Probe-based real-time PCR method for multilocus melt typing of Xylella fastidiosa strains

Brady, Jeff A.; Faske, Jennifer B.; Ator, Rebecca A.; Castañeda-Gill, Jessica M.; Mitchell, Forrest L.

doi:10.1016/j.mimet.2012.02.002

Cited by 6 publications

(3 citation statements)

References 22 publications

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“…Dicho protocolo se probó en ocho cepas de EP, seis de OLS y seis de ALS que podrían colocarse con éxito en el grupo de cepas respectivo mediante el análisis de la curva de Tm (Bextine y Child, 2007). De manera similar, Brady et al (2012) utilizando un conjunto de sondas fluorescentes, desarrolló un sistema de tipificación en fusión multilocus (MLMT) para discriminar las subespecies y cepas de X. fastidiosa en reacciones rápidas en tiempo real. Estos enfoques son potencialmente muy interesantes, porque teóricamente es posible detectar variaciones genéticas determinadas por tan solo una alteración de un solo par de bases.…”

Section: Nomenclatura Taxonómica Molecular Internacionalunclassified

Xylella fastidiosa: UN ANÁLISIS MOLECULAR DEL ESTADO DE LA ENFERMEDAD BACTERIANA A NIVEL INTERNACIONAL

Brito-Vega¹,

López-Ferrer²,

Gómez-Méndez³

et al. 2021

Trop Subtrop Agroecosyst

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Background: Xylella fastidiosa is a bacterium considered native to the American continent, which affects the vascular ducts of the xylem, causing diseases with an economically important cost in plantations. This species is distributed in Asia, America and Europe. The bacteria can be transmitted with the help of vector insects. Objective. The objective of this work was to carry out an analysis of the main theoretical and practical aspects of the X. fastidiosa species and its impact on agriculture. Methodology. The method used was a review of the literature and information available on the bacterium Xylella fastidiosa and its subspecies internationally and nationally. Main findings. The first known syndrome caused by this bacterium was described in 1892 by Newton Barris Pierce, when a strange pathology devastated thousands of hectares of vine in Los Angeles. In Mexico, Pierce's disease was detected in 1980 in vineyards in Baja California Norte and in 1995 in vineyards in Valle de Guadalupe, in the municipality of Ensenada, Baja California. X. fastidiosa entered the genomic era when in the year 2000 the first genome of a bacterium associated with plants, the 9a5c strain of Citrus Variegated Chlorosis, was sequenced. Since the first half of the 1990s, specific PCR primers have been used to identify X. fastidiosa from infected plants. Implications. Six subspecies of Xylella fastidiosa are currently considered: fastidiosa, multiplex, sandyi, tashke, pauca and morus; fastidiosa and pauca specifically affect citrus fruits and the related insect vectors are: Bucephalagonia xanthohis, Diloboterus costalimaik, Acrogonia citrina, Oncometopia facialis, Ferrariana trivittata, Plesiommata corniculata, Homalodisca ignorata, Parathona virescens, Sonesimia groscens and Acrogonia virescens. Once the insect contains the bacteria, at least 200 viable bacteria are enough to infect the target plant. Conclusions. Currently there are still no solutions or established techniques to fully protect plantations, it is important to strengthen surveillance to limit the spread. DNA-based molecular biology is a valuable tool for the detection and characterization of X. fastidiosa.

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Section: Nomenclatura Taxonómica Molecular Internacionalunclassified

Xylella fastidiosa: UN ANÁLISIS MOLECULAR DEL ESTADO DE LA ENFERMEDAD BACTERIANA A NIVEL INTERNACIONAL

Brito-Vega¹,

López-Ferrer²,

Gómez-Méndez³

et al. 2021

Trop Subtrop Agroecosyst

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“…Several immunological and molecular methods for specific detection of X. fastidiosa have been developed by diverse research groups (comprehensively reviewed by Baldi & La Porta (2017)). Some of the PCR-based methods were designed to detect the pathogen at the species level using primers targeted to genomic regions conserved among all subspecies (Francis et al, 2006), others to differentiate among a subset of subspecies (Hernandez-Martinez et al, 2006), and yet others to detect a specific subspecies (Pooler & Hartung, 1995;Brady et al, 2012). Although it is believed that the method that best discriminates among X. fastidiosa strains is MLST (Almeida et al, 2008;Yuan et al, 2010;Nunney et al, 2012), lack of correlation has been observed between detection using subspecies-specific primers and MLST (Denanc e et al, 2017).…”

