As illustrated in Fig 2, the 4 most predominant lineages comprised both PGG1 and PGG2/3 lineages: Latin-American Mediterranean (LAM), n = 165 or 37.1% (PGG 2/3); ancestral East African-Indian (EAI), n = 132 or 29.7% (PGG1); an evolutionary recent but yet ill-defined T clade, n = 52 or 11.7% (PGG 2/3); and the globally-emerging Beijing clone, n = 31 or 7% (PGG1). The rest of the lineages were in the following order: Haarlem (H), n = 14 or 3.1% (PGG2/3); X clade, n = 13 or 2.9% (PGG2/3); Central Asian (CAS), n = 11 or 2.5% (PGG1). Moreover, we found 5 isolates with Manu patterns (2 isolates with Manu1 pattern and 3 isolates with Manu2 pattern) or 1.1% (PGG1),
that were further investigated for Region of Difference (RD) 105 polymorphism. A high spoligotype diversity was documented for EAI, LAM and T lineages (Fig 2). Indeed, GDC-0994 datasheet out of the 12 sublineages reported so far worldwide for the LAM clade [5], a total of 8 sublineages were present in our 1 year recruitment. BX-795 chemical structure A high diversity was also evidenced for other PGG1 clades (CAS), as well as PGG2/3 clades (X clade
and H). Furthermore, no M. africanum or M. bovis were found in this study. We also attempted to describe the worldwide distribution of predominant SITs (and lineages) encountered in this study. As shown in Table 1, we observed that many of the predominant SITs in our study belonging both to ancient PGG1 strains (SIT8/EAI5, SIT48/EAI1-SOM, SIT129/EAI6-BGD, SIT702/EAI6-BGD1, SIT806/EAI1-SOM) and evolutionary recent PGG2/3 strains (SIT33/LAM3, SIT59/LAM11-ZWE, SIT92/X3, SIT811/LAM11-ZWE, SIT815/LAM11-ZWE) were more frequently
present in Eastern and Gemcitabine molecular weight Southern Africa (mostly among its immediate neighbours Zimbabwe, Zambia, South Africa, Malawi, and to a lesser extent to Tanzania, Namibia, and PF299 order Somalia). Furthermore, 8 lineages or sublineages in Table 1 were made-up of their prototypes in the SITVIT2 database; these concerned SIT20 for LAM1, SIT33 for LAM3, SIT42 for LAM9, SIT48 for EAI1-SOM, SIT53 for T1, SIT59 for LAM11-ZWE, and SIT92 for X3 sublineages. Table 1 Description of predominant SITs (representing 8 or more strains) in our study, and their worldwide distribution SIT (Clade) Number (%) in this study % in this study as compared to SITVIT2 Distribution in Regions with 5% of a given SITs * Distribution in countries with ≥5% of a given SITs ** 1 (Beijing) 30 (6.74) 0.46 AMER-N 30.72, ASIA-SE 13.92, AFRI-S 11.76, ASIA-E 11.21, ASIA-N 8.36 USA 30.65, ZAF 11.77, RUS 8.36, JPN 8.19, VNM 5.96 8 (EAI5) 12 (2.70) 10.26 AFRI-E 26.50, EURO-N 24.79, AMER-N 24.79, ASIA-W 6.84, AFRI-S 5.13 USA 24.79, DNK 13.68, MOZ 10.26, TZA 9.40, GBR 8.55, ZMB 6.84, SAU 5.13, ZAF 5.13 20 (LAM1) 14 (3.15) 2.02 AMER-S 24.68, AMER-N 24.68, AFRI-S 12.84, EURO-S 11.40, EURO-W 8.23, CARI 6.20, AFRI-E 5.05 USA 22.94, BRA 14.29, NAM 8.95, PRT 7.07, VEN 6.06 33 (LAM3) 8 (1.80) 0.83 AFRI-S 32.60, AMER-S 23.33, AMER-N 16.77, EURO-S 14.37, EURO-W 5.73 ZAF 32.60, USA 16.56, BRA 9.48, ESP 9.