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Background  Insecticide resistance in  Anopheles coluzzii  mosquitoes has become widespread throughout West Africa including in Burkina Faso. The insecticide resistance allele ( kdr  or L1014F) is a prime indicator that is highly correlated with phenotypic resistance in West Africa. Studies from Benin, Ghana and Mali have suggested that the source of the L1014F is introgression of the 2L divergence island via interspecific hybridization with  Anopheles gambiae.  The goal of this study was to characterize local mosquito populations in the Nouna Department, Burkina Faso with respect to: (i) the extent of introgression between  An. coluzzii  and  An. gambiae , (ii) the frequency of the L1014F mutation and (iii)  Plasmodium  infection rates.    Methods  A total of 95 mosquitoes were collected from ten sites surrounding Nouna town in Kossi Province, Burkina Faso in 2012. The species composition, the extent of introgression in  An. coluzzii  mosquitoes and their  Plasmodium  infection rates were identified with a modified version of the “Divergence Island SNP” (DIS) genotyping assay.    Results  The mosquito collection contained 70.5%  An. coluzzii , 89.3% of which carried a 3 Mb genomic region on the 2L chromosome with L1014F insecticide resistance mutation that was introgressed from  An. gambiae . In addition, 22.4% in the introgressed  An. coluzzii  specimens were infected with  Plasmodium falciparum , whereas none of the non-introgressed (“pure”)  An. coluzzii  were infected.    Conclusion  This paper is the first report providing divergence island SNP genotypes for natural population of Burkina Faso and corresponding  Plasmodium  infection rates. These observations warrant further study and could have a major impact on future malaria control strategies in Burkina Faso.    Electronic supplementary material  The online version of this article (10.1186/s12936-019-2759-1) contains supplementary material, which is available to authorized users.

Introgression between Anopheles gambiae and Anopheles coluzzii in Burkina Faso and its associations with kdr resistance and Plasmodium infection