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Rapid and precise detection of cryptic tea pathogen Exobasidium vexans: RealAmp validation of LAMP approach. World J Microbiol Biotechnol 2022; 39:52. [PMID: 36564678 DOI: 10.1007/s11274-022-03506-y] [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: 07/27/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
This work embodies the development of a real time loop mediated isothermal amplification (RealAmp) assay for the rapid detection of the cryptic tea phytopathogen, Exobasidium vexans, the causal organism of blister blight disease. Due to the widespread popularity of tea as a beverage and the associated agro-economy, the rapid detection and management of the fast-spreading blister blight disease have been a longstanding necessity. Loop-mediated isothermal amplification (LAMP) primers were designed targeting the E. vexans ITS rDNA region and the reaction temperature was optimized at 62 °C with a 60 min reaction time. Amplification of the E. vexans isolates in the initial LAMP reactions was confirmed by both agarose gel electrophoresis and SYBR Green I dye based colour change visualization. The specificity of the LAMP primers for E. vexans was validated by negative testing of seven different phytopathogenic test fungi using LAMP and RealAmp assay. The positive findings in RealAmp assay for E. vexans strain were corroborated via detecting fluorescence signals in real-time. Further, the LAMP assays performed with gDNA isolated from infected tea leaves revealed positive amplification for the presence of E. vexans. The results demonstrate that this rapid and precise RealAmp assay has the potential to be applied for field-based detection of E. vexans in real-time.
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Liang Z, Liu H, Xu Z, Zhang LH. First Report of Pectobacterium aroidearum Causing Soft Rot in Olecranon Honey Peach ( Prunus persica) in China. PLANT DISEASE 2022; 106:PDIS10212238PDN. [PMID: 34844444 DOI: 10.1094/pdis-10-21-2238-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Zhibin Liang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Huidi Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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Yang L, Zhang L, Cao J, Wang L, Shi H, Zhu F, Ji Z. Rapid Detection of Peach Shoot Blight Caused by Phomopsis amygdali Utilizing a New Target Gene Identified from Genome Sequences Within Loop-Mediated Isothermal Amplification. PLANT DISEASE 2022; 106:669-675. [PMID: 34597154 DOI: 10.1094/pdis-08-21-1645-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Peach shoot blight (PSB), caused by Phomopsis amygdali, is a serious threat to the healthy development of the peach industry and leads to 30 to 50% damage to peach production in southern China. In this study, loop-mediated isothermal amplification (LAMP) technology was used to detect the P. amygdali target of a gene of GME6801 that was unique in the whole genome of the pathogen compared with that of Diaporthe (Phomopsis) longicolla TWH P74, Fusarium graminearum PH-1, Colletotrichum gloeosporioides SMCG1 and Magnaporthe oryzae 70-15. Blast comparison of this gene sequence in NCBI database showed that no homologous sequences were found. Therefore, the gene sequence of GME6801 was used to design two pairs of LAMP primers and one pair of PCR primers. The results showed that both primer sets were specific to the 15 strains of P. amygdali, and the other 15 fungal strains presented negative reactions, similar to the control. In addition, 50 pg of genomic DNA of P. amygdali in a 25-μl reaction system could be detected by LAMP assay, which was 100 times more sensitive than PCR. Furthermore, the GME6801 LAMP assay was used to detect artificially inoculated twigs of the pathogen, disease twigs within significantly symptomatic PSB in the fields, and healthy twigs in the same orchard, with detection rates of 100, 75, and 20.8%, respectively. However, detection rates of conventional PCR were separately 100, 62.5, and 16.7%. The results indicated that GME6801-based LAMP could be used for P. amygdali detection as its specificity, sensitivity, and simplicity. This study provides a rapid experimental basis for the identification and prediction of P. amygdali that causes PSB and is beneficial for precise prevention and control of the disease.
