Table 3.
Incidence estimates of MDR iNTS disease in sub-Saharan Africa
| Country* | Age group in years | PYO estimation† | Recruitment proportion† | Genome-sequenced iNTS cases | Crude MDR iNTS cases | Crude MDR iNTS incidence per 100 000 PYO | Adjusted MDR iNTS cases | Adjusted MDR iNTS incidence per 100 000 PYO (95% CI)‡ |
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| Proportion of catchment population visiting study facility in case of fever (95% CI) | Catchment population | Catchment population adjusted by health-seeking behaviour | PYO | ||||||||
| Burkina Faso | |||||||||||
| Nioko II | 0–1 | 81% (74 to 88) | 2208 | 1788 | 2097 | 247/1297 (19) | 2 | 1 | 48 | 5 | 251 (107 to 590) |
| 2–4 | 81% (75 to 86) | 1823 | 1477 | 2097 | 235/1259 (19) | 3 | 3 | 143 | 16 | 753 (460 to 1233) | |
| 5–14 | 81% (78 to 84) | 4295 | 3479 | 4889 | 228/889 (26) | 2 | 1 | 20 | 4 | 79 (29 to 214) | |
| <15 | n.a. | 8326 | 6744 | 9083 | n.a. | 7 | 5 | 55 | 25 | 274 (185 to 406) | |
| ≥15 | 81% (79 to 83) | 9428 | 7637 | 10 676 | 208/759 (27) | 1 | 1 | 9 | 4 | 35 (13 to 96) | |
| All | n.a. | 17 754 | 14 381 | 19 759 | n.a. | 8 | 6 | 30 | 29 | 145 (100 to 209) | |
| Polesgo | 0–1 | 92% (86 to 99) | 896 | 824 | 929 | 117/475 (25) | 1 | 1 | 108 | 4 | 431 (162 to 1147) |
| 2–4 | 83% (76 to 89) | 856 | 710 | 992 | 148/466 (32) | 2 | 2 | 202 | 6 | 630 (288 to 1380) | |
| 5–14 | 87% (83 to 91) | 1734 | 1509 | 2104 | 252/510 (49) | 0 | 0 | 0 | 0 | 0 | |
| <15 | n.a. | 3486 | 3043 | 4025 | n.a. | 3 | 3 | 75 | 10 | 255 (138 to 470) | |
| ≥15 | 87% (84 to 89) | 4088 | 3557 | 4917 | 239/629 (38) | 1 | 1 | 20 | 3 | 54 (16 to 179) | |
| All | n.a. | 7574 | 6600 | 8942 | n.a. | 4 | 4 | 45 | 13 | 144 (83 to 249) | |
| Ghana§ | |||||||||||
| AAN | 0–1 | 16% (14 to 18) | 11 222 | 1760 | 4080 | 41 | 88 | 24 | 588 | 59 | 1435 (1110 to 1854) |
| 2–4 | 16% (13 to 18) | 8086 | 1268 | 2940 | 41 | 23 | 9 | 306 | 22 | 747 (491 to 1135) | |
| 0–4 | n.a. | n.a. | n.a. | n.a. | n.a. | 111 | 33 | n.a. | n.a. | n.a. | |
| 5–14 | 16% (15 to 17) | 34 439 | 5415 | 12 554 | 623/1657 (38) | 6 | 6 | 48 | 16 | 126 (77 to 206) | |
| <15 | n.a. | 53 747 | 8443 | 19 574 | n.a. | 117 | 39 | 147 | 81 | 414 (333 to 515) | |
| ≥15 | n.a. | n.a. | n.a. | n.a. | n.a. | 16 | 10 | n.a. | n.a. | n.a. | |
| All_TSAP | n.a. | n.a. | n.a. | n.a. | n.a. | 133 | 49 | n.a. | n.a. | n.a. | |
| Non_TSAP¶ | n.a. | n.a. | n.a. | n.a. | n.a. | 49 | 39 | n.a. | n.a. | n.a. | |
| All | n.a. | n.a. | n.a. | n.a | n.a. | 182 | 88 | n.a. | n.a. | n.a. | |
| Guinea-Bissau | |||||||||||
| Bandim | 0–1 | 46% (39 to 54) | 10 852 | 4992 | 5198 | 206/631 (33) | 7 | 2 | 96 | 15 | 291 (176 to 482) |
| 2–4 | 43% (37 to 48) | 7307 | 3142 | 3866 | 175/359 (49) | 1 | 0 | 26 | 2 | 53 (13 to 208) | |
