Comparative genomics and pathogenicity of Pantoea stewartii subsp. stewartii reveal multiple introductions and limited distribution in Europe

Pantoea stewartii subsp. stewartii (Pss), the causal agent of Stewart’s wilt in maize, is native to North America but has been detected on several occasions also in Europe, including in Italy in association with seed maize production. These findings have raised concern due to the bacterium’s quarantine status in the EU. To investigate its diversity and possible introduction routes, we performed whole-genome sequencing of Slovenian and other Pss isolates and compared them with publicly available genomes. Comparative genomics revealed that Pss forms a distinct clade within P. stewartii, exhibiting high average nucleotide identity (>99.9%). Most of the Slovenian isolates clustered closely together, forming a separate branch consistent with at least two independent introduction events. They were genetically distinct from recent Italian isolates. Additionally, several unique plasmids and prophages were identified in Pss isolates, with notable diversity in mobile genetic elements despite overall genomic homogeneity. Pangenome analysis confirmed an open pangenome for P. stewartii, with greater genomic diversity among non-Pss strains. Functional analysis identified multiple secretion systems in Pss, which are likely to contribute to its pathogenicity and insect-mediated transmission. Our findings highlight previously unrecognised diversity within the subspecies and confirm the presence of at least two distinct clades within P. stewartii. So far, the detections in Slovenia remain confined to the Vipava Valley with evidence of multiple introduction events. Together, these findings cannot definitely conclude whether Pss is already established in Slovenia. This suggests that eradication remains achievable through continued surveillance and preventive phytosanitary measures.