Phylogenetics and molecular evolution
By sequencing the complete genomes of pathogen isolates from a given outbreak, molecular epidemiologists are now able to identify the small handful of mutations that distinguish isolates from other and that can be used as markers of transmission. This “genomic epidemiology” approach has been to used to identify person-to-person transmission of an infectious disease, trace hospital outbreaks back to unique environmental sources, and explore the dynamics of regional epidemics including Ebolavirus. However, the evolutionary processes that allow us to describe outbreak dynamics at such high resolution also introduce complications when interpreting genomic data through an epidemiological lens, particularly for pathogens with long periods of latency or chronic carriage. This talk will cover opportunities and challenges for genomic epidemiology, using a long outbreak of tuberculosis amongst the homeless population as a guiding example.