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Lucas ER, Nagi SC, Kabula B, Batengana B, Kisinza W, Egyir-Yawson A, Essandoh J, Dadzie S, Chabi J, Van't Hof AE, Rippon EJ, Pipini D, Harding NJ, Dyer NA, Clarkson CS, Miles A, Weetman D, Donnelly MJ. Copy number variants underlie the major selective sweeps in insecticide resistance genes in Anopheles arabiensis from Tanzania. bioRxiv 2024:2024.03.11.583874. [PMID: 38559088 PMCID: PMC10979859 DOI: 10.1101/2024.03.11.583874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
To keep ahead of the evolution of resistance to insecticides in mosquitoes, national malaria control programmes must make use of a range of insecticides, both old and new, while monitoring resistance mechanisms. Knowledge of the mechanisms of resistance remains limited in Anopheles arabiensis, which in many parts of Africa is of increasing importance because it is apparently less susceptible to many indoor control interventions. Furthermore, comparatively little is known in general about resistance to non-pyrethroid insecticides such as pirimiphos-methyl (PM), which are crucial for effective control in the context of resistance to pyrethroids. We performed a genome-wide association study to determine the molecular mechanisms of resistance to deltamethrin (commonly used in bednets) and PM, in An. arabiensis from two regions in Tanzania. Genomic regions of positive selection in these populations were largely driven by copy number variants (CNVs) in gene families involved in resistance to these two insecticides. We found evidence of a new gene cluster involved in resistance to PM, identifying a strong selective sweep tied to a CNV in the Coeae2g-Coeae6g cluster of carboxylesterase genes. Using complementary data from An. coluzzii in Ghana, we show that copy number at this locus is significantly associated with PM resistance. Similarly, for deltamethrin, resistance was strongly associated with a novel CNV allele in the Cyp6aa / Cyp6p cluster. Against this background of metabolic resistance, target site resistance was very rare or absent for both insecticides. Mutations in the pyrethroid target site Vgsc were at very low frequency in Tanzania, yet combining these samples with three An. arabiensis individuals from West Africa revealed a startling diversity of evolutionary origins of target site resistance, with up to 5 independent origins of Vgsc-995 mutations found within just 8 haplotypes. Thus, despite having been first recorded over 10 years ago, Vgsc resistance mutations in Tanzanian An. arabiensis have remained at stable low frequencies. Overall, our results provide a new copy number marker for monitoring resistance to PM in malaria mosquitoes, and reveal the complex picture of resistance patterns in An. arabiensis.
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Affiliation(s)
- Eric R Lucas
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Sanjay C Nagi
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Bilali Kabula
- National Institute for Medical Research, Amani Research Centre, P.O. Box 81, Muheza, Tanzania
| | - Bernard Batengana
- National Institute for Medical Research, Amani Research Centre, P.O. Box 81, Muheza, Tanzania
| | - William Kisinza
- National Institute for Medical Research, Amani Research Centre, P.O. Box 81, Muheza, Tanzania
| | | | - John Essandoh
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Sam Dadzie
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Joseph Chabi
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Arjen E Van't Hof
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Emily J Rippon
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Dimitra Pipini
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Nicholas J Harding
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Naomi A Dyer
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Chris S Clarkson
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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Lucas ER, Nagi SC, Egyir-Yawson A, Essandoh J, Dadzie S, Chabi J, Djogbénou LS, Medjigbodo AA, Edi CV, Kétoh GK, Koudou BG, Van't Hof AE, Rippon EJ, Pipini D, Harding NJ, Dyer NA, Cerdeira LT, Clarkson CS, Kwiatkowski DP, Miles A, Donnelly MJ, Weetman D. Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae and Anopheles coluzzii. Nat Commun 2023; 14:4946. [PMID: 37587104 PMCID: PMC10432508 DOI: 10.1038/s41467-023-40693-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023] Open
Abstract
Resistance to insecticides in Anopheles mosquitoes threatens the effectiveness of malaria control, but the genetics of resistance are only partially understood. We performed a large scale multi-country genome-wide association study of resistance to two widely used insecticides: deltamethrin and pirimiphos-methyl, using sequencing data from An. gambiae and An. coluzzii from ten locations in West Africa. Resistance was highly multi-genic, multi-allelic and variable between populations. While the strongest and most consistent association with deltamethrin resistance came from Cyp6aa1, this was based on several independent copy number variants (CNVs) in An. coluzzii, and on a non-CNV haplotype in An. gambiae. For pirimiphos-methyl, signals included Ace1, cytochrome P450s, glutathione S-transferases and the nAChR target site of neonicotinoid insecticides. The regions around Cyp9k1 and the Tep family of immune genes showed evidence of cross-resistance to both insecticides. These locally-varying, multi-allelic patterns highlight the challenges involved in genomic monitoring of resistance, and may form the basis for improved surveillance methods.
