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Wang S, Chen K, Guo J, Zhang P, Li Y, Xu Z, Cui L, Qiang Y. Identification of Pathogen Causing Bulb Rot in Fritillaria taipaiensis P. Y. Li and Establishment of Detection Methods. PLANTS (BASEL, SWITZERLAND) 2024; 13:2236. [PMID: 39204672 PMCID: PMC11360731 DOI: 10.3390/plants13162236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Revised: 08/04/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
Fritillaria taipaiensis P. Y. Li (F. taipaiensis) is a traditional Chinese herbal medicine that has been used for over two millennia to treat cough and expectoration. However, the increasing cultivation of F. taipaiensis has led to the spread of bulb rot diseases. In this study, pathogens were isolated from rotten F. taipaiensis bulbs. Through molecular identification, pathogenicity testing, morphological assessment, and microscopy, Fusarium solani was identified as the pathogen causing bulb rot in F. taipaiensis. The colonization of F. solani in the bulbs was investigated through microscopic observation. The rapid and accurate detection of this pathogen will contribute to better disease monitoring and control. Loop-mediated isothermal amplification (LAMP) and qPCR methods were established to quickly and specifically identify this pathogen. These results provide valuable insights for further research on the prediction, rapid detection, and effective prevention and control of bulb rot in F. taipaiensis.
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Affiliation(s)
- Shijie Wang
- National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an 710119, China; (S.W.); (J.G.); (P.Z.); (Y.L.); (Z.X.)
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Keke Chen
- School of Biological and Environmental Engineering, Xi’an University, Xi’an 710065, China;
| | - Jiaqi Guo
- National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an 710119, China; (S.W.); (J.G.); (P.Z.); (Y.L.); (Z.X.)
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Panwang Zhang
- National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an 710119, China; (S.W.); (J.G.); (P.Z.); (Y.L.); (Z.X.)
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Yuchen Li
- National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an 710119, China; (S.W.); (J.G.); (P.Z.); (Y.L.); (Z.X.)
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Zhenghao Xu
- National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an 710119, China; (S.W.); (J.G.); (P.Z.); (Y.L.); (Z.X.)
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Langjun Cui
- National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an 710119, China; (S.W.); (J.G.); (P.Z.); (Y.L.); (Z.X.)
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Yi Qiang
- National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an 710119, China; (S.W.); (J.G.); (P.Z.); (Y.L.); (Z.X.)
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
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Petrović K, Orzali L, Krsmanović S, Valente MT, Tolimir M, Pavlov J, Riccioni L. Genetic Diversity and Pathogenicity of the Fusarium Species Complex on Soybean in Serbia. PLANT DISEASE 2024; 108:1851-1860. [PMID: 38311795 DOI: 10.1094/pdis-11-23-2450-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Using morphological and cultural characteristics for identification, 36 Fusarium isolates were recovered from diseased roots, stems, and seeds of soybean from several localities throughout Vojvodina Province, Serbia. Based on molecular characterization, 12 Fusarium species were identified: F. acuminatum, F. avenaceum, F. commune, F. equiseti, F. graminearum, F. incarnatum, F. oxysporum, F. proliferatum, F. solani, F. sporotrichioides, F. subglutinans, and F. tricinctum. The elongation factor 1-α-based phylogeny grouped the isolates into 12 well-supported clades, but polymorphisms among sequences in some clades suggested the use of the species complex concept: (i) F. incarnatum-equiseti species complex (FIESC)-F. incarnatum and F. equiseti; (ii) F. oxysporum species complex (FOSC)-F. oxysporum; (iii) F. solani species complex (FSSC)-F. solani; and (iv) F. acuminatum/F. avenaceum/F. tricinctum species complex (FAATSC)-F. acuminatum, F. avenaceum, and F. tricinctum. Pathogenicity tests showed that the most aggressive species causing soybean seed rot were F. sporotrichioides, F. graminearum, FIESC, and F. avenaceum. Furthermore, F. subglutinans, FSSC, and F. proliferatum showed a high percentage of pathogenicity on soybean seeds (80 to 100%), whereas variability in pathogenicity occurred within isolates of F. tricinctum. FOSC, F. commune, and F. acuminatum had the lowest pathogenicity. To our knowledge, this is the first study of the characterization of Fusarium species on soybean in Serbia. This study provides valuable information about the composition of Fusarium species and pathogenicity that will be used in further research on soybean resistance to Fusarium-based diseases.
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Affiliation(s)
- Kristina Petrović
- Maize Research Institute "Zemun Polje", Belgrade 11185, Serbia
- BioSense Institute, University of Novi Sad, Novi Sad 21001, Serbia
| | - Laura Orzali
- Council for Agricultural Research and Economics (CREA), Research Center for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy
| | | | - Maria Teresa Valente
- Council for Agricultural Research and Economics (CREA), Research Center for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy
| | - Miodrag Tolimir
- Maize Research Institute "Zemun Polje", Belgrade 11185, Serbia
| | - Jovan Pavlov
- Maize Research Institute "Zemun Polje", Belgrade 11185, Serbia
| | - Luca Riccioni
- Council for Agricultural Research and Economics (CREA), Research Center for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy (deceased)
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Senatore MT, Prodi A, Tini F, Balmas V, Infantino A, Onofri A, Cappelletti E, Oufensou S, Sulyok M, Covarelli L, Beccari G. Different diagnostic approaches for the characterization of the fungal community and Fusarium species complex composition of Italian durum wheat grain and correlation with secondary metabolite accumulation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:4503-4521. [PMID: 36828788 DOI: 10.1002/jsfa.12526] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 02/06/2023] [Accepted: 02/24/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND The evolution of the fungal communities associated with durum wheat was assessed using different diagnostic approaches. Durum wheat grain samples were collected in three different Italian cultivation macro-areas (north, center and south). Fungal isolation was realized by potato dextrose agar (PDA) and by deep-freezing blotter (DFB). Identification of Fusarium isolates obtained from PDA was achieved by partial tef1α sequencing (PDA + tef1α), while those obtained from DFB were identified from their morphological characteristics (DFB + mc). The fungal biomass of eight Fusarium species was quantified in grains by quantitative polymerase chain reaction (qPCR). Fungal secondary metabolites were analyzed in grains by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Correlations between Fusarium detection techniques (PDA + tef1α; DFB + mc and qPCR) and mycotoxins in grains were assessed. RESULTS Alternaria and Fusarium showed the highest incidence among the fungal genera developed from grains. Within the Fusarium community, PDA + tef1α highlighted that F. avenaceum and F. graminearum were the most represented members, while, DFB + mc detected a high presence of F. proliferatum. Alternaria and Fusarium mycotoxins, principally enniatins, were particularly present in the grain harvested in central Italy. Deoxynivalenol was mainly detected in northern-central Italy. CONCLUSIONS The adoption of the different diagnostic techniques of Fusarium detection highlighted that, for some species, qPCR was the best method of predicting their mycotoxin contamination in grains. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Maria Teresa Senatore