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Affiliation(s)
- Lina Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Liang Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jun Cao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Lingyun Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hengsong Shi
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Feng Zhu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zhaolin Ji
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
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Arizala D, Dobhal S, Babler B, Crockford AB, Rioux RA, Alvarez AM, Arif M. Development of a multiplex TaqMan qPCR targeting unique genomic regions for the specific and sensitive detection of Pectobacterium species and P. parmentieri. J Appl Microbiol 2022; 132:3089-3110. [PMID: 35026058 DOI: 10.1111/jam.15447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/13/2021] [Accepted: 01/06/2022] [Indexed: 11/26/2022]
Abstract
AIM The newly defined species P. parmentieri has emerged as an aggressive pathogen that causes soft rot and blackleg diseases on potato and has been widely disseminated across the globe, jeopardizing the productivity and potato food safety. The implementation of a fast and accurate detection tool is imperative to control, monitor and prevent further spread of these pathogens. The objective of this work was to develop a specific and sensitive multiplex TaqMan qPCR to detect P. parmentieri and distinguish it from all known Pectobacterium species. A universal internal control (UIC) was included to enhance the reliability of the assay. METHODS AND RESULTS A comparative genomics approach was used to identify O-acetyltransferase and the XRE family transcriptional regulator as specific targets for primers/probe design for the detection of the Pectobacterium genus and P. parmentieri, respectively. Specificity was assessed with 35 and 25 strains included inclusivity and exclusivity panels, respectively, isolated from different geographic locations and sources. The assay specifically detected all 35 strains of Pectobacterium sp. and all 15 P. parmentieri strains. No cross-reactivity was detected during assay validation. Our assay detected up to 10 fg genomic DNA and 1 CFU ml-1 bacterial culture. No change in the detection threshold (1 CFU ml-1 ) was observed in spiked assays after adding host tissue to the reactions. The assay was validated with naturally and artificially infected host tissues and soil rhizosphere samples. All infected plant samples containing the target pathogens were accurately amplified. CONCLUSION The presented multiplex TaqMan qPCR diagnostic assay is highly specific, sensitive, reliable for the detection of Pectobacterium species and P. parmentieri with no false positives or false negatives. SIGNIFICANCE AND IMPACT The developed assay can be adopted for multiple purposes such as seed certification programs, surveillance, biosecurity, microbial forensics, quarantine, border protection, inspections, and epidemiology.
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Affiliation(s)
- Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu
| | - Brooke Babler
- Department of Plant Pathology, University of Wisconsin-Madison
| | | | - Renee A Rioux
- Department of Plant Pathology, University of Wisconsin-Madison
| | - Anne M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu
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Xu P, Wang H, Qin C, Li Z, Lin C, Liu W, Miao W. Analysis of the Taxonomy and Pathogenic Factors of Pectobacterium aroidearum L6 Using Whole-Genome Sequencing and Comparative Genomics. Front Microbiol 2021; 12:679102. [PMID: 34276610 PMCID: PMC8282894 DOI: 10.3389/fmicb.2021.679102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/07/2021] [Indexed: 11/24/2022] Open
Abstract
Soft rot pectobacteria are devastating plant pathogens with a global distribution and a broad host range. Pectobacterium aroidearum L6, previously isolated from leaves of Syngonium podophyllum, is a pectolytic bacterial pathogen that causes typical soft rot on S. podophyllum. There is a shortage for genome data of P. aroidearum, which seriously hinders research on classification and pathogenesis of Pectobacterium. We present here the complete genome sequence of P. aroidearum L6. The L6 strain carries a single 4,995,896-bp chromosome with 53.10% G + C content and harbors 4,306 predicted protein-coding genes. We estimated in silico DNA-DNA hybridization and average nucleotide identity values in combination with the whole-genome-based phylogeny from 19 Pectobacterium strains including P. aroidearum L6. The results showed that L6 and PC1 formed a population distinct from other populations of the Pectobacterium genus. Phylogenetic analysis based on 16S rRNA and genome sequences showed a close evolutionary relationship among Pectobacterium species. Overall, evolutionary analysis showed that L6 was in the same branch with PC1. In comparison with 18 Pectobacterium spp. reference pathogens, strain L6 had 2,712 gene families, among which 1,632 gene families were identified as orthologous to those strains, as well as 1 putative unique gene family. We discovered 478 genes, 10.4% of the total of predicted genes, that were potentially related to pathogenesis using the Virulence Factors of Pathogenic Bacteria database. A total of 25 genes were related to toxins, 35 encoded plant cell-wall degrading enzymes, and 122 were involved in secretion systems. This study provides a foundation for a better understanding of the genomic structure of P. aroidearum and particularly offers information for the discovery of potential pathogenic factors and the development of more effective strategies against this pathogen.