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Affiliation(s)
- Eric R Lucas
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - Sanjay C Nagi
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | | | - John Essandoh
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Samuel Dadzie
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Joseph Chabi
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Luc S Djogbénou
- Tropical Infectious Diseases Research Centre (TIDRC), Université d'Abomey-Calavi (UAC), 01 B.P. 526, Cotonou, Benin
| | - Adandé A Medjigbodo
- Tropical Infectious Diseases Research Centre (TIDRC), Université d'Abomey-Calavi (UAC), 01 B.P. 526, Cotonou, Benin
| | - Constant V Edi
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, 01 BP 1303, Abidjan, Côte d'Ivoire
| | - Guillaume K Kétoh
- Laboratory of Ecology and Ecotoxicology, Department of Zoology, Faculty of Sciences, Université de Lomé, 01 B.P. 1515, Lomé, Togo
| | - Benjamin G Koudou
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, 01 BP 1303, Abidjan, Côte d'Ivoire
| | - Arjen E Van't Hof
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Emily J Rippon
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Dimitra Pipini
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Nicholas J Harding
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Naomi A Dyer
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Louise T Cerdeira
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | | | | | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
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Lucas ER, Nagi SC, Egyir-Yawson A, Essandoh J, Dadzie S, Chabi J, Djogbénou LS, Medjigbodo AA, Edi CV, Ketoh GK, Koudou BG, Van't Hof AE, Rippon EJ, Pipini D, Harding NJ, Dyer NA, Cerdeira LT, Clarkson CS, Kwiatkowski DP, Miles A, Donnelly MJ, Weetman D. Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae s.l. bioRxiv 2023:2023.01.13.523889. [PMID: 36712022 PMCID: PMC9882144 DOI: 10.1101/2023.01.13.523889] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Resistance to insecticides in Anopheles mosquitoes threatens the effectiveness of the most widespread tools currently used to control malaria. The genetic underpinnings of resistance are still only partially understood, with much of the variance in resistance phenotype left unexplained. We performed a multi-country large scale genome-wide association study of resistance to two insecticides widely used in malaria control: deltamethrin and pirimiphos-methyl. Using a bioassay methodology designed to maximise the phenotypic difference between resistant and susceptible samples, we sequenced 969 phenotyped female An. gambiae and An. coluzzii from ten locations across four countries in West Africa (Benin, Côte d'Ivoire, Ghana and Togo), identifying single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) segregating in the populations. The patterns of resistance association were highly multiallelic and variable between populations, with different genomic regions contributing to resistance, as well as different mutations within a given region. While the strongest and most consistent association with deltamethrin resistance came from the region around Cyp6aa1 , this resistance was based on a combination of several independent CNVs in An. coluzzii , and on a non-CNV bearing haplotype in An. gambiae . Further signals involved a range of cytochrome P450, mitochondrial, and immunity genes. Similarly, for pirimiphos-methyl, while the strongest signal came from the region of Ace1 , more widespread signals included cytochrome P450s, glutathione S-transferases, and a subunit of the nAChR target site of neonicotinoid insecticides. The regions around Cyp9k1 and the Tep family of immune genes were associated with resistance to both insecticide classes, suggesting possible cross-resistance mechanisms. These locally-varying, multigenic and multiallelic patterns highlight the challenges involved in genomic monitoring and surveillance of resistance, and form the basis for improvement of methods used to detect and predict resistance. Based on simulations of resistance variants, we recommend that yet larger scale studies, exceeding 500 phenotyped samples per population, are required to better identify associated genomic regions.
