of São Paulo, Brazil; LIM 54, Institute of Tropical Medicine of the University of São Paulo, Brazil.
| | - Cleison Taira
- Laboratory of Pathogenic Dimorphic Fungi - Institute of Biomedical Sciences, University of São Paulo, Brazil; Laboratory of Medical Investigation 53, Faculty of Medicine, University of São Paulo, Brazil.
| | - Silvia F Costa
- Department of Infectious Diseases, Faculty of Medicine, University of São Paulo, Brazil; LIM 54, Institute of Tropical Medicine of the University of São Paulo, Brazil.
| | - Anna S Levin
- Department of Infectious Diseases, Faculty of Medicine, University of São Paulo, Brazil; LIM 54, Institute of Tropical Medicine of the University of São Paulo, Brazil.
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Muraosa Y, Toyotome T, Yahiro M, Watanabe A, Shikanai-Yasuda MA, Kamei K. Detection of Histoplasma capsulatum from clinical specimens by cycling probe-based real-time PCR and nested real-time PCR. Med Mycol 2015; 54:433-8. [PMID: 26705837 DOI: 10.1093/mmy/myv106] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 11/19/2015] [Indexed: 11/13/2022] Open
Abstract
We developed new cycling probe-based real-time PCR and nested real-time PCR assays for the detection of Histoplasma capsulatum that were designed to detect the gene encoding N-acetylated α-linked acidic dipeptidase (NAALADase), which we previously identified as an H. capsulatum antigen reacting with sera from patients with histoplasmosis. Both assays specifically detected the DNAs of all H. capsulatum strains but not those of other fungi or human DNA. The limited of detection (LOD) of the real-time PCR assay was 10 DNA copies when using 10-fold serial dilutions of the standard plasmid DNA and 50 DNA copies when using human serum spiked with standard plasmid DNA. The nested real-time PCR improved the LOD to 5 DNA copies when using human serum spiked with standard plasmid DNA, which represents a 10-fold higher than that observed with the real-time PCR assay. To assess the ability of the two assays to diagnose histoplasmosis, we analyzed a small number of clinical specimens collected from five patients with histoplasmosis, such as sera (n = 4), formalin-fixed paraffin-embedded (FFPE) tissue (n = 4), and bronchoalveolar lavage fluid (BALF) (n = 1). Although clinical sensitivity of the real-time PCR assay was insufficiently sensitive (33%), the nested real-time PCR assay increased the clinical sensitivity (77%), suggesting it has a potential to be a useful method for detecting H. capsulatum DNA in clinical specimens.
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Affiliation(s)
- Yasunori Muraosa
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Takahito Toyotome
- Research Unit for Risk Analysis, Diagnostic Center for Animal Health and Food Safety, Obihiro University of Agriculture and Veterinary Medicine, Hokkaido, Japan
| | - Maki Yahiro
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Akira Watanabe
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Maria Aparecida Shikanai-Yasuda
- Laboratory of Immunology, Hospital das Clínicas, Faculdade de Medicina, University of São Paulo and Department of Infectious and Parasitic Diseases, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
| | - Katsuhiko Kamei
- Medical Mycology Research Center, Chiba University, Chiba, Japan
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van Diepeningen AD, Brankovics B, Iltes J, van der Lee TAJ, Waalwijk C. Diagnosis of Fusarium Infections: Approaches to Identification by the Clinical Mycology Laboratory. CURRENT FUNGAL INFECTION REPORTS 2015; 9:135-143. [PMID: 26301000 PMCID: PMC4537702 DOI: 10.1007/s12281-015-0225-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Infections caused by the genus Fusarium have emerged over the past decades and range from onychomycosis and keratitis in healthy individuals to deep and disseminated infections with high mortality rates in immune-compromised patients. As antifungal susceptibility can differ between the different Fusarium species, identification at species level is recommended. Several clinical observations as hyaline hyphae in tissue, necrotic lesions in the skin and positive blood tests with fungal growth or presence of fungal cell wall components may be the first hints for fusariosis. Many laboratories rely on morphological identification, but especially multi-locus sequencing proves better to discriminate among members of the species complexes involved in human infection. DNA-based diagnostic tools have best discriminatory power when based on translation elongation factor 1-α or the RNA polymerase II second largest subunit. However, assays based on the detection of other fusarial cell compounds such as peptides and cell wall components may also be used for identification. The purpose of this review is to provide an overview and a comparison of the different tools currently available for the diagnosis of fusariosis.
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Affiliation(s)
| | - Balázs Brankovics
- />CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Jearidienne Iltes
- />CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Theo A. J. van der Lee
- />Plant Research International Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Cees Waalwijk
- />Plant Research International Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Kawakami H, Inuzuka H, Hori N, Takahashi N, Ishida K, Mochizuki K, Ohkusu K, Muraosa Y, Watanabe A, Kamei K. Inhibitory effects of antimicrobial agents againstFusariumspecies. Med Mycol 2015; 53:603-11. [DOI: 10.1093/mmy/myv016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/10/2015] [Indexed: 11/12/2022] Open
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32
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Trabasso P, Matsuzawa T, Fagnani R, Muraosa Y, Tominaga K, Resende MR, Kamei K, Mikami Y, Schreiber AZ, Moretti ML. Isolation and drug susceptibility of Candida parapsilosis sensu lato and other species of C. parapsilosis complex from patients with blood stream infections and proposal of a novel LAMP identification method for the species. Mycopathologia 2014; 179:53-62. [PMID: 25481844 DOI: 10.1007/s11046-014-9830-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/31/2014] [Indexed: 11/28/2022]
Abstract
Candida parapsilosis complex (CPC) is the third Candida species isolated in blood cultures of patients from our Hospital, following C. albicans and C. tropicalis. From 2006 to 2010, the median annual distribution of CPC was 8 cases/year. Records of 36 patients were reviewed. CPC were 31 (86.1%) C. parapsilosis; 4 (11.1%) C. orthopsilosis; and 1 (2.8%) C. metapsilosis. Clinical characteristics were central venous catheter, 34 (94.4%); parental nutrition, 25 (70%); surgery, 27 (57.9%); prior bacteremia, 20 (51.3%); malignancy, 18 (50%). General mortality was 47.2%. Death was higher in immunosuppressed patients (17 vs. 11; p = 0.003). Three out four (75%) patients with C. orthopsilosis and 14 out 31 (45.2%) with C. parapsilosis died (p = 0.558). Thirty-nine individual isolates were tested for susceptibility to seven antifungal drugs, with MICs values showing susceptibility to all of them. Two isolates, one C. orthopsilosis and one C. parapsilosis, had fluconazole MIC = 4 μg/mL. Differentiation among CPC has implication in caring for patients with invasive candidiasis since there are differences in virulence, pathogenicity and drug susceptibility. A method targeting the topoisomerase II gene based on loop-mediated isothermal amplification (LAMP) was developed. LAMP emerges as a promising tool for the identification of fungal species due to the high sensitivity and specificity. LAMP can be performed at the point-of-care, being no necessary the use of expensive equipment. In our study, the method was successful comparing to the DNA sequencing and proved to be a reliable and fast assay to distinguish the three species of CPC.
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Affiliation(s)
- Plinio Trabasso
- Infectious Diseases Division, School of Medical Sciences, University of Campinas, Rua Tessália Vieira de Carvalho, 126 Cidade Universitária Zeferino Vaz, Campinas, Sao Paulo, 13083-887, Brazil,
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