Leonilde M. Moreira, PhD, has been studying the Burkholderia complex for 15 years. The bacteria, known for causing pneumonia or septicemia in some individuals, can survive for prolonged periods in moist environments. During the last 10 years, it has become one of the more predominant bacteria seen in cystic fibrosis patients.
“Sometimes, the patients just get rid of it,” says Moreira, an assistant professor at the Instituto Superior Técnico in Lisbon, Portugal, “but in most patients it turns to chronic infection and is in the lungs for years and years. Like other bacteria, it is very difficult to eradicate by antibiotics.” Burkholdreria multivorans, for example, is the most commonly isolated Burkholderia species from chronic infections of the airways of CF patients worldwide, with an overall prevalence in the U.S. of 0.68%, Moreira says, yet understanding of the traits required for bacterial colonization and persistence, as well as the molecular mechanisms underlying this adaptation, are limited.
A sabbatical in 2006 led Moreira to the laboratory of David Speert, MD, head of the University of British Columbia’s Centre for Understanding and Preventing Infection in Children. There, in the Vancouver lab, she was introduced to “a beautiful collection of clinical isolates” taken from Canadian cystic fibrosis patients over the last 30 years or so.
“I became interested in seeing what is going on, and why does this species in particular stay within the patient for so many years,” Moreira says.
Studying a series of isolates collected from one female CF patient over 20 years, Moreira and colleagues may have found some clues. By analyzing sputum samples from the patient and comparing them to her medical records, they found that B. multivorans evolves and adapts in bursts to survive in the lungs of cystic fibrosis patients. The work, published this week in mSystems, suggests that B. multivorans directly or indirectly targets adherence, metabolism and changes to the cell envelope to stick around and evade antibiotics.
The team sequenced and analyzed the genomes of 22 B. multivorans isolates taken from the patient --- who was hospitalized once due to CF-related respiratory illness and treated on multiple occasions with antibiotics --- and looked for correlations in the patient’s medical records, finding that several distinct bacterial lineages coexisted at any given time but evolved at different rates. One family quickly diversified into three others. The new lineages evolved mainly by mutations in genes with regulatory/signaling roles, and in genes whose proteins are involved in lipid, amino acid and carbohydrate metabolism. A slow and steady population-wide rate of genetic changes occurred over the course of infection, at a rate of about two single nucleotide polymorphisms per year.
The evidence suggests that mutations in several of these genes were adaptive to allow the bacteria to survive, Moreira notes: “These mutations corresponded to what was happening physically with the patient, so we could see that those mutations were not just random – they were specific targets that affected the physiology of the bacteria.”
B. multivorans was first isolated from the patient in 1993 and recovered periodically until 2013. She was initially infected by Staphylococcus aureus, Haemophilus influenzae and Pseudomonas aeruginosa in 1989-1993, followed by a period of co-infection of these microorganisms with B. multivorans from 1993-1996. Overall, the evolution was marked by periods of strong diversification followed by periods of relative stability. The period of the most diversification within the B. multivorans infection was associated with more rapid deterioration of the patient’s lung function, Moreira says.
The work not only sheds new light onto Burkholderia evolution but “this dynamic suggests that monitoring these evolutionary and molecular patterns could be used to design responsive therapies designed to limit population diversity and disease progression,” Moreira says. Her team is continuing studies of the bacteria in samples from an additional 10 CF patients provided by Speert’s lab.
-- Karen Blum