Growing insecticide resistance in malaria vectors is threatening the effectiveness of insecticide-based interventions, including Long Lasting Insecticidal Nets (LLINs). However, the impact of metabolic resistance on the effectiveness of these tools remains poorly characterized. Using experimental hut trials and genotyping of a glutathione S-transferase resistance marker (L119F-GSTe2), we established that GST-mediated resistance is reducing the efficacy of LLINs against Anopheles funestus. Hut trials performed in Cameroon revealed that Piperonyl butoxide (PBO)-based nets induced a significantly higher mortality against pyrethroid resistant An. funestus than pyrethroid-only nets. Blood feeding rate and deterrence were significantly higher in all LLINs than control. Genotyping the L119F-GSTe2 mutation revealed that, for permethrin-based nets, 119F-GSTe2 resistant mosquitoes have a greater ability to blood feed than susceptible while the opposite effect is observed for deltamethrin-based nets. For Olyset Plus, a significant association with exophily was observed in resistant mosquitoes (OR = 11.7; p < 0.01). Furthermore, GSTe2-resistant mosquitoes (cone assays) significantly survived with PermaNet 2.0 (OR = 2.1; p < 0.01) and PermaNet 3.0 (side) (OR = 30.1; p < 0.001) but not for Olyset Plus. This study shows that the efficacy of PBO-based nets (e.g., blood feeding inhibition) against pyrethroid resistant malaria vectors could be impacted by other mechanisms including GST-mediated metabolic resistance not affected by the synergistic action of PBO. Mosaic LLINs incorporating a GST inhibitor (diethyl maleate) could help improve their efficacy in areas of GST-mediated resistance.

Resistance is threatening the effectiveness of insecticide-based interventions in use for malaria control. Pinpointing genes associated with resistance is crucial for evidence-based resistance management targeting the major malaria vectors. Here, a combination of RNA-seq based genome-wide transcriptional analysis and RNA-silencing in vivo functional validation were used to identify key insecticide resistance genes associated with DDT and DDT/permethrin cross-resistance across Africa. A cluster of glutathione-S-transferase from epsilon group were found to be overexpressed in resistant populations of Anopheles funestus across Africa including GSTe1 [Cameroon (fold change, FC: 2.54), Ghana (4.20), Malawi (2.51)], GSTe2 [Cameroon (4.47), Ghana (7.52), Malawi (2.13)], GSTe3 [Cameroon (2.49), Uganda (2.60)], GSTe4 in Ghana (3.47), GSTe5 [Ghana (2.94), Malawi (2.26)], GSTe6 [Cameroun (3.0), Ghana (3.11), Malawi (3.07), Uganda (3.78)] and GSTe7 (2.39) in Ghana. Validation of GSTe genes expression profiles by qPCR confirmed that the genes are differentially expressed across Africa with a greater overexpression in DDT-resistant mosquitoes. RNAi-based knock-down analyses supported that five GSTe genes are playing a major role in resistance to pyrethroids (permethrin and deltamethrin) and DDT in An. funestus, with a significant recovery of susceptibility observed when GSTe2, 3, 4, 5 and GSTe6 were silenced. These findings established that GSTe3, 4, 5 and 6 contribute to DDT resistance and should be further characterized to identify their specific genetic variants, to help design DNA-based diagnostic assays, as previously done for the 119F-GSTe2 mutation. This study highlights the role of GSTes in the development of resistance to insecticides in malaria vectors and calls for actions to mitigate this resistance.

Background: Insecticide resistance in malaria vectors is a serious challenge to malaria control and elimination. Elucidation of the role of detoxification genes in resistance is necessary to develop targeted strategies to reduce malaria burden. Glutathione S-transferase epsilon clusters (GSTe genes) are upregulated in DDT- and pyrethroid-resistant Anopheles funestus mosquitoes across Africa. However, except for GSTe2, the molecular mechanisms behind this upregulation remain unclear. Here, we established that overexpression and allelic variation of GSTe genes contribute to insecticide resistance in African malaria vector An. funestus s.s. Methods: Transcriptomic and genomic analyses of GSTe genes were conducted, followed by in silico structural analysis, and functional characterization of GSTe3, GSTe4 and GSTe6 using metabolic assay and transgenic expression in Drosophila flies. Results: Transcriptomic and genomic analyses reveal changes in gene expression and genetic diversity of GSTes cluster in An. funestus across Africa. Cloning of cDNAs of GSTes from different regions of Africa detected allelic variants under selection, including A¹⁷D²⁶T¹⁵⁸-GSTe3, L¹³⁵H¹⁹¹A¹⁸⁹-GSTe4 in West/Central Africa, and T¹⁶⁹S²⁰¹ E²¹⁰-GSTe6 present only in West/Southern Africa. Furthermore, in silico analysis of BN-GSTe3, MWI-GSTe3, BN-GSTe4, MWI-GSTe4, CMR-GSTe6 and, BN-GSTe6 alleles revealed that allelic variations increase the binding cavity in the active site of these GSTes with stronger affinities observed towards DDT and permethrin. All recombinant GSTes significantly metabolize DDT (41–63%) and permethrin (13–25%). Additionally, BN-GSTe4 (L¹³⁵H¹⁹¹A¹⁸⁹-GSTe4) variant significantly metabolizes deltamethrin (28.75%), compared to the wild-type allele (15.99%; p < 0.05). Transgenic expression of the GSTes in Drosophila melanogaster flies revealed reduced DDT mortalities in flies expressing the selected alleles (39–55%; p˂0.001), compared to control group (98%). Similar resistance patterns were observed toward permethrin and deltamethrin. Conclusion: These findings established the role of GSTes in conferring cross-resistance to pyrethroids and DDT, highlighting the role of these genes in metabolic resistance in An. funestus, which complicates malaria control using the above key insecticides.

