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Background  The emergence of pyrethroid resistance in the malaria vector,  Anopheles arabiensis , threatens to undermine the considerable gains made towards eliminating malaria on Zanzibar. Previously, resistance was restricted to the island of Pemba while mosquitoes from Unguja, the larger of the two islands of Zanzibar, were susceptible. Here, we characterised the mechanism(s) responsible for resistance on Zanzibar using a combination of gene expression and target-site mutation assays.    Methods  WHO resistance bioassays were conducted using 1-5d old adult  Anopheles gambiae s.l.  collected between 2011 and 2013 across the archipelago. Synergist assays with the P450 inhibitor piperonyl-butoxide were performed in 2013. Members of the  An. gambiae  complex were PCR-identified and screened for target-site mutations ( kdr  and  Ace-1 ). Gene expression in pyrethroid resistant  An. arabiensis  from Pemba was analysed using whole-genome microarrays.    Results  Pyrethroid resistance is now present across the entire Zanzibar archipelago. Survival to the pyrethroid lambda-cyhalothrin in bioassays conducted in 2013 was 23.5-54.3% on Unguja and 32.9-81.7% on Pemba. We present evidence that resistance is mediated, in part at least, by elevated P450 monoxygenases. Whole-genome microarray scans showed that the most enriched gene terms in resistant  An. arabiensis  from Pemba were associated with P450 activity and synergist assays with PBO completely restored susceptibility to pyrethroids in both islands.  CYP4G16  was the most consistently over-expressed gene in resistant mosquitoes compared with two susceptible strains from Unguja and Dar es Salaam. Expression of this P450 is enriched in the abdomen and it is thought to play a role in hydrocarbon synthesis. Microarray and qPCR detected several additional genes putatively involved in this pathway enriched in the Pemba pyrethroid resistant population and we hypothesise that resistance may be, in part, related to alterations in the structure of the mosquito cuticle. None of the  kdr  target-site mutations, associated with pyrethroid/DDT resistance in  An. gambiae  elsewhere in Africa, were found on the islands.    Conclusion  The consequences of this resistance phenotype are discussed in relation to future vector control strategies on Zanzibar to support the ongoing malaria elimination efforts on the islands.

The dynamics of pyrethroid resistance in Anopheles arabiensis from Zanzibar and an assessment of the underlying genetic basis