A forgotten disease

Ubon, a city in Northeast Thailand, has the unenviable title of being the world’s capital of melioidosis. Caused by a bacterial infection, it’s estimated that 165,000 people a year around the world develop the disease, and more than half of those affected die from it. The numbers are likely to be a huge underestimate, as testing for the presence of the bacteria isn’t always possible. Despite the high mortality rate, and the fact that prevention and treatment are possible, the condition is not well studied, and does not make it onto lists of neglected tropical diseases. However, the bacterium does make it on to the Centers for Disease Control and Prevention ‘Tier 1 select agent’ list as a potential bioweapon¹.

Dr Claire Chewapreecha began studying melioidosis after visiting a hospital in Ubon and seeing patients affected. She is a computational biologist based at the Mahidol Oxford Tropical Medicine Research Unit in Bangkok, Thailand, and an International Fellow at the Wellcome Sanger Institute. She works to understand the genetics of the Burkholderia pseudomallei bacterium that causes the disease. She is also investigating why some people infected become ill and others don’t. In collaboration with researchers around the world, she is involved in vaccine trials for the disease and public health initiatives to raise awareness of the condition.

The burden of melioidosis

We started by discussing the impacts of melioidosis around the world. The bacterium responsible for the disease, Burkholderia pseudomallei, lives in the environment, in soil and water. In Southeast Asia, many people who catch it are farmers working in rice paddy fields. The bacterium can enter the skin through a cut or graze, though it might also be caught by consuming contaminated food or water, or by inhalation. People with diabetes are at a much greater risk of melioidosis. Diagnosis is difficult, as symptoms of the infection mimic those of many other diseases. To confirm melioidosis, a bacterial culture test, where bacteria are isolated from blood, sputum or urine of suspected cases is still employed. Results can take several days to come back, by which time, the patient has often died from the infection.

Burkholderia pseudomallei in the laboratory. Credit: Claire Chewapreecha

“Timely diagnosis and a vaccine are key clinical interventions that could save many lives from melioidosis. Both are still under development. While we wait for that research to be done, people are working on public health interventions – promoting protective clothing for farmers, for example,” says Claire.

“Thai people love to take selfies, so that’s been incorporated into public health campaigns.”²

Bacterial genetics

Claire’s current work in collaboration with the Sanger Institute is focusing on the genetics of Burkholderia pseudomallei. She is seeking to uncover what makes it so virulent, as well as so variable in its effects. It is a species with high levels of genetic recombination – which means that the bacteria regularly ‘swap’ their DNA. This process facilitates bacterial survival across different geographical locations, and results in a diverse population³.  Claire uses genome-wide association studies (GWAS) to compare the genomes of Burkholderia pseudomallei in the environment to those from infected patients. The team has been able to identify genes associated with different properties of these bacteria⁴.

“We found genetic variations associated with disease-causing isolates in a gene that codes for hemolysin-coregulated protein (Hcp)⁴. The protein is both a substrate and a component of Type VI Secretion System -  a ‘needle’ that the bacterium uses to puncture and enter human cells. Reassuringly, Hcp is already part of the conjugate vaccine that is currently in trial, as well as the target for a rapid diagnostic test^5,6.  It’s good to see our findings match up. However, it is possible that a genetic change at this location would create both vaccine and rapid test escape bacteria at the same time”

To predict the vaccine lifespan, Claire is working to assess if any bacterial variants could escape the vaccine. She is also investigating selection pressures on the bacterium.

Using genome-wide epistasis and co-selection studies (GWES), the team identified the mutation pairs in genes that are passed on to bacterial descendants together – termed co-selection. They found that genes active during physical stress, particularly those essential for bacterial survival under nutrient depletion, were co-selected⁷. Claire reasoned that if the co-selected genes are co-regulated under physical stresses, then these conditions should reflect the selective pressures the bacteria faces.

Claire explains: “Soil sampling studies have shown that the bacteria are commonly found in nutrient depleted soil. Agricultural practice that induces loss of soil nutrients, such as crop rotations with short-term fallows and post-harvest residue burning, is not uncommon in melioidosis endemic areas. This has been linked to soil nutrient depletion and may contribute to the prevalence of B. pseudomallei.”