- Department of Agricultural and Food Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Antonio Prodi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Francesco Tini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Virgilio Balmas
- Department of Agriculture, University of Sassari, Sassari, Italy
| | - Alessandro Infantino
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Rome, Italy
| | - Andrea Onofri
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Eleonora Cappelletti
- Department of Agricultural and Food Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Safa Oufensou
- Department of Agriculture, University of Sassari, Sassari, Italy
| | - Michael Sulyok
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Institute of Bionalytics and Agro-Metabolomics, Tulln, Austria
| | - Lorenzo Covarelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Giovanni Beccari
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
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Niessen L, Fritze M, Wibbelt G, Puechmaille SJ. Development and Application of Loop-Mediated Isothermal Amplification (LAMP) Assays for Rapid Diagnosis of the Bat White-Nose Disease Fungus Pseudogymnoascus destructans. Mycopathologia 2022; 187:547-565. [PMID: 35931867 DOI: 10.1007/s11046-022-00650-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/01/2022] [Indexed: 11/28/2022]
Abstract
Pseudogymnoascus destructans (= Geomyces destructans) is a psychrophilic filamentous fungus that causes White-Nose Disease (WND; the disease associated with White-Nose Syndrome, WNS) in hibernating bats. The disease has caused considerable reductions in bat populations in the USA and Canada since 2006. Identification and detection of the pathogen in pure cultures and environmental samples is routinely based on qPCR or PCR after DNA isolation and purification. Rapid and specific direct detection of the fungus in the field would strongly improve prompt surveillance, and support control measures. Based on the genes coding for ATP citrate lyase1 (acl1) and the 28S-18S ribosomal RNA intergenic spacer (IGS) in P. destructans, two independent LAMP assays were developed for the rapid and sensitive diagnosis of the fungus. Both assays could discriminate P. destructans from 159 tested species of filamentous fungi and yeasts. Sensitivity of the assays was 2.1 picogram per reaction (pg/rxn) and 21 femtogram per reaction (fg/rxn) for the acl1 and IGS based assays, respectively. Moreover, both assays also work with spores and mycelia of P. destructans that are directly added to the master mix without prior DNA extraction. For field-diagnostics, we developed and tested a field-applicable version of the IGS-based LAMP assay. Lastly, we also developed a protocol for preparation of fungal spores and mycelia from swabs and tape liftings of contaminated surfaces or infected bats. This protocol in combination with the highly sensitive IGS-based LAMP-assay enabled sensitive detection of P. destructans from various sources.
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Affiliation(s)
- Ludwig Niessen
- TUM School of Life Sciences, Technical University of Munich, Gregor-Mendel-Str. 4, 85354, Freising, Germany.
| | - Marcus Fritze
- Applied Zoology and Nature Conservation, University of Greifswald, Loitzer Str. 26, 17489, Greifswald, Germany.,German Bat Observatory, Am Juliusturm 64, 13599, Berlin, Germany
| | - Gudrun Wibbelt
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Sebastien J Puechmaille
- Applied Zoology and Nature Conservation, University of Greifswald, Loitzer Str. 26, 17489, Greifswald, Germany.,ISEM, CNRS, EPHE, IRD, University of Montpellier, Montpellier, France.,Institut Universitaire de France, 75005, Paris, France
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5
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Wang Y, Wang R, Sha Y. Distribution, pathogenicity and disease control of Fusarium tricinctum. Front Microbiol 2022; 13:939927. [PMID: 35958126 PMCID: PMC9360978 DOI: 10.3389/fmicb.2022.939927] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/07/2022] [Indexed: 11/25/2022] Open
Abstract
Plant pathogenic fungi such as Fusarium tricinctum cause various plant diseases worldwide, especially in temperate regions. In cereals, F. tricinctum is one of the most common species causing Fusarium head blight (FHB) and root rot. Infection with F. tricinctum results in high yield losses and reduction in quality, mainly due to mycotoxin contamination of grain. Mycotoxins produced by F. tricinctum, such as enniatins (ENs) and moniliformin (MON), which are the most studied mycotoxins, have been reported to have multiple toxic effects on humans and animals. Although chemical control of Fusarium infection has been applied to grains, it is not always effective in controlling disease or reducing the level of mycotoxins in wheat grains. To the contrary, chemical control may significantly increase infection of F. tricinctum in fungicide-treated plots after treatment. Our studies show that the bacterium Bacillus amyloliquefaciens, has good control effects against F. tricinctum. Therefore, its use as a biological control agent against various plant pathogens may be an effective strategy to control the spread of Fusarium pathogens. Here, we conduct a review of the literature involving this plant pathogen, its diversity, virulence, and methods to control.
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Affiliation(s)
- Yun Wang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Ruoyu Wang
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Lanzhou, China
- Gaolan Station of Agricultural and Ecological Experiment, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- *Correspondence: Ruoyu Wang,
| | - Yuexia Sha
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
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6
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Laraba I, Busman M, Geiser DM, O'Donnell K. Phylogenetic Diversity and Mycotoxin Potential of Emergent Phytopathogens Within the Fusarium tricinctum Species Complex. PHYTOPATHOLOGY 2022; 112:1284-1298. [PMID: 34989594 DOI: 10.1094/phyto-09-21-0394-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Recent studies on multiple continents indicate members of the Fusarium tricinctum species complex (FTSC) are emerging as prevalent pathogens of small-grain cereals, pulses, and other economically important crops. These understudied fusaria produce structurally diverse mycotoxins, among which enniatins (ENNs) and moniliformin (MON) are the most frequent and of greatest concern to food and feed safety. Herein a large survey of fusaria in the Fusarium Research Center and Agricultural Research Service culture collections was undertaken to assess species diversity and mycotoxin potential within the FTSC. A 151-strain collection originating from diverse hosts and substrates from different agroclimatic regions throughout the world was selected from 460 FTSC strains to represent the breadth of FTSC phylogenetic diversity. Evolutionary relationships inferred from a five-locus dataset, using maximum likelihood and parsimony, resolved the 151 strains as 24 phylogenetically distinct species, including nine that are new to science. Of the five genes analyzed, nearly full-length phosphate permease sequences contained the most phylogenetically informative characters, establishing its suitability for species-level phylogenetics within the FTSC. Fifteen of the species produced ENNs, MON, the sphingosine analog 2-amino-14,16-dimethyloctadecan-3-ol (AOD), and the toxic pigment aurofusarin (AUR) on a cracked corn kernel substrate. Interestingly, the five earliest diverging species in the FTSC phylogeny (i.e., F. iranicum, F. flocciferum, F. torulosum, and Fusarium spp. FTSC 8 and 24) failed to produce AOD and MON, but synthesized ENNs and/or AUR. Moreover, our reassessment of nine published phylogenetic studies on the FTSC identified 11 additional novel taxa, suggesting this complex comprises at least 36 species.
