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Hancock PA, Ochomo E, Messenger LA. Genetic surveillance of insecticide resistance in African Anopheles populations to inform malaria vector control. Trends Parasitol 2024; 40:604-618. [PMID: 38760258 DOI: 10.1016/j.pt.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/19/2024]
Abstract
Insecticide resistance in malaria vector populations poses a major threat to malaria control, which relies largely on insecticidal interventions. Contemporary vector-control strategies focus on combatting resistance using multiple insecticides with differing modes of action within the mosquito. However, diverse genetic resistance mechanisms are present in vector populations, and continue to evolve. Knowledge of the spatial distribution of these genetic mechanisms, and how they impact the efficacy of different insecticidal products, is critical to inform intervention deployment decisions. We developed a catalogue of genetic-resistance mechanisms in African malaria vectors that could guide molecular surveillance. We highlight situations where intervention deployment has led to resistance evolution and spread, and identify challenges in understanding and mitigating the epidemiological impacts of resistance.
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Affiliation(s)
- Penelope A Hancock
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Eric Ochomo
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya; Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Louisa A Messenger
- Department of Environmental and Occupational Health, School of Public Health, University of Nevada, Las Vegas, USA; Parasitology and Vector Biology (PARAVEC) Laboratory, School of Public Health, University of Nevada, Las Vegas, USA
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Mapua SA, Samb B, Nambunga IH, Mkandawile G, Bwanaly H, Kaindoa EW, Odero JO, Masalu JP, Kahamba NF, Hape EE, Govella NJ, Okumu FO, Tripet F. Entomological survey of sibling species in the Anopheles funestus group in Tanzania confirms the role of Anopheles parensis as a secondary malaria vector. Parasit Vectors 2024; 17:261. [PMID: 38886827 PMCID: PMC11181546 DOI: 10.1186/s13071-024-06348-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Malaria transmission in Tanzania is driven by mosquitoes of the Anopheles gambiae complex and Anopheles funestus group. The latter includes An. funestus s.s., an anthropophilic vector, which is now strongly resistant to public health insecticides, and several sibling species, which remain largely understudied despite their potential as secondary vectors. This paper provides the initial results of a cross-country study of the species composition, distribution and malaria transmission potential of members of the Anopheles funestus group in Tanzania. METHODS Mosquitoes were collected inside homes in 12 regions across Tanzania between 2018 and 2022 using Centres for Disease Control and Prevention (CDC) light traps and Prokopack aspirators. Polymerase chain reaction (PCR) assays targeting the noncoding internal transcribed spacer 2 (ITS2) and 18S ribosomal DNA (18S rDNA) were used to identify sibling species in the An. funestus group and presence of Plasmodium infections, respectively. Where DNA fragments failed to amplify during PCR, we sequenced the ITS2 region to identify any polymorphisms. RESULTS The following sibling species of the An. funestus group were found across Tanzania: An. funestus s.s. (50.3%), An. parensis (11.4%), An. rivulorum (1.1%), An. leesoni (0.3%). Sequencing of the ITS2 region in the nonamplified samples showed that polymorphisms at the priming sites of standard species-specific primers obstructed PCR amplification, although the ITS2 sequences closely matched those of An. funestus s.s., barring these polymorphisms. Of the 914 samples tested for Plasmodium infections, 11 An. funestus s.s. (1.2%), and 2 An. parensis (0.2%) individuals were confirmed positive for P. falciparum. The highest malaria transmission intensities [entomological inoculation rate (EIR)] contributed by the Funestus group were in the north-western region [108.3 infectious bites/person/year (ib/p/y)] and the south-eastern region (72.2 ib/p/y). CONCLUSIONS Whereas An. funestus s.s. is the dominant malaria vector in the Funestus group in Tanzania, this survey confirms the occurrence of Plasmodium-infected An. parensis, an observation previously made in at least two other occasions in the country. The findings indicate the need to better understand the ecology and vectorial capacity of this and other secondary malaria vectors in the region to improve malaria control.
