Structural and phenotypical diversities of Erwinia amylovora populations in Washington

The fire blight pathogen Erwinia amylovora is genetically homogeneous but exhibits substantial variations in virulence, motility, and amylovoran production. A possible explanation for these functional diversities could be due to large chromosomal inversions (LCIs), structural rearrangements associated with ribosomal RNA (rrn) operons. This study investigated the distribution of LCI types in E. amylovora populations from Washington state (WA) and their associated phenotypic diversities. A total of 191 isolates collected from WA between 2022 and 2024 were analyzed using PCR-based molecular markers targeting rrn operons. These isolates were classified into four most prevalent LCI types: Ea1189, CFBP1430, Ea273, and Ea401. Temporal analysis revealed diversity of LCI occurrence in different years, with up to four LCI types co-occurring within a single orchard in 2024. Phenotypic assays demonstrated significant differences among the isolates of the LCI types in amylovoran production and virulence. Differences in motility and disease severity development further emphasized the diversity among isolates even within each LCI type. Overall, our findings showed the primary population structure of E. amylovora in WA and highlighted measurable functional variations within the E. amylovora population. This study also demonstrated that multiple LCI types could coexist in a single orchard, highlighting that chromosomal structural variations could shape E. amylovora population diversity, adaptation, and pathogenic potential, which might help understand fire blight epidemiology and pathogen evolution.