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Background  Determining the source of malaria outbreaks in Ecuador and identifying remaining transmission foci will help in malaria elimination efforts. In this study, the genetic signatures of  Plasmodium falciparum  isolates, obtained from an outbreak that occurred in northwest Ecuador from 2012 to 2013, were characterized.    Methods  Molecular investigation of the outbreak was performed using neutral microsatellites, drug resistance markers and  pfhrp2  and  pfhrp3  genotyping.    Results  A majority of parasite isolates (31/32) from this outbreak were of a single clonal type that matched a clonal lineage previously described on the northern coast of Peru and a historical isolate from Ecuador. All but one isolate carried a chloroquine-resistant  pfcrt  genotype and sulfadoxine- and pyrimethamine-sensitive  pfdhps  and  pfdhfr  genotypes.  Pfmdr1  mutations were identified in codons 184 and 1042. In addition, most samples (97 %) showed presence of  pfhrp2  gene.    Conclusions  This study indicates that parasites from a single clonal lineage largely contributed to this outbreak and this lineage was found to be genetically related to a lineage previously reported in the Peruvian coast and historical Ecuadorian parasites.    Electronic supplementary material  The online version of this article (doi:10.1186/s12936-015-1019-2) contains supplementary material, which is available to authorized users.

Clonal population expansion in an outbreak of Plasmodium falciparum on the northwest coast of Ecuador