Isolation and genetic characterization of Erwinia amylovora bacteria from Kyrgyzstan

Fire Blight, an economically relevant disease of apple, pear, and quince trees that is caused by the Gram-negative bacterium Erwinia amylovora, was first reported from Kyrgyzstan in 2008. One decade later, the disease has spread across the northern part of the country, affecting fruit orchards mainly in Chuy and Issyk-kul regions. Using semi-selective cultural media, bacteria have been isolated from plant material sampled in infested orchards from different locations in Kyrgyzstan, and 16S rRNA gene sequence determination together with diagnostic PCR have been used to identify E. amylovora bacteria among isolates. The assignment to this taxonomic species has been corroborated by phylogenetic reconstruction using multilocus sequence analysis, and a short-sequence repeat (SSR) marker has been employed to estimate genetic diversity across the isolates. CRISPR analysis has revealed both a previously unreported CRISPR-2 array pattern and a close relationship of Kyrgyz E. amylovora isolates to strains present in Europe and the Middle East. This study presents the first consistent molecular taxonomic characterization of E. amylovora bacteria from Kyrgyzstan.