A MLVA Genotyping Scheme for Global Surveillance of the Citrus Pathogen Xanthomonas Citri Pv. Citri Suggests a Worldwide Geographical Expansion of a Single Genetic Lineage

PLoS One. 2014 Jun 4;9(6):e98129. doi: 10.1371/journal.pone.0098129. eCollection 2014.


MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epidemics on a global scale. Xanthomonas citri pv. citri is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of Xanthomonas citri pv. citri strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these in silico data, an optimized MLVA scheme was developed to assess the global diversity of this monomorphic bacterium. Thirty-one minisatellite loci (MLVA-31) were selected to assess the genetic structure of 129 strains representative of the worldwide pathological and genetic diversity of X. citri pv. citri. Based on Discriminant Analysis of Principal Components (DAPC), four pathotype-specific clusters were defined. DAPC cluster 1 comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31. MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the Xanthomonas citri genotyping database (http://www.biopred.net/MLVA/).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Typing Techniques
  • Citrus / microbiology*
  • Genes, Bacterial*
  • Genetic Variation*
  • Genome, Bacterial
  • Genotype
  • Plant Diseases / microbiology*
  • Sequence Analysis, DNA
  • Tandem Repeat Sequences
  • Xanthomonas / genetics*

Grant support

We thank C. Boyer, P. Grygiel, J. Hoareau, C. Juhasz, I. Robène and A. Dereeper for their contributions. The European Union (ERDF; http://europa.eu/legislation_summaries/agriculture/general_framework/g24234_en.htm), Conseil Régional de La Réunion (http://www.regionreunion.com/fr/spip/), the French Agence Nationale de la Recherche (ANR-2010-BLAN-1723; http://www.agence-nationale-recherche.fr/suivi-bilan/recherches-exploratoires-et-emergentes/blanc-generalite-et-contacts/blanc-presentation-synthetique-du-projet/?tx_lwmsuivibilan_pi2%5BCODE%5D=ANR-10-BLAN-1723), the French Direction Générale de l'Armement (contract n° 2010 34 006; http://www.defense.gouv.fr/dga), and CIRAD (http://www.cirad.fr) provided financial support. AL acknowledges support from the French Direction Générale de l'Armement (contract n° 2011 60 080) and CIRAD. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.