Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis

The bacterium <i>Burkholderia ubonensis</i> is commonly co-isolated from environmental specimens harbouring the melioidosis pathogen, <i>Burkholderia pseudomallei. B. ubonensis</i> has been reported in northern Australia and Thailand but not North America, suggesting similar geographic distribution to <i>B. pseudomallei</i>. Unlike most other <i>Burkholderia cepacia</i> complex (Bcc) species, <i>B. ubonensis</i> is considered non-pathogenic, although its virulence potential has not been tested. Antibiotic resistance in <i>B. ubonensis, particularly towards drugs used to treat the most severe B. pseudomallei infections</i>, has also been poorly characterised. This study examined the population biology of <i>B. ubonensis</i>, and includes the first reported isolates from the Caribbean. Phylogenomic analysis of 264 <i>B. ubonensis</i> genomes identified distinct clades that corresponded with geographic origin, similar to <i>B. pseudomallei</i>. A small proportion (4%) of strains lacked the 920kb chromosome III replicon, with discordance of presence/absence amongst genetically highly related strains, demonstrating that the third chromosome of <i>B. ubonensis</i>, like other Bcc species, probably encodes for a nonessential pC3 megaplasmid. Multilocus sequence typing using the <i>B. pseudomallei</i> scheme revealed that one-third of strains lack the "housekeeping" <i>narK</i> locus. In comparison, all strains could be genotyped using the Bcc scheme. Several strains possessed high-level meropenem resistance (≥32 μg/mL), a concern due to potential transmission of this phenotype to <i>B. pseudomallei. In silico</i> analysis uncovered a high degree of heterogeneity among the lipopolysaccharide O-antigen cluster loci, with at least 35 different variants identified. Finally, we show that Asian <i>B. ubonensis</i> isolate RF23-BP41 is avirulent in the BALB/c mouse model via a subcutaneous route of infection. Our results provide several new insights into the biology of this understudied species.