| 5–14 | 42% (41 to 48) | 19 905 | 8360 | 11 101 | 187/380 (49) | 1 | 0 | 18 | 4 | 37 (14 to 97) | |
| <15 | n.a. | 38 064 | 16 494 | 20 165 | n.a. | 9 | 2 | 40 | 21 | 105 (69 to 161) | |
| ≥15 | 45% (43 to 47) | 62 694 | 28 212 | 37 109 | 105/163 (64%) | 0 | 0 | 0 | 0 | 0 | |
| All | n.a. | 100 758 | 44 706 | 57 274 | n.a. | 9 | 2 | 14 | 21 | 37 (24 to 57) | |
| Kenya | |||||||||||
| Kibera | 0–1 | 42% (38 to 47) | 3467 | 1456 | 2031 | 99/99 (100) | 0 | 0 | 0 | 0 | 0 |
| 2–4 | 39% (36 to 43) | 3070 | 1197 | 2039 | 312/312 (100) | 0 | 0 | 0 | 0 | 0 | |
| 5–14 | 43% (39 to 47) | 7514 | 3231 | 5722 | 539/539 (100) | 0 | 0 | 0 | 0 | 0 | |
| <15 | n.a. | 14 051 | 5884 | 9792 | n.a. | 0 | 0 | 0 | 0 | 0 | |
| ≥15 | 35% (32 to 38) | 15 263 | 5342 | 9228 | 301/301 (100) | 1 | 1 | 11 | 1 | 11 (2 to 77) | |
| All | n.a. | 29 314 | 11 227 | 19 020 | n.a. | 1 | 1 | 5 | 1 | 5 (1 to 37) | |
| Senegal** | |||||||||||
| Pikine | 0–1 | 39% (32 to 46) | 20 120 | 7837 | 11 194 | n.a. | 0 | 0 | n.a. | n.a. | n.a. |
| 2–4 | 37% (33 to 41) | 30 180 | 11 097 | 15 851 | n.a. | 1 | 1 | n.a. | n.a. | n.a. | |
| 5–14 | 31% (28 to 34) | 96 152 | 29 807 | 42 577 | n.a. | 0 | 0 | n.a. | n.a. | n.a. | |
| <15 | n.a. | 146 452 | 48 741 | 69 623 | n.a. | 1 | 1 | n.a. | n.a. | n.a. | |
| ≥15 | 30% (28 to 31) | 195 726 | 58 718 | 83 874 | n.a. | 1 | 0 | n.a. | n.a. | n.a. | |
| All | n.a. | 342 178 | 107 459 | 153 496 | n.a. | 2 | 1 | n.a. | n.a. | n.a. | |
*TSAP was performed in 10 countries, of which 8 countries (Burkina Faso, Ghana, Guinea-Bissau, Kenya, Madagascar, Senegal, South Africa and Tanzania in alphabetical order) exhibited positive iNTS isolates confirmed via whole genome sequencing. MDR iNTS were found in 5/8 countries presented in this table. No MDR iNTS were detected via whole genome sequencing from the isolates yielded from Madagascar, South Africa and Tanzania.
†PYO estimation methodologies have been published in detail in the TSAP typhoid burden paper (Marks et al, Lancet Global Health, 2017).
‡Adjusted MDR iNTS incidence per 100 000 PYO (95% CI): adjustments for case recruitment and error factors.
§Ghana samples included in this estimation of MDR iNTS are from the TSAP only.
¶Non-TSAP includes other fever surveillance performed in Agogo (‘IsolateAgogo’, ‘FISA’ and ‘zTYSA’). Refer to the Methods section.
**Adjusted MDR incidence of iNTS per 100 000 PYO could not be estimated for the study site in Senegal due to unavailable data on the recruitment proportion. The one MDR iNTS patient confirmed and presented in this table (crude MDR iNTS case) was a male infant aged 17 months, infected in 2012 with S. Enteritidis ST11. The one non-MDR iNTS patient presented in this table (genome-sequenced iNTS case) was a male adult aged 66 years, infected in 2012 with S. Typhimurium.
n.a., not available; PYO, person-years-of-observation.