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Although plant growth-promoting (PGP) bacteria possess numerous attributes beneficial to host plants, many of these bacteria also harbor ARGs, necessitating a focused assessment of their negative implications. In this context, here we performed whole genome sequencing of 14 PGP endophytic strains isolated from root nodules of faba beans, belonging to three <jats:italic>Klebsiella oxytoca<\/jats:italic> species complex (KoSC): <jats:italic>K. grimontii<\/jats:italic> (<jats:italic>n<\/jats:italic>\u2009=\u20095), <jats:italic>K. michiganensis<\/jats:italic> (<jats:italic>n<\/jats:italic>\u2009=\u20095), and <jats:italic>K. pasteurii<\/jats:italic> (<jats:italic>n<\/jats:italic>\u2009=\u20094). We performed comparative genomics, molecular typing, and pangenome analyses on these strains. We identified significant diversity within the KoSC population, classifying the strains into five 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 indicated 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 findings disclosed that the 14 assembled genomes harbored multiple ARGs, conferring resistance to various antibiotic classes, with 71% of the population classified as multidrug-resistant based on the in vitro antibiotic susceptibility assay. Furthermore, all genomes contained an array of virulence factors critical for survival, pathogenesis, biofilm formation, and root colonization. In conclusion, this study substantiates the hypothesis that certain PGP bacteria may serve as potential reservoirs of multidrug resistance, posing significant public health risks. Thus, the future advancement of bacteria-based biofertilizers should integrate environmental considerations and monitor their impact on antibiotic resistance dissemination in soil ecosystems.<\/jats:p>","DOI":"10.1186\/s12866-025-04002-7","type":"journal-article","created":{"date-parts":[[2025,5,15]],"date-time":"2025-05-15T05:37:41Z","timestamp":1747287461000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Nodules-associated Klebsiella oxytoca complex: genomic insights into plant growth promotion and health risk assessment"],"prefix":"10.1186","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8309-4764","authenticated-orcid":false,"given":"Sameh H.","family":"Youseif","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fayrouz H. 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