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Affiliation(s)
- Eric R Lucas
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Sanjay C Nagi
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | | | - John Essandoh
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Sam Dadzie
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Joseph Chabi
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Luc S Djogbénou
- Tropical Infectious Diseases Research Centre (TIDRC), Université d'Abomey-Calavi (UAC), 01 B.P. 526, Cotonou, Benin
| | - Adandé A Medjigbodo
- Tropical Infectious Diseases Research Centre (TIDRC), Université d'Abomey-Calavi (UAC), 01 B.P. 526, Cotonou, Benin
| | - Constant V Edi
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, 01 BP 1303 Abidjan 01, Côte d'Ivoire
| | - Guillaume K Ketoh
- Laboratory of Ecology and Ecotoxicology, Department of Zoology, Faculty of Sciences, Université de Lomé, 01 B.P: 1515 Lomé 01, Togo
| | - Benjamin G Koudou
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, 01 BP 1303 Abidjan 01, Côte d'Ivoire
| | - Arjen E Van't Hof
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Emily J Rippon
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Dimitra Pipini
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Nicholas J Harding
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Naomi A Dyer
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Louise T Cerdeira
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Chris S Clarkson
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | | | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
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Lucas ER, Rockett KA, Lynd A, Essandoh J, Grisales N, Kemei B, Njoroge H, Hubbart C, Rippon EJ, Morgan J, Van't Hof AE, Ochomo EO, Kwiatkowski DP, Weetman D, Donnelly MJ. A high throughput multi-locus insecticide resistance marker panel for tracking resistance emergence and spread in Anopheles gambiae. Sci Rep 2019; 9:13335. [PMID: 31527637 PMCID: PMC6746726 DOI: 10.1038/s41598-019-49892-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/03/2019] [Indexed: 01/11/2023] Open
Abstract
The spread of resistance to insecticides in disease-carrying mosquitoes poses a threat to the effectiveness of control programmes, which rely largely on insecticide-based interventions. Monitoring mosquito populations is essential, but obtaining phenotypic measurements of resistance is laborious and error-prone. High-throughput genotyping offers the prospect of quick and repeatable estimates of resistance, while also allowing resistance markers to be tracked and studied. To demonstrate the potential of highly-mulitplexed genotypic screening for measuring resistance-association of mutations and tracking their spread, we developed a panel of 28 known or putative resistance markers in the major malaria vector Anopheles gambiae, which we used to screen mosquitoes from a wide swathe of Sub-Saharan Africa (Burkina Faso, Ghana, Democratic Republic of Congo (DRC) and Kenya). We found resistance association in four markers, including a novel mutation in the detoxification gene Gste2 (Gste2-119V). We also identified a duplication in Gste2 combining a resistance-associated mutation with its wild-type counterpart, potentially alleviating the costs of resistance. Finally, we describe the distribution of the multiple origins of kdr resistance, finding unprecedented diversity in the DRC. This panel represents the first step towards a quantitative genotypic model of insecticide resistance that can be used to predict resistance status in An. gambiae.
