Extended Data Fig. 2: Risk ratio framework sensitivity analyses to determine geographic structure when sub-sampling and only including disease isolates.

Risk ratio of being the same GPSC within a province (blue), between different provinces over increasing distance (red), compared to geographically distant pairs (>1000 km) (reference) (top) and the risk ratio of having a tMRCA 0–5, 5–10, 10–20, or 20–200 years ago within South African provinces (blue), across larger distances within South Africa (red), from South Africa to other countries in Africa (green), and from South Africa to countries outside of Africa (purple) (South Africa; N = 6910). (a) Including all isolates from each province (left) compared with sub-sampling to 300 with replacement to compensate for biased sampling in each province. (b) Including only isolates sampled from patients with pneumococcal disease. All plots use a reference of pairs which are from distant provinces in South Africa (open triangle). Error bars represent 2.5 to 97.5 CIs.