Bentley says it’s not yet clear where the new chunks of DNA are coming from, though they likely originated in other types of pneumoniae bacteria inhabiting the same niche, namely, the nose.
The research also sheds light on how this population of microbes has evolved in response to the introduction, in 2000, of a vaccine against seven of the most common disease-causing subtypes in the United States. Scientists already knew that those subtypes were virtually eradicated once vaccination became popular, and that others arose to take their place. But it hadn’t been clear whether the new variants were present before 2000 and grew to fill a niche left by those that had been eradicated, or whether they had evolved in response to the vaccine, says Hervé Tettelin, associate professor of microbiology and immunology at the University of Maryland School of Medicine. Scientists now know that the variants most likely existed before 2000.
“If we understand how those things are evolving, we can better decide on future vaccines and antibiotic treatment regimens so that we don’t make matters worse or displace the problem,” says Tettelin.
The newest version of the vaccine targets 13 of the most common subtypes. But given that there are more than 90 varieties of this strain of microbe, the researchers now predict that the microbial population will respond the same way it has responded to the previous vaccine.
Another option is to develop a vaccine that targets a protein shared by all strains, one that is vital to the microbes’ survival. Sequencing studies such as this one could help scientists identify such a protein. “If you sequence hundreds or thousands of genomes, this is when you can start defining the true core genome,” says Tettelin. “Then you can make a decision about what proteins to use in a vaccine.”
The strain under study in this project is just one of many disease-causing varieties of pneumococci. Bentley, Tettelin, and others are now analyzing other strains using a similar approach. Researchers are also using sequencing to look even more closely at the evolution of the bacteria. Bentley plans to analyze samples collected from a refugee camp in Thailand over 15 years. That should give a much higher resolution picture than the one the current project produced. That improved picture will, in turn, help trace how the bugs are transmitted from person to person.