Using targeted next-generation sequencing to characterize genetic differences associated with insecticide resistance in Culex quinquefasciatus populations from the southern U.S

Insecticide resistance of Miami-Dade Culex quinquefasciatus populations and initial field efficacy of a new resistance-breaking adulticide formulation

Sporadic outbreaks of human cases of West Nile virus (WNV), primarily vectored by Culex quinquefasciatus Say in suburban and urban areas, have been reported since introduction of the virus into Florida in 2001. Miami-Dade County, Florida is part of one of the largest metropolitan areas in the United States, supports Cx. quinquefasciatus year-round, and recently experienced over 60 human cases of WNV during one outbreak. To facilitate more effective integrated vector management and public health protection, we used the Centers for Disease Control and Prevention (CDC) bottle bioassay method to evaluate the susceptibility of adult Cx. quinquefasciatus collected from 29 locations throughout Miami-Dade County to pyrethroid and organophosphate adulticide active ingredients (AIs) used by Miami-Dade County Mosquito Control. We also determined the frequency of the 1014 knockdown resistance (kdr) mutation for Cx. quinquefasciatus from a subset of 17 locations. We detected resistance to two pyrethroid AIs in all tested locations (permethrin: 27 locations, deltamethrin: 28 locations). The 1014F allele was widely distributed throughout all 17 locations sampled; however, 29.4% of these locations lacked 1014F homozygotes even though phenotypic pyrethroid resistance was present. Organophosphate resistance was more variable; 20.7% of the locations tested were susceptible to malathion, and 33.3% of the populations were susceptible to naled. We subsequently conducted a field trial of ReMoa Tri, a recently approved multiple AI adulticide formulation labelled for resistant mosquitoes, against a mixed location field population of Miami-Dade Cx. quinquefasciatus. Average 24-hr mortality was 65.1 ± 7.2% and 48-hr mortality increased to 85.3 ± 9.1%, indicating good control of these resistant Cx. quinquefasciatus. This current study shows that insecticide resistance is common in local Cx. quinquefasciatus but effective options are available to maintain control during active disease transmission in Miami-Dade County.

Potential key genes involved in metabolic resistance to malathion in the southern house mosquito, Culex quinquefasciatus, and functional validation of CYP325BC1 and CYP9M12 as candidate genes using RNA interference

BACKGROUND

Metabolic detoxification is one of the major mechanisms contributing to the development of resistance in mosquitoes, including the southern house mosquito, Culex quinquefasciatus. The three major detoxification supergene families, cytochrome P450s, glutathione S-transferases and general esterases, have been demonstrated to play an important role in metabolic resistance. In this study, we performed differential gene expression analysis based on high-throughput transcriptome sequencing on samples from four experimental groups to give insight into key genes involved in metabolic resistance to malathion in Cx. quinquefasciatus. We conducted a whole transcriptome analysis of field captured wild Cx. quinquefasciatus from Harris County (WI), Texas and a malathion susceptible laboratory-maintained Sebring colony (CO) to investigate metabolic insecticide resistance. Field captured mosquitoes were also phenotypically classified into the malathion resistant and malathion susceptible groups following a mortality response measure conducted using a Centers for Disease Control and Prevention (CDC) bottle assay. The live (MR) and dead (MS) specimens from the bottle assay, along with an unselected WI sample and a CO sample were processed for total RNA extraction and subjected to whole-transcriptome sequencing.

RESULTS

We demonstrated that the genes coding for detoxification enzymes, particularly cytochrome P450s, were highly up-regulated in the MR group compared to the MS group with similar up-regulation observed in the WI group compared to the CO group. A total of 1,438 genes were differentially expressed in comparison between MR and MS group, including 614 up-regulated genes and 824 down-regulated genes. Additionally, 1,871 genes were differentially expressed in comparison between WI and CO group, including 1,083 up-regulated genes and 788 down-regulated genes. Further analysis on differentially expressed genes from three major detoxification supergene families in both comparisons resulted in 16 detoxification genes as candidates potentially associated with metabolic resistance to malathion. Knockdown of CYP325BC1 and CYP9M12 using RNA interference on the laboratory-maintained Sebring strain significantly increased the mortality of Cx. quinquefasciatus after exposure to malathion.

