By MITZI BAKER

Taking advantage of the open-air laboratory that is San Francisco, Peter Small, MD, has collected samples of virtually every case of tuberculosis that has occurred in the city for the last 13 years -- almost 3,000 total. In this week's advance online edition of the Proceedings of the National Academy of Sciences, the associate professor of infectious diseases and geographic medicine at the School of Medicine and his colleagues present a genetic analysis of 100 of these samples.

The findings suggest ways the bacteria can escape a host's immune system or develop antibiotic resistance.

The team took its analysis a step further in a second paper, which appears in the same edition of the journal. They found that people from different regions of the world carry different strains of tuberculosis, pointing out the importance of sociological interactions in infectious disease transmission. This also raises the possibility that the pathogen evolves within a geographic population and doesn't spread to other groups.

“It was remarkable how well the genetics mapped to global geography,” said Small. “Co-evolution is highly speculative, but it's an intriguing possibility. Most importantly, it's a hypothesis we now have the technology to address.”

Tuberculosis causes more adult deaths than any other infectious disease. Worldwide, one person in three is infected, but it remains a problem primarily in the developing world. However, the emergence of tuberculosis strains resistant to multiple drugs in industrialized countries is prompting renewed interest in vaccination.

There has long been anecdotal evidence that tuberculosis bacteria differ throughout the world, said Small, who is currently on leave from Stanford serving as a senior program officer in the Global Health Program of the Bill and Melinda Gates Foundation. Additionally, he said, studies testing tuberculosis vaccines have varied widely in how well they work when conducted in different regions of the world, which suggests that each area may require its own vaccine.

Through genetic analysis, Small's group could discriminate between cases of tuberculosis that someone contracted from another person in San Francisco and cases that arose from a much earlier infection. The bacteria have genetic “fingerprints” by which researchers can track transmission through a community, said Aaron Hirsh, PhD, a postdoctoral scholar and lead author of the second paper.

Small's laboratory examined the genomes of 100 distinct strains of the disease isolated from patients in San Francisco using microarrays -- glass slides containing pieces of DNA that span the entire sequence of tuberculosis -- to comprehensively identify specific, irreversible genetic changes that serve as fingerprints.

At the time of these studies, Hirsh was a graduate student in the lab of Marcus Feldman, PhD, the Burnet C. and Mildred Finley Wohlford Professor in the Department of Biological Sciences. Hirsh applied his molecular evolution expertise to combine the tuberculosis genetic information into a simple graphic akin to a family tree to illustrate commonalities between the strains.

Once the tree was drawn with 100 strains represented, researchers assigned each strain its own color based on the national origin of the infected person. “It was amazing how clearly the tree was pink in one branch and blue in another branch and black in another branch,” said Hirsh. “It fell out so neatly, based on where a person was born, even though half those people had gotten their tuberculosis after they arrived in the city.”

The lack of bacterial exchange between people of varying national origins living in San Francisco was surprising.

“I suspect the most reasonable explanation has to do with sociology. Immigrants from Asia don't really commingle with immigrants from other parts of the world or with native-born Americans,” Small said. “But the puzzling part is that Asian tuberculosis must have been introduced around the time of the Gold Rush and you'd think in the intervening 150 years, there'd be ample opportunity for those strains to spread around. We simply didn't see that.”

A pragmatic outcome of their analysis, said Small, is the ability to address whether there are strain-to-strain differences in how people's immune systems respond to tuberculosis, such as those that have been demonstrated in HIV.

“This has profound implications for vaccine development,” Small said. “We may ultimately need to develop different vaccines for different parts of the world. It's a completely open question, but we can start to answer it now.”

Anthony Tsolak, PhD, first author of the genetic analysis paper, was a postdoctoral scholar in Peter Small's lab and has since returned to England. Seven additional Stanford researchers were involved in these studies, which were funded by grants from the National Institutes of Health.