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Affiliation(s)
- Imane Laraba
- ORISE Fellow, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit (MPM), Peoria, IL 61604
| | - Mark Busman
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit (MPM), Peoria, IL 61604
| | - David M Geiser
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802
| | - Kerry O'Donnell
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit (MPM), Peoria, IL 61604
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Development of Loop-Mediated Isothermal Amplification Assay for Rapid Detection and Analysis of the Root-Knot Nematode Meloidogyne hapla in Soil. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Soil analysis is crucial for estimating the risk of crop damage by the root-knot nematode Meloidogyne hapla. Here, we developed an analysis assay based on Loop-mediated Isothermal Amplification (LAMP). The LAMP primers were verified for specificity against 10 different nematode species. A manual soil DNA extraction, referred to as SKMM, was developed and compared with a FastDNA kit followed by DNA purification. DNA was extracted with both methods from artificially inoculated soils as well as from naturally infested soil collected from farm fields. The primers exclusively amplified DNA from M. hapla with both colorimetric and real-time LAMP. The detection limit was 193 gene copies and 0.0016 juveniles (12 pg µL−1) per reaction. DNA concentrations and purity (A260/A230) were significantly higher using the SKMM procedure compared with the kit. From the field samples collected in 2019, DNA was amplified from 16% of samples extracted with SKMM and from 11% of samples using the kit. Occurrence of M. hapla DNA was confirmed in soil samples from two out of six field soils in 2020 using both real-time LAMP and qPCR. In conclusion, the developed real-time LAMP is a fast and specific assay for detection and quantification of M. hapla DNA in soil.
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Du R, Huang Y, Zhang J, Yang L, Wu M, Li GQ. LAMP Detection and Identification of the Blackleg Pathogen Leptosphaeria biglobosa 'brassicae'. PLANT DISEASE 2021; 105:3192-3200. [PMID: 33560882 DOI: 10.1094/pdis-08-20-1819-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Blackleg of oilseed rape is a damaging invasive disease caused by the species complex Leptosphaeria maculans (Lm)/L. biglobosa (Lb), which is composed of at least two and seven phylogenetic subclades, respectively. Generally, Lm is more virulent than Lb, but under certain conditions, Lb can cause a significant yield loss in oilseed rape. Lb 'brassicae' (Lbb) has been found to be the causal agent for blackleg of oilseed rape in China, whereas Lm and Lb 'canadensis' (Lbc) were frequently detected in imported seeds of oilseed rape, posing a risk of spread into China. To monitor the blackleg-pathogen populations, a diagnostic tool based on loop-mediated isothermal amplification (LAMP) was developed using a 615-bp-long DNA sequence from Lbb that was derived from a randomly amplified polymorphic DNA assay. The LAMP was optimized for temperature and time, and tested for specificity and sensitivity using the DNA extracted from Lbb, Lbc, Lm, and 10 other fungi. The results showed that the optimal temperature and time were 65°C and 40 min, respectively. The LAMP primer set was specific to Lbb and highly sensitive as it detected the Lbb DNA as low as 132 fg per reaction. The LAMP assay was validated using the DNA extracted from mycelia and conidia of a well-characterized Lbb isolate, and its utility was evaluated using the DNA extracted from leaves, stems, pods, and seeds of oilseed rape. The LAMP assay developed herein will help for monitoring populations of the blackleg pathogens in China and in developing strategies for management of the blackleg disease.
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Affiliation(s)
- Ran Du
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongju Huang
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB UK
| | - Jing Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Long Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingde Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guo-Qing Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
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9
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Köck J, Gottschalk C, Ulrich S, Schwaiger K, Gareis M, Niessen L. Rapid and selective detection of macrocyclic trichothecene producing Stachybotrys chartarum strains by loop-mediated isothermal amplification (LAMP). Anal Bioanal Chem 2021; 413:4801-4813. [PMID: 34129076 PMCID: PMC8318954 DOI: 10.1007/s00216-021-03436-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/28/2022]
Abstract
Cytotoxic macrocyclic trichothecenes such as satratoxins are produced by chemotype S strains of Stachybotrys chartarum. Diseases such as stachybotryotoxicosis in animals and the sick building syndrome as a multifactorial disease complex in humans have been associated with this mold and its toxins. Less toxic non-chemotype S strains of S. chartarum are morphologically indistinguishable from chemotype S strains, which results in uncertainties in hazard characterization of isolates. To selectively identify macrocyclic trichothecene producing S. chartarum isolates, a set of sat14 gene-specific primers was designed and applied in a loop-mediated isothermal amplification (LAMP) assay using neutral red for visual signal detection. The assay was highly specific for S. chartarum strains of the macrocyclic trichothecene producing chemotype and showed no cross-reaction with non-macrocyclic trichothecene producing S. chartarum strains or 152 strains of 131 other fungal species. The assay's detection limit was 0.635 pg/rxn (picogram per reaction) with a reaction time of 60 min. Its high specificity and sensitivity as well as the cost-saving properties make the new assay an interesting and powerful diagnostic tool for easy and rapid testing.
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Affiliation(s)
- Johannes Köck
- Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Christoph Gottschalk
- Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Sebastian Ulrich
- Institute for Infectious Diseases and Zoonoses, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinaerstraße 13, 80539, Munich, Germany
| | - Karin Schwaiger
- Institute for Food Safety, Food Technology and Veterinary Public Health, Unit of Food Hygiene and Technology, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria
| | - Manfred Gareis
- Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Ludwig Niessen
- TUM School of Life Sciences, Technical University of Munich, Gregor-Mendel-Str. 4, 85354, Freising, Germany.
