Résumé
Asiatic Citrus Canker disease is induced by #Xanthomonas citri# pv. #citri# (Xcc) and threatens most of Citrus species and cultivars in many citrus-producing countries. Two pathogenic variants with different host range were described within Xcc. The pathotype Xcc-A infects a wide range of citrus and some related genera, has a worldwide distribution and is a permanent threat for citriculture. In contrast, Xcc-A* is naturally restricted to two Citrus species, limes (C. aurantifolia) and alemow (C. macrophylla) in limited areas. A rapid and reliable test using molecular methods is useful for accurate identification at pathotype level of this bacterium, classified as quarantine organism. Several PCR-based diagnostic tools have been developed for the identification of Xcc. In a preliminary study, we showed a lack of specificity for most of them when assayed on a large collection of Xcc strains and non-target strains. The aim of this study was to propose a new diagnostic tool for detection and identification of pathotypes of X. citri pv. citri. A multiplex quantitative real-time PCR assay (qPCR) was developed using hydrolysis probes targeting two markers of the bacterium. PCR primers targeting genes involved in pathogenicity and/or plant interactions were designed from the complete sequence of the Xcc-pathotype A strain IAPAR 306. Their specificity was assayed on a collection of Xcc-A strains (n=21), Xcc-A* (n=14) and other genetically related Xanthomonas (n=23) (1). A specific Xcc sequence encoding a conserved hypothetical protein related to chemotaxism and a specific Xcc-A sequence in a housekeeping gene were retained for the qPCR assay. The specificity of the qPCR assay was verified on the same strains collection of Xcc strains and non-target Xanthomonas. The qPCR assay detected all the Xcc strains and identified the pathotypes from cultures and citrus plant samples artificially infected with the bacterium: a sample is tested positive for the presence of A strains if both markers are amplified. No amplification or amplification of the housekeeping gene marker alone led to a negative result for Xcc. Amplification of the Xcc-specific marker alone is the signature for A* strains. Standard curves with high correlation coefficients (R2>0,99) were obtained from 10-fold bacterial suspensions dilutions. The qPCR assay allowed the detection of 107 to 103 CFU per ml of bacterial suspension or per g of lime leaves (Citrus aurantifolia) with calculated amplification efficiencies around 90% and 80% respectively. This qPCR assay is a powerful tool that allows distinguishing pathotypes with different economic incidence. It would be useful for indexing propagation material in nurseries and for surveillance of international movement of Xanthomonas citri pv. Citri. (Résumé d'auteur)