A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics

Gétaz, Michael; Bühlmann, Andreas; Schneeberger, Pierre H. H.; Van Malderghem, Cinzia; Duffy, Brion; Maes, Martine; Pothier, Joël F.; Cottyn, Bart

doi:10.1111/ppa.12665

Publication type:	Article in scientific journal
Type of review:	Peer review (publication)
Title:	A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics
Authors:	Gétaz, Michael Bühlmann, Andreas Schneeberger, Pierre H. H. Van Malderghem, Cinzia Duffy, Brion Maes, Martine Pothier, Joël F. Cottyn, Bart
DOI:	10.1111/ppa.12665
Published in:	Plant Pathology
Volume(Issue):	66
Issue:	7
Page(s):	1094
Pages to:	1102
Issue Date:	Sep-2017
Publisher / Ed. Institution:	Wiley
ISSN:	0032-0862 1365-3059
Language:	English
Subjects:	Detection; In-field; LAMP; Strawberry
Subject (DDC):	570: Biology
Abstract:	Molecular diagnostics of plant pathogens are crucial to prevent disease spread and to enhance food quality and security. A comparative genomics approach using genomes of different Xanthomonas species and pathovars was applied to identify highly specific targets in the genome of Xanthomonas fragariae, the causal agent of angular leaf spot of strawberry, listed under quarantine regulations in Europe. A reliable and sensitive loop-mediated isothermal amplification (LAMP) assay was designed using a unique marker providing a highly specific and rapid detection, making this technique convenient for on-site detection. Specificity of the designed assay was tested on 37 culture collection strains of X. fragariae, 82 strains of other Xanthomonas species and pathovars and 11 strains of other bacterial genera isolated from strawberry leaves. A detection limit of 10^2 fg was achieved, approximating 20 genome copies per reaction. When performing analyses with crude plant material, a consistent lower detection efficiency of 10^2 CFU ml−1 was achieved. The LAMP assay designed in this study was adapted to work on crude plant material without any prior extensive extraction steps or incubation period. Moreover, it does not require advanced analytical knowledge or a fully equipped laboratory. Results were produced within 7 to 20 min depending on the pathogen concentration, thus providing a high throughput and user-friendly method for detection and screening of plant material in support of quarantine regulations.
URI:	https://digitalcollection.zhaw.ch/handle/11475/1642
Fulltext version:	Published version
License (according to publishing contract):	Licence according to publishing contract
Departement:	Life Sciences and Facility Management
Organisational Unit:	Institute of Natural Resource Sciences (IUNR)
Published as part of the ZHAW project:	DROPSA: Strategies to develop effective, innovative and practical approaches to protect major European fruit crops from pests and pathogens
Appears in collections:	Publikationen Life Sciences und Facility Management

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Gétaz, M., Bühlmann, A., Schneeberger, P. H. H., Van Malderghem, C., Duffy, B., Maes, M., Pothier, J. F., & Cottyn, B. (2017). A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics. Plant Pathology, 66(7), 1094–1102. https://doi.org/10.1111/ppa.12665

Gétaz, M. et al. (2017) ‘A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics’, Plant Pathology, 66(7), pp. 1094–1102. Available at: https://doi.org/10.1111/ppa.12665.

M. Gétaz et al., “A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics,” Plant Pathology, vol. 66, no. 7, pp. 1094–1102, Sep. 2017, doi: 10.1111/ppa.12665.

GÉTAZ, Michael, Andreas BÜHLMANN, Pierre H. H. SCHNEEBERGER, Cinzia VAN MALDERGHEM, Brion DUFFY, Martine MAES, Joël F. POTHIER und Bart COTTYN, 2017. A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics. Plant Pathology. September 2017. Bd. 66, Nr. 7, S. 1094–1102. DOI 10.1111/ppa.12665

Gétaz, Michael, Andreas Bühlmann, Pierre H. H. Schneeberger, Cinzia Van Malderghem, Brion Duffy, Martine Maes, Joël F. Pothier, and Bart Cottyn. 2017. “A Diagnostic Tool for Improved Detection of Xanthomonas Fragariae Using a Rapid and Highly Specific LAMP Assay Designed with Comparative Genomics.” Plant Pathology 66 (7): 1094–1102. https://doi.org/10.1111/ppa.12665.

Gétaz, Michael, et al. “A Diagnostic Tool for Improved Detection of Xanthomonas Fragariae Using a Rapid and Highly Specific LAMP Assay Designed with Comparative Genomics.” Plant Pathology, vol. 66, no. 7, Sept. 2017, pp. 1094–102, https://doi.org/10.1111/ppa.12665.