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Applied and Environmental Microbiology, February 2009, p. 1173-1184, Vol. 75, No. 4
0099-2240/09/$08.00+0 doi:10.1128/AEM.02245-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
From Local Surveys to Global Surveillance: Three High-Throughput Genotyping Methods for Epidemiological Monitoring of Xanthomonas citri pv. citri Pathotypes 
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Lan Bui Thi Ngoc,1
Christian Vernière,1
Philippe Jarne,2
Sylvain Brisse,3
Fabien Guérin,1
Sébastien Boutry,1
Lionel Gagnevin,1 and
Olivier Pruvost1*
CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 7 chemin de l'Irat, 97410 Saint Pierre, La Réunion, France,1 Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, campus CNRS, 1919 route de Mende, 34293 Montpellier Cedex 5, France,2 Unité Biodiversité des Bactéries Pathogènes Emergentes, Institut Pasteur, 25-28 rue du Dr Roux, 75724 Paris Cedex 15, France3
Received 30 September 2008/ Accepted 10 December 2008
Asiatic citrus canker is a major disease worldwide, and its causal agent, Xanthomonas citri pv. citri, is listed as a quarantine organism in many countries. Analysis of the molecular epidemiology of this bacterium is hindered by a lack of molecular typing techniques suitable for surveillance and outbreak investigation. We report a comparative evaluation of three typing techniques, amplified fragment length polymorphism (AFLP) analysis, insertion sequence ligation-mediated PCR (IS-LM-PCR) typing, and multilocus variable-number tandem-repeat analysis (MLVA), with 234 strains originating from Asia, the likely center of origin of the pathogen, and reference strains of pathotypes A, A*, and Aw, which differ in host range. The typing techniques were congruent in describing the diversity of this strain collection, suggesting that the evolution pattern of the bacterium may be clonal. Based on a hierarchical analysis of molecular variance, the AFLP method best described the genetic variation found among pathotypes whereas MLVA best described the variation found among individual strains from the same countries or groups of neighboring countries. IS-LM-PCR data suggested that the transposition of insertion sequences in the genome of X. citri pv. citri occurs rarely enough not to disturb the phylogenetic signal. This technique may be useful for the global surveillance of non-epidemiologically related strains. Although pathological characteristics of strains could be most often predicted from genotyping data, we report the occurrence in the Indian peninsula of strains genetically related to pathotype A* strains but with a host range similar to that of pathotype A, which makes the classification of this bacterium even more complicated.
* Corresponding author. Mailing address: CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 7 chemin de l'Irat, 97410 Saint Pierre, La Réunion, France. Phone: 262 262 49 92 20. Fax: 262 262 49 92 93. E-mail: olivier.pruvost{at}cirad.fr
Published ahead of print on 16 December 2008.
Supplemental material for this article may be found at http://aem.asm.org/.
Applied and Environmental Microbiology, February 2009, p. 1173-1184, Vol. 75, No. 4
0099-2240/09/$08.00+0 doi:10.1128/AEM.02245-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
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