Comparative genomic and phenotypic biosafety assessment of plant-associated Klebsiella pneumoniae species complex strains isolated from faba bean root nodules

Abstract

Plant-associated members of the Klebsiella pneumoniae species complex (KpSC) may harbor genomic traits of potential agricultural relevance while also carrying resistance- and virulence-associated determinants of biosafety concern. Here, whole-genome sequencing and comparative genomic analyses were used to characterize nine KpSC strains isolated from Vicia faba root nodules, comprising three Klebsiella quasipneumoniae and six Klebsiella variicola isolates. Genome-based taxonomic analysis identified four sequence types (ST-355, ST-3956, ST-4200, and ST-4574), with phylogenomic analysis indicating that genomic relatedness was more strongly associated with sequence type than isolation source. Comparative analyses revealed lineage-associated differences in resistance- and virulence-associated genomic profiles, while multidrug non-susceptibility was phenotypically observed in K. quasipneumoniae NGB-FR79 and K. variicola NGB-FR73 and NGB-FR75. The genomes also carried genes putatively associated with agriculturally relevant traits, including nitrogen fixation, phosphorus metabolism, iron acquisition, auxin-associated pathways, and adaptation to abiotic stresses. Phenotypic assays further evaluated tolerance to salt and elevated temperature. Collectively, these findings demonstrate that nodule-associated KpSC strains combine putative plant-beneficial genomic traits with resistance- and virulence-associated determinants, emphasizing the need for strain-level genomic and phenotypic biosafety assessment before consideration for agricultural applications.