An onion, paddy-fields in South-east Asia and the human lung may not have much in common, but they are all home to members of a highly adaptable genus of bacteria, Burkholderia. These bacteria are so widespread in the environment that no one knows just how many species there are. But the genomes of two of them – B. cenocepacia and B. pseudomallei – have recently been sequenced at the Wellcome Trust Sanger Institute. And the sequences are exposing an extensive genetic toolkit that may account for their great adaptability.

“B. cenocepacia and B. pseudomallei have mechanisms for surviving both in the soil and in the mammalian host, and these are quite challenging environments,”explains the Sanger Institute’s Dr Matt Holden. “And not only are they very good at causing disease, they can also survive unnoticed in the host for a long time.”

To do all this, the organisms have stockpiled an array of genetic tools to equip them for life’s challenges. They have very large genomes and, unlike most other bacteria, which have one chromosome, B. pseudomallei has two and B. cenocepacia three. The bacteria are also adept at incorporating new genes, acquired from other organisms. Strains that inherit gene clusters known as pathogenicity islands are often particularly deadly.

Burkholderia cenocepacia

Burkholderia cenocepacia was first isolated in 1949 from rotting onions. It naturally inhabits soil and water, and particularly favours the area around plant roots (rhizosphere). But in the last 30 years it has emerged as a dangerous pathogen for people with cystic fibrosis (CF), killing one in five patients.

The first case of B. cenocepacia in humans probably occurred when a CF patient came into contact with contaminated soil or plant roots. But once established in the CF population, it spread easily from patient to patient through direct contact. Its rapid spread in these vulnerable patients – who overproduce mucus in their lungs and are very susceptible to bacterial infections – has been aided by its inbuilt resistance to commonly used antibiotics.

“People with cystic fibrosis are on continual antimicrobial therapy for Pseudomonas and other bacterial infections,” explains Dr Eshwar Mahenthiralingam, Lecturer in Microbiology at Cardiff University. And because these people are vulnerable to infection, highly resistant organisms such as Burkholderia sp. can grow and cause disease. “The strains of B. cenocepacia that cause disease are those with particular features such as pathogenicity islands, which give them a greater capacity to spread in CF patients and other vulnerable individuals.”

One consequence has been the demise of aerobics classes for people with cystic fibrosis. The high density of people exercising in an enclosed space created perfect conditions for infection to spread.

As well as its resistance to antibiotics, B. cenocepacia has evolved the ability to live off many carbon sources, and can even survive in phenolic disinfectants – a feature that has seen it spread through hospital intensive care units, transmitted by the very disinfectant used to reduce infections.

Dr Mahenthiralingam, funded by the Natural Environment Research Council, is using the B. cenocepacia genome sequence data to pinpoint the genes it uses to break down organic compounds such as oil, and to kill pathogenic fungi, as well as those that make the bacteria virulent. His goals are to develop environmentally friendly ways of breaking down pollutants and to produce a new family of ‘biopesticides’.

“If we can understand which genes are important for virulence, such as those encoded on pathogenicity islands, we can knock out these genes and engineer the bacteria so they are ecologically useful but unable to cause infection,” he says.

But introducing B. cenocepacia bacteria into the environment is a sensitive issue, as many people believe the disabled bacteria could pick up new genes and become pathogenic again. Others disagree: “If there is already a reservoir of these organisms in the soil and these organisms are already effective pathogens, and do not require any mutation to cause disease, then to some extent, the risk is already there,” points out Chris Dowson, Professor of Microbiology at the University of Warwick.

However, he agrees that a proper risk assessment is necessary – something he plans to do as part of a Wellcome-funded project. “We will look at about 1200 B. cenocepacia strains from across the world, from as diverse a range of sources as possible. We will thoroughly characterise the organisms to understand the relationship between the clinical and environmental strains.” This study should also lead to new diagnostic tools to help identify particularly prevalent or resistant strains.

B. pseudomallei

B. pseudomallei is found mainly in South-east Asia, where it causes a devastating disease called melioidosis. In north-east Thailand, where the disease accounts for one in five cases of septicaemia, most people become infected when exposed to contaminated wet soil in paddy fields. In general,people with underlying conditions such as diabetes or kidney failure succumb to melioidosis – a disease that takes several forms and kills almost half those infected.

“Some people infected with B.pseudomallei die from fulminant septicaemia within 24 hours, whereas others might have a chronic lesion that grumbles on for years and years,” explains Sharon Peacock, Head of Microbiology at the Wellcome International Research Programme in Bangkok, Thailand.

But the bacterium can also lie unnoticed in the body for many years before causing clinical disease. This first came to light during the US–Vietnam conflict, when soldiers fell ill after returning home. B. pseudomallei became known as the ‘Vietnam timebomb’, and in one case a helicopter pilot developed disease 26 years after returning to the USA.

Dr Peacock wants to understand how the bacteria can cause different types of disease as well as lie dormant. “Understanding the degree of variability within natural populations of B. pseudomallei is likely to make an important contribution to the development of preventive strategies, including vaccines,” she says. She is investigating how B. pseudomallei changes its appearance, both when cultured in the lab and during the course of an infection. And in collaboration with Matt Holden and Julian Parkhill at the Sanger Institute, Dr Peacock hopes to find the genes responsible for these changes.

Developing vaccines against B. pseudomallei is high on the research agenda, not least because it is classed as a potential bio-weapon by the US Centers for Disease Control and Prevention. In collaboration with Matt Holden, a team headed by Richard Titball at the Government’s Defence Science and Technology Laboratory in Porton Down is investigating whether any of the possible virulence genes might be exploited as vaccine candidates.

Enter the horse

The work on the Burkholderia species affecting people has been helped by a parallel sequencing project. The genome of B. mallei, a close relative of B. pseudomallei that causes a disease called glanders in horses, has been sequenced at The Institute for Genomic Research (TIGR) in the USA.

“Comparing the two genomes has been very interesting,” enthuses Dr Holden. “Like B. pseudomallei, B. mallei has two chromosomes, but they are much smaller. It seems that since the two evolved from a common ancestor, B. mallei has lost a large chunk of its genome and it is now very host restricted.”

The comparisons suggest which genes are crucial to the human pathogen’s flexibility. “We’ve been able to identify virulence genes that may be important in causing disease, and also genes important for survival n the environment – something that B. pseudomallei can do, but B. mallei can’t,” explains Dr Holden.

So it would seem there is at least one Burkholderia species that is not adaptable. As Dr Holden puts it: “B. mallei has a genome in decay – it has backed itself into an evolutionary corner.” Interestingly, though, B. mallei has already been used as a bio-weapon – in World War I horses were deliberately infected to disrupt supply convoys and artillery movements.

External links

• Burkholderia cenocepacia genome sequencing at the Sanger Institute
• Burkholderia pseudomallei genome sequencing at the Sanger Institute
• Defence Science and Technology Laboratory, Porton Down
• Institute for Genomic Research (TIGR), USA
• Dr Eshwar Mahenthiralingam at Cardiff University: Research interests
• Professor Chris Dowson at the University of Warwick: Research interests