A new multi-level genome typing scheme for X.citri
Xanthomonas citri is a phytopathogenic bacterium associated with diverse plant hosts and causes a wide range of economically significant plant diseases. Historically, its identification was based upon host plant association and disease symptoms. Additionally, numerous typing and classification systems such as pathovar, phylogroup, pathotype and race have been used to classify X. citri subgroups. DNA-based methods, such as genomics, can not only identify X. citri subgroups but also provide highly discriminative typing useful for epidemiology and disease control. Here, we developed a unified Multilevel Genome Typing (MGT) scheme for classifying X. citri at population and outbreak levels with a focus on pv. malvacearum. MGT builds upon classical multilocus sequence typing (MLST) and incorporates multiple levels with increasing numbers of loci for improved identification and monitoring of pathogens at different levels. Our X. citri MGT consists of eight levels, from the lowest level (MGT1) that builds on 7 loci equivalent to classical MLST to MGT7 consisting of 2,027 loci representing X. citri core genes, and the highest level, MGT8 consisting of all genes and intergenic regions of the pv. malvacearum core genome (3,977 loci). We constructed the X. citri MGT scheme using 415 genomes, with lower levels, MGT2 and MGT3, associated with genetic lineages, pathotypes and races of pvs fuscans, citri and malvacearum that were isolated from different regions. Higher levels (MGT4-8) require increasing numbers of loci and discrimination of related X. citri clusters as scheme level increases, with the highest level, MGT8, allowing for tracing of highly similar isolates consistent with an outbreak cluster. The X. citri MGT scheme provides a unified genomic epidemiology system that can be used for rapid pathovar identification and can simultaneously provide analysis of broad disease trends at the population and outbreak levels.