CONCLUSION

We generated substantial transcriptomic evidence on metabolic detoxification of malathion in Cx. quinquefasciatus. We also validated the functional roles of two candidate P450 genes identified through DGE analysis. Our results are the first to demonstrate that knockdown of CYP325BC1 and CYP9M12 both significantly increased malathion susceptibility in Cx. quinquefasciatus, indicating involvement of these two genes in metabolic resistance to malathion.

The Invasive Mosquitoes of Canada: An Entomological, Medical, and Veterinary Review

Several invasive mosquitoes have become established in Canada, including important pathogen vectors such as Aedes albopictus, Ae. japonicus, and Culex pipiens. Some species have been present for decades, while others are recent arrivals. Several species present new health concerns and may result in autochthonous seasonal outbreaks of pathogens, particularly in southern Canada, that were previously restricted to imported cases. This review provides an overview of current knowledge of the biological, medical, and veterinary perspectives of these invasive species and highlights the need for increased monitoring efforts and information sharing.

A gene-based capture assay for surveying patterns of genetic diversity and insecticide resistance in a worldwide group of invasive mosquitoes

Understanding patterns of diversification, genetic exchange, and pesticide resistance in arthropod disease vectors is necessary for effective population management. With the availability of next-generation sequencing technologies, one of the best approaches for surveying such patterns involves the simultaneous genotyping of many samples for a large number of genetic markers. To this end, the targeting of gene sequences of known function can be a cost-effective strategy. One insect group of substantial health concern are the mosquito taxa that make up the Culex pipiens complex. Members of this complex transmit damaging arboviruses and filariae worms to humans, as well as other pathogens such as avian malaria parasites that are detrimental to birds. Here we describe the development of a targeted, gene-based assay for surveying genetic diversity and population structure in this mosquito complex. To test the utility of this assay, we sequenced samples from several members of the complex, as well as from distinct populations of the relatively under-studied Culex quinquefasciatus. The data generated was then used to examine taxonomic divergence and population clustering between and within these mosquitoes. We also used this data to investigate genetic variants present in our samples that had previously been shown to correlate with insecticide-resistance. Broadly, our gene capture approach successfully enriched the genomic regions of interest, and proved effective for facilitating examinations of taxonomic divergence and geographic clustering within the Cx. pipiens complex. It also allowed us to successfully survey genetic variation associated with insecticide resistance in Culex mosquitoes. This enrichment protocol will be useful for future studies that aim to understand the genetic mechanisms underlying the evolution of these ubiquitous and increasingly damaging disease vectors.

The mosquito taxa that make up the Culex pipiens complex are important vectors of the agents of several human diseases such as West Nile and St. Louis encephalitides, and lymphatic filariasis. They are also important vectors of avian malaria, which impacts livestock and wildlife. The development of effective strategies for the control of these mosquitoes requires knowledge of their origins, distribution, dispersal patterns, and the extent to which discreet taxonomic entities within the complex interbreed. To achieve these objectives, it is necessary to compare patterns of genetic diversity across many mosquito samples, which can be cost-prohibitive. To address this limitation, we developed a targeted, gene-based assay that allowed us to cost-effectively genotype a large number of genetic variants from a representative global sampling of individual Cx. pipiens complex mosquitoes. We show that this assay is a powerful tool for examining genetic structure and hybridization among populations. We also explore its utility for surveying alleles previously shown to be associated with insecticide resistance. Future use of this enrichment assay and the bioinformatics methods described here will allow researchers to study evolutionary patterns across the Cx. pipiens complex as well as monitor the presence of genetic variation that could affect control efforts.

Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution

The advent of NGS-based methods has been profoundly transforming entomological research. Through continual development and improvement of different methods and sequencing platforms, NGS has promoted mass elucidation of partial or whole genetic materials associated with beneficial insects, pests (of agriculture, forestry and animal, and human health), and species of conservation concern, helping to unravel ecological and evolutionary mechanisms and characterizing survival, trophic interactions, and dispersal. It is shifting the scale of biodiversity and environmental analyses from individuals and biodiversity indicator species to the large-scale study of communities and ecosystems using bulk samples of species or a mixed "soup" of environmental DNA. As the NGS-based methods have become more affordable, complexity demystified, and specificity and sensitivity proven, their use in entomological research has spread widely. This article presents several examples on how NGS-based methods have been used in entomology to provide incentives to apply them when appropriate and to open our minds to the expected advances in entomology that are yet to come.

High insecticide resistance mediated by different mechanisms in Culex quinquefasciatus populations from the city of Yaoundé, Cameroon

Culex mosquitoes particularly Culex quinquefasciatus are important arboviral and filariasis vectors, however despite this important epidemiological role, there is still a paucity of data on their bionomics. The present study was undertaken to assess the insecticide resistance status of Cx. quinquefasciatus populations from four districts of Yaoundé (Cameroon). All Culex quinquefasciatus populations except one displayed high resistance to bendiocarb and malathion with mortalities ranging from 0 to 89% while high resistance intensity against both permethrin and deltamethrin was recorded. Molecular analyses revealed high frequencies of the ACE-1 G119S mutation (ranging from 0 to 33%) and kdr L1014F allele (ranging from 55 to 74%) in all Cx. quinquefasciatus populations. Significant overexpression was detected for cytochrome P450s genes CYP6AA7 and CYP6Z10, as well as for Esterase A and Esterase B genes. The total cuticular hydrocarbon content, a proxy of cuticular resistance, was significantly increased (compared to the S-lab strain) in one population. The study confirms strong insecticide resistance mediated by different mechanisms in Cx. quinquefasciatus populations from the city of Yaoundé. The expansion of insecticide resistance in Culex populations could affect the effectiveness of current vector control measures and stress the need for the implementation of integrated vector control strategies in urban settings.

Whole-genome assembly of Culex tarsalis

The mosquito, Culex tarsalis, is a key vector in the western United States due to its role in transmission of zoonotic arboviruses that affect human health. Extensive research has been conducted on Cx. tarsalis ecology, feeding behavior, vector competence, autogeny, diapause, genetics, and insecticide resistance. Population genetic analyses in the western U.S. have identified at least three genetic clusters that are geographically distinct. However, in-depth genetic studies have been hindered by the lack of a reference genome. In this study, we present the first whole-genome assembly of this mosquito species (CtarK1) based on PacBio HiFi reads from high-molecular-weight DNA extracted from a single male. The CtarK1 assembly is 790 Mb with an N50 of 58 kb, which is 27% larger than Culex quinquefasciatus (578 Mb). This difference appears to be mostly composed of transposable elements. To annotate CtarK1, we used a previously assembled Cx. tarsalis transcriptome and approximately 17,456 protein genes from Cx. quinquefasciatus (N = 17,456). Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 84.8% of the 2799 Dipteran BUSCO genes. Using a Bayesian phylogeny based on mitochondrial genomes, we place Cx. tarsalis in the context of other mosquito species and estimate the divergence between Cx. tarsalis and Cx. quinquefasciatus to be between 15.8 and 22.2 million years ago (MYA). Important next steps from this work include characterizing the genetic basis of diapause and sex determination in Culex mosquitoes.