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10
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Senatore MT, Ward TJ, Cappelletti E, Beccari G, McCormick SP, Busman M, Laraba I, O'Donnell K, Prodi A. Species diversity and mycotoxin production by members of the Fusarium tricinctum species complex associated with Fusarium head blight of wheat and barley in Italy. Int J Food Microbiol 2021; 358:109298. [PMID: 34210546 DOI: 10.1016/j.ijfoodmicro.2021.109298] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/26/2021] [Accepted: 06/05/2021] [Indexed: 11/29/2022]
Abstract
Fusarium head blight (FHB) is a global cereal disease caused by a complex of Fusarium species. In Europe, the main species responsible for FHB are F. graminearum, F. culmorum and F. poae. However, members of the F. tricinctum species complex (FTSC) have become increasingly important. FTSC fusaria can synthesize mycotoxins such as moniliformin (MON), enniatins (ENNs) and several other biologically active secondary metabolites that could compromise food quality. In this study, FTSC isolates primarily from Italian durum wheat and barley, together with individual strains from four non-graminaceous hosts, were collected to assess their genetic diversity and determine their potential to produce mycotoxins in vitro on rice cultures. A multilocus DNA sequence dataset (TEF1, RPB1 and RPB2) was constructed for 117 isolates from Italy and 6 from Iran to evaluate FTSC species diversity and their evolutionary relationships. Phylogenetic analyses revealed wide genetic diversity among Italian FTSC isolates. Among previously described FTSC species, F. avenaceum (FTSC 4) was the most common species in Italy (56/117 = 47.9%) while F. tricinctum (FTSC 3), and F. acuminatum (FTSC 2) accounted for 11.1% (13/117) and the 8.5% (10/117), respectively. The second most detected species was a new and unnamed Fusarium sp. (FTSC 12; 32/117 = 19%) resolved as the sister group of F. tricinctum. Collectively, these four phylospecies accounted for 111/117 = 94.9% of the Italian FTSC collection. However, we identified five other FTSC species at low frequencies, including F. iranicum (FTSC 6) and three newly discovered species (Fusarium spp. FTSC 13, 14, 15). Of the 59 FTSC isolates tested for mycotoxin production on rice cultures, 54 and 55 strains, respectively, were able to produce detectable levels of ENNs and MON. In addition, we confirmed that the ability to produce bioactive secondary metabolites such as chlamydosporol, acuminatopyrone, longiborneol, fungerin and butanolide is widespread across the FTSC.
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Affiliation(s)
- M T Senatore
- Department of Agricultural and Food Sciences, Alma Mater Studiorum University of Bologna, Viale G. Fanin, 44, 40127 Bologna, Italy
| | - T J Ward
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 North University Street, Peoria, IL 60604-3999, USA
| | - E Cappelletti
- Department of Agricultural and Food Sciences, Alma Mater Studiorum University of Bologna, Viale G. Fanin, 44, 40127 Bologna, Italy
| | - G Beccari
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
| | - S P McCormick
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 North University Street, Peoria, IL 60604-3999, USA
| | - M Busman
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 North University Street, Peoria, IL 60604-3999, USA
| | - I Laraba
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 North University Street, Peoria, IL 60604-3999, USA
| | - K O'Donnell
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 North University Street, Peoria, IL 60604-3999, USA
| | - A Prodi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum University of Bologna, Viale G. Fanin, 44, 40127 Bologna, Italy.
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11
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Khan IUH, Becker A, Cloutier M, Plötz M, Lapen DR, Wilkes G, Topp E, Abdulmawjood A. Loop-mediated isothermal amplification: Development, validation and application of simple and rapid assays for quantitative detection of species of Arcobacteraceae family- and species-specific Aliarcobacter faecis and Aliarcobacter lanthieri. J Appl Microbiol 2020; 131:288-299. [PMID: 33174331 PMCID: PMC8359143 DOI: 10.1111/jam.14926] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 11/29/2022]
Abstract
Aim The family Arcobacteraceae formerly genus Arcobacter has recently been reclassified into six genera. Among nine species of the genus Aliarcobacter, Aliarcobacter faecis and Aliarcobacter lanthieri have been identified as emerging pathogens potentially cause health risks to humans and animals. This study was designed to develop/optimize, validate and apply Arcobacteraceae family‐ and two species‐specific (A. faecis and A. lanthieri) loop‐mediated isothermal amplification (LAMP) assays to rapidly detect and quantify total number of cells in various environmental niches. Methods and Results Three sets of LAMP primers were designed from conserved and variable regions of 16S rRNA (family‐specific) and gyrB (species‐specific) genes. Optimized Arcobacteraceae family‐specific LAMP assay correctly amplified and detected 24 species, whereas species‐specific LAMP assays detected A. faecis and A. lanthieri reference strains as well as 91 pure and mixed culture isolates recovered from aquatic and faecal sources. The specificity of LAMP amplification of A. faecis and A. lanthieri was further confirmed by restriction fragment length polymorphism analysis. Assay sensitivities were tested using variable DNA concentrations extracted from simulated target species cells in an autoclaved agricultural water sample by achieving a minimum detection limit of 10 cells mL−1 (10 fg). Direct DNA‐based quantitative detection, from agricultural surface water, identified A. faecis (17%) and A. lanthieri (1%) at a low frequency compared to family‐level (93%) with the concentration ranging from 2·1 × 101 to 2·2 × 105 cells 100 mL−1. Conclusions Overall, these three DNA‐based rapid and cost‐effective novel LAMP assays are sensitive and can be completed in less than 40 min. They have potential for on‐site quantitative detection of species of family Arcobacteraceae, A. faecis and A. lanthieri in food, environmental and clinical matrices. Significance and Impact of the Study The newly developed LAMP assays are specific, sensitive, accurate with higher reproducibility that have potential to facilitate in a less equipped lab setting and can help in early quantitative detection and rate of prevalence in environmental niches. The assays can be adopted in the diagnostic labs and epidemiological studies.
