Xylella fastidiosa genetic and phenotypic diversity exists at different taxonomic levels. This genus has only one species, although it has been known for over a decade that a divergent genotype infecting pears in Taiwan is highly divergent and will, eventually, be assigned its own species. Within the species fastidiosa, multi-locus sequence typing (MLST) is currently used as the method of choice to study within species diversity. MLST has two advantages, first it is robust in the presence of homologous recombination, which is important as X. fastidiosa is naturally competent. Second, virtually all currently known diversity of this bacterium is represented and archived in a publicly available database. MLST has really helped solve significant problems that prohibited a reasonably good understanding of X. fastidiosa genetic diversity, however it is now being replaced by genomic sequences.
There are today five broadly accepted X. fastidiosa subspecies, although this is and will continue to be a point of academic discussion. One of them, sandyi, is probably going to be folded into the larger subspecies fastidiosa (three papers in 2016 suggest that- 1 2 3). Subspecies morus is so far an interesting case, as it seems to have originated from massive recombination events between isolates in fastidiosa and multiplex; it needs to be better studied. The other three groups are, today, taxonomically robust: fastidiosa, pauca, and multiplex.
We expect that X. fastidiosa taxonomy at the subspecies level will change in the near future, as additional genetic diversity reported during the last couple of years, primarily from Central and South America, suggests that will occur. These new data will be very important in improving our understanding of X. fastidiosa evolution. In addition, it is possible that genomic sequences will help resolve some problems (more data per genotype will probably be better), but so far genomic data has largely supported the MLST-based conclusions.