Pneumococcal genome sequencing

Bacterial genome sequencing is used to track current pneumococcal epidemics, such as pneumonia, in a study reported this week in Nature Genetics. Steptococcus pneumoniae is a major cause of pneumonia as well as other invasive pneumococcal diseases including bacterial meningitis. Peter Donnelly and colleagues report sequencing of 62 isolates of S. pneumoniae. These isolates were selected for epidemiological interest from within a CDC national monitoring program that included 27,000 samples isolated from patients at ten different locales in the United States from 2000-2007. The authors consider the effects of the introduction of the PCV7 pneumococcal vaccine in the US in 2000, and the selection that this imposed on the bacterial genome. They examine the pneumococcal evolution in these populations over time, and identify an important role for multi-fragment recombination.