Figure 1. Maximum-likelihood phylogeny of household index cases and contacts’ sequences with 1,000 ultrafast bootstrap replicates rooted to the reference sequence with a scaled bar of 2 SNP (6.6 × 10 ^-5 substitutions/site).

The dotted line at bottom left indicates where a single long branch was collapsed for visualisation. The non-grey shading on the outer ring represents non-clustered households where sequences are coloured by their households. HH002 and HH007 were the only households where none of the contacts’ sequences clustered with that of their household’s index case and this is evidence that the contact could have acquired the infection elsewhere and is thus excluded from the analysis. SNP, Single Nucleotide Polymorphism.