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Affiliation(s)
- Peidong Xu
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
- School of Life Sciences, Hainan University, Haikou, China
| | - Huanwei Wang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Chunxiu Qin
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Zengping Li
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Chunhua Lin
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Wenbo Liu
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Weiguo Miao
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
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Zhou Y, Fan F, Wang L, Chaisiri C, Yin LF, Yin WX, Luo CX. Development of a loop-mediated isothermal amplification method for the rapid detection of Venturia carpophila on peach. PEST MANAGEMENT SCIENCE 2021; 77:1383-1391. [PMID: 33098187 DOI: 10.1002/ps.6154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/12/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Peach scab, caused by Venturia carpophila, can significantly reduce both the yield and quality of peach fruit. It is difficult to distinguish peach scab from other peach diseases such as black spot and bacterial spot. An efficient assay is needed to identify V. carpophila in order to develop scientific management strategies. RESULTS A set of loop-mediated isothermal amplification (LAMP) primers was designed based on the internal transcribed spacer (rDNA-ITS) sequence to detect V. carpophila. Compared with the conventional polymerase chain reaction (PCR) method, the LAMP method not only exhibited higher sensitivity and specificity in the detection of V. carpophila, but also required simpler equipment and less operational time. The minimum detectable concentration of V. carpophila genomic DNA with the LAMP method was 56.6 fg μl-1 , which was 100 times lower than with the conventional PCR method. When eight fungal species including V. carpophila (23 isolates from 14 provinces) and one bacterial species were used with LAMP detection, only V. carpophila showed a color change, from brown to yellowish green, and ladder-like bands in electrophoresis, indicating successful amplification. Moreover, when crude DNAs of peach fruit samples were used in LAMP detection, amplification was observed only from diseased fruits, and not from healthy fruits and the negative control. CONCLUSION The LAMP assay shows simplicity, rapidity, high sensitivity and specificity, and will be useful in distinguishing scab caused by Venturia carpophila from other diseases with similar symptoms. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Yang Zhou
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fei Fan
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Wang
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chingchai Chaisiri
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liang-Fen Yin
- Experimental Teaching Center of Crop Science, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wei-Xiao Yin
- Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chao-Xi Luo
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Hu L, Zhu X, Shang L, Teng Y, Li J, Li B. Inhibit the intrinsic bacteria from konjac glucomannan hydrosol for its improved viscosity stability. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Oulghazi S, Sarfraz S, Zaczek-Moczydłowska MA, Khayi S, Ed-Dra A, Lekbach Y, Campbell K, Novungayo Moleleki L, O’Hanlon R, Faure D. Pectobacterium brasiliense: Genomics, Host Range and Disease Management. Microorganisms 2021; 9:E106. [PMID: 33466309 PMCID: PMC7824751 DOI: 10.3390/microorganisms9010106] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Pectobacterium brasiliense (Pbr) is considered as one of the most virulent species among the Pectobacteriaceae. This species has a broad host range within horticulture crops and is well distributed elsewhere. It has been found to be pathogenic not only in the field causing blackleg and soft rot of potato, but it is also transmitted via storage causing soft rot of other vegetables. Genomic analysis and other cost-effective molecular detection methods such as a quantitative polymerase chain reaction (qPCR) are essential to investigate the ecology and pathogenesis of the Pbr. The lack of fast, field deployable point-of-care testing (POCT) methods, specific control strategies and current limited genomic knowledge make management of this species difficult. Thus far, no comprehensive review exists about Pbr, however there is an intense need to research the biology, detection, pathogenicity and management of Pbr, not only because of its fast distribution across Europe and other countries but also due to its increased survival to various climatic conditions. This review outlines the information available in peer-reviewed literature regarding host range, detection methods, genomics, geographical distribution, nomenclature and taxonomical evolution along with some of the possible management and control strategies. In summary, the conclusions and a further directions highlight the management of this species.
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Affiliation(s)
- Said Oulghazi
- Department of Biology, Faculty of Sciences, Moulay Ismaïl University, BP.11201, Zitoune Meknes 50000, Morocco; (S.O.); (A.E.-D.)
- Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Sohaib Sarfraz
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Maja A. Zaczek-Moczydłowska
- Institute for Global Food Security, School of Biological Sciences, Queen’s University, Belfast BT9 5DL, UK; (M.A.Z.-M.); (K.C.)
| | - Slimane Khayi
- Biotechnology Research Unit, CRRA-Rabat, National Institute for Agricultural Research (INRA), Rabat 10101, Morocco;
| | - Abdelaziz Ed-Dra
- Department of Biology, Faculty of Sciences, Moulay Ismaïl University, BP.11201, Zitoune Meknes 50000, Morocco; (S.O.); (A.E.-D.)
| | - Yassir Lekbach
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, China;
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen’s University, Belfast BT9 5DL, UK; (M.A.Z.-M.); (K.C.)
