Approaching the micro-evolution of bacterial pathogens of plants using MLVA: invasive outbreaks vs endemic diseases

Abstract

The movement of goods around the world and broad borders have facilitated the diffusion of plant diseases through the movement of pathogens into a new area, and climate change has helped the emergence or re-emergence of new pathogens that negatively affect food production. In this thesis, we have dealt with three important pathogens Pseudomonas syringae pv. actinidiae, Xylella fastidiosa , as invasive outbreaks pathogens and Pseudomonas savastanoi an endemic pathogen. These pathogens have a very important impact on food production not only in Italy but also worldwide. In order to understand the genetic characteristics, various methods have been developed for analysing plant pathogenic bacteria, these methods are based on either restriction enzymes or DNA segments amplified by PCR. These methods have differed in their discriminative power, reproducibility, and ease of results interpretation. Hence, we have developed and applied MLVA (Multiple Loci Variable Number of Tandem Repeats Analysis) for genotyping the three pathogens. To develop a robust MLVA (Multiple Loci Variable Number of Tandem Repeats Analysis) scheme suitable for global and local studies of three main bacterial diseases (endemic and invasive) in Italy: Knot disease on olive, oleander, and ash which is caused by Pseudomonas savastanoi pathovars, as an endemic pathogen, then canker of kiwifruit which is caused by P. syringae pv. actinidiae (Psa), and the new emerge olive quick decline syndrome which is caused by Xylella fastidiosa subspecies pauca st53 as an invasive outbreak. Then, we used this approach to understand differences in populations of each pathogen, elucidate the diffusion and movements of these populations. The results obtained in these studies point out that MLVA represents a very promising first-line assay for large-scale routine genotyping prior to whole-genome sequencing of only the most relevant samples in case of outbreaks. In addition, its ability to differentiate the pathovars, biovars, and subspecies, `the method went beyond that when it was able to differentiate the sequence types of the same subspecies. MLVA assay has great potential as an easy and effective tool not only to recognize and schedule the presence of the above-mentioned types of bacterial species all over the world but above all to trace their movements on local and to international scale, in addition to its ability supporting the simple detection of contaminated materials with key information concerning specific haplotypes populations.