Background
Methods
Study sites
Sample collection
Study Site | Classification | No. of samples tested | No. presumptively diagnosed based on symptoms | No. confirmed by microscopy |
---|---|---|---|---|
Terre Noire | Urban | 232 | 196 | 36 |
Leogane | Rural | 31 | 0 | 31 |
Artibonite | Rural | 25 | 0 | 25 |
Hinche | Rural | 10 | 0 | 10 |
Cap Haitien | Rural | 10 | 0 | 10 |
Jacmel | Rural | 11 | 0 | 11 |
Total | -- | 319 | 0 | 123 |
DNA extraction
PCR amplification
Gene | Primer | Sequence‡ | Nucleotide location | |
---|---|---|---|---|
dhfr
| PCR1 | M1* | TTTATGATGGAACAAGTCTGC | −3 to 18 |
M5* | AGTATATACATCGCTAACAGA | 625 to 645 | ||
PCR2 | M3* | TTTATGATGGAACAAGTCTGCGACGTT | −3 to 24 | |
F/* | AAATTCTTGATAAACAACGGAACCTTTTA | 491 to 519 | ||
dhps
| PCR1 | R2* | AACCTAAACGTGCTGTTCAA | 223 to 242 |
R/* | AATTGTGTGATTTGTCCACAA | 913 to 933 | ||
PCR2 | K* | TGCTAGTGTTATAGATATAGGATGAGCATC | 269 to 298 | |
K/* | CTATAACGAGGTATTGCATTTAATGCAAGAA | 676 to 706 | ||
Seq | Kb† | ATTGGTTTCGCATCACATTT | 408 to 427 |
Sequencing and alignment
Gene | Codon | Wild type codon(s) (amino acid) | Resistance codon(s) (amino acid) |
---|---|---|---|
dhfr
| 51 | AAT, AAC (N) | ATT (I) |
59 | TGT (C) | CGT (R) | |
108 | AGC (S) | AAC (N), ACC (T) | |
164 | ATA(I) | TTA (L) | |
dhps
| 436 | TCT (S) | GCT (A), TTT (F) |
437 | GCT (A) | GGT (G) | |
540 | AAA (K) | GAA (E) |
Statistical analysis
Results
Sampling summary and positive amplification results
Study Site | Total samples | # Positive amplifications | # Sequenced | ||||
---|---|---|---|---|---|---|---|
ssu rRNA
|
dhfr
|
dhps
|
dhfr
|
dhps
|
Both dhfr and dhps
| ||
Terre Noire † | 232 | 39 (SS1 =13, SS2 =26) | 33 (SS1 =12, SS2 =21) | 31 (SS1 = 10, SS2 = 21) | 30 (SS1 = 12, SS2 = 18) | 23 (SS1 = 10, SS2 = 13) | 21 (SS1 = 10, SS2 = 11) |
Leogane | 31 | 24 | 14 | 18 | 13 | 13 | 10 |
Hinche | 10 | 6 | 5 | 8 | 5 | 8 | 4 |
Cap Haitien | 10 | 1 | 4 | 8 | 4 | 7 | 4 |
Jacmel | 11 | 6 | 9 | 8 | 9 | 7 | 7 |
Total* | 294 | 76 | 65 | 73 | 61 | 58 | 46 |
Dhfr and dhps mutations
Study Site | # DHFR sequenced | S108N mutants (%) |
---|---|---|
Terre Noire | 30 | 11 (36.67%) |
Leogane | 13 | 2 (13.33%) |
Hinche | 5 | 0 (0%) |
Cap Haitien | 4 | 1 (25%) |
Jacmel | 9 | 6 (66.67%) |
Total | 61 | 20 (32.79%) |