| Summary: | <p>Abstract</p> <p>Background</p> <p>The mutations in <it>Plasmodium falciparum</it> chloroquine resistance transporter (<it>pfcrt</it>), multidrug resistance 1 (<it>pfmdr1</it>), dihydrofolate reductase (<it>pfdhfr</it>), dihydropteroate synthase (<it>pfdhps</it>) and ATPase (<it>pfatp6</it>) genes were associated with anti-malaria drug resistance. The aim of this study was to investigate the prevalence of polymorphisms in <it>pfcrt</it>, <it>pfmdr1</it>, <it>pfdhfr</it>, <it>pfdhps</it> and <it>pfatp6</it> in Yunnan Province. Finger-prick blood samples were collected from malaria-positive patients from Yunnan Province in 2009-2010. Single-nucleotide polymorphisms (SNPs) in the resistance-related genes were analysed by various PCR-based methods.</p> <p>Results</p> <p>A total of 108 blood samples were collected. Although chloroquine has not been used to treat falciparum malaria for nearly 30 years, 95.3% of the parasites still carried the <it>pfcrt</it> K76T mutation, whereas the majority of isolates displayed the wild-type <it>pfmdr1</it> N86 and D1246 sequences. The molecular level of sulphadoxine–pyrimethamine resistance in <it>P. falciparum</it> was high. The most prevalent mutation was <it>pfdhfr</it> C59R (95.9%), whereas the frequencies of the quadruple, triple and double mutants were 22.7% (N51I/C59R/S108N/I164L), 51.5% (N51I/C59R/S108N, N51I/C59R/I164L and C59R/S108N/ I164L) and 21.6% (N51I/ C59R, C59R/S108N and C59R/I164L), respectively. A437G (n = 77) and K540E (n = 71) were the most prevalent mutations in <it>pfdhps</it>, and 52.7% of the samples were double mutants, among which A437G/K540E was the most common double mutation (37/49). Quadruple mutants were found in 28.0% (26/93) of samples. A total of 8.6% of isolates (8/93) carried the S436A/A437G/A581G triple mutation. No mutations were found in <it>pfatp6</it> codons 623 or 769, but another two mutations (N683K and R756K) were found in 4.6% (3/97) and 9.2% (6/97) of parasite isolates, respectively.</p> <p>Conclusions</p> <p>This study identified a high frequency of mutations in <it>pfcrt</it>, <it>pfdhfr</it> and <it>pfdhps</it> associated with CQ and SP resistance in <it>P. falciparum</it> and no mutations linked to artemisinin resistance (<it>pfatp6</it>). Molecular epidemiology should be included in routine surveillance protocols and used to provide complementary information to assess the appropriateness of the current national anti-malarial drug policy.</p>
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