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Background  Tanzania abandoned sulfadoxine-pyrimethamine (SP) as the first-line treatment for uncomplicated malaria in 2006 due to high levels  Plasmodium falciparum  resistance. However, SP is still being used for intermittent preventive treatment during pregnancy (IPTp-SP). This study aimed to assess the pattern of  P. falciparum  dihydrofolate reductase  (Pfdhfr)  and  dihydropteroate synthetase (Pfdhps)  mutations and associated haplotypes in areas with different malaria transmission intensities in mainland Tanzania, 6 years after withdrawal of SP as a first-line treatment regimen for uncomplicated malaria.    Methods  A total of 264 samples were collected during cross-sectional surveys in three districts of Muheza, Muleba and Nachingwea in Tanga, Kagera and Lindi regions, respectively. Parasite genomic DNA was extracted from  P. falciparum  positive samples. The  Pfdhfr, Pfdhps  single nucleotide polymorphisms (SNPs) were amplified using nested polymerase chain reaction and detected by sequence specific oligonucleotide probe-enzyme linked immunosorbent assay (SSOP-ELISA).    Results  The prevalence of the mutant  Pfdhfr - Pfdhps  haplotypes was heterogenous and transmission dependent. The triple  Pfdhfr  mutant haplotypes (C  IRN  I) were predominant in all sites with significantly higher frequencies at Muheza (93.3 %) compared to Muleba (75.0 %) and Nachingwea districts (70.6 %), (p < 0.001). Overall, the prevalence of the wild-type  Pfdhps  (SAKAA) haplotype was lowest at Muheza (1.3 %), (p = 0.002). Double  Pfdhps  haplotype S  GE  AA was significantly high at Muheza (27.2 %) and Muleba (20.8 %) while none (0 %) was detected at Nachingwea (p < 0.001). The prevalence of triple  Pfdhps  S  GEG  A haplotype was significantly higher at Muheza compared to Muleba and Nachingwea (p < 0.001). In contrast, Nachingwea and Muleba had significantly higher prevalence of another triple  Pfdhps   AGE  AA haplotype (χ 2  = 39.9, p < 0.001). Conversely,  Pfdhfr - Pfdhps  as quintuple and sextuple haplotypes were predominant including the emergence of a septuple mutant haplotype C  IRN  I-  AGEG  A (n = 11) observed at Muheza and Muleba.    Conclusion  These results ascertain the high prevalence and saturation of  Pfdhfr  and  Pfdhps  haplotypes conferring SP resistance in areas with changing malaria epidemiology; and this could undermine the use of IPTp-SP in improving pregnancy outcomes. In these settings where high level SP resistance is documented, additional control efforts are needed and evaluation of an alternative drug for IPTp is an urgent priority.

High-level Plasmodium falciparum sulfadoxine-pyrimethamine resistance with the concomitant occurrence of septuple haplotype in Tanzania