A distinct Erwinia amylovora lineage in Kazakhstan associated with a pEA29 transposase mutation

Fire blight, caused by Erwinia amylovora, continues to spread across apple-producing regions worldwide. Genomic analyses have revealed that most global isolates belong to the “Widely Prevalent” (WP) lineage, which underwent a bottleneck during its dissemination from North America to Eurasia. Within this lineage, a distinct cluster of strains from Kazakhstan, designated the Za clade, was identified previously. In this study, we report that all Za strains share a single-base deletion in the conserved plasmid pEA29 gene EAMY_3738, encoding a putative ISNCY family transposase. The deletion causes a frameshift and truncation of the protein, predicted to abolish its function. The Za strains also display a distinctive CRISPR genotype, further supporting their peculiar evolutionary status. PCR testing of a set of isolates from 2023 to 2024 showed that the Za lineage is still present as a minor population in the region. This lineage may thus represent a distinct evolutionary variant.