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Affiliation(s)
- Eric R Lucas
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Amy Lynd
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - John Essandoh
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.,Department of Wildlife and Entomology, University of Cape Coast, Cape Coast, Ghana
| | - Nelson Grisales
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.,Abt Associates, 6130 Executive BLVD, Rockville, MD, United States
| | - Brigid Kemei
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research, Kisumu, Kenya
| | - Harun Njoroge
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Emily J Rippon
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - John Morgan
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Arjen E Van't Hof
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Eric O Ochomo
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research, Kisumu, Kenya
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.,Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - David Weetman
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Martin J Donnelly
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.,Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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Odero JO, Fillinger U, Rippon EJ, Masiga DK, Weetman D. Using sibship reconstructions to understand the relationship between larval habitat productivity and oviposition behaviour in Kenyan Anopheles arabiensis. Malar J 2019; 18:286. [PMID: 31443645 PMCID: PMC6708163 DOI: 10.1186/s12936-019-2917-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/17/2019] [Indexed: 11/10/2022] Open
Abstract
Background Strategies for combatting residual malaria by targeting vectors outdoors are gaining importance as the limitations of primary indoor interventions are reached. Strategies to target ovipositing females or her offspring are broadly applicable because all mosquitoes require aquatic habitats for immature development irrespective of their biting or resting preferences. Oviposition site selection by gravid females is frequently studied by counting early instar larvae in habitats; an approach which is valid only if the number of larvae correlates with the number of females laying eggs. This hypothesis was tested against the alternative, that a higher abundance of larvae results from improved survival of a similar or fewer number of families. Methods In a controlled experiment, 20 outdoor artificial ponds were left uncovered for 4 days to allow oviposition by wild mosquitoes, then covered with netting and first and second instar larvae sampled daily. Natural Anopheles habitats of two different types were also identified, and all visible larvae sampled. All larvae were identified to species, and most samples of the predominant species, Anopheles arabiensis, were genotyped using microsatellites for sibling group reconstructions using two contrasting softwares, BAPS and COLONY. Results In the ponds, the number of families reconstructed by each software significantly predicted larval abundance (BAPS R2 = 0.318, p = 0.01; COLONY R2 = 0.476, p = 0.001), and suggested that around 50% of females spread larvae across multiple ponds (skip oviposition). From natural habitats, the mean family size again predicted larval abundance using BAPS (R2 = 0.829, p = 0.017) though not using COLONY (R2 = 0.218, p = 0.68), but both softwares once more suggested high rates of skip oviposition (in excess of 50%). Conclusion This study shows that, whether in closely-located artificial habitats or natural breeding sites, higher early instar larval densities result from more females laying eggs in these sites. These results provide empirical support for use of early instar larval abundance as an index for oviposition site preference. Furthermore, the sharing of habitats by multiple females and the high skip-oviposition rate in An. arabiensis suggest that larviciding by auto-dissemination of insecticide may be successful.
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Affiliation(s)
- Joel O Odero
- Human Health Theme, International Centre of Insect Physiology and Ecology, Nairobi, Kenya. .,Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Ulrike Fillinger
- Human Health Theme, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Emily J Rippon
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Daniel K Masiga
- Human Health Theme, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - David Weetman
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK
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Wilson AL, Pinder M, Bradley J, Donnelly MJ, Hamid-Adiamoh M, Jarju LBS, Jawara M, Jeffries D, Kandeh B, Rippon EJ, Salami K, D'Alessandro U, Lindsay SW. Correction to: Emergence of knock-down resistance in the Anopheles gambiae complex in the Upper River Region, The Gambia, and its relationship with malaria infection in children. Malar J 2018; 17:227. [PMID: 29879981 PMCID: PMC5992667 DOI: 10.1186/s12936-018-2374-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
| | - Margaret Pinder
- Durham University, Durham, UK.,Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - John Bradley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Majidah Hamid-Adiamoh
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | | | - Musa Jawara
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - David Jeffries
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Ballah Kandeh
- National Malaria Control Programme, Banjul, The Gambia
| | | | - Kolawole Salami
