Genetic diversity and population structure ofPseudomonas savastanoi, an endemic pathogen of the Mediterranean area, revealed up to strain level by the MLVA assay

Pseudomonas savastanoiis a bacterial species included in thePseudomonas syringaecomplex. It is further sub-typed in pathovars which are the causal agents of a group of diseases of woody plants, such as the knot disease on olive and oleander and the bacterial canker on ash. Given its long-established presence in the Mediterranean area, the pathogen causing the afore-mentioned diseases can be considered endemic. Here, an MLVA approach was developed to assess the genetic relationships among and within those pathovars, with a specific focus onP. savastanoipv.savastanoi. By analyzing the genome of theP.savastanoipv.savastanoistrain NCPPB 3335 (accession n degrees CP008742), 14 Tandem Repeat (TR) loci were identified and the corresponding primers were designed and used for the amplification of genomic DNAs from 84 strains belonging toPseudomonas savastanoipathovars. Data were analyzed using different approaches, such as hierarchical clustering, STRUCTURE, and k-means clustering with DAPC to evaluate the effectiveness of the assay in describing pathovars and population structure of the pathogen. Results reveal a very complex articulation of genetic relationships, as expected from a long-time evolving pathogen, while providing the possibility to discriminate the pathovars between each other. At intra-pathovar level, the MLVA assay clusters isolates mainly according to their hosts and geographic origin. This resulted particularly useful in the identification and tracking ofP. savastanoipopulations at local level.