Comparative Genomic Insights into Antibiotic Resistance and Virulence in Some Indigenously Isolated Plant Growth Promoting Rhizobacteria
Authors: Ajibade O.A, Akintoyese O.T, Akinmolayan T.A, Chijioke U.O, Ukaegbu C. J and Oyawoye O.MThe rapid advancement of whole-genome sequencing has revolutionized microbiology, enabling detailed comparative analyses that uncover the genetic underpinnings of bacterial evolution, adaptation, and pathogenicity. This study presents a comparative genomic analysis of three distinct bacteria: Enterobacter sichuanensis strain AJI2411, a plant-associated rhizobacterium; Burkholderia vietnamiensis AU2011, a nitrogen-fixing species; and Burkholderia contaminans OYA0603, a member of the opportunistic Burkholderia cepacia complex. Phylogenetic relationships were inferred from 16S rRNA gene sequences extracted using barrnap (v0.9) and aligned with MAFFT (v7.490), with Maximum Likelihood tree reconstruction performed in IQ-TREE 2 under the GTR+G substitution model selected via ModelFinder and supported by 1,000 ultrafast bootstrap replicates (UFBoot).Our findings highlight the distinct evolutionary trajectories and functional capacities shaped by niche adaptation. The two Burkholderia species formed a strongly supported sister clade (bootstrap = 98). Analysis reveals the presence of sophisticated regulatory systems, such as quorum sensing in B. vietnamiensis, and the production of toxic secondary metabolites in B. contaminans. Furthermore, evidence of antibiotic resistance mechanisms, including efflux pumps in B. vietnamiensis and putative β-lactamases in B. contaminans, underscores the clinical relevance of these species. This report synthesizes existing genomic information to provide a comprehensive comparison, contributing to a deeper understanding of the genetic diversity and functional potential within these important bacterial genera. The study underscores the power of in-silico analysis for predicting bacterial phenotypes and informing both agricultural and clinical strategies.