The versatility of cytochrome P450 reductase (CPR) in transferring electrons to P450s from other closely related species has been extensively exploited, e.g., by using An. gambiae CPR (AgCPR), as a homologous surrogate, to validate the role of An. funestus P450s in insecticide resistance. However, genomic variation between the AgCPR and An. funestus CPR (AfCPR) suggests that the full metabolism spectrum of An. funestus P450s might be missed when using AgCPR. To test this hypothesis, we expressed AgCPR and AfCPR side-by-side with CYP6P9a and CYP6P9b and functionally validated their role in the detoxification of insecticides from five different classes. Major variations were observed within the FAD- and NADP-binding domains of AgCPR and AfCPR, e.g., the coordinates of the second FAD stacking residue AfCPR-Y⁴⁵⁶ differ from that of AgCPR-His⁴⁵⁶. While no significant differences were observed in the cytochrome c reductase activities, when co-expressed with their endogenous AfCPR, the P450s significantly metabolized higher amounts of permethrin and deltamethrin, with CYP6P9b-AfCPR membrane metabolizing α-cypermethrin as well. Only the CYP6P9a-AfCPR membrane significantly metabolized DDT (producing dicofol), bendiocarb, clothianidin, and chlorfenapyr (bioactivation into tralopyril). This demonstrates the broad substrate specificity of An. funestus CYP6P9a/-b, capturing their role in conferring cross-resistance towards unrelated insecticide classes, which can complicate resistance management.

Deciphering the molecular drivers of insecticide resistance is paramount to extending the effectiveness of malaria vector control tools. Here, we demonstrate that a P450 haplotype spanning a Glu ²⁰⁵ →Asp (E205D) amino acid point mutation in the CYP6P3 gene drives pyrethroid insecticide resistance in the mosquito malaria vector Anopheles gambiae . Pooled whole-genome DNA sequencing data from A. gambiae mosquitoes detected a major P450-linked locus (CYP6 haplotype) on chromosome 2R adjacent to the locus encoding a sodium channel. In vitro metabolism assays with recombinantly expressed CYP6P3 protein revealed that the catalytic efficiency of the 205D variant for the pyrethroid insecticide permethrin was 3.7 times higher than that of the E205 variant. Similar findings were made for the related insecticide α-cypermethrin. Overexpression of the 205D variant in transgenic flies conferred higher resistance to pyrethroids compared with flies expressing the susceptible E205 variant. A DNA-based assay confirmed that the CYP6P3 -E205D variant correlates with pyrethroid resistance in field mosquito populations [odds ratio (OR): 26.4; P < 0.0001] and reduces the efficacy of pyrethroid-only long-lasting insecticide bed nets. The homozygous resistance genotype of A. gambiae exhibited higher survival after exposure to the PermaNet 3.0 bed net compared with the susceptible SS genotype (OR: 6.1; P = 0.011). Furthermore, the CYP6P3 -E205D variant together with the kdr target-site resistance mechanism exacerbated the loss of bed net efficacy. The 205D variant is predominant in West and Central Africa but less abundant or absent in East and South Africa, with signs of introgression with Anopheles coluzzii in Ghana.

Aggravation of pyrethroid resistance threatens malaria control; yet, its molecular basis remains elusive. This study used a comprehensive multi-omics framework integrating 7-year gap temporal RNA-Seq, PoolSeq Whole Genome, and functional analyses, to uncover resistance escalation mechanisms in Anopheles funestus Africa-wide. Spatiotemporal analyses (2014–2021) reveal massive overexpression of novel genes (V-ATPase, tubulin alpha-1, transposase), alongside canonical resistance genes (P450s, cuticular proteins, chemosensory). Epigenetic regulators (histone H3/4, glycine N-methyltransferase) were greatly overexpressed in highly resistant mosquitoes, suggesting resistance modulation. P450-based signatures of selective sweep were detected with a drastic change in the rp1 and the P450 CYP9K1 in Central Africa. Noticeably, genomic variations at the cytochrome P450 reductase (CPR) gene were selected including a N70I mutation in Malawi [0% (2009)–80% (2021)] and a 5.9 kb promoter duplication in Ghana. Transgenic expression in Drosophila confirmed CPR-70I enhances pyrethroid resistance when co-expressed with P450-CYP6P9a, uncovering a novel CPR-mediated mechanism in intensely resistant mosquitoes. This study highlights novel candidate genes for marker development to track the spread of intensely resistant mosquitoes across Africa.