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Affiliation(s)
- I U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - A Becker
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Foundation, Hannover, Germany
| | - M Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - M Plötz
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Foundation, Hannover, Germany
| | - D R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - G Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada.,Natural Resources Canada, Ottawa, ON, Canada
| | - E Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - A Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Foundation, Hannover, Germany
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12
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Pollard AT, Okubara PA. Real-time PCR quantification of Fusarium avenaceum in soil and seeds. J Microbiol Methods 2019; 157:21-30. [DOI: 10.1016/j.mimet.2018.12.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/11/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
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13
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Yli-Mattila T, Hussien T, Gavrilova O, Gagkaeva T. Morphological and Molecular Variation Between Fusarium avenaceum, Fusarium arthrosporioides and Fusarium anguioides Strains. Pathogens 2018; 7:pathogens7040094. [PMID: 30501049 PMCID: PMC6313738 DOI: 10.3390/pathogens7040094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 10/26/2018] [Indexed: 12/04/2022] Open
Abstract
Fusarium avenaceum and closely related species are common fungi on various plants, cultivated in different climatic regions. The aim of this study was to determine the taxonomic affiliations of the F. avenaceum, Fusarium arthrosporioides, and Fusarium anguioides strains by using morphological, physiological and molecular-genetic approaches. Twenty-six single-spored morphologically identified strains, which were mainly from cereals, were investigated in order to find out, if they belong to a separate species. Pathogenicity of strains to wheat seedlings and ISSR (Inter Simple Sequence Repeats) fingerprint and beta-tubulin DNA sequence patterns were analyzed. According to phylogenetic analyses, the strains could be divided into two big groups consisting of mostly F. avenaceum or F. anguioides strains. F. arthrosporioides was not detected as a separate species by the sum of the characters. F. anguioides was characterized as a separate species, which could be identified by morphological and molecular data. High genetic diversity of the F. avenaceum and related species was revealed. One F. anguioides strain (rudbeckia, Vladivostok, Russia), had an identical beta-tubulin sequence with two previously sequenced strains of Fusarium tricinctum species complex, which were isolated from dicotyledonous plants in Asia.
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Affiliation(s)
| | - Taha Hussien
- Department of Biochemistry, University of Turku, Turku 20014, Finland.
- National Research Center, Cairo 80301, Egypt.
| | - Olga Gavrilova
- All-Russian Institute of Plant Protection (VIZR), St. Petersburg-Pushkin 196608, Russia.
| | - Tatiana Gagkaeva
- All-Russian Institute of Plant Protection (VIZR), St. Petersburg-Pushkin 196608, Russia.
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14
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Pieczul K, Perek A, Kubiak K. Detection of Tilletia caries, Tilletia laevis and Tilletia controversa wheat grain contamination using loop-mediated isothermal DNA amplification (LAMP). J Microbiol Methods 2018; 154:141-146. [PMID: 30393029 DOI: 10.1016/j.mimet.2018.10.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/12/2018] [Accepted: 10/26/2018] [Indexed: 11/25/2022]
Abstract
The study describes a novel diagnostic protocol based on a loop-mediated isothermal DNA amplification (LAMP) for identification of wheat grains infection by Tilletia laevis, Tilletia caries (common bunt) and Tilletia controversa (draft bunt). The presented data showed that the LAMP analysis is a simple, specific and rapid method that could be used for detection of Tilletia spp. in contaminated grain samples. The lowest DNA concentration required for the successful detection of Tilletia spp. strains were estimated to be 0.001 ng/μl. Simultaneously the detection limit for wheat grain contamination by T. caries and T. laevis teliospores was estimated at 20 μg per 100 g of grain. For T. controversa detection limit was lower and was approximately 20 mg of teliospores per 100 g of grain. The negative results of the LAMP reactions were achieved for the most common fungal species colonizing wheat grain like Fusarium spp., Alternaria sp., Cladosporium sp., Helminthosporium sp., and Penicillium sp.
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Affiliation(s)
- Katarzyna Pieczul
- Institute of Plant Protection - National Research Institute, Władysława Węgorka, Poznań 2060-318, Poland.
| | - Agnieszka Perek
- Institute of Plant Protection - National Research Institute, Władysława Węgorka, Poznań 2060-318, Poland.
| | - Krzysztof Kubiak
- Institute of Plant Protection - National Research Institute, Władysława Węgorka, Poznań 2060-318, Poland.
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15
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The application of loop-mediated isothermal amplification (LAMP) assays for the rapid diagnosis of food-borne mycotoxigenic fungi. Curr Opin Food Sci 2018. [DOI: 10.1016/j.cofs.2018.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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16
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Regional differences in the composition of Fusarium Head Blight pathogens and mycotoxins associated with wheat in Mexico. Int J Food Microbiol 2018; 273:11-19. [DOI: 10.1016/j.ijfoodmicro.2018.03.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 03/07/2018] [Accepted: 03/10/2018] [Indexed: 12/28/2022]
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17
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LAMP-based group specific detection of aflatoxin producers within Aspergillus section Flavi in food raw materials, spices, and dried fruit using neutral red for visible-light signal detection. Int J Food Microbiol 2017; 266:241-250. [PMID: 29272724 DOI: 10.1016/j.ijfoodmicro.2017.12.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 01/10/2023]
Abstract
Aflatoxins can be produced by 21 species within sections Flavi (16 species), Ochraceorosei (2), and Nidulantes (3) of the fungal genus Aspergillus. They pose risks to human and animal health due to high toxicity and carcinogenicity. Detecting aflatoxin producers can help to assess toxicological risks associated with contaminated commodities. Species specific molecular assays (PCR and LAMP) are available for detection of major producers, but fail to detect species of minor importance. To enable rapid and sensitive detection of several aflatoxin producing species in a single analysis, a nor1 gene-specific LAMP assay was developed. Specificity testing showed that among 128 fungal species from 28 genera, 15 aflatoxigenic species in section Flavi were detected, including synonyms of A. flavus and A. parasiticus. No cross reactions were found with other tested species. The detection limit of the assay was 9.03pg of A. parasiticus genomic DNA per reaction. Visual detection of positive LAMP reactions under daylight conditions was facilitated using neutral red to allow unambiguous distinction between positive and negative assay results. Application of the assay to the detection of A. parasiticus conidia revealed a detection limit of 211 conidia per reaction after minimal sample preparation. The usefulness of the assay was demonstrated in the analysis of aflatoxinogenic species in samples of rice, nuts, raisins, dried figs, as well as powdered spices. Comparison of LAMP results with presence/absence of aflatoxins and aflatoxin producing fungi in 50 rice samples showed good correlation between these parameters. Our study suggests that the developed LAMP assay is a rapid, sensitive and user-friendly tool for surveillance and quality control in our food industry.
