Given the emergence of drug resistance and the high rate of polyclonal microorganism infections, the availability of a fast and sensitive test to detect minority mutant populations would be an improvement in the diagnosis of infectious diseases. A clamped-probe real-time PCR assay to diagnose the Plasmodium falciparum K76T mutation in clone populations was developed, using a wild-type-specific locked-nucleic-acid-containing oligomer to suppress wild-type PCR amplification and to enhance melting analysis with a mutation-specific detection probe.In the last few decades, the emergence of drug resistance has become a major problem for the treatment of various infectious diseases. Bacterial, viral, or parasitic infections are often polyclonal (4,10,12,25,27). Drug-resistant individuals may hide among a sensitive population and the identification of a resistant clone may have implications for epidemiology and treatment. Molecular diagnosis of resistant microorganisms by mutation detection is a routine examination in virology (17,20) and has started to be used in bacteriology (5,19,23) and parasitology (24). Recent virology studies have indicated that the presence of minority drug-resistant variants may be an independent predictor of treatment failure (8, 9). The emergence of nosocomial infections caused by drug-resistant bacteria also represents a significant threat for debilitated patients (22). As a consequence, a need exists to have a fast and sensitive diagnostic test to identify minority populations of resistant organisms. In order to improve the efficacy of such a genotype-assisted diagnosis, methods have been developed to lower the detection threshold of minority populations among a wild-type one. This trend was demonstrated by two recent studies. First, a rapid and accurate method of duplex real-time PCR used to detect ampicillin-resistant Enterococcus faecium, a major cause of nosocomial infections, was recently published (19). Second, an RNA heteroduplex generator tracking assay elicited a decrease in the detection threshold of type 1 human immunodeficiency virus mutant populations from 20 to 0.5% (12). Concerning the diagnosis of Plasmodium falciparum malaria, the detection of a minority population has become important with the discovery of Pfcrt K76T mutation, which has been correlated with in vitro chloroquine resistance (1,7,26).Chloroquine has proved to be one of the most successful drugs ever deployed against P. falciparum malaria, mainly because it is well tolerated and available at a very low cost. Over the last three decades, P. falciparum chloroquine resistance has significantly increased, and many countries have discarded this drug from the antimalarial weaponry. In these areas, it has recently been observed that the reappearance of chloroquinesensitive P. falciparum strains has followed chloroquine withdrawal (15, 21). This phenomenon, if confirmed in the future, could make reusing chloroquine as the first line treatment of malaria possible (18, 21), e.g., in combination with artemisinin derivati...