Genome-informed diagnostics for specific and rapid detection of Pectobacterium species using recombinase polymerase amplification coupled with a lateral flow device

Abstract Pectobacterium species cause serious bacterial soft rot diseases worldwide on economically important fruit and vegetable crops including tomato and potato. Accurate and simple methods are essential for rapid pathogen identification and timely management of the diseases. Recombinase polymera...

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Autores principales:	Firas A. Ahmed, Adriana Larrea-Sarmiento, Anne M. Alvarez, Mohammad Arif
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Recombinase Polymerase Amplification (RPA) Lateral Flow Devices (LFD) Pectobacterium Species Host Control Loop-mediated Isothermal Amplification (LAMP) Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1d4c61a51648499196831d4ccd40214d
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spelling	oai:doaj.org-article:1d4c61a51648499196831d4ccd40214d2021-12-02T15:08:04ZGenome-informed diagnostics for specific and rapid detection of Pectobacterium species using recombinase polymerase amplification coupled with a lateral flow device10.1038/s41598-018-34275-02045-2322https://doaj.org/article/1d4c61a51648499196831d4ccd40214d2018-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-34275-0https://doaj.org/toc/2045-2322Abstract Pectobacterium species cause serious bacterial soft rot diseases worldwide on economically important fruit and vegetable crops including tomato and potato. Accurate and simple methods are essential for rapid pathogen identification and timely management of the diseases. Recombinase polymerase amplification (RPA) combined with a lateral flow device (LFD) was developed for specific detection of Pectobacterium sp. directly from infected plant materials with no need for DNA isolation. The specificity of RPA-LFD was tested with 26 Pectobacterium sp. strains and 12 non-Pectobacterium species and no false positive or false negative outcomes were observed. RPA primers and probe for host control were also developed to detect the host genome for enhanced reliability and accuracy of the developed assay. The detection limit of 10 fg was obtained with both sensitivity and spiked sensitivity assays. No inhibitory effects were observed on the RPA assay when targets (pathogen and host) were directly detected from infected potato and tomato sap. The developed RPA assay has numerous applications from routine diagnostics at point-of-care, biosecurity, surveillance and disease management to epidemiological studies. In addition, this tool can also be used to discover reservoir hosts for Pectobacterium species.Firas A. AhmedAdriana Larrea-SarmientoAnne M. AlvarezMohammad ArifNature PortfolioarticleRecombinase Polymerase Amplification (RPA)Lateral Flow Devices (LFD)Pectobacterium SpeciesHost ControlLoop-mediated Isothermal Amplification (LAMP)MedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-11 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Recombinase Polymerase Amplification (RPA) Lateral Flow Devices (LFD) Pectobacterium Species Host Control Loop-mediated Isothermal Amplification (LAMP) Medicine R Science Q
spellingShingle	Recombinase Polymerase Amplification (RPA) Lateral Flow Devices (LFD) Pectobacterium Species Host Control Loop-mediated Isothermal Amplification (LAMP) Medicine R Science Q Firas A. Ahmed Adriana Larrea-Sarmiento Anne M. Alvarez Mohammad Arif Genome-informed diagnostics for specific and rapid detection of Pectobacterium species using recombinase polymerase amplification coupled with a lateral flow device
description	Abstract Pectobacterium species cause serious bacterial soft rot diseases worldwide on economically important fruit and vegetable crops including tomato and potato. Accurate and simple methods are essential for rapid pathogen identification and timely management of the diseases. Recombinase polymerase amplification (RPA) combined with a lateral flow device (LFD) was developed for specific detection of Pectobacterium sp. directly from infected plant materials with no need for DNA isolation. The specificity of RPA-LFD was tested with 26 Pectobacterium sp. strains and 12 non-Pectobacterium species and no false positive or false negative outcomes were observed. RPA primers and probe for host control were also developed to detect the host genome for enhanced reliability and accuracy of the developed assay. The detection limit of 10 fg was obtained with both sensitivity and spiked sensitivity assays. No inhibitory effects were observed on the RPA assay when targets (pathogen and host) were directly detected from infected potato and tomato sap. The developed RPA assay has numerous applications from routine diagnostics at point-of-care, biosecurity, surveillance and disease management to epidemiological studies. In addition, this tool can also be used to discover reservoir hosts for Pectobacterium species.
format	article
author	Firas A. Ahmed Adriana Larrea-Sarmiento Anne M. Alvarez Mohammad Arif
author_facet	Firas A. Ahmed Adriana Larrea-Sarmiento Anne M. Alvarez Mohammad Arif
author_sort	Firas A. Ahmed
title	Genome-informed diagnostics for specific and rapid detection of Pectobacterium species using recombinase polymerase amplification coupled with a lateral flow device
title_short	Genome-informed diagnostics for specific and rapid detection of Pectobacterium species using recombinase polymerase amplification coupled with a lateral flow device
title_full	Genome-informed diagnostics for specific and rapid detection of Pectobacterium species using recombinase polymerase amplification coupled with a lateral flow device
title_fullStr	Genome-informed diagnostics for specific and rapid detection of Pectobacterium species using recombinase polymerase amplification coupled with a lateral flow device
title_full_unstemmed	Genome-informed diagnostics for specific and rapid detection of Pectobacterium species using recombinase polymerase amplification coupled with a lateral flow device
title_sort	genome-informed diagnostics for specific and rapid detection of pectobacterium species using recombinase polymerase amplification coupled with a lateral flow device
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/1d4c61a51648499196831d4ccd40214d
work_keys_str_mv	AT firasaahmed genomeinformeddiagnosticsforspecificandrapiddetectionofpectobacteriumspeciesusingrecombinasepolymeraseamplificationcoupledwithalateralflowdevice AT adrianalarreasarmiento genomeinformeddiagnosticsforspecificandrapiddetectionofpectobacteriumspeciesusingrecombinasepolymeraseamplificationcoupledwithalateralflowdevice AT annemalvarez genomeinformeddiagnosticsforspecificandrapiddetectionofpectobacteriumspeciesusingrecombinasepolymeraseamplificationcoupledwithalateralflowdevice AT mohammadarif genomeinformeddiagnosticsforspecificandrapiddetectionofpectobacteriumspeciesusingrecombinasepolymeraseamplificationcoupledwithalateralflowdevice
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Genome-informed diagnostics for specific and rapid detection of Pectobacterium species using recombinase polymerase amplification coupled with a lateral flow device

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