TABLE 3.
Molecular typing of N. meningitidis in specimens from the 2019 Togo and Burkina Faso meningitis outbreaka
| Specimen | Sequencing method | CT, sodC | Genome assembly size (kb) | No. of cgMLST loci identified | No. of molecular typing loci | No. of MLST loci | Sequence type; clonal complexb |
|---|---|---|---|---|---|---|---|
| BF_1 | Unenr | 17 | 2,136,395 | 1,559 | 14 | 7 | ST-10217; CC10217 |
| BF_2 | Unenr | 19 | 2,132,672 | 1,556 | 14 | 7 | ST-10217; CC10217 |
| BF_3 | Unenr | 17 | 2,132,682 | 1,557 | 14 | 7 | ST-10217; CC10217 |
| BF_4 | Unenr | 16 | 2,064,493 | 1,560 | 14 | 7 | ST-10217; CC10217 |
| BF_5 | Unenr | 16 | 2,063,009 | 1,564 | 14 | 7 | ST-10217; CC10217 |
| BF_6 | Unenr | 19 | 2,052,439 | 1,559 | 14 | 7 | ST-10217; CC10217 |
| BF_7 | Unenr | 18 | 2,064,961 | 1,556 | 14 | 7 | ST-10217; CC10217 |
| BF_8 | Unenr | 19 | 2,069,327 | 1,563 | 14 | 7 | ST-10217; CC10217 |
| BF_9 | Unenr | 16 | 2,069,218 | 1,560 | 14 | 7 | ST-10217; CC10217 |
| BF_10 | Unenr/SWGA_1c | 17 | 2,093,455 | 1,553 | 14 | 7 | ST-10217; CC10217 |
| BF_11 | SWGA_1 | 21 | 2,104,298 | 1,530 | 14 | 7 | ST-10217; CC10217 |
| BF_12 | SWGA_1 | 30 | 2,059,934 | 1,509 | 14 | 7 | ST-10217; CC10217 |
| BF_13 | SWGA_1 | 25 | 1,351,960 | 534 | 9 | 5 | — |
| BF_14 | SWGA_1 | 30 | 2,133,478 | 1,535 | 14 | 7 | ST-10217; CC10217 |
| BF_15 | SWGA_1 | 22 | 2,064,379 | 1,520 | 13 | 6 | ST-ND; CC10217 |
| BF_16 | SWGA_1 | 33 | 2,095,986 | 1,551 | 14 | 7 | ST-10217; CC10217 |
| BF_17 | SWGA_1 | 26 | 2,085,832 | 1,549 | 14 | 7 | ST-10217; CC10217 |
| Togo_1 | Unenr | 17 | 2,121,115 | 1,552 | 14 | 7 | ST-9367; CC10217 |
| Togo_2 | SWGA_1 | 20 | 2,508,337 | 1,222 | 13 | 6 | — |
| Togo_3 | SWGA_1 | 33 | 1,081,654 | 442 | 4 | 2 | — |
| Togo_4 | SWGA_1 | 25 | 2,084,690 | 1,517 | 14 | 7 | ST-9367; CC10217 |
| Togo_5 | SWGA_1 | 32 | 1,077,209 | 410 | 4 | 2 | — |
| Togo_6 | SWGA_1 | 30 | 1,923,570 | 1,375 | 12 | 7 | ST-9367; CC10217 |
| Togo_7 | SWGA_1 | 22 | 2,114,107 | 1,539 | 14 | 7 | ST-9367; CC10217 |
| Togo_8 | SWGA_1 | 26 | 2,153,980 | 1,236 | 14 | 7 | ST-9367; CC10217 |
| Togo_9 | SWGA_1 | 25 | 2,114,641 | 1,533 | 14 | 7 | ST-9367; CC10217 |
| Togo_10 | SWGA_2 | 26 | 2,210,580 | 1,263 | 11 | 7 | New |
| Togo_11 | SWGA_1 | 22 | 1,679,000 | 952 | 10 | 4 | — |
| Togo_12 | SWGA_1 | 23 | 2,116,610 | 1,540 | 14 | 7 | ST-9367; CC10217 |
| Togo_13 | SWGA_1 | 28 | 2,003,579 | 1,413 | 12 | 6 | ST-ND; CC10217 |
| Togo_14 | SWGA_1 | 27 | 2,014,369 | 1,424 | 11 | 5 | ST-ND; CC10217 |
| Togo_15 | SWGA_1 | 21 | 2,107,985 | 1,544 | 14 | 7 | ST-9367; CC10217 |
| Togo_16 | SWGA_2 | 26 | 842,874 | 159 | 4 | 0 | — |
| Togo_17 | SWGA_1 | 23 | 2,365,275 | 1,377 | 14 | 7 | New |
| Togo_18 | SWGA_1 | 22 | 1,828,557 | 1,224 | 12 | 7 | New |
| Togo_19 | SWGA_1 | 20 | 2,061,090 | 1,557 | 14 | 7 | ST-9367; CC10217 |
a
Specimens which did not meet an accuracy cutoff of 1,400 in cgMLST are highlighted with gray shading. Unenr, unenriched; SWGA_1, SWGA protocol 1; SWGA_2, SWGA protocol 2.
b
ND, not determined (not enough information to identify the ST for the strain). “New” indicates a new sequence type (ST) or clonal complex (CC). A dash indicates nonavailability of ST and CC due to poor sequencing data. Full data are available in Table S6.
c
All but one locus was identified by sequencing of not enriched specimen. The missing locus (NhbA) was determined from the corresponding SWGA-enriched backup of the specimen.