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Umberto D'Alessandro
- London School of Hygiene and Tropical Medicine, London, UK.,Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Steven W Lindsay
- Durham University, Durham, UK.,London School of Hygiene and Tropical Medicine, London, UK
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Wilson AL, Pinder M, Bradley J, Donnelly MJ, Hamid-Adiamoh M, Jarju LBS, Jawara M, Jeffries D, Kandeh B, Rippon EJ, Salami K, D'Alessandro U, Lindsay SW. Emergence of knock-down resistance in the Anopheles gambiae complex in the Upper River Region, The Gambia, and its relationship with malaria infection in children. Malar J 2018; 17:205. [PMID: 29776361 PMCID: PMC5960171 DOI: 10.1186/s12936-018-2348-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/07/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Insecticide resistance threatens malaria control in sub-Saharan Africa. Knockdown resistance to pyrethroids and organochlorines in Anopheles gambiae sensu lato (s.l.) is commonly caused by mutations in the gene encoding a voltage-gated sodium channel which is the target site for the insecticide. The study aimed to examine risk factors for knockdown resistance in An. gambiae s.l. and its relationship with malaria infection in children in rural Gambia. Point mutations at the Vgsc-1014 locus, were measured in An. gambiae s.l. during a 2-year trial. Cross-sectional surveys were conducted at the end of the transmission season to measure malaria infection in children aged 6 months-14 years. RESULTS Whilst few Anopheles arabiensis and Anopheles coluzzii had Vgsc-1014 mutations, the proportion of An. gambiae sensu stricto (s.s.) mosquitoes homozygous for the Vgsc-1014F mutation increased from 64.8 to 90.9% during the study. The Vgsc-1014S or 1014F mutation was 80% higher in 2011 compared to 2010, and 27% higher in the villages with indoor residual spraying compared to those without. An increase in the proportion of An. gambiae s.l. mosquitoes with homozygous Vgsc-1014F mutations and an increase in the proportion of An. gambiae s.s. in a cluster were each associated with increased childhood malaria infection. Homozygous Vgsc-1014F mutations were, however, most common in An. gambiae s.s. and almost reached saturation during the study meaning that the two variables were colinear. CONCLUSIONS As a result of colinearity between homozygous Vgsc-1014F mutations and An. gambiae s.s., it was not possible to determine whether insecticide resistance or species composition increased the risk of childhood malaria infection.
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Affiliation(s)
| | - Margaret Pinder
- Durham University, Durham, UK.,Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - John Bradley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Majidah Hamid-Adiamoh
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | | | - Musa Jawara
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - David Jeffries
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Ballah Kandeh
- National Malaria Control Programme, Banjul, The Gambia
| | | | - Kolawole Salami
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Umberto D'Alessandro
- London School of Hygiene and Tropical Medicine, London, UK.,Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Steven W Lindsay
- Durham University, Durham, UK.,London School of Hygiene and Tropical Medicine, London, UK
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Kabula B, Tungu P, Rippon EJ, Steen K, Kisinza W, Magesa S, Mosha F, Donnelly MJ. A significant association between deltamethrin resistance, Plasmodium falciparum infection and the Vgsc-1014S resistance mutation in Anopheles gambiae highlights the epidemiological importance of resistance markers. Malar J 2016; 15:289. [PMID: 27216484 PMCID: PMC4877992 DOI: 10.1186/s12936-016-1331-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/06/2016] [Indexed: 11/16/2022] Open
Abstract
Background The success of malaria vector control is threatened by widespread pyrethroid insecticide resistance. However, the extent to which insecticide resistance impacts transmission is unclear. The objective of this study was to examine the association between the DDT/pyrethroid knockdown resistance mutation Vgsc-1014S, commonly termed kdr, and infection with Plasmodium falciparum sporozoites in Anopheles gambiae. Methods WHO standard methods were used to characterize susceptibility of wild female mosquitoes to 0.05 % deltamethrin. PCR-based molecular diagnostics were used to identify mosquitoes to species and to genotype at the Vgsc-L1014S locus. ELISAs were used to detect the presence of P.falciparum sporozoites and for blood meal identification. Results Anopheles mosquitoes were resistant to deltamethrin with mortality rates of 77.7 % [95 % CI 74.9–80.3 %]. Of 545 mosquitoes genotyped 96.5 % were A. gambiaes.s. and 3.5 % were Anopheles arabiensis. The Vgsc-1014S mutation was detected in both species. Both species were predominantly anthropophagic. In A. gambiaes.s., Vgsc-L1014S genotype was significantly associated with deltamethrin resistance (χ2 = 11.2; p < 0.001). The P. falciparum sporozoite infection rate was 4.2 %. There was a significant association between the presence of sporozoites and Vgsc-L1014S genotype in A. gambiaes.s. (χ2 = 4.94; p = 0.026). Conclusions One marker, Vgsc-1014S, was associated with insecticide resistance and P. falciparum infection in wild-caught mixed aged populations of A. gambiaes.s. thereby showing how resistance may directly impact transmission.