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Affiliation(s)
- Salum Abdallah Mapua
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P. O. Box 53, Morogoro, Tanzania.
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK.
| | - Badara Samb
- Laboratoire d'Écologie Vectorielle et Parasitaire, Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop de Dakar, 5005, Dakar-Fann, BP, Senegal
| | - Ismail Hassan Nambunga
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P. O. Box 53, Morogoro, Tanzania
| | - Gustav Mkandawile
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P. O. Box 53, Morogoro, Tanzania
| | - Hamis Bwanaly
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P. O. Box 53, Morogoro, Tanzania
| | - Emmanuel Wilson Kaindoa
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P. O. Box 53, Morogoro, Tanzania
| | - Joel Ouma Odero
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P. O. Box 53, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G61 1QH, UK
| | - John Paliga Masalu
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P. O. Box 53, Morogoro, Tanzania
| | - Najat Feruz Kahamba
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P. O. Box 53, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G61 1QH, UK
| | - Emmanuel Elirehema Hape
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P. O. Box 53, Morogoro, Tanzania
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicodem James Govella
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P. O. Box 53, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G61 1QH, UK
- School of Life Science and Bioengineering, The Nelson Mandela African Institution of Science and Technology, P. O. Box 447, Arusha, Tanzania
| | - Fredros Oketch Okumu
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P. O. Box 53, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G61 1QH, UK
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Life Science and Bioengineering, The Nelson Mandela African Institution of Science and Technology, P. O. Box 447, Arusha, Tanzania
| | - Frederic Tripet
- Swiss Tropical and Public Health Institute, Kreuzgasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
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Bouafou L, Makanga BK, Rahola N, Boddé M, Ngangué MF, Daron J, Berger A, Mouillaud T, Makunin A, Korlević P, Nwezeobi J, Kengne P, Paupy C, Lawniczak MKN, Ayala D. Host preference patterns in domestic and wild settings: Insights into Anopheles feeding behavior. Evol Appl 2024; 17:e13693. [PMID: 38828055 PMCID: PMC11143308 DOI: 10.1111/eva.13693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 06/05/2024] Open
Abstract
The adaptation of Anopheles malaria vectors to domestic settings is directly linked to their ability to feed on humans. The strength of this species-habitat association is unequal across the species within the genus, with the major vectors being particularly dependent on humans. However, our understanding of how blood-feeding behavior interacts with and adapts to environmental settings, including the presence of humans, remains limited. Using a field-based approach, we first investigated Anopheles community structure and feeding behavior patterns in domestic and sylvatic settings in La Lopé National Park in Gabon, Central Africa. We characterized the preference indices using a dual-host choice sampling approach across mosquito species, habitats, and seasons. We then quantified the plastic biting behavior of mosquito species in each habitat. We collected individuals from 16 Anopheles species that exhibited significant differences in species composition and abundance between sylvatic and domestic settings. The host-seeking behavior also varied among the seven most abundant species. The general attractiveness to each host, human or animal, remained relatively constant for each species, but with significant variations between habitats across species. These variations, to more generalist and to more anthropophilic behavior, were related to seasonal changes and distance from the village, respectively. Finally, we pointed out that the host choice of major malaria vectors changed in the absence of humans, revealing a plastic feeding behavior of these species. This study highlights the effect of humans on Anopheles distribution and feeding evolution. The characterization of feeding behavior in wild and domestic settings provides opportunities to better understand the interplay between genetic determinants of host preference and ecological factors. Our findings suggest that protected areas may offer alternative thriving conditions to major malaria vectors.
