Multilocus sequence typing and whole genome single-nucleotide polymorphisms reveal phylogenetic diversity and population structure of Xanthomonas citri subsp. citri

AIMS: Xanthomonas citri subsp. citri (Xcc), the bacteria responsible for citrus canker, is widely distributed worldwide and causes severe losses to the citrus industry. Understanding the emergence and spread of Xcc requires reliable strain identification and tracking methods. This study aimed to develop a robust multilocus sequence typing (MLST) scheme for Xcc. METHODS AND RESULTS: 123 Xcc strains from diverse geographic origins were molecularly typed using seven conserved loci. Twenty-seven sequence types (STs) were identified, revealing a high level of genetic diversity within the population. eBURST clustering further grouped these STs into three major clonal complexes (CC1, CC2, and CC3). To evaluate the resolution of MLST, a whole-genome single-nucleotide polymorphism (wgSNP) analysis was also performed. Phylogenetic reconstruction of 49 representative strains resolved them into seven clades, largely consistent with the MLST results but offering superior accuracy and resolution. Geographical structuring was evident in the evolutionary patterns; however, strains from different host varieties shared identical types, and multiple types were observed among strains collected from the same variety, indicating weak host variety associations. CONCLUSIONS: The MLST scheme developed in this study provides a reliable framework for identifying and tracking Xcc strains, while wgSNP analysis offers enhanced resolution for fine-scale epidemiological studies. Together, these approaches highlight the geographic structuring of Xcc populations, thereby advancing understanding of the pathogen's evolutionary dynamics and spread.