Whole-genome sequencing used to track the evolution of a bacterial pathogen during a Burkholderia dolosa outbreak amongst cystic fibrosis patients is reported this week in Nature Genetics. This provides an example of the utility of high-throughput sequencing technologies in a clinical epidemic setting and provides insights into pathogen genomic evolution during infection of their human hosts.
Roy Kishony and colleagues examined a historical epidemic of B. dolosa — that can cause pneumonia — that occurred amongst patients with cystic fibrosis tracked in a single Boston hospital in the 1990s. They sequenced the whole-genomes of B. dolosa isolates obtained from 14 cystic fibrosis patients from this outbreak, including 112 bacterial isolates collected over the course of 16 years. They conducted evolutionary and epidemiological analyses, and are able to infer the network of transmission amongst these patients. They further identified 17 genes as targets of selection, suggesting that they play a role in B. dolosa pathogenesis and adaptation to their human host.