Fire blight, caused by Erwinia amylovora, is a critical quarantine disease that emerged in China over the past decade. To characterize the population structure, genetic diversity, and virulence differentiation of E.amylovora, we performed CRISPR-based genotyping on 270 isolates collected from Xinjiang and Gansu between 2016 and 2025, China. All isolates contained three CRISPR loci (CR1, CR2, and CR4), revealing 15 distinct genotypes. Notably, 14 genotypes were identified in China for the first time, all differing from the North American reference strain Ea055 (A, a, α). The identified genotypes clustered into eight distinct lineages, with Lineage I comprising the dominant A-type (A, t, α) and three related genotypes, representing 86.7% of the total isolates. The dominant Central Asian genotype (A, t, α) represented 84.1% of isolates and remains the primary invasive lineage. However, significant regional differentiation was observed: Lineages III and V were unique to Zhangye, Gansu (2023–2025), where genotype (ie, t, α) became regionally dominant (63.3%). Furthermore, our data suggest that genotypes A and D, originating from Central Asian populations, were independently introduced into the Ili and Aksu regions of Xinjiang, China, respectively. Pathogenicity assays on detached pear leaves (Pyrus sinkiangensis) showed 61.5% of strains were highly/strongly virulent; no direct correlation was observed between CRISPR genotypes and virulence levels. These findings reveal that since its introduction, E. amylovora has undergone localized adaptation, and population differentiation has occurred at the CRISPR genotype level, resulting in a complex genetic landscape. This decadal analysis provides a critical scientific foundation for tracing fire blight spread and management strategies.
Du et al. (2026) studied this question.