Toxicological Evaluation of Novel Butenolide Pesticide Flupyradifurone Against Culex quinquefasciatus (Diptera: Culicidae) Mosquitoes

The impact of increasing resistance of mosquitoes to conventional pesticides has led to investigate various unique tools and pest control strategies. Herein, we assessed the potency of flupyradifurone, a novel pesticide, on fourth instar larvae of Culex quinquefasciatus Say. Further, we evaluated the synergistic action of piperonyl butoxide (PBO) and the octopamine receptor agonists (OR agonists) chlordimeform (CDM) and amitraz (AMZ) on the toxicity of flupyradifurone in comparison with sulfoxaflor and nitenpyram to increase their toxicity on Cx. quinquefasciatus. Results demonstrated that flupyradifurone was the most potent pesticide followed by sulfoxaflor and nitenpyram. Further, the synergetic effect of PBO, CDM, and AMZ was significant for all selected pesticides especially flupyradifurone. However, AMZ had the most significant effect in combination with the selected pesticides followed by CDM and PBO. The toxicity of the pesticides was time-dependent and increased over time from 24, 48, to 72 h of exposure in all experiments. The results indicate that flupyradifurone is a promising component in future mosquito control programs.

Detection of the Nav channel kdr-like mutation and modeling of factors affecting survivorship of Culex quinquefasciatus mosquitoes from six areas of Harris County (Houston), Texas, after permethrin field-cage tests

Culex quinquefasciatus is one of the most important mosquito vectors of arboviruses. Currently, the fastest approach to control disease transmission is the application of synthetic adulticide insecticides. However, in highly populated urban centers the development of insecticide resistance in mosquito populations could impair insecticide efficacy and therefore, disease control. To assess the effect of resistance on vector control, females of Cx. quinquefasciatus collected from six mosquito control operational areas in Harris County, Texas, were treated in field cage tests at three different distances with the pyrethroid Permanone® 31-66 applied at the operational rate. Females were analyzed by sequencing and/or diagnostic PCR using de novo designed primers for detecting the kdr-like mutation in the voltage-gated sodium channel (L982F; TTA to TTT) (house fly kdr canonical mutation L1014F). Females from the Cx. quinquefasciatus susceptible Sebring strain and those from the six operational areas placed at 30.4 m from the treatment source were killed in the tests, while 14% of field-collected mosquitoes survived at 60.8 m, and 35% at 91.2 m from the source. The diagnostic PCR had a with 97.5% accuracy to detect the kdr-like mutation. Pyrethroid resistant mosquitoes carrying the L982F mutation were broadly distributed in Harris County at high frequency. Among mosquitoes analyzed (n = 1,028), the kdr-kdr genotype was prevalent (81.2%), the kdr-s genotype was 18%, and s-s mosquitoes were less than 1% (n = 8). A logistic regression model estimated an equal probability of survival for the genotypes kdr-kdr and kdr-s in all areas analyzed. Altogether, our results point to a high-risk situation for the pyrethroid-based arboviral disease control in Harris County.

Genomic Variant Analyses in Pyrethroid Resistant and Susceptible Malaria Vector, Anopheles sinensis

Anopheles sinensis is a major malaria vector in Southeast Asia. Resistance to pyrethroid insecticides in this species has impeded malaria control in the region. Previous studies found that An. sinensis populations from Yunnan Province, China were highly resistant to deltamethrin and did not carry mutations in the voltage-gated sodium channel gene that cause knockdown resistance. In this study, we tested the hypothesis that other genomic variants are associated with the resistance phenotype. Using paired-end whole genome sequencing (DNA-seq), we generated 108 Gb of DNA sequence from deltamethrin -resistant and -susceptible mosquito pools with an average coverage of 83.3× depth. Using a stringent filtering method, we identified a total of 916,926 single nucleotide variants (SNVs), including 32,240 non-synonymous mutations. A total of 958 SNVs differed significantly in allele frequency between deltamethrin -resistant and -susceptible mosquitoes. Of these, 43 SNVs were present within 37 genes that code for immunity, detoxification, cuticular, and odorant proteins. A subset of 12 SNVs were randomly selected for genotyping of individual mosquitoes by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and showed consistent allele frequencies with the pooled DNA-seq derived allele frequencies. In addition, copy number variations (CNVs) were detected in 56 genes, including 33 that contained amplification alleles and 23 that contained deletion alleles in resistant mosquitoes compared to susceptible mosquitoes. The genomic variants described here provide a useful resource for future studies on the genetic mechanism of insecticide resistance in this important malaria vector species.