Mapped Pneumonia Genome Will Improve Vaccine Design

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Medical vaccine
Close up of doctor's hands vaccinating child

The most common bacterial cause of pneumonia around the world, Streptococcus pneumoniae,has been mapped by an international collaboration led by scientists from the Wellcome Sanger Institute, Emory University, and the U.S. Centers for Disease Control and Prevention.

The Global Pneumococcal Sequencing Project (GPS) found 621 strains of the bacterium across 51 countries. The researchers sequenced more than 20,000 S. pneumoniae patient samples. They also examined how the organism evolves in response to vaccination. One study based on their work was published in The Lancet Infectious Diseases (June 10). A sister paper appeared in EBioMedicine.

Their studies reveal which strains of S. pneumoniae (also known as the pneumococcus) are circulating around the world and help explain why the disease is still common despite existing vaccines. The GPS’s work is expected to help predict which strains will be important for new vaccines. It also underlines the importance of global genomic surveillance of infectious diseases.

Rebecca Gladstone, Ph.D., from the Wellcome Sanger Institute, is one of the papers’ authors. She said: “Our study gives the first genomic description of the S. pneumoniae population of the world. This has never been possible before, as previously only samples from individual populations had been studied. Now we have global data, showing which strains are present in each country, and can use this to understand pneumococcal infection on a world-wide scale.”

Many countries have introduced the pneumococcal conjugate vaccine (PCV) over the last ten years. This vaccine targets the coat (or capsule) around each S. pneumoniae bacterium. That coat is the most important factor influencing the virulence of each strain. PCV and has greatly reduced the number of childhood infections, but it is currently only highly effective against up to 13 of the 100s of coat types known.

To study the impact of vaccination on evolution of the bacterium, GPS collected patient samples both before and after the vaccine’s introduction. Both bacterial DNA sequences and patients’ health data were compared, making it possible to track changes influencing the vaccine’s effectiveness. The researchers also determined whether new strains are emerging that would impact disease severity and ease of treatment.

They found that the levels of non-vaccine type bacteria rose after the introduction of PCV, suggesting the bacteria evolve in response to the vaccine.

Pneumonia is an infection of the lungs responsible for the deaths of hundreds of thousands of people a year globally. It is the single largest infectious cause of death of children under 5 years old worldwide. Healthy people often carry these bacteria without becoming ill. But the bacteria can cause fatal infections such as sepsis, in the brain or blood, particularly in young children and some adults.

Reducing the transmission of S. pneumoniae between children is therefore a big public health priority. Vaccination also reduces the number of adult infections through herd immunity.

Robert Breiman, M.D., Director of the Emory Global Health Institute and Principal Investigator for the project, said “GPS turns a spotlight onto a new era in which the intersection of genomics and public health enables unparalleled capacity for optimizing prevention strategies, while providing an immensely valuable tool for forecasting and addressing new challenges ahead.”

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