Section: Pathogen Detectionmentioning

confidence: 99%

Coffee bacterial diseases: a plethora of scientific opportunities

Badel

Zambolim

2019

Plant Pathology

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Coffee is a very important crop for several tropical countries across different continents. The diseases bacterial halo blight (BHB), bacterial leaf spot (BLS), bacterial leaf blight (BLB) and coffee leaf scorch (CLS), caused by the bacterial pathogens Pseudomonas syringae pv. garcae (Psgc), P. syringae pv. tabaci (Psta), Pseudomonas cichorii (Pch) and Xylella fastidiosa subsp. pauca (Xfp), respectively, cause significant reductions in coffee production, although other minor bacterial diseases have also been reported in some countries. Little research progress has been made on aspects that are relevant for control and management of these diseases. In all cases, there is an urgent need to develop rapid and more reliable methods for early detection of the pathogens in order to minimize their negative impact on coffee production. Because of the high rate of intra‐ and intersubspecific recombination occurring in X. fastidiosa, a permanent revision of the detection methods is necessary. Greater efforts should be made to understand the genetic and virulence diversity of Psgc, Psta and Pch populations. Early studies reported the identification of potential sources of resistance against Psgc and Psta, but, to date, no resistance gene has been isolated. Little effort has been made to understand the biology and molecular mechanisms underlying the interaction between Coffea spp. and these pathogenic bacteria. This review discusses the recent progress on the molecular mechanisms used by these bacteria to cause diseases on other plant species, in order to provide a guideline for the establishment of future research programmes.

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“…Such protocol was tested on eight PD, six OLS, and six ALS strains that could be successfully placed into the respective strain group by the analysis of T m curve (Bextine and Child, 2007). Similarly but using a set of fluorescent probes, Brady et al developed a multilocus melt typing (MLMT) system to discriminate X. fastidiosa subspecies and strains in rapid real time reactions (Brady et al, 2012). These approaches are potentially very interesting, as theoretically it is possible to detect genetic variations determined by as few as a single base pair alteration.…”

Section: Hosts and Diseasesmentioning

confidence: 99%

Xylella fastidiosa: Host Range and Advance in Molecular Identification Techniques

Baldi

Porta

2017

Front. Plant Sci.

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In the never ending struggle against plant pathogenic bacteria, a major goal is the early identification and classification of infecting microorganisms. Xylella fastidiosa, a Gram-negative bacterium belonging to the family Xanthmonadaceae, is no exception as this pathogen showed a broad range of vectors and host plants, many of which may carry the pathogen for a long time without showing any symptom. Till the last years, most of the diseases caused by X. fastidiosa have been reported from North and South America, but recently a widespread infection of olive quick decline syndrome caused by this fastidious pathogen appeared in Apulia (south-eastern Italy), and several cases of X. fastidiosa infection have been reported in other European Countries. At least five different subspecies of X. fastidiosa have been reported and classified: fastidiosa, multiplex, pauca, sandyi, and tashke. A sixth subspecies (morus) has been recently proposed. Therefore, it is vital to develop fast and reliable methods that allow the pathogen detection during the very early stages of infection, in order to prevent further spreading of this dangerous bacterium. To this purpose, the classical immunological methods such as ELISA and immunofluorescence are not always sensitive enough. However, PCR-based methods exploiting specific primers for the amplification of target regions of genomic DNA have been developed and are becoming a powerful tool for the detection and identification of many species of bacteria. The aim of this review is to illustrate the application of the most commonly used PCR approaches to X. fastidiosa study, ranging from classical PCR, to several PCR-based detection methods: random amplified polymorphic DNA (RAPD), quantitative real-time PCR (qRT-PCR), nested-PCR (N-PCR), immunocapture PCR (IC-PCR), short sequence repeats (SSRs, also called VNTR), single nucleotide polymorphisms (SNPs) and multilocus sequence typing (MLST). Amplification and sequence analysis of specific targets is also mentioned. The fast progresses achieved during the last years in the DNA-based classification of this pathogen are described and discussed and specific primers designed for the different methods are listed, in order to provide a concise and useful tool to all the researchers working in the field.

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Probe-based real-time PCR method for multilocus melt typing of Xylella fastidiosa strains

Cited by 6 publications

References 22 publications

Xylella fastidiosa: UN ANÁLISIS MOLECULAR DEL ESTADO DE LA ENFERMEDAD BACTERIANA A NIVEL INTERNACIONAL

Xylella fastidiosa: UN ANÁLISIS MOLECULAR DEL ESTADO DE LA ENFERMEDAD BACTERIANA A NIVEL INTERNACIONAL

Coffee bacterial diseases: a plethora of scientific opportunities

Xylella fastidiosa: Host Range and Advance in Molecular Identification Techniques

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