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18
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Evaluation of antifungal, phosphate solubilisation, and siderophore and chitinase release activities of endophytic fungi from Pistacia vera. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1315-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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19
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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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20
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Four-locus phylogeny of Fusarium avenaceum and related species and their species-specific identification based on partial phosphate permease gene sequences. Int J Food Microbiol 2016; 225:27-37. [DOI: 10.1016/j.ijfoodmicro.2016.02.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 02/01/2016] [Accepted: 02/15/2016] [Indexed: 11/20/2022]
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21
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Bec S, Ward T, Farman M, O'Donnell K, Hershman D, Van Sanford D, Vaillancourt LJ. Characterization of Fusarium Strains Recovered From Wheat With Symptoms of Head Blight in Kentucky. PLANT DISEASE 2015; 99:1622-1632. [PMID: 30695966 DOI: 10.1094/pdis-06-14-0610-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fusarium graminearum species complex (FGSC) members cause Fusarium head blight (FHB) of wheat (Triticum aestivum L.) and small grains in the United States. The U.S. population is diverse and includes several genetically distinct local emergent subpopulations, some more aggressive and toxigenic than the majority population. Kentucky is a transition zone between the Mid-Atlantic and Midwestern wheat production areas. Sixty-eight Fusarium strains were isolated from symptomatic wheat heads from central and western Kentucky and southern Indiana in 2007. A multilocus genotyping assay and a variety of additional molecular markers, including some novel markers developed using the F. graminearum genome sequence, were used to characterize the pathogen population. Five of the isolates were identified as members of two non-FGSC species, F. acuminatum and F. cf. reticulatum, but they did not cause symptoms in greenhouse tests. All the FGSC isolates belonged to the 15-ADON chemotype of F. graminearum. Comparative genetic analysis using variable nuclear tandem repeat (VNTR) markers indicated that the population in Kentucky and Indiana belonged to the dominant North American population, with some diversification likely due to local evolution. Telomere and RFLP fingerprinting markers based on repetitive sequences revealed a high degree of genetic diversity within the population, with unique genotypes found at each location, and multiple genotypes isolated from the same head.
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Affiliation(s)
- S Bec
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546-0312
| | - T Ward
- Bacterial Foodborne Pathogens and Mycology Research Unit, USDA-ARS, Peoria, IL 61604-3999
| | - M Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546-0312
| | - K O'Donnell
- Bacterial Foodborne Pathogens and Mycology Research Unit, USDA-ARS, Peoria, IL 61604-3999
| | - D Hershman
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546-0312
| | - D Van Sanford
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312
| | - L J Vaillancourt
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546-0312
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22
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Niessen L. Current state and future perspectives of loop-mediated isothermal amplification (LAMP)-based diagnosis of filamentous fungi and yeasts. Appl Microbiol Biotechnol 2014; 99:553-74. [PMID: 25492418 DOI: 10.1007/s00253-014-6196-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 11/30/2022]
Abstract
Loop-mediated isothermal amplification is a rather novel method of enzymatic deoxyribonucleic acid amplification which can be applied for the diagnosis of viruses, bacteria, and fungi. Although firmly established in viral and bacterial diagnosis, the technology has only recently been applied to a noteworthy number of species in the filamentous fungi and yeasts. The current review gives an overview of the literature so far published on the topic by discussing the different groups of fungal organisms to which the method has been applied. Moreover, the method is described in detail as well as the different possibilities available for signal detection and quantification and sample preparation. Future perspective of loop-mediated isothermal amplification-based assays is discussed in the light of applicability for fungal diagnostics.
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Affiliation(s)
- Ludwig Niessen
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Gregor-Mendel-Straße 4, 85354, Freising, Germany,
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23
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Franke J, Geary B, Meyer SE. Identification of the Infection Route of a Fusarium Seed Pathogen into Nondormant Bromus tectorum Seeds. PHYTOPATHOLOGY 2014; 104:1306-1313. [PMID: 25389704 DOI: 10.1094/phyto-03-14-0077-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The genus Fusarium has a wide host range and causes many different forms of plant disease. These include seed rot and seedling blight diseases of cultivated plants. The diseases caused by Fusarium on wild plants are less well-known. In this study, we examined disease development caused by Fusarium sp. n on nondormant seeds of the important rangeland weed Bromus tectorum as part of broader studies of the phenomenon of stand failure or "die-off" in this annual grass. We previously isolated an undescribed species in the F. tricinctum species complex from die-off soils and showed that it is pathogenic on seeds. It can cause high mortality of nondormant B. tectorum seeds, especially under conditions of water stress, but rarely attacks dormant seeds. In this study, we used scanning electron microscopy (SEM) to investigate the mode of attack used by this pathogen. Nondormant B. tectorum seeds (i.e., florets containing caryopses) were inoculated with isolate Skull C1 macroconidia. Seeds were then exposed to water stress conditions (-1.5 MPa) for 7 days and then transferred to free water. Time lapse SEM photographs of healthy versus infected seeds revealed that hyphae under water stress conditions grew toward and culminated their attack at the abscission layer of the floret attachment scar. A prominent infection cushion, apparent macroscopically as a white tuft of mycelium at the radicle end of the seed, developed within 48 h after inoculation. Seeds that lacked an infection cushion completed germination upon transfer to free water, whereas seeds with an infection cushion were almost always killed. In addition, hyphae on seeds that did not initiate germination lacked directional growth and did not develop the infection cushion. This strongly suggests that the fungal attack is triggered by seed exudates released through the floret attachment scar at the initiation of germination. Images of cross sections of infected seeds showed that the fungal hyphae first penetrated the caryposis wall, then entered the embryo, and later ramified throughout the endosperm, completely destroying the seed.
