TABLE 3.
Description of clustered M. tuberculosis complex isolates (2 or more isolates in this study) from HIV+ and HIV- patients in Ibadan, Nigeria, and their worldwide distribution in the SITVIT2 database
| SIT (clade)a | Total (%) in subgroup | % in subgroup vs. SITVIT2 | Distribution (%) in regions with: |
|
|---|---|---|---|---|
| ≥5% of a given SITb | ≥5% of a given SITc | |||
| Clustered isolates in the HIV+ patient subgroup (n = 49) | ||||
| 53 (T1) | 4 (8.2) | 0.1 | AMER-N, 19.95; AMER-S, 14.67; EURO-W, 13.0; EURO-S, 10.16; ASIA-W, 8.81; AFRI-S, 6.04 | USA, 17.56; ZAF, 5.89; ITA, 5.20 |
| 61 (LAM10-CAM) | 6 (12.2) | 0.9 | AFRI-M, 27.59; AFRI-W, 25.39; AMER-N, 12.54; EURO-W, 10.97; ASIA-W, 6.90 | CMR, 26.49; NGA, 22.57; USA, 12.54; SAU, 6.90; FRA, 6.27 |
| 373 (T1) | 16 (32.7) | 29.1 | AFRI-W, 29.09; EURO-W, 16.36; AFRI-S, 14.55; AMER-S, 10.91; EURO-S, 9.09; EURO-E, 9.09; AMER-N, 7.27 | NGA, 29.09; ZAF, 14.55; CZE, 9.09; USA, 7.27; BEL, 7.27; PER, 5.45; AUT, 5.45; BRA, 5.45 |
| 403 (LAM10-CAM) | 6 (12.2) | 17.6 | AFRI-M, 44.12; AFRI-W, 26.47; AMER-N, 8.82; EURO-W, 8.82; ASIA-S, 5.88 | CMR, 44.12; NGA, 26.47; USA, 8.82; IND, 5.88 |
| Clustered isolates in the HIV− patient subgroup (n = 114) | ||||
| 42 (LAM9) | 2 (1.75) | 0.08 | AMER-S, 29.83; AMER-N, 16.28; EURO-S, 12.78; EURO-W, 7.02; AFRI-N, 5.07 | USA, 15.24; BRA, 10.33; COL, 7.87; ITA, 6.72 |
| 53 (T1) | 7 (6.14) | 0.15 | AMER-N, 19.95; AMER-S, 14.67; EURO-W, 13.0; EURO-S, 10.16; ASIA-W, 8.81; AFRI-S, 6.04 | USA, 17.56; ZAF, 5.89; ITA, 5.20 |
| 61 (LAM10-CAM) | 43 (37.72) | 6.36 | AFRI-M, 27.59; AFRI-W, 25.39; AMER-N, 12.54; EURO-W, 10.97; ASIA-W, 6.90 | CMR, 26.49; NGA, 22.57; USA, 12.54; SAU, 6.90; FRA, 6.27 |
| 181 (AFRI_1) | 2 (1.75) | 0.60 | AFRI-W, 80.06; AMER-N, 6.34; EURO-W, 6.04 | GNB, 51.06; GMB, 25.38; USA, 6.34 |
| 320 (AFRI_2) | 2 (1.75) | 22.22 | AFRI-W, 44.44; AMER-N, 22.22; AFRI-M, 22.22; EURO-S, 11.11 | NGA, 44.44; USA, 22.22; CMR, 22.22; ESP, 11.11 |
| 330 (AFRI_2) | 2 (1.75) | 33.33 | AFRI-W, 33.33; AFRI-M, 33.33; EURO-W, 16.67; AFRI-N, 16.67 | NGA, 33.33; CAF, 16.67; CMR, 16.67; TUN, 16.67; BEL, 16.67 |
| 331 (AFRI_2) | 5 (4.39) | 11.90 | AFRI-W, 64.29; AMER-N, 23.81; AFRI-M, 7.14 | NGA, 54.76; USA, 23.81; CIV, 7.14; CMR, 7.14 |
| 342 (EAI5) | 2 (1.75) | 12.50 | AFRI-W, 43.75; EURO-W, 25.00; EURO-N, 18.75; AMER-N, 12.50 | NGA, 31.25; GBR, 12.50; GMB, 12.50; USA, 12.50; BEL, 12.50; NLD, 6.25; DNK, 6.25; DEU, 6.25 |
| 438 (AFRI_3) | 4 (3.51) | 50.00 | AFRI-W, 75.00; AMER-N, 25.00 | NGA, 62.50; USA, 25.00; SLE, 12.50 |
| 504 (T3) | 2 (1.75) | 15.38 | AMER-N, 53.85; AFRI-W, 15.38; EURO-W, 7.69; EURO-S, 7.69; ASIA-S, 7.69; AFRI-E, 7.69 | USA, 53.85; NGA, 15.38; TZA, 7.69; FXX, 7.69; IND, 7.69; ITA, 7.69 |
| 1592 (AFRI_2) | 2 (1.75) | 33.33 | AFRI-W, 66.67; EURO-W, 33.33 | NGA, 66.67; DEU, 16.67; FRA, 16.67 |
| 2550 (LAM10-CAM) | 4 (3.51) | 26.67 | CARI, 46.67; AFRI-W, 26.67; ASIA-W, 6.67; AMER-S, 6.67; AMER-N, 6.67; AFRI-E, 6.67 | TTO, 46.67; NGA, 26.67; USA, 6.67; BRA, 6.67; TUR, 6.67; MDG, 6.67 |
| 2823d (AFRI_3) | 2 (1.75) | 66.67 | AFRI-W, 100.00 | NGA, 100.00 |
| 2825d (LAM10-CAM) | 2 (1.75) | 100.00 | AFRI-W, 100.00 | NGA, 100.00 |
| 2829d (AFRI_2) | 2 (1.75) | 100.00 | AFRI-W, 100.00 | NGA, 100.00 |
| 2831d (LAM10-CAM) | 3 (2.63) | 100.00 | AFRI-W, 100.00 | NGA, 100.00 |
| 2835d (EAI) | 3 (2.63) | 75.00 | AFRI-W, 100.00 | NGA, 100.00 |
SITs simultaneously present in HIV-positive and HIV-negative subgroups are in boldface.
Worldwide distribution is reported for regions with ≥5% of a given SIT compared to the total number in the SITVIT2 database. The definitions of regions and subregions are according to those of the United Nations (http://unstats.un.org/unsd/methods/m49/m49regin.htm): regions, AFRI (Africa), AMER (Americas), ASIA (Asia), EURO (Europe), and OCE (Oceania), subdivided into E (eastern), M (middle), C (central), N (northern), S (southern), SE (southeastern), and W (western). Furthermore, CARIB (Caribbean) belongs to the Americas, while Oceania is subdivided into 4 subregions, AUST (Australasia), MEL (Melanesia), MIC (Micronesia), and POLY (Polynesia). Note that in our classification scheme, Russia has been assigned a new subregion by itself (Northern Asia) instead of including it with the rest of Eastern Europe. This reflects its geographical location, as well as the similarity of specific TB genotypes circulating in Russia (a majority of Beijing genotypes) to those prevalent in Central, Eastern, and Southeast Asia.
The 3-letter country codes are defined in wikipedia (http://en.wikipedia.org/wiki/ISO_3166-1_alpha-3); countrywide distribution is shown only for SITs with ≥5% compared to their total number in the SITVIT2 database.
Newly created shared type (for details, see note d to Table 2).