A MLVA Genotyping Scheme for Global Surveillance of the Citrus Pathogen <i>Xanthomonas citri</i> pv. <i>citri</i> Suggests a Worldwide Geographical Expansion of a Single Genetic Lineage

<div><p>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. <i>Xanthomonas citri</i> pv. <i>citri</i> is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of <i>Xanthomonas citri</i> pv. <i>citri</i> strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these <i>in silico</i> 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 <i>X. citri</i> pv. <i>citri</i>. 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 <i>X. citri</i> pv. <i>citri</i> during the 20^th 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 <i>X. citri</i> pv. <i>citri</i>, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international <i>X. citri</i> pv. <i>citri</i> genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the <i>Xanthomonas citri</i> genotyping database (<a href="http://www.biopred.net/MLVA/" target="_blank">http://www.biopred.net/MLVA/</a>).</p>