Insecticide resistant Anopheles from Ethiopia but not Burkina Faso show a microbiome composition shift upon insecticide exposure

Malaria remains a key contributor to mortality and morbidity across Africa, with the highest burden in children under five. Insecticide based vector control tools, which target the adult Anopheles mosquito are the most efficacious tool in disease prevention. Due to the widespread use of these interventions, insecticide resistance is now ubiquitous across Africa. Understanding the underlying mechanisms contributing to this phenotype is necessary to both track the spread of resistance and to design new tools to overcome resistance. Here, we show that the microbiome composition of insecticide resistant populations of An. gambiae, An. coluzzii and An. arabiensis originating in Burkina Faso from field caught populations and colonies across two countries show no changes in microbial composition compared to their susceptible counterparts. In contrast, An. arabiensis from Ethiopia demonstrates clear differences in microbiome composition in those dying and surviving insecticide exposure. To further understand resistance in this An. arabiensis population, we performed RNAseq and saw differential expression of detoxification genes associated with insecticide resistance and changes to respiration, metabolism and synapse-related ion channels. Taken together, these results indicate that in addition to changes to the transcriptome, the microbiome can contribute to insecticide resistance in certain settings.