(A) Clustering of the single nucleotide polymorphism (SNP) types of the isolates of the Harlingen IS6110 restriction fragment length polymorphism (RFLP) cluster. Application of the SNP markers to the isolates of the Harlingen cluster divided the IS6110 RFLP cluster into SNP clusters. The SNP types of the clusters are shown as an eight-position SNP code. Positions one to four indicate SNPs that were identified between strains SH1 and SH5 and positions five to eight represent SNPs that were identified between strains SH1 and SH9 (Table 1). Positions in red represent acquired SNPs, and underlined positions represent mutation events. (B) Dendrogram of clustered SNP types with integration of a time scale. All bacterial strains are designated with an “S” followed by the respective patient number. Only isolates of patients of one of the contact chains or strains with an SNP type different from the SNP type of SH1 were used for clustering. Branches in bold indicate the neighbor-joining-based clustering of the SNP types. Other horizontal branches indicate the number of days that have passed since the isolation date of the first patient isolate in each transmission cluster. Samples with the same color belong to one SNP cluster. Black, Harlingen cluster; red, SNP cluster with index case H3; purple, SNP cluster with index case H4.a; blue, SNP cluster with index case H4.c; green, SNP cluster with index case H9. A bacterial isolate of patient H6 (SH6) is missing from the Dutch tuberculosis database, because this patient was not diagnosed in the Netherlands.

Schematic depiction of two contact chains from the Harlingen (H) cluster suggested by contact tracing. Time is depicted by the horizontal bar; patients are numbered H1 to H9. Bacterial isolates of patients marked with an asterisk were subjected to genome sequencing. The bacterial isolates are designated with an “S” (for strain) followed by the patient number (e.g., SH1, SH5, and SH9). A bacterial isolate of patient H6 was not available for analysis. #, after being diagnosed with tuberculosis in 2003, patient H4 experienced two relapses of the disease in 2004 and 2005 (referred to as H4.a, H4.b, and H4.c in Fig. 3).

Most likely transmission scheme suggested by single nucleotide polymorphism (SNP) typing, temporal, and contact tracing data. Black arrows indicate the most likely transmission events based on the SNP type clustering and integration of temporal data and supported by contact tracing information. Arrows with dashed lines indicate transmission events suspected based only on contact tracing information. Stickmen with the same color belong to the same SNP cluster. Black, Harlingen cluster with index case H1; red, SNP cluster with index case H3; purple, SNP cluster with index case H4.a; blue, SNP cluster with index case H4.c; green, SNP cluster with index case H9.