Nodules-associated Klebsiella oxytoca complex: genomic insights into plant growth promotion and health risk assessment

Abstract

The swift emergence of antibiotic resistance genes (ARGs) across interconnected One Health compartments poses a signifcant global threat. Although plant growth-promoting (PGP) bacteria possess numerous attributes benefcial to host plants, many of these bacteria also harbor ARGs, necessitating a focused assessment of their negative implica‑ tions. In this context, here we performed whole genome sequencing of 14 PGP endophytic strains isolated from root nodules of faba beans, belonging to three Klebsiella oxytoca species complex (KoSC): K. grimontii (n=5), K. michiganensis (n=5), and K. pasteurii (n=4). We performed comparative genomics, molecular typing, and pangenome analyses on these strains. We identifed signifcant diversity within the KoSC population, classifying the strains into fve sequence types (STs), three of which are novel to this study (ST-542, ST-569, and ST-629). Phylogenomic analysis revealed that the bacterial strains clustered more closely by ST than by their source of isolation. Annotation of gene clusters indi‑ cated that all assembled genomes are enriched with genes involved in PGP activities, alongside a robust array of genes conferring tolerance to abiotic stresses. Importantly, our fndings disclosed that the 14 assembled genomes harbored multiple ARGs, conferring resistance to various antibiotic classes, with 71% of the population classifed as multidrugresistant based on the in vitro antibiotic susceptibility assay. Furthermore, all genomes contained an array of virulence factors critical for survival, pathogenesis, bioflm formation, and root colonization. In conclusion, this study substantiates the hypothesis that certain PGP bacteria may serve as potential reservoirs of multidrug resistance, posing signifcant public health risks. Thus, the future advancement of bacteria-based biofertilizers should integrate environmental con‑ siderations and monitor their impact on antibiotic resistance dissemination in soil ecosystems.