Fig. 1.

Phylogenetic tree of 686 carriage isolates from healthy children in Cambodia, isolated between 2013 and 2017. GPSCs with N>20 in the population are highlighted. The tree was built from a nucleotide alignment in FastTree using a generalized time reversible model. Branches are coloured by GPSC corresponding with the first colour strip. ermB and mefA are macrolide (e.g. erythromycin) resistance genes, cat causes resistance to chloramphenicol, tet results in resistance to tetracycline and refers to presence of either tet(M) or tet(O), and folA I20L and folP cause resistance to trimethoprim and sulfamethoxazole (the components of co-trimoxazole), respectively. Antimicrobials are coloured as follows: resistant, red; susceptible, blue; and in the case of co-trimoxazole – intermediate, pink. This figure can be visualized interactively using webtool Microreact at: https://microreact.org/project/mvgn3EvNgmxAcPjPBnyFMj/a32e0dc6.