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
| | - Richard O’Hanlon
- Agri-Food and Biosciences Institute, 18a Newforge Lane, Belfast BT9 5PX, UK;
- Department of Agriculture, Food and the Marine, D02 WK12 Dublin 2, Ireland
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, 91190 Gif-sur-Yvette, France
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Tegli S, Biancalani C, Ignatov AN, Osdaghi E. A Powerful LAMP Weapon against the Threat of the Quarantine Plant Pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens. Microorganisms 2020; 8:microorganisms8111705. [PMID: 33142784 PMCID: PMC7716198 DOI: 10.3390/microorganisms8111705] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/23/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022] Open
Abstract
Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff) is a Gram-positive phytopathogenic bacterium attacking leguminous crops and causing systemic diseases such as the bacterial wilt of beans and bacterial spot of soybeans. Since the early 20th century, Cff is reported to be present in North America, where it still causes high economic losses. Currently, Cff is an emerging plant pathogen, rapidly spreading worldwide and occurring in many bean-producing countries. Infected seeds are the main dissemination pathway for Cff, both over short and long distances. Cff remains viable in the seeds for long times, even in field conditions. According to the most recent EU legislation, Cff is included among the quarantine pests not known to occur in the Union territory, and for which the phytosanitary inspection consists mainly of the visual examination of imported bean seeds. The seedborne nature of Cff combined with the globalization of trades urgently call for the implementation of a highly specific diagnostic test for Cff, to be routinely and easily used at the official ports of entry and into the fields. This paper reports the development of a LAMP (Loop-Mediated Isothermal Amplification) specific for Cff, that allows the detection of Cff in infected seeds, both by fluorescence and visual monitoring, after 30 min of reaction and with a detection limit at around 4 fg/μL of pure Cff genomic DNA.
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Affiliation(s)
- Stefania Tegli
- Laboratorio di Patologia Vegetale Molecolare, Dipartimento di Scienze e Tecnologie Agrarie, Alimentari Ambientali e Forestali (DAGRI), Università degli Studi di Firenze, Via della Lastruccia 10, 50019 Sesto Fiorentino (Firenze), Italy;
- Correspondence: ; Tel.: +39-0554573427
| | - Carola Biancalani
- Laboratorio di Patologia Vegetale Molecolare, Dipartimento di Scienze e Tecnologie Agrarie, Alimentari Ambientali e Forestali (DAGRI), Università degli Studi di Firenze, Via della Lastruccia 10, 50019 Sesto Fiorentino (Firenze), Italy;
| | - Aleksandr N. Ignatov
- Agrarian and Technological Institute (ATI), Peoples’ Friendship University of Russia, Miklukho-Maklaya str.8, 117198 Moscow, Russia;
| | - Ebrahim Osdaghi
- Department of Plant Protection, University of Tehran, Karaj 31587-77871, Iran;
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Goudarzi R, Mortazavi MM. Loop-mediated isothermal amplification: a rapid molecular technique for early diagnosis of Pseudomonas syringae pv. syringae of stone fruits. J Genet Eng Biotechnol 2020; 18:55. [PMID: 33009592 PMCID: PMC7532232 DOI: 10.1186/s43141-020-00062-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/20/2020] [Indexed: 12/02/2022]
Abstract
Background Pathogenic bacteria cause significant economic damages in agriculture. The detection of such bacteria is considered as a continual interest for plant pathologists to prevent disease dissemination. Pseudomonas syringae pv. syringae is one of the most important bacterial pathogens infecting yield and quality of stone fruits throughout the world. Biochemical assays such as a LOPAT and GATTa are common methods to detect this pathogen. Serological tests and culturing on King’s B selective medium also used to isolate this bacterium. Selective media is composed of specific and effective ingredients to inhibit the growth of certain species of microbes in a mixed culture while allowing others to grow. These are used for the growth of only selected microorganisms. King’s B medium can be used as a general medium for the non-selective isolation cultivation and pigment production of Pseudomonas species from foods, cosmetic samples, plants, etc. Nevertheless, the mentioned methods are not enough accurate to differentiate the strains. On the other hand, PCR-based techniques are sensitive and efficient in detecting plant diseases. However, these techniques are not practicable for those researchers who do not have access to a thermal cycler. We have used loop-mediated isothermal amplification to couple with a target. The amplification of syrD gene using loop and bumper primers can be used to prevent disease dissemination. Results The outcome of this investigation indicated more sensitivity of LAMP in comparison to PCR. The direct addition of SYBR Gold in microtube is more sensitive than gel in both LAMP and PCR byproducts so we can eliminate gel electrophoresis, while the LAMP showed high sensitivity and high specificity in comparison to results obtained by cultivation. The described molecular test could detect Pseudomonas syringae pv. syringae type in nearly 1 h, and this is the first time that Lamp molecular detection of Pseudomonas syringae pv. syringae particularly on stone fruits is described and introduced. Conclusions The obtained data confirmed that LAMP is a fast, cheap, and high specific method for the rapid detection of Pseudomonas syringae pv. syringae to the comparison of PCR and culture.
