Screening and genomic identification of the bacterial pathogens from an apple orchard in Kazakhstan

Apple production in Kazakhstan faces increasing threats from bacterial pathogens, including Erwinia amylovora, the causal agent of fire blight, and members of the Pseudomonas syringae species complex. These diseases not only cause substantial economic losses but also endanger the endemic wild apple Malus sieversii. In this study, apple leaves displaying symptoms of a bacterial infection were collected near Almaty and analyzed using molecular and genomic approaches. The preliminary low coverage genome sequencing and targeted 16S amplicon sequencing indicated the presence of E. amylovora and Pseudomonas spp. Subsequently, whole-genome sequencing (WGS) was performed on two Erwinia amylovora isolates and three Pseudomonas spp. isolates for definitive identification and phylogenetic placemenet. Two isolates were confirmed as E. amylovora, closely related to widely prevalent (WP) group, while three isolates belonged to P. syringae species group and included P. fragariae, P. syringae, and P. tremae. The presence of P. tremae and P. fragariae was reported for the first time in Kazakhstan. The results highlight the challenges of differentiating phenotypically similar phytopathogens and the need for the correct choice of diagnostic approach. Immunological tests and species-specific polymerase chain reaction (PCR) allow reliable detection and discrimination of E. amylovora, whereas genomic methods are particularly important for accurate taxonomic resolution of closely related isolates and for assessing the genetic variability of local populations. These data expand the genomic resources on plant pathogens in Central Asia and provide a foundation for management strategies by enabling more accurate pathogen identification and confirming the composition of regional Pseudomonas populations, thereby improving the interpretation of monitoring results and the selection of appropriate control measures.