PCR genotyping In areas of intense transmission, where multiple genotype infections are common , a second episode of malaria or a recurrent parasitaemia during the drug-free follow-up period may be due to the same infection or a different infection (a recrudescence, thus a treatment failure, or a new infection, respectively). To distinguish these two events, polymorphic P. falciparum genes, such as the merozoite surface protein 1 and 2 genes (msp1 and msp2) and the glutamate-rich protein gene (glurp) were genotyped by PCR, as previously described. PCR analyses, conducted at the Epicentre research base, Mbarara, Uganda, were performed using paired samples from all patients experiencing late clinical or parasitologic failure. Blood was collected on filter paper (Whatman FTA® Cards) on the day of enrollment and the day treatment failure occurred. The genotypic profiles for pre- and post-treatment parasites were compared; patients in which pre- and post-treatment genotypes were identical were considered as recrudescences and patients in which pre- and post-treatment genotypes were different were considered as new infections.