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Affiliation(s)
- Lemonde Bouafou
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
- CIRMFFrancevilleGabon
| | | | - Nil Rahola
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
| | | | | | - Josquin Daron
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
| | - Audric Berger
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
| | - Theo Mouillaud
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
| | | | | | | | - Pierre Kengne
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
- CIRMFFrancevilleGabon
| | - Christophe Paupy
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
| | | | - Diego Ayala
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
- Medical Entomology UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
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Nelder MP, Schats R, Poinar HN, Cooke A, Brickley MB. Pathogen prospecting of museums: Reconstructing malaria epidemiology. Proc Natl Acad Sci U S A 2024; 121:e2310859121. [PMID: 38527214 PMCID: PMC11009618 DOI: 10.1073/pnas.2310859121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Mark P. Nelder
- Enteric, Zoonotic and Vector-Borne Diseases, Health Protection, Public Health Ontario, Toronto, ONM5G 1M1, Canada
| | - Rachel Schats
- Laboratory for Human Osteoarchaeology, Faculty of Archaeology, Leiden University, 2333 CCLeiden, The Netherlands
| | - Hendrik N. Poinar
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
- Department of Biochemistry, McMaster University, Hamilton, ONL8S 4L9, Canada
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Amanda Cooke
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Megan B. Brickley
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
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Moraes Zenker M, Portella TP, Pessoa FAC, Bengtsson-Palme J, Galetti PM. Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity. Sci Rep 2024; 14:7432. [PMID: 38548880 PMCID: PMC10978826 DOI: 10.1038/s41598-024-58071-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/25/2024] [Indexed: 04/01/2024] Open
Abstract
Mosquitoes (Culicidae) represent the main vector insects globally, and they also inhabit many of the terrestrial and aquatic habitats of the world. DNA barcoding and metabarcoding are now widely used in both research and routine practices involving mosquitoes. However, these methodologies rely on information available in databases consisting of barcode sequences representing taxonomically identified voucher specimens. In this study, we assess the availability of public data for mosquitoes in the main online databases, focusing specifically on the two most widely used DNA barcoding markers in Culicidae: COI and ITS2. In addition, we test hypotheses on possible factors affecting species coverage (i.e., the percentage of species covered in the online databases) for COI in different countries and the occurrence of the DNA barcode gap for COI. Our findings showed differences in the data publicly available in the repositories, with a taxonomic or species coverage of 28.4-30.11% for COI in BOLD + GenBank, and 12.32% for ITS2 in GenBank. Afrotropical, Australian and Oriental biogeographic regions had the lowest coverages, while Nearctic, Palearctic and Oceanian had the highest. The Neotropical region had an intermediate coverage. In general, countries with a higher diversity of mosquitoes and higher numbers of medically important species had lower coverage. Moreover, countries with a higher number of endemic species tended to have a higher coverage. Although our DNA barcode gap analyses suggested that the species boundaries need to be revised in half of the mosquito species available in the databases, additional data must be gathered to confirm these results and to allow explaining the occurrence of the DNA barcode gap. We hope this study can help guide regional species inventories of mosquitoes and the completion of a publicly available reference library of DNA barcodes for all mosquito species.
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Affiliation(s)
- Maurício Moraes Zenker
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil.
| | - Tatiana Pineda Portella
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Felipe Arley Costa Pessoa
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz Amazônia, Manaus, Brazil
| | - Johan Bengtsson-Palme
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, 412 96, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), Gothenburg, Sweden
| | - Pedro Manoel Galetti
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil
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Acford-Palmer H, Campos M, Bandibabone J, N'Do S, Bantuzeko C, Zawadi B, Walker T, Phelan JE, Messenger LA, Clark TG, Campino S. Detection of insecticide resistance markers in Anopheles funestus from the Democratic Republic of the Congo using a targeted amplicon sequencing panel. Sci Rep 2023; 13:17363. [PMID: 37833354 PMCID: PMC10575962 DOI: 10.1038/s41598-023-44457-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023] Open
Abstract
Vector control strategies have been successful in reducing the number of malaria cases and deaths globally, but the spread of insecticide resistance represents a significant threat to disease control. Insecticide resistance has been reported across Anopheles (An.) vector populations, including species within the An. funestus group. These mosquitoes are responsible for intense malaria transmission across sub-Saharan Africa, including in the Democratic Republic of the Congo (DRC), a country contributing > 12% of global malaria infections and mortality events. To support the continuous efficacy of vector control strategies, it is essential to monitor insecticide resistance using molecular surveillance tools. In this study, we developed an amplicon sequencing ("Amp-seq") approach targeting An. funestus, and using multiplex PCR, dual index barcoding, and next-generation sequencing for high throughput and low-cost applications. Using our Amp-seq approach, we screened 80 An. funestus field isolates from the DRC across a panel of nine genes with mutations linked to insecticide resistance (ace-1, CYP6P4, CYP6P9a, GSTe2, vgsc, and rdl) and mosquito speciation (cox-1, mtND5, and ITS2). Amongst the 18 non-synonymous mutations detected, was N485I, in the ace-1 gene associated with carbamate resistance. Overall, our panel represents an extendable and much-needed method for the molecular surveillance of insecticide resistance in An. funestus populations.
