Genomic characterization of an environmental Burkholderia thailandensis strain from Kerala, India reveals virulence and antimicrobial resistance signatures

Background: Burkholderia thailandensis is an environmental Gram-negative bacterium closely related to the highly pathogenic B. pseudomallei, the causative agent of melioidosis. Although B. thailandensis is generally considered avirulent, sporadic human infections and genomic features suggest potential for pathogenic adaptation. We report the whole-genome sequencing and comparative analysis of a B. thailandensis strain (BUR-TH_250524) isolated from soil in Kerala, India, to assess its taxonomic identity, genetic composition, and potential for antimicrobial resistance and virulence. Genomic DNA was extracted from a biochemically identified isolate, which was subsequently confirmed as B. thailandensis through 16S rRNA gene sequencing. Whole-genome sequencing was performed using Illumina paired-end technology. The genome was assembled de novo and functionally annotated using Bakta, KEGG, GO, CARD, and VFDB databases. Comparative analyses included ANI, variant calling, prophage prediction, and mobile genetic element profiling. Results: The Ragout-scaffolded draft genome (6.93 Mb) exhibited a genome fraction of 94.67%, with 280,948 undetermined bases (N’s) corresponding to unresolved gaps, that represent ~ 4.05% of the total assembly, reflecting a high overall completeness. The assembled genome comprises two chromosomes with high completeness (95.1%, BUSCO). Annotation revealed 5,647 coding sequences, including 225 virulence-related genes and 8 high-confidence antimicrobial resistance genes. Seven prophage regions and 215 mobileOG elements were identified, highlighting genomic plasticity. ANI values (≥ 99.6%) and phylogenetic analysis confirmed close relatedness to reference B. thailandensis strains, yet the isolate shared features with B. pseudomallei and B. mallei. Conclusion: This study provides the first genomic insights into an Indian B. thailandensis environmental isolate. The detection of virulence and resistance-associated determinants underscores the importance of genomic surveillance of environmental Burkholderia populations and warrants genomic surveillance and awareness of the potential for misidentification with B. pseudomallei in regions where melioidosis is endemic.