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Background  Sulphadoxine-pyrimethamine (SP) and chloroquine (CQ) have been used in treatment of falciparum and vivax malaria in Nepal. Recently, resistance to both drugs have necessitated a change towards artemisinin combination therapy (ACT) against  Plasmodium falciparum  in highly endemic areas. However, SP is still used against  P. falciparum  infections in low endemic areas while CQ is used in suspected cases in areas with lack of diagnostic facilities. This study examines the prevalence of molecular markers of CQ and SP resistance in  P. falciparum  and  Plasmodium vivax  to determine if high levels of  in vivo  resistance are reflected at molecular level as well.    Methods  Finger prick blood samples (n = 189) were collected from malaria positive patients from two high endemic districts and analysed for single nucleotide polymorphisms (SNPs) in the resistance related genes of  P. falciparum  and  P. vivax  for CQ ( Pfcrt, Pfmdr1, Pvmdr1 ) and SP ( Pfdhfr, Pfdhps, Pvdhfr ), using various PCR-based methods.    Results and discussion  Positive  P. vivax  and  P. falciparum  infections were identified by PCR in 92 and 41 samples respectively. However, some of these were negative in subsequent PCRs. Based on a few  P. falciparum  samples, the molecular level of CQ resistance in  P. falciparum  was high since nearly all parasites had the  Pfcrt  mutant haplotypes CVIET (55%) or SVMNT (42%), though frequency of the  Pfmdr1  wild type haplotype was relatively low (35%). Molecular level of SP resistance in  P. falciparum  was found to be high. The most prevalent  Pfdhfr  haplotype was double mutant CNRNI (91%), while frequency of  Pfdhps  double mutant SGEAA and AGEAA were 38% and 33% respectively. Combined, the frequency of quadruple mutations (CNRNI-SGEAA/AGEAA) was 63%. Based on  P. vivax  samples, low CQ and SP resistance were most likely due to low prevalence of  Pvmdr1  Y976F mutation (5%) and absence of triple/quadruple mutations in  Pvdhfr .    Conclusions  Based on the limited number of samples, prevalence of CQ and SP resistance at molecular levels in the population in the study area were determined as high in  P. falciparum  and low in  P. vivax . Therefore, CQ could still be used in the treatment of  P. vivax  infections, but this remains to be tested  in vivo  while the change to ACT for  P. falciparum  seems justified.

Prevalence of molecular markers of anti-malarial drug resistance in Plasmodium vivax and Plasmodium falciparum in two districts of Nepal