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Affiliation(s)
- Bilali Kabula
- Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania.,Amani Research Centre, National Institute for Medical Research, Muheza, Tanzania.,Tukuyu Research Centre, National Institute for Medical Research, Tukuyu, Tanzania
| | - Patrick Tungu
- Amani Research Centre, National Institute for Medical Research, Muheza, Tanzania
| | - Emily J Rippon
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Keith Steen
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - William Kisinza
- Amani Research Centre, National Institute for Medical Research, Muheza, Tanzania
| | - Stephen Magesa
- Amani Research Centre, National Institute for Medical Research, Muheza, Tanzania.,Global Health Division, RTI International, Dar es Salaam, Tanzania
| | - Franklin Mosha
- Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania
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Weetman D, Mitchell SN, Wilding CS, Birks DP, Yawson AE, Essandoh J, Mawejje HD, Djogbenou LS, Steen K, Rippon EJ, Clarkson CS, Field SG, Rigden DJ, Donnelly MJ. Contemporary evolution of resistance at the major insecticide target site gene Ace-1 by mutation and copy number variation in the malaria mosquito Anopheles gambiae. Mol Ecol 2015; 24:2656-72. [PMID: 25865270 PMCID: PMC4447564 DOI: 10.1111/mec.13197] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 12/27/2022]
Abstract
Functionally constrained genes are ideal insecticide targets because disruption is often fatal, and resistance mutations are typically costly. Synaptic acetylcholinesterase (AChE) is an essential neurotransmission enzyme targeted by insecticides used increasingly in malaria control. In Anopheles and Culex mosquitoes, a glycine–serine substitution at codon 119 of the Ace-1 gene confers both resistance and fitness costs, especially for 119S/S homozygotes. G119S in Anopheles gambiae from Accra (Ghana) is strongly associated with resistance, and, despite expectations of cost, resistant 119S alleles are increasing significantly in frequency. Sequencing of Accra females detected only a single Ace-1 119S haplotype, whereas 119G diversity was high overall but very low at non-synonymous sites, evidence of strong purifying selection driven by functional constraint. Flanking microsatellites showed reduced diversity, elevated linkage disequilibrium and high differentiation of 119S, relative to 119G homozygotes across up to two megabases of the genome. Yet these signals of selection were inconsistent and sometimes weak tens of kilobases from Ace-1. This unexpected finding is attributable to apparently ubiquitous amplification of 119S alleles as part of a large copy number variant (CNV) far exceeding the size of the Ace-1 gene, whereas 119G alleles were unduplicated. Ace-1 CNV was detectable in archived samples collected when the 119S allele was rare in Ghana. Multicopy amplification of resistant alleles has not been observed previously and is likely to underpin the recent increase in 119S frequency. The large CNV compromised localization of the strong selective sweep around Ace-1, emphasizing the need to integrate CNV analysis into genome scans for selection.
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Affiliation(s)
- David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Sara N Mitchell
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Craig S Wilding
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Daniel P Birks
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Alexander E Yawson
- Biotechnology and Nuclear Agriculture Research Institute, Ghana Atomic Energy Commission, Kwabenya, Accra, Ghana.,Department of Molecular Biology and Biotechnology, University of Cape Coast, Cape Coast, Ghana
| | - John Essandoh
- Department of Wildlife and Entomology, University of Cape Coast, Cape Coast, Ghana
| | | | - Luc S Djogbenou
- Institut Regional de Sante Publique de Ouidah, Ouidah, Benin.,Universite d'Abomey-Calavi, Cotonou, Benin
| | - Keith Steen
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Emily J Rippon
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Christopher S Clarkson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Stuart G Field
- Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO, USA
| | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.,Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
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Weetman D, Steen K, Rippon EJ, Mawejje HD, Donnelly MJ, Wilding CS. Contemporary gene flow between wild An. gambiae s.s. and An. arabiensis. Parasit Vectors 2014; 7:345. [PMID: 25060488 PMCID: PMC4124135 DOI: 10.1186/1756-3305-7-345] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/21/2014] [Indexed: 11/10/2022] Open
Abstract
