Within-Host Evolution of Burkholderia pseudomallei over a Twelve-Year Chronic Carriage Infection

Abstract

Burkholderia pseudomallei causes the potentially fatal disease melioidosis. It is generally accepted that B. pseudomallei is a noncommensal bacterium and that any culture-positive clinical specimen denotes disease requiring treatment. Over a 23-year study of melioidosis cases in Darwin, Australia, just one patient from 707 survivors has developed persistent asymptomatic B. pseudomallei carriage. To better understand the mechanisms behind this unique scenario, we performed whole-genome analysis of two strains isolated 139 months apart. During this period, B. pseudomallei underwent several adaptive changes. Of 23 point mutations, 78% were nonsynonymous and 43% were predicted to be deleterious to gene function, demonstrating a strong propensity for positive selection. Notably, a nonsense mutation inactivated the universal stress response sigma factor RpoS, with pleiotropic implications. The genome underwent substantial reduction, with four deletions in chromosome 2 resulting in the loss of 221 genes. The deleted loci included genes involved in secondary metabolism, environmental survival, and pathogenesis. Of 14 indels, 11 occurred in coding regions and 9 resulted in frameshift mutations that dramatically affected predicted gene products. Disproportionately, four indels affected lipopolysaccharide biosynthesis and modification. Finally, we identified a frameshift mutation in both P314 isolates within wcbR, an important component of the capsular polysaccharide I locus, suggesting virulence attenuation early in infection. Our study illustrates a unique clinical case that contrasts a high-consequence infectious agent with a long-term commensal infection and provides further insights into bacterial evolution within the human host.

Tracing Melioidosis Back to the Source: Using Whole-Genome Sequencing To Investigate an Outbreak Originating from a Contaminated Domestic Water Supply

“…MSHR6137 was also subjected to WGS using the 454 GS FLX ϩ platform (454 Life Sciences, Branford, CT, USA). Genome assembly for this strain was performed as previously described (12). The final genome contains 65 contigs totaling 7,208,016 bp, with an N50 of 258,651 bp, and encodes a predicted 6,656 proteins.…”

“…To obtain greater resolution, we performed whole-genome sequencing (WGS) on B. pseudomallei obtained from these two cases, from their water supply, and from other melioidosis patients and environmental samples from the surrounding region. PCR-based multilocus variable-number tandem repeat (VNTR) analysis (MLVA) of four loci (10) was incorporated to augment WGS short read data, which are unable to span paralogous or certain highly repetitive loci in B. pseudomallei (11,12). As a novel aspect of this study, we performed genomewide phylogenetic analysis of small insertions/deletions (indels), which largely comprise short read-mappable VNTRs across the B. pseudomallei genome, to increase our resolution among closely related isolates.…”

Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs

“…Previous studies on long-term bacterial adaptation have reported genome reduction by deletion of genes encoding nonessential functions, particularly for environmental-opportunistic pathogens (Rau et al 2012;Price et al 2013;Sharma et al 2014). Longterm mutation accumulation studies showed that B. cenocepacia has low genome-wide mutation rates, with many of the mutations biased toward deletions (Dillon et al 2015).…”

Burkholderia pseudomallei: Challenges for the Clinical Microbiology Laboratory

“…These relatively large chromosomes encode several putative virulence factors, including quorum sensing, type III secretion systems, and the capsular polysaccharide (13). The chromosomes are thought to be highly dynamic, evidenced by the presence of several recently acquired mobile genetic elements in the chromosome (6,12) and the extensive genetic diversification observed over time in a single patient (14,15). The portion of the genome with high variability between strains may contribute to virulence and antibiotic resistance (16).…”