Fig. 2.

a: Within host and between host observed allelic diversity across paired isolates. From left to right, paired isolates from within host (pulmonary and non-pulmonary sampled within 6 months of each other); paired pulmonary isolates sampled >6 months apart from within individual hosts; pairwise distances between patients within households; and pairwise distances between patients across 11 different community clusters, stratified by type of epidemiological link. 22 of the 38 links within the 25 household clusters also occur within community clusters (ie, known linkage) but are shown with household isolates and not with community isolates. Top horizontal dashed line indicates the threshold above which direct transmission can be judged to be unlikely; bottom horizontal dashed line indicates the threshold below which transmission should be investigated. b: All against all comparison of the number of allele differences and MIRU-VNTR locus differences for genomes for which full 24-locus MIRU-VNTR profiles were available. Zero MIRU-VNTR differences implies identical MIRU-VNTR profiles. The size of the blue circles indicates the number of comparisons with X MIRU-VNTR locus differences and Y allele differences.