Background In areas where the morphologically indistinguishable malaria mosquitoes Anopheles gambiae Giles and An. arabiensis Patton are sympatric, hybrids are detected occasionally via species-diagnostic molecular assays. An. gambiae and An. arabiensis exhibit both pre- and post-reproductive mating barriers, with swarms largely species-specific and male F1 (first-generation) hybrids sterile. Consequently advanced-stage hybrids (back-crosses to parental species), which would represent a route for potentially-adaptive introgression, are expected to be very rare in natural populations. Yet the use of one or two physically linked single-locus diagnostic assays renders them indistinguishable from F1 hybrids and levels of interspecific gene flow are unknown. Methods We used data from over 350 polymorphic autosomal SNPs to investigate post F1 gene flow via patterns of genomic admixture between An. gambiae and An. arabiensis from eastern Uganda. Simulations were used to investigate the statistical power to detect hybrids with different levels of crossing and to identify the hybrid category significantly admixed genotypes could represent. Results A range of admixture proportions were detected for 11 field-collected hybrids identified via single-locus species-diagnostic PCRs. Comparison of admixture data with simulations indicated that at least seven of these hybrids were advanced generation crosses, with backcrosses to each species identified. In addition, of 36 individuals typing as An. gambiae or An. arabiensis that exhibited outlying admixture proportions, ten were identified as significantly mixed backcrosses, and at least four of these were second or third generation crosses. Conclusions Our results show that hybrids detected using standard diagnostics will often be hybrid generations beyond F1, and that in our study area around 5% (95% confidence intervals 3%-9%) of apparently ‘pure’ species samples may also be backcrosses. This is likely an underestimate because of rapidly-declining detection power beyond the first two backcross generations. Post-F1 gene flow occurs at a far from inconsequential rate between An. gambiae and An. arabiensis, and, especially for traits under strong selection, could readily lead to adaptive introgression of genetic variants relevant for vector control. Electronic supplementary material The online version of this article (doi:10.1186/1756-3305-7-345) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Craig S Wilding
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK.
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Mawejje HD, Wilding CS, Rippon EJ, Hughes A, Weetman D, Donnelly MJ. Insecticide resistance monitoring of field-collected Anopheles gambiae s.l. populations from Jinja, eastern Uganda, identifies high levels of pyrethroid resistance. Med Vet Entomol 2013; 27:276-283. [PMID: 23046446 PMCID: PMC3543752 DOI: 10.1111/j.1365-2915.2012.01055.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Insecticide resistance in the malaria vector Anopheles gambiae s.l. (Diptera: Culicidae) threatens insecticide-based control efforts, necessitating regular monitoring. We assessed resistance in field-collected An. gambiae s.l. from Jinja, Uganda using World Health Organization (WHO) bioassays. Only An. gambiae s.s. and An. arabiensis (≈70%) were present. Female An. gambiae exhibited extremely high pyrethroid resistance (permethrin LT50 > 2 h; deltamethrin LT50 > 5 h). Female An. arabiensis were resistant to permethrin and exhibited reduced susceptibility to deltamethrin. However, while An. gambiae were DDT resistant, An. arabiensis were fully susceptible. Both species were fully susceptible to bendiocarb and fenitrothion. Kdr 1014S has increased rapidly in the Jinja population of An. gambiae s.s. and now approaches fixation (≈95%), consistent with insecticide-mediated selection, but is currently at a low frequency in An. arabiensis (0.07%). Kdr 1014F was also at a low frequency in An. gambiae. These frequencies preclude adequately-powered tests for an association with phenotypic resistance. PBO synergist bioassays resulted in near complete recovery of pyrethroid susceptibility suggesting involvement of CYP450s in resistance. A small number (0.22%) of An. gambiae s.s. ×An. arabiensis hybrids were found, suggesting the possibility of introgression of resistance alleles between species. The high levels of pyrethroid resistance encountered in Jinja threaten to reduce the efficacy of vector control programmes which rely on pyrethroid-impregnated bednets or indoor spraying of pyrethroids.
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Affiliation(s)
| | - Craig S. Wilding
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Emily J. Rippon
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Angela Hughes
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - David Weetman
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Martin J. Donnelly
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
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