Whole-genome sequencing of Burkholderia glumae strains from Thailand reveals potential horizontal gene transfer with Burkholderia pseudomallei

Abstract

Burkholderia glumae is an emerging phytopathogen that causes bacterial panicle blight in rice and has been implicated in rare human infections. In Thailand, B. glumae and the human pathogen Burkholderia pseudomallei coexist in rice fields. Given the high genomic plasticity of Burkholderia species, including frequent genome rearrangements, variability in mobile genetic elements, and recombination events that facilitate horizontal gene transfer, there are concerns about the emergence of novel traits that may affect both plant and human health. In this study, we performed whole-genome sequencing and a comparative genomic analysis of 16 B. glumae strains isolated from rice fields across seven Thai provinces. Our phylogenomic analysis, based on core-genome single-nucleotide polymorphisms, revealed high genetic diversity and a polyclonal population structure, with evidence of a globally distributed clonal lineage. All isolates harbored plasmids and diverse prophage elements, which indicated extensive mobilome variability. A total of 572 putative horizontally transferred genes were identified. Most of these genes originated from unclassified or plant-associated Burkholderia species. Notably, two strains shared a chromosomal island that carried genes that were very similar to those found in B. pseudomallei. This genomic region contained genes associated with mobile genetic elements, phage defense, and a type VI secretion system, including genes that encode a PAAR domain-containing protein, a putative nuclease, and an immunity protein. Our findings highlight the genomic heterogeneity of B. glumae in Thailand and provide evidence of interspecies horizontal gene acquisition from human pathogenic B. pseudomallei. The presence of B. pseudomallei-derived genes in B. glumae chromosomes underscores the potential for genetic exchange in shared environmental niches, which could affect the evolutionary dynamics and pathogenicity of B. glumae. Hence, our findings also emphasize the critical need for environmental surveillance and genome-based monitoring to track emerging genomic combinations relevant to both plant and human health.