Whole-genome characterization and analysis of Pantoea agglomerans R6: a genomic insight into its pathogenicity and resistance as a potential opportunistic plant pathogen

Abstract

Pantoea agglomerans is a Gram-negative bacterium increasingly recognised as an opportunistic pathogen, yet the molecular basis underpinning its host-interaction capacity remains poorly understood. Here, we report the whole-genome sequencing and integrative characterisation of P. agglomerans strain R6, isolated from Lactuca serriola. The 4.7 Mb draft genome (GC content 55.6%) encodes 4,349 genes, including secretion system components, siderophore clusters, adhesins, and multidrug efflux pumps. Comparative genomic analysis against previously characterised Pantoea strains revealed an open pan-genome shaped by horizontal gene transfer, with multiple genomic islands harbouring putative virulence- and resistance-associated loci. Notably, homologues of type VI secretion system components, iron acquisition systems, and stress response pathways suggest adaptive potential during host colonisation. Complementary phenotypic assays supported these genomic predictions, demonstrating swarming motility, biofilm formation, extracellular polysaccharide production, and enzymatic activities associated with host interaction in related strains. While R6 displayed susceptibility to β-lactams, its genomic repertoire indicates potential for adaptive resilience under selective pressure. This integrative genomic and phenotypic characterisation identifies candidate molecular features associated with opportunistic behaviour and highlights the genomic potential of R6, rather than experimentally validated causal determinants of pathogenicity.