Table 3.
Pathogen Detection by 3 Testing Methods, Chad
| Latex | Culture | rt-PCRd | |||||
|---|---|---|---|---|---|---|---|
| Result | Total No. of Confirmed Pathogensa | No. Testedb (%) | No. Positivec (%) | No. Tested (%) | No. Positive (%) | No. Tested (%) | No. Positive (%) |
| 2010–2012 | |||||||
| Nm | 278 | 206 (74.1) | 204 (99.0) | 274 (98.6) | 151 (55.1) | … | … |
| NmA | 254 | 184 (72.4) | 183 (99.5) | 250 (98.4) | 145 (58.0) | … | … |
| NmWe | 20 | 20 (100.0) | 19 (95.0) | 20 (100.0) | 4 (20.0) | … | … |
| NmXf | 2 | 0 (0.0) | 0 (0.0) | 2 (100.0) | 2 (100.0) | … | … |
| Other Nm | 2 | 2 (100.0) | 2 (100.0) | 2 (100.0) | 0 (0.0) | … | … |
| Hig | 1 | 1 (100.0) | 1 (100.0) | 1 (100.0) | 0 (0.0) | … | … |
| Sp | 15 | 9 (60.0) | 8 (88.9) | 12 (80.0) | 10 (83.3) | … | … |
| Total confirmed | 294 | 216 (73.5) | 213 (98.6) | 287 (97.6) | 161 (56.1) | … | … |
| 2013–2015 | |||||||
| Nmh | 20 | 18 (90.0) | 17 (94.4) | 20 (100.0) | 6 (30.0) | … | … |
| NmA | 2 | 1 (50.0) | 1 (100.0) | 2 (100.0) | 1 (50.0) | … | … |
| NmWe | 16 | 16 (100.0) | 15 (93.8) | 16 (100.0) | 5 (31.3) | … | … |
| NmXf,i | 1 | 0 (0.0) | 0 (0.0) | 1 (100.0) | 0 (0.0) | … | … |
| Other Nm | 1 | 1 (100.0) | 1 (100.0) | 1 (100.0) | 0 (0.0) | … | … |
| Hig | 10 | 8 (80.0) | 5 (62.5) | 10 (100.0) | 7 (70.0) | … | … |
| Sp | 58 | 40 (69.0) | 31 (77.5) | 57 (98.3) | 42 (73.7) | … | … |
| Total confirmed | 88 | 66 (75.0) | 53 (80.3) | 87 (98.9) | 55 (63.2) | … | … |
| 2016–2018 | |||||||
| Nm | 86 | 14 (16.3) | 7 (50.0) | 73 (84.9) | 17 (23.3) | 85 (98.8) | 79 (92.9) |
| NmA | 0 | 0 (0.0) | 0 (0.0) | 0 (0.0) | 0 (0.0) | 0 (0.0) | 0 (0.0) |
| NmWe | 17 | 4 (23.5) | 4 (100.0) | 16 (94.1) | 2 (12.5) | 17 (100.0) | 16 (94.1) |
| NmXf | 58 | 6 (10.3) | 0 (0.0) | 46 (79.3) | 13 (28.3) | 58 (100.0) | 57 (98.3) |
| Other Nm | 10 | 3 (30.0) | 2 (66.7) | 10 (100.0) | 2 (20.0) | 9 (90.0) | 6 (66.7) |
| Hig | 39 | 6 (15.4) | 5 (83.3) | 38 (97.4) | 15 (39.5) | 38 (97.4) | 35 (92.1) |
| Sp | 136 | 18 (13.2) | 12 (66.7) | 132 (97.1) | 52 (39.4) | 135 (99.3) | 124 (91.9) |
| Total confirmed | 261 | 38 (14.6) | 24 (63.2) | 243 (93.1) | 84 (34.6) | 258 (98.9) | 238 (92.2) |
Abbreviations: Hi, Haemophilus influenzae; NmA, Neisseria meningitidis serogroup A; NmW, Neisseria meningitidis serogroup W; NmX, Neisseria meningitidis serogroup X; Other Nm, other Neisseria meningitidis groups, which are nongroupable, polyagglutinate, and autoagglutinate; rt-PCR, real-time polymerase chain reaction; Sp, Streptococcus pneumoniae.
aDistribution of pathogens is from the final case interpretations, which use the results from all test methods. The definition of final case interpretation is included in the “Methods” section.
bPercentage of specimens tested is calculated using the total number of pathogens (second column) as the denominator.
cThe percentage of positive cases is calculated using the number of specimens tested (third column) as the denominator.
drt-PCR was not implemented prior to 2016.
eTest results are reported as NmW/Y for latex because the test cannot differentiate between NmW and NmY.
fLatex does not test for NmX.
gAll of the identified Hi were Hib. Hi non-b has not been detected during these time periods.
hOne specimen was positive for NmB/Escherichia coli by latex in 2017 (post-MenAfriNet). The specimen tested negative for Nm, Hib, and Sp by culture and rt-PCR, and is excluded from the table.
iOne NmX case, collected in 2013, was tested and confirmed in 2017 using rt-PCR.