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Affiliation(s)
- Holly Acford-Palmer
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Monica Campos
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Janvier Bandibabone
- Centre de Recherche en Sciences Naturelles de Lwiro, Sud-Kivu, Democratic Republic of the Congo
| | - Sévérin N'Do
- Médecins Sans Frontières (MSF) OCBA, Barcelona, Spain
- Institut de Recherche en Sciences de La Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Chimanuka Bantuzeko
- Centre de Recherche en Sciences Naturelles de Lwiro, Sud-Kivu, Democratic Republic of the Congo
- Université Officielle de Bukavu (UOB), Bukavu, Democratic Republic of the Congo
| | - Bertin Zawadi
- Centre de Recherche en Sciences Naturelles de Lwiro, Sud-Kivu, Democratic Republic of the Congo
| | - Thomas Walker
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Jody E Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Louisa A Messenger
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Department of Environmental and Occupational Health, School of Public Health, University of Nevada, Las Vegas, Las Vegas, USA
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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Acford-Palmer H, Phelan JE, Tadesse FG, Kristan M, Collins E, Spadar A, Walker T, Bousema T, Messenger LA, Clark TG, Campino S. Identification of two insecticide resistance markers in Ethiopian Anopheles stephensi mosquitoes using a multiplex amplicon sequencing assay. Sci Rep 2023; 13:5612. [PMID: 37019918 PMCID: PMC10076309 DOI: 10.1038/s41598-023-32336-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/26/2023] [Indexed: 04/07/2023] Open
Abstract
Since its first detection in 2012 in Djibouti, Anopheles stephensi has invaded and established in the Horn of Africa, and more recently Nigeria. The expansion of this vector poses a significant threat to malaria control and elimination efforts. Integrated vector management is the primary strategy used to interrupt disease transmission; however, growing insecticide resistance is threatening to reverse gains in global malaria control. We present a next-generation amplicon-sequencing approach, for high-throughput monitoring of insecticide resistance genes (ace1, GSTe2, vgsc and rdl), species identification and characterization of genetic diversity (its2 and cox1) in An. stephensi. Ninety-five An. stephensi mosquitoes, collected in Ethiopia, were screened, identifying 104 SNPs, including the knock-down mutation L958F (L1014F in Musca domestica), and for the first time in this vector species, the A296S substitution (A301S in Drosophila melanogaster) in the rdl locus. Two other amino acid substitutions (ace1-N177D, GSTe2-V189L) were also identified but have not been previously implicated in insecticide resistance. Genetic diversity in the mitochondrial cox1 gene revealed shared haplotypes between Ethiopian An. stephensi with samples from Pakistan, Sudan, and Djibouti. Overall, we present a reliable, cost-effective strategy using amplicon-sequencing to monitor known insecticide resistance mutations, with the potential to identify new genetic variants, to assist in the high-throughput surveillance of insecticide resistance in An. stephensi populations.