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Khiyami MA, Almoammar H, Awad YM, Alghuthaymi MA, Abd-Elsalam KA. Plant pathogen nanodiagnostic techniques: forthcoming changes? BIOTECHNOL BIOTEC EQ 2014; 28:775-785. [PMID: 26740775 PMCID: PMC4684063 DOI: 10.1080/13102818.2014.960739] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 06/09/2014] [Indexed: 01/17/2023] Open
Abstract
Plant diseases are among the major factors limiting crop productivity. A first step towards managing a plant disease under greenhouse and field conditions is to correctly identify the pathogen. Current technologies, such as quantitative polymerase chain reaction (Q-PCR), require a relatively large amount of target tissue and rely on multiple assays to accurately identify distinct plant pathogens. The common disadvantage of the traditional diagnostic methods is that they are time consuming and lack high sensitivity. Consequently, developing low-cost methods to improve the accuracy and rapidity of plant pathogens diagnosis is needed. Nanotechnology, nano particles and quantum dots (QDs) have emerged as essential tools for fast detection of a particular biological marker with extreme accuracy. Biosensor, QDs, nanostructured platforms, nanoimaging and nanopore DNA sequencing tools have the potential to raise sensitivity, specificity and speed of the pathogen detection, facilitate high-throughput analysis, and to be used for high-quality monitoring and crop protection. Furthermore, nanodiagnostic kit equipment can easily and quickly detect potential serious plant pathogens, allowing experts to help farmers in the prevention of epidemic diseases. The current review deals with the application of nanotechnology for quicker, more cost-effective and precise diagnostic procedures of plant diseases. Such an accurate technology may help to design a proper integrated disease management system which may modify crop environments to adversely affect crop pathogens.
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Affiliation(s)
- Mohammad A Khiyami
- King Abdulaziz City for Science and Technology (KACST) , Riyadh , Saudi Arabia
| | - Hassan Almoammar
- King Abdulaziz City for Science and Technology (KACST) , Riyadh , Saudi Arabia
| | - Yasser M Awad
- Department of Agricultural Botany, Faculty of Agriculture, Suez Canal University , Ismailia , Egypt
| | - Mousa A Alghuthaymi
- Biology Department, Science and Humanities College, Shaqra University , Alquwayiyah , Saudi Arabia
| | - Kamel A Abd-Elsalam
- Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza, Egypt; Unit of Excellence in Nano-Molecular Plant Pathology Research (ARC), Giza, Egypt
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25
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Denschlag C, Rieder J, Vogel RF, Niessen L. Real-time loop-mediated isothermal amplification (LAMP) assay for group specific detection of important trichothecene producing Fusarium species in wheat. Int J Food Microbiol 2014; 177:117-27. [PMID: 24631635 DOI: 10.1016/j.ijfoodmicro.2014.02.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 01/29/2014] [Accepted: 02/14/2014] [Indexed: 10/25/2022]
Abstract
Trichothecene mycotoxins such as deoxynivaneol (DON), nivalenol (NIV) and T2-Toxin are produced by a variety of Fusarium spp. on cereals in the field and may be ingested by consumption of commodities and products made thereof. The toxins inhibit eukaryotic protein biosynthesis and may thus impair human and animal health. Aimed at rapid and sensitive detection of the most important trichothecene producing Fusarium spp. in a single analysis, a real-time duplex loop-mediated isothermal amplification (LAMP) assay was set up. Two sets of LAMP primers were designed independently to amplify a partial sequence of the tri6 gene in Fusarium (F.) graminearum and of the tri5 gene in Fusarium sporotrichioides, respectively. Each of the two sets detected a limited number of the established trichothecene producing Fusarium-species. However, combination of the two sets in one duplex assay enabled detection of F. graminearum, Fusarium culmorum, Fusarium cerealis, F. sporotrichioides, Fusarium langsethiae and Fusarium poae in a group specific manner. No cross reactions were detected with purified DNA from 127 other fungal species or with cereal DNA. To demonstrate the usefulness of the assay, 100 wheat samples collected from all over the German state of Bavaria were analyzed for the trichothecene mycotoxin DON by HPLC and for the presence of trichothecene producers by the new real-time duplex LAMP assay in parallel analyses. The LAMP assay showed positive results for all samples with a DON concentration exceeding 163ppb. The major advantage of the duplex LAMP assay is that the presence of six of the major trichothecene producing Fusarium spp. can be detected in a rapid and user-friendly manner with only one single assay. To our knowledge this is the first report of the use of a multiplex LAMP assay for fungal organisms.
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Affiliation(s)
- Carla Denschlag
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Gregor-Mendel-Str. 4, 85354 Freising, Germany
| | - Johann Rieder
- Bavarian State Research Center for Agriculture, Department for Quality Assurance and Analytics, Lange Point 6, 85354 Freising, Germany
| | - Rudi F Vogel
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Gregor-Mendel-Str. 4, 85354 Freising, Germany
| | - Ludwig Niessen
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Gregor-Mendel-Str. 4, 85354 Freising, Germany.
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26
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Moradi A, Almasi MA, Jafary H, Mercado-Blanco J. A novel and rapid loop-mediated isothermal amplification assay for the specific detection of Verticillium dahliae. J Appl Microbiol 2013; 116:942-54. [PMID: 24329885 DOI: 10.1111/jam.12407] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/21/2013] [Accepted: 11/22/2013] [Indexed: 11/29/2022]
Abstract
AIMS In this study, a loop-mediated isothermal amplification (LAMP) assay has been developed and evaluated for the rapid and sensitive detection of Verticillium dahliae Kleb., the causal agent of vascular wilts in many economically important crops. METHODS AND RESULTS LAMP primers were designed based on a previously described RAPD marker, and the LAMP assay was applied for direct detection of V. dahliae grown on medium and from soil samples without DNA purification steps (direct-LAMP). Thirty-two agricultural soil samples from various olive orchards were collected, and the presence of pathogen was detected by LAMP, direct-LAMP and nested-PCR methods. The LAMP methodology could successfully detect V. dahliae with high specificity, and cross-reaction was not observed with different pathogenic and nonpathogenic fungi and bacteria. The LAMP assay was capable of detecting a minimum of 500 and 50 fg of purified target DNA per reaction of V. dahliae ND and D pathotypes, respectively. In contrast, nested-PCR could only detect 5 pg reaction(-1) for both pathotypes. In artificially infested soil samples, the LAMP method detected 5 microsclerotia per gram of soil. Conversely, nested-PCR assay detected 50 microsclerotia g(-1) soil. The detection ratios of LAMP and direct-LAMP protocols were better (26 and 24 positive samples out of 32 agricultural soils analysed, respectively) than that obtained for nested-PCR method (22 positive results). Moreover, direct-LAMP yielded positive detection of V. dahliae in agricultural soil samples within 60-80 min. CONCLUSIONS The newly developed LAMP method was proved to be an effective, simple and rapid method to detect V. dahliae without the need for either expensive equipment or DNA purification. SIGNIFICANCE AND IMPACT OF STUDY This technique can be considered as an excellent standard alternative to plating and nested-PCR assays for the early, sensitive and low-cost detection of V. dahliae as well as other soilborne pathogens in the field.
