Genetic characterization of Erwinia amylovora isolates detected in the wild walnut-fruit forest of South Kyrgyzstan

Erwinia amylovora, the causal agent of fire blight, was first reported in Kyrgyz orchards in 2008 and, within a few years, the disease has spread throughout most of the northern part of the country. As fire blight expanded and penetrated new areas, it also reached the unique ecosystem constituted by the Arslonbob wild walnut-fruit forests in South Kyrgyzstan. Here, we present the results of field surveys in the forests and in the nearby orchards and gardens of the Jalal-Abad region during the 2019 season. Further, we use genetic profiling of the CRISPR regions to compare the genotypes of the obtained isolates to those of previous outbreaks in the north of the country and in nearby Kazakhstan. While fire blight was found in twelve of the twenty-six sites investigated in and around the Arslonbob walnut-fruit forest, it was mostly located on domesticated varieties of quince, apple or pear in gardens, orchards or nurseries. Plants in the forest and especially endangered wild species were not affected by the disease, but their proximity to the current infection herds is cause of major concern and calls for immediate protective action. Genetic analysis suggests that the main introduction route for fire blight to Central Asia was import of contaminated plant material from already affected countries in the Eurasian continent, which probably occurred on multiple independent instances. Nonetheless, indications of natural spread of the disease were identified between the regions of South Kazakhstan and North Kyrgyzstan.