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. 2009 Oct 21;47(12):4006–4020. doi: 10.1128/JCM.01270-09

FIG. 1.

FIG. 1.

Data for the 79 PETRA lineage strains of this study. The leftmost column (ID) contains the strain identification codes (a number followed by the year of isolation). The next column shows the country of origin of the patient with tuberculosis as follows: IRN, Iran; ERI, Eritrea; ETH, Ethiopia; IND, India; JOR, Jordan; SUD, Sudan; NEP, Nepal; ISR, Israel; EGY, Egypt; YEM, Yemen; GEO, Georgia; IRQ, Iraq. The type of tuberculosis specimen (TB type) is shown as follows: P, pulmonary; EP, extrapulmonary. In the RES column, resistance to first line anti-tuberculosis drugs (RES) is shown as follows: I, isoniazid; S, streptomycin; n a, information not available. The MIRU-VNTR loci column shows the MIRU-VNTR copy number profile for each strain, by locus in the following order: 2, 4, 10, 16, 20, 23, 24, 26, 27, 31, 39, 40, A, B, C, and QUB11b, which are clustered in Fig. 2. Note that 0 indicates an absence of the amplicon (terminology which facilitates data manipulation by Excel and Bionumerics). The column labeled MST MIRU Group shows the MIRU-VNTR minimum spanning tree (MST) group as visualized in Fig. 4. The SPOLIGO Octal column shows the octal equivalent of the 43-spacer spoligotype. The column labeled SPOLIGO Spacers shows the character representation of the 43-spacer spoligotype profiles for each strain, which are clustered in Fig. 3, as follows: 1 for hybridization and 0 for no hybridization. The MST Spoligo Group column shows the spoligotype MST group as visualized in Fig. 5. The strains with gray shaded backgrounds have identical spoligotypes and MIRU-VNTR types that vary only at locus ETR A. To the right of the figure, the MIRU-VNTR subclusters that also share spoligotype identity (MIRU-spo-identity) are shown. ETR A amplicons of various copy numbers are shown (for example, amplicons of copy number 4 are represented by A = 4). Since it is difficult in places to distinguish among zero, Q, and capital O, we note for the sake of clarity that the country of origin for strain 0753-06 is Iraq (IRQ), the MST MIRU group for strain 2039-00 is A0, the MST MIRU group for strain 0346-08 is AO, the MST MIRU group for strain 0493-06 is AQ, the MST spoligo group for strain 0854-08 is Q, and the MST spoligo group for strain 0346-08 is O.