tuberculosis strains with zero-copy-numbers of IS6110; H37Rv, M. tuberculosis H37Rv; BGC, M. bovis BCG; ♦, M. bovis strains. *, Reference strains used as controls. ■, INH-resistant MTb strains Spoligotyping To determine lineage, the 57 strains (48 MTb and 9 M. bovis) from the MTC were spoligotyped and binary outcomes were compared with the shared type (ST)

number and lineages and sublineages reported by Brudey et al [26]. Spoligotype analysis of 48 MTb strains yielded 21 patterns (Figure 1). Thirty-nine MTb strains (81.3%) were grouped into 12 clusters (2 to 10 strains per cluster) while 9 strains selleck chemical showed Osimertinib order unique patterns. Thirty-four MTb strains showed 12 spoligotyping patterns that matched with: Shared-type (ST) number 2 (lineage name H2; n = 1), ST42 (LAM9; n = 10), ST47 (H1; n = 2), ST50 (H3; n =

2), ST53 (T1; n = 5), ST119 (X1; n = 3), ST137 (X2; n = 2), ST274 (U; n = 1), ST508 G418 mouse (T1; n = 4), ST732 (T1; n = 2), ST948 (H3; n = 1), and ST1626 (T1; n = 1). A further 14 MTb strains showed 9 patterns that did no exist in the SpolDB4.0 database (see question marks, Figure 1). Spoligotyping allows discrimination of MTb strains with low-copy-numbers of IS6110 (see Figure 1; for example, strains MEX-IPN 15, MEX-IPN 16, MEX-IPN17 and MEX-IPN 44). Nine M. bovis strains yielded 7 spoligotyping patterns; 5 unique patterns and 2 clusters with 2 strains in each one (Figure 1). The M. bovis spoligotyping patterns matched with ST409 (BOVIS2; n = 2), ST479 (BOVIS3; n = 2), ST683 (BOVIS2; n = 1), ST1306 (BOV; n = 1), ST1625 (BOVIS2; n = 1), and 2 new patterns were identified (Figure 1). MIRU-VNTR patterns Clustering of MIRU-VNTR patterns by the UPGMA method showed a greater diversity of patterns in the mycobacterial strains studied. A total of 40 patterns were produced from 48 MTb strains, 5 clusters were identified (2 clusters with 4 and 3 strains, respectively, and 3 clusters with 2 strains in each). The remaining 35

strains showed unique patterns. Nine M. bovis strains produced a total of 7 patterns (Figure 1), 1 cluster was identified with 3 PDK4 strains, while 6 strains presented unique patterns. Genomic diversity of MTb isolates The discriminatory power of MIRU-VNTR typing was compared to that of IS6110 RFLP and spoligotyping by analyzing only MTb strains. Overall, MIRU-VNTR typing discriminated 40 different patterns (Figure 1); in comparison, only 27 different patterns were obtained with IS6110 RFLP and 21 patterns were obtained with spoligotyping. MIRU-VNTR typing performed even better than a combination of spoligotyping and IS6110 RFLP, which discriminated 36 patterns. The maximal discrimination was apparently achieved by combining MIRU-VNTR and IS6110 RFLP typing, resulting in 46 patterns. Spoligotypes could often be distinguished by MIRU-VNTR typing; for instance, the single ST42 spoligotype corresponded to 9 distinct MIRU-VNTR genotypes (Figure 1).