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Affiliation(s)
- R Goudarzi
- Department of Agriculture, Damghan Islamic Azad University, Damghan, Iran
| | - M M Mortazavi
- Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran. .,Ehya Bone Company, Growth Center, Golestan University of Medical Sciences, Gorgan, Iran. .,Transmission Electron Microscope Lab, Biomedical Technology Wing, SCTIMSTs, Trivandrum, India.
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Cai S, Kong F, Xu S. Detection of porcine-derived ingredients from adulterated meat based on real-time loop-mediated isothermal amplification. Mol Cell Probes 2020; 53:101609. [PMID: 32485233 DOI: 10.1016/j.mcp.2020.101609] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 11/28/2022]
Abstract
Increasingly globalized and complex food supply chains contribute to a growing problem of meat fraud. Meat adulteration with pork is especially exceptionable to the global population for health concern and religious faith reasons. To prevent unfair competition and protect consumer rights, an efficient and rapid assay to identify the species of meat products is crucial. In this study, a real-time loop-mediated isothermal amplification (real-time LAMP) assay was developed for the detection of a porcine gene in meat products. The designed primers were highly selective for the porcine gene. The amplification showed no cross-reactivity with 11 other meats. The established method required 20 min with an initial amplification curve of approximately 10 min and demonstrated a detection limit of 1.76 pg/μL porcine DNA, which is 1000 times more sensitive than PCR. This study is the first attempt at detecting porcine-derived ingredients using a real-time LAMP assay in commercial products. This method meets specificity, rapidness, robustness, and sensitivity criteria; its practical application will greatly aid in battling adulteration in the food industry.
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Affiliation(s)
- Shaoxin Cai
- Fisheries College, Jimei University, Xiamen, 361021, China; Inspection and Quarantine Technology Center of Cross-Strait Agricultural Products in Xiamen, Xiamen, 361021, China.
| | - Fande Kong
- Inspection and Quarantine Technology Center of Cross-Strait Agricultural Products in Xiamen, Xiamen, 361021, China
| | - Shufei Xu
- Inspection and Quarantine Technology Center of Cross-Strait Agricultural Products in Xiamen, Xiamen, 361021, China.
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A Simple and Multiplex Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid Detection of SARS-CoV. BIOCHIP JOURNAL 2019; 13:341-351. [PMID: 32226589 PMCID: PMC7097549 DOI: 10.1007/s13206-019-3404-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 08/23/2019] [Indexed: 12/29/2022]
Abstract
The current diagnosis of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) relies on laboratory-based tests since its clinical features are nonspecific, unlike other respiratory pathogens. Therefore, the development of a rapid and simple method for on-site detection of SARS-CoV is crucial for the identification and prevention of future SARS outbreaks. In this study, a simple colorimetric and multiplex loop-mediated isothermal amplification (LAMP) assay was developed to rapid screening of severe acute respiratory syndrome-associated coronavirus (SARS-CoV). It can be visually detected based on color change and monitored in real-time with fluorescent signals. The performance of this assay, based on six primers targeting open reading frame (ORF1b) and nucleocapsid (N) genes located in different regions of the SARS-CoV, was compared with real-time RT-PCR assay using various concentrations of target genes. The detection limit of the LAMP assay was comparable to that of real-time RT-PCR assay and therefore a few target RNA to 104-105 copies could be detected within a short period of time (20–25 min). In addition, we established a multiplex real-time LAMP assay to simultaneously detect two target regions within the SARS-CoV genome. Two target sequences were amplified by specific primers in the same reaction tube and revealed that it was able to detect down to 105 copies. The standard curve had a linear relationship with similar amplification efficiencies. The LAMP assay results in shorter “sample-to-answer” time than conventional PCR method. Therefore, it is suitable not only for diagnosis of clinical test, but also for surveillance of SARS virus in developing countries.
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