By Nicholas Schou
According to the National Institutes of Health, the southern African nation of Botswana has one of the highest tuberculosis infection rates in the world. Officially a sparsely populated country of 2.58 million people, most of Botswana’s inhabitants are actually crowded into roughly a third of its available land, the remainder of which consists of the inhospitable and non-arable Kalahari desert.
Currently, 353 people out of 100 000 people in Botswana are infected with the highly transmissible TB bacteria, and 60 percent of those also test positive for HIV. Yet although Botswana is among the countries with the highest TB infection rates in the world, there remains a startling lack of data on the disease and its effect on populations at the local level in the country–data which is necessary to any effective effort to better understand and combat the spread of the illness.
A new UC Irvine study, published in Emerging Infectious Diseases, a monthly journal of the Centers for Disease Control and Prevention, has provided important new data that will greatly impact the effort to study and treat TB in Botswana and other affected nations. The lead author for the project is Chelsea Baker, a Ph.D. candidate in the Sue & Bill Gross School of Nursing; co-authors include partners at UCI and the Centers for Disease Control, as well as in Germany and Botswana.
The paper challenges the general scientific assumption that TB is simply an endemic disease which spreads evenly throughout the population. By using cutting edge spatial analysis methods to analyze data involving just under 1500 participants in Botswana, Baker’s work reveals that different communities in the country were in fact plagued by multiple distinct outbreaks of TB.
Dr. Sanghyuk Shin, director of UCI’s Infectious Disease Science Initiative and associate professor at the Sue & Bill Gross School of Nursing, said Baker used advanced whole genome sequencing to identify distinct TB variants in Botswana. “She then integrated spatial analysis and modeling to map out the distinct patterns of spread across the TB variants,” Shin explained. “Her approach to integrated analysis of genomic and spatial data could potentially be used by public health agencies to track the spread of TB outbreaks in real time and implement targeted measures to stop these outbreaks from spreading.”
According to Baker, her paper was a collaborative effort, and its results were made possible by combining data from UCI’s partners in Botswana, who provided clinical and geographic data, and that she used advanced whole genome sequencing which was performed by the paper’s co-authors in Germany.
“The integration of genomic and geospatial data is a promising approach for
studying TB transmission in high-burden settings,” Baker said, adding that methods for
analyzing these types of data together are still evolving. “We were fortunate to have
access to really high-resolution geographic and genomic data. Employing spatial
analysis allowed us to see some interesting patterns that could potentially be useful for
public health planning.”
UCI’s Infectious Disease Science Initiative aims to position the university as a global leader in infectious disease research and education by funding work that probes the dynamics of infectious diseases and drug resistance. The program seeks to use data-driven science to resolve questions about how infectious disease outbreaks occur and what can be done to predict and prevent them.
Dr. Shin also emphasized the fact that the nursing school couldn’t have carried out its ground-breaking research without help. “We relied on partners in Botswana and Germany to do this research,” he said. “It really shows the exceptional value of international collaborations in generating highly significant scientific knowledge for tackling global health problems.”