Comparison of Different Methods of Molecular Detection of Erwinia amylovora in Plant Material

Fire blight, caused by <i>Erwinia amylovora</i>, is one of the most damaging bacterial diseases affecting apple production and the safety of wild <i>Malus sieversii</i> populations in Central Asia. Effective monitoring relies on accurate molecular diagnostics; however, comparative data on commonly used detection methods remain limited for the region. In this study, we evaluated the performance of three molecular assays-LAMP, real-time PCR, and targeted nanopore sequencing of a 16S rRNA gene fragment-using 124 plant samples exhibiting fire blight symptoms collected from 30 sites across Southern Kazakhstan and Kyrgyzstan. The results of LAMP, real-time PCR, and the amplification of 16S sequences were highly consistent with each other. Targeted 16S nanopore sequencing reliably identified <i>E. amylovora</i> in all PCR-positive samples, yielding high read counts and consistent species-level classification, although the analyzed 16S region provided limited resolution for intraspecies variation. Across sampling locations, abandoned orchards represented major reservoirs of infection compared to maintained orchards and wild populations. Our results confirm that all three approaches are robust tools for detecting <i>E. amylovora</i>. These findings support the importance of different molecular diagnostic methods to assist fire blight surveillance in the region.