Mapping the Evolution of Louse-Borne Bacteria Using Genomic Time Series

Louse-borne diseases are an under-recognised burden, disproportionately affecting populations facing health inequalities, and are expected to increase as human displacement intensifies. Three bacterial pathogens transmitted by human lice, Borrelia recurrentis, Bartonella quintana, and Rickettsia prowazekii, have caused outbreaks throughout history, yet the correlates and drivers of their evolution remain poorly understood. Each of these species represents a separate evolutionary shift from tick- or flea-borne ancestors to strictly louse-borne transmission. This transition has been accompanied by increased virulence, epidemic potential, and substantial genome reduction. However, the genomic features underlying these changes are largely unknown and cannot be recovered from limited contemporary genomic datasets. My Wellcome ECA combines contemporary, historical and ancient pathogen genomes, including material recovered from archaeological remains and archival collections, to reconstruct how and when these bacterial pathogens adapted to lice. Using a pan-genomic, time-calibrated evolutionary framework across genomic time series, I will identify the genes and functional pathways that were lost or gained during this transition and place these changes within their historical context. By analysing each genus independently and comparatively, my work will identify convergent evolutionary pathways, providing insight into the genomic processes that have shaped the emergence, spread and epidemic potential of these louse-borne diseases.