Clonal complexes identified in each study location.

a. Clonal complexes are named with the sequence type (ST) predicted to be the ancestral ST. When the ancestral ST could not be determined, all STs in the clonal complex are indicated (e.g. 6025/7595). When an ST had no related variants it is marked as “STxx_Single”. The first 10 CCs listed were considered to be major CCs and the remainder were minor CCs.b. KAT = Kathmandu; OKH = Okhaldhunga.c. One serotype was unknown because the isolate was PCR-negative for the serotyping primers and the culture was nonviable (and thus unavailable for serotyping by Quellung).d. Clonal complexes with: 4 isolates each, n = 15; 3 isolates each, n = 18; 2 isolates each, n = 30; and 1 isolate each, n = 123.