Epidemiological description of fire blight introduction patterns to Central Asia and the Caucasus region based on CRISPR spacer typing and genome analysis

In the last two decades, fire blight has progressively spread eastward from Europe and the Mediterranean area to several pome-fruit producing regions of Asia. Its causative agent, the bacterial pathogen <i>Erwinia amylovora</i>, was detected in several new countries, including Georgia, Kyrgyzstan, and Kazakhstan. In the latter two states, the disease creates a threat not only to the commercial apple and pear production, but also to the wild <i>Malus</i> and <i>Pyrus</i> species that constitute the basis of the local forest ecosystems. In this study, we investigated the genetic diversity of the pathogen in Central Asia and the Caucasus region utilizing CRISPR Repeat Regions (CRRs) genotyping and genome sequencing, with the aim to understand its dissemination patterns across the continent. Genome sequence analysis revealed that all strains from these two regions exclusively derived from the archetypal CRR1 genotype A. Our analysis revealed three main <i>E. amylovora</i> clades in Central Asia, with distinct yet partial overlapping geographical distributions. Genomic relationships among isolates indicate that Central Asian strains are genetically closest to those from the Persian region and the Middle East, while the Georgian population is genetically more distant and can align with strains from the Volga District in southern Russia and the Eastern Mediterranean area. Notably, this study also includes strains from the first confirmed occurrences of fire blight in Uzbekistan, Tajikistan, and China. Our findings highlight the importance of phylogenetic analysis and genome sequencing in understanding the phytopathogen epidemics and protecting key agricultural species and the genetic resources of their wild counterparts in the forest.