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Affiliation(s)
- A Moradi
- Department of Biotechnology, Research Institute of Physiology and Biotechnology, University of Zanjan, Zanjan, Iran
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27
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Comparison of conventional PCR, multiplex PCR, and loop-mediated isothermal amplification assays for rapid detection of Arcobacter species. J Clin Microbiol 2013; 52:557-63. [PMID: 24478488 DOI: 10.1128/jcm.02883-13] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study aimed to develop a loop-mediated isothermal amplification (LAMP) method for the rapid detection of Arcobacter species. Specific primers targeting the 23S ribosomal RNA gene were used to detect Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii. The specificity of the LAMP primer set was assessed using DNA samples from a panel of Arcobacter and Campylobacter species, and the sensitivity was determined using serial dilutions of Arcobacter species cultures. LAMP showed a 10- to 1,000-fold-higher sensitivity than multiplex PCR, with a detection limit of 2 to 20 CFU per reaction in vitro. Whereas multiplex PCR showed cross-reactivity with Campylobacter species, the LAMP method developed in this study was more sensitive and reliable than conventional PCR or multiplex PCR for the detection of Arcobacter species.
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28
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Gräfenhan T, Patrick SK, Roscoe M, Trelka R, Gaba D, Chan JM, McKendry T, Clear RM, Tittlemier SA. Fusarium damage in cereal grains from Western Canada. 1. Phylogenetic analysis of moniliformin-producing fusarium species and their natural occurrence in mycotoxin-contaminated wheat, oats, and rye. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:5425-5437. [PMID: 23683177 DOI: 10.1021/jf400651p] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Harvest samples of common wheat (Triticum aestivum), oats (Avena sativa), and rye (Secale cereale) from producers in western Canada were analyzed for fungal infection by toxigenic Fusarium species and contamination by trichothecenes and moniliformin (MON). Fusarium graminearum and F. avenaceum were the two most frequently isolated species from samples of rye and wheat collected in 2010. F. poae and F. sporotrichioides were more commonly detected in randomly selected oat seeds. Other toxigenic Fusarium species including F. acuminatum, F. culmorum, and F. pseudograminearum as well as Phaeosphaeria nodorum (a.k.a. Septoria nodorum) were recovered primarily from fusarium-damaged kernels of wheat. Pure cultures of F. avenaceum, F. acuminatum, and other related species known to produce moniliformin were isolated from incubated seeds based on micro- and macromorphological criteria. The phylogenetic analysis inferred from partial DNA sequences of the acl1 and tef-1α genes revealed two major clades representing F. avenaceum and F. acuminatum, respectively. These clades comprised all Canadian isolates of the two species and a number of reference cultures studied earlier for their propensity to form moniliformin in vitro and in planta. However, some reference cultures previously reported to produce significant amounts of moniliformin formed minor phylogenetic lineages that represent rather distinct but closely related species. Concomitantly, cereal samples were analyzed for the presence of deoxynivalenol and moniliformin. These two Fusarium toxins were observed most frequently in common wheat, at concentrations up to 1.1 and 4.0 mg/kg, respectively. There was no apparent relationship between moniliformin concentrations and detection of F. avenaceum and F. acuminatum in rye and oat samples. Geographical analysis of the distribution of moniliformin and F. avenaceum and F. acuminatum across the Canadian Prairies also did not indicate a strong relationship.
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Affiliation(s)
- Tom Gräfenhan
- Grain Research Laboratory, Canadian Grain Commission, Winnipeg, Manitoba, Canada.
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Focke F, Haase I, Fischer M. Loop-mediated isothermal amplification (LAMP): methods for plant species identification in food. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:2943-2949. [PMID: 23432417 DOI: 10.1021/jf304295b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a DNA-based analytical method that can be used as an isothermal alternative to polymerase chain reaction (PCR). In comparison to PCR, the advantage of LAMP is the possibility to perform the isothermal reaction without any sophisticated technical equipment; only a water bath is needed, and naked eye detection is sufficient. Up to now, an application of LAMP methods for the detection of even closely related plant species in food or feed matrices has not been described, whereas a large number of PCR methods for that topic are cited in the literature. The aim of the study was the evaluation of LAMP-based methods for plant species identification with respect to method parameters such as R(2), LOD, and LOQ. An existing (real-time) PCR method (for the detection of spices) was used for comparison. It could be shown that the developed LAMP methods have potential as alternative strategies to PCR in DNA-based analysis.
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Affiliation(s)
- Felix Focke
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg , Grindelallee 117, 20146 Hamburg, Germany
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Development and application of a loop-mediated isothermal amplification assay for rapid identification of aflatoxigenic molds and their detection in food samples. Int J Food Microbiol 2012; 159:214-24. [PMID: 23107500 DOI: 10.1016/j.ijfoodmicro.2012.08.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 08/24/2012] [Accepted: 08/28/2012] [Indexed: 11/21/2022]
Abstract
Aflatoxins are the most thoroughly studied mycotoxins. They are produced by several members of the genus Aspergillus in section Flavi with Aspergillus flavus, Aspergillus parasiticus, and Aspergillus nomius being frequently isolated from contaminated food sources. In this work, we describe the development and evaluation of loop-mediated isothermal amplification (LAMP) assays for rapid detection of the three species in separate analyses. The acl1-gene of A. flavus and amy1-genes of A. nomius and A. parasiticus were used as target genes. The detection limits were 2.4, 7.6 and 20pg of pure DNA/reaction for A. flavus, A. nomius and A. parasiticus, respectively. For specificity testing, DNA extracted from mycelia of representative strains of 39 Aspergillus species, 23 Penicillium species, 75 Fusarium species and 37 other fungal species was used as a template for the specific LAMP primer sets developed for the three target species. The LAMP assay was combined with a DNA extraction method for the analysis of pure fungal cultures as well as artificially contaminated Brazil nuts, peanuts and green coffee beans. It is suggested that the developed LAMP assay is a promising tool in the prediction of a potential aflatoxin risk in food and food raw materials and may therefore be suitable for high throughput analysis in the food industry.
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