Co-evolutionary signals fromBurkholderia pseudomalleigenomics identify its survival strategies and highlight improving environmental health as prevention policy

SummaryBackgroundThe soil bacteriumBurkholderia pseudomalleiis the causative agent of melioidosis. It kills up to 40% of cases and contributes to human morbidity and mortality in many tropical and sub-tropical countries. As no vaccines are currently available, prevention is the key health policy and is achieved by avoiding direct contact with soil and standing water. The pathogen notoriously persists in ranges of environmental conditions which make disease prevention difficult. We aimed to scanB. pseudomalleigenomes for signals of evolutionary adaptations that allow it to thrive across environmental conditions, which should ultimately inform prevention policy.MethodsWe conducted three layers of analyses: a genome-wide epistasis and co-selection study (GWES) on 2,011B. pseudomalleigenomes to detect signals of co-selection; gene expression analyses across 82 diverse physical, chemical, biological and infectious conditions to identify specific conditions in which such selection might have acted; and gene knockout assays to confirm the function of the co-selection hotspot.FindingsWe uncovered 13,061 mutation pairs in distinct genes and non-coding RNA that have been repeatedly co-selected throughB. pseudomalleievolution. Genes under co-selection displayed marked expression correlation whenB. pseudomalleiwas subjected to physical stress conditions including temperature stress, osmotic stress, UV radiation, and nutrient deprivation; highlighting these conditions as the major evolutionary driving forces for this bacterium. We identified a putative adhesin (BPSL1661) as a hub of co-selection signals, experimentally confirmed the role ofBPSL1661under nutrient deprivation, and explored the functional basis of the co-selection gene network surroundingBPSL1661in facilitating bacterial survival under nutrient depletion.InterpretationOur findings suggest thatB. pseudomalleihas a selective advantage to survive nutrient-limited conditions. Anthropogenic activities such as shifting cultivation systems with more frequent rotations of cropping and shortened fallow periods or continuous cultivation of cash crops could directly or indirectly contribute to loss of soil nutrient; these may lead to the preferential survival ofB. pseudomalleiand a subsequent rise of melioidosis. Successful disease control for melioidosis needs to consider improving environmental health in addition to current preventive efforts.FundingWellcome Trust, European Research Council, UK Department of Health, Thailand Research Fund and Khon Kaen UniversityResearch in contextEvidence before this studyWe searched PubMed with terms (co-selection AND bacteria AND population) with no date or language restrictions from database inception until April 11, 2021. We identified 44 publications of which four were conducted at a genome-wide scale. These four studies were performed on human-restricted pathogens, detected co-selection of antibiotic resistance gene networks which highlight the use of antibiotics as major selection pressures and further inform treatment options. However, none of these studies were performed onBurkholderia pseudomalleior other opportunistic pathogens that have been adapted to both natural and host environments. The selection pressures exerted on these pathogens and the genetic determinants allowed for their adaptations remain unclear, which limit our understanding on the bacterial biology and the information used for disease control.Added value of this studyBased on genomes of 2,011B. pseudomalleicollected from melioidosis endemic areas, we identified and confirmed genetic signals for co-selection. Using transcriptome profiling covering a broad spectrum of conditions and exposures, we showed that genes under co-selection displayed marked expression correlation under physical stress conditions with the gene at the co-selection hotspot conditionally expressed under nutrient starvation. Furthermore, we experimentally validated the function of the hotspot gene and demonstrated that unlike host-restricted pathogens, theB. pseudomalleico-selection network does not facilitate host infection but is focused on bacterial survival in a harsh environment, particularly under nutrient depletion. Aside from providing a data resource, the study also showcases the power of combined genetics, transcriptomics and functional analysis as a tool for biology discovery.Implications of all available evidenceOur findings provide evolutionary and biological evidence for preferential survival ofB. pseudomalleiunder nutrient starvation. Agricultural practice that induces soil loss, which is not uncommon in melioidosis endemic areas has been linked to soil nutrient depletion and may contribute to the prevalence ofB. pseudomalleiand a consequent rise of melioidosis in these regions. Successful melioidosis control has to consider environmental health in addition to existing prevention policy.