Fig 1.
Phylogenomic analysis of 264 Burkholderia ubonensis genomes.
A midpoint-rooted maximum parsimony phylogeny was constructed using 589,433 biallelic core-genome SNPs. A) Strains lacking the B. pseudomallei multilocus sequence typing (MLST) gene narK are labelled with blue branches, and those lacking pC3 (previously known as chromosome III) are in bold italics. Highly related strains retrieved from single environmental samples are outlined by green boxes. Red branches indicate instances where isolates could be differentiated by the B. pseudomallei MLST scheme, but not the Bcc scheme. B) Heatmap of the meropenem minimum inhibitory concentration values for 40 tested B. ubonensis isolates. In both trees, the six distinct clades (I, II, III, IV, V and VI) are labelled. Consistency index = 0.25. Bootstrap values below 80% are labelled on their corresponding branches.
Fig 2.
Example Etest results in Burkholderia ubonensis towards meropenem.
Left, sensitive isolate MSMB2152 at a minimum inhibitory concentration (MIC) of 3 μg/mL; centre, intermediate isolate MSMB1183 at an MIC of 6 μg/mL; right, resistant isolate MSMB1162 at an MIC of ≥32 μg/mL.
Fig 3.
Heatmap of variably present Burkholderia ubonensis genes across the MSMB0022 genome.
A presence/absence matrix was constructed across 1kb windows of the MSMB0022 reference genome for each of the 264 taxa. Green = 100% mapped reads; red = 0% mapped reads. Taxa are in rows and the 1kb windows are in columns. Only regions containing <80% window coverage for at least one strain are shown, representing 2.78Mbp of the MSMB0022 B. ubonensis genome. The absence of pC3 in 4% of strains demonstrates that this megaplasmid can occasionally segregate, a finding consistent with pC3 in other Bcc species [15].