Identification of pyrimethamine- and chloroquine-resistant Plasmodium falciparum in Africa between 1984 and 1998: genotyping of archive blood samples

Abstract

Background: Understanding the geographical distribution of drug resistance of Plasmodium falciparum is important for the effective treatment of malaria. Drug resistance has previously been inferred mainly from records of clinical resistance. However, clinical resistance is not always consistent with the parasite's genetic resistance. Thus, molecular identification of the parasite's drug resistance is required. In Africa, clinical resistance to pyrimethamine (Pyr) and chloroquine (CQ) was evident before 1980 but few studies investigating the genetic resistance to these drugs were conducted before the late 1990s. In this study, genotyping of genes involved in resistance to Pyr and CQ was performed using archive blood samples from Africa between 1984 and 1998.

Methods: Parasite DNA was extracted from P. falciparum-infected blood smears collected from travellers returning to Japan from Africa between 1984 and 1998. Genotypes of the dihydrofolate reductase gene (dhfr) and CQ-resistance transporter gene (pfcrt) were determined by polymerase chain reaction amplification and sequencing.

Results: Genotyping of dhfr and pfcrt was successful in 59 and 80 samples, respectively. One wild-type and seven mutant dhfr genotypes were identified. Three dhfr genotypes lacking the S108N mutation (NRSI, ICSI, IRSI; amino acids at positions 51, 59, 108, and 164 with mutations underlined) were highly prevalent before 1994 but reduced after 1995, accompanied by an increase in genotypes with the S108N mutation. The dhfr IRNI genotype was first identified in Nigeria in 1991 in the present samples, and its frequency gradually increased. However, two double mutants (ICNI and NRNI), the latter of which was exclusively found in West Africa, were more frequent than the IRNI genotype. Only two pfcrt genotypes were found, the wild-type and a Southeast Asian type (CVIET; amino acids at positions 72-76 with mutations underlined). The CVIET genotype was already present as early as 1984 in Tanzania and Nigeria, and appeared throughout Africa between 1984 and 1998.

Conclusions: This study is the first to report the molecular identification of Pyr- and CQ-resistant genotypes of P. falciparum in Africa before 1990. Genotyping of dhfr and pfcrt using archive samples has revealed new aspects of the evolutionary history of Pyr- and CQ-resistant parasites in Africa.

Figure 1

Yearly change in the number of dhfr- and pfcrt-genotypes in Africa between 1984 and 1998. (a) Wild-type (NCSI), pyrimethamine-sensitive (NRSI, ICSI, IRSI) and pyrimethamine-resistant (NCNI, ICNI, NRNI, IRNI) dhfr genotypes were identified in blood samples collected from cases of Plasmodium falciparum malaria in Africa between 1984 and 1998. The height of each coloured bar shows the number of samples in that year infected with that particular genotype. (b) Wild-type (CVMNK; white bars) and chloroquine-resistant (CVIET; black bars) pfcrt genotypes were identified in blood samples collected as above. The height of each bar shows the number of samples in that year infected with that genotype.

Figure 2

Time-line scheme for dhfr and pfcrt genotypes determined using samples from Africa between 1984 and 1998. (a) Wild-type (NCSI), pyrimethamine-sensitive (NRSI, ICSI, IRSI) and pyrimethamine-resistant (NCNI, ICNI, NRNI, IRNI) dhfr genotypes of Plasmodium falciparum are shown by the different coloured symbols, as listed at the bottom of the figure. In samples with mixed genotype infections, the different genotypes are listed together and underlined. Values in parentheses are the number of samples. *One individual that returned from Ghana in 1993 also visited Burkina Faso in the same trip. (b) Wild-type (CVMNK) and chloroquine-resistant (CVIET) pfcrt genotypes of P. falciparum are shown by white and black circles, respectively. In samples with mixed genotype infections, the different genotypes are listed together and underlined. Values in parentheses are the number of samples. *One individual returning from Ghana in 1993 and one individual returning from Togo in 1990 also visited Burkina Faso in the same trip.