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Affiliation(s)
- Holly Acford-Palmer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Fitsum G Tadesse
- Malaria and NTD Directorate, Armauer Hansen Research Institute, ALERT Hospital Compound, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Mojca Kristan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Emma Collins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Thomas Walker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Teun Bousema
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Louisa A Messenger
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Environmental and Occupational Health, School of Public Health, University of Nevada, Las Vegas, Las Vegas, USA
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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Kirby R, Giesbrecht D, Karema C, Watson O, Lewis S, Munyaneza T, Butera JDD, Juliano JJ, Bailey JA, Mazarati JB. Examining the Early Distribution of the Artemisinin-Resistant Plasmodium falciparum kelch13 R561H Mutation in Areas of Higher Transmission in Rwanda. Open Forum Infect Dis 2023; 10:ofad149. [PMID: 37096145 PMCID: PMC10122489 DOI: 10.1093/ofid/ofad149] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/15/2023] [Indexed: 04/26/2023] Open
Abstract
Background Artemisinin resistance mutations in Plasmodium falciparum kelch13 (Pfk13) have begun to emerge in Africa, with Pfk13-R561H being the first reported in Rwanda in 2014, but limited sampling left questions about its early distribution and origin. Methods We genotyped P. falciparum positive dried blood spot (DBS) samples from a nationally representative 2014-2015 Rwanda Demographic Health Surveys (DHS) HIV study. DBS were subsampled from DHS sampling clusters with >15% P. falciparum prevalence, as determined by rapid testing or microscopy done during the DHS study (n clusters = 67, n samples = 1873). Results We detected 476 parasitemias among 1873 residual blood spots from a 2014-2015 Rwanda Demographic Health Survey. We sequenced 351 samples: 341/351 were wild-type (97.03% weighted), and 4 samples (1.34% weighted) harbored R561H that were significantly spatially clustered. Other nonsynonymous mutations found were V555A (3), C532W (1), and G533A (1). Conclusions Our study better defines the early distribution of R561H in Rwanda. Previous studies only observed the mutation in Masaka as of 2014, but our study indicates its presence in higher-transmission regions in the southeast of the country at that time.
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Affiliation(s)
| | | | - Corine Karema
- Quality Equity Health Care, Kigali, Rwanda
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Oliver Watson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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Collins EL, Phelan JE, Hubner M, Spadar A, Campos M, Ward D, Acford-Palmer H, Gomes AR, Silva K, Ferrero Gomez L, Clark TG, Campino S. A next generation targeted amplicon sequencing method to screen for insecticide resistance mutations in Aedes aegypti populations reveals a rdl mutation in mosquitoes from Cabo Verde. PLoS Negl Trop Dis 2022; 16:e0010935. [PMID: 36512510 PMCID: PMC9746995 DOI: 10.1371/journal.pntd.0010935] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/06/2022] [Indexed: 12/15/2022] Open
Abstract
Aedes mosquito vectors transmit many viruses of global health concern, including dengue, chikungunya and Zika. These vector-borne viral diseases have a limited number of treatment options, and vaccines vary in their effectiveness. Consequently, integrated vector management is a primary strategy for disease control. However, the increasing emergence and spread of insecticide resistance is threatening the efficacy of vector control methods. Identifying mutations associated with resistance in vector populations is important to monitor the occurrence and evolution of insecticide resistance and inform control strategies. Rapid and cost-effective genome sequencing approaches are urgently needed. Here we present an adaptable targeted amplicon approach for cost-effective implementation within next generation sequencing platforms. This approach can identify single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) in genes involved in insecticide resistance in Aedes aegypti mosquitoes. We designed and tested eleven amplicons, which included segments of the ace-1 (carbamate target), the Voltage-Gated Sodium Channel (vgsc; pyrethroids, DDT and organochlorines), and rdl (dieldrin) genes; thereby covering established knockdown resistance (kdr) mutations (e.g., S989P, I1011M/V, V1016G/I and F1534C), with the potential to identify novel ones. The amplicon assays were designed with internal barcodes, to facilitate multiplexing of large numbers of mosquitoes at low cost, and were sequenced using an Illumina platform. Our approach was evaluated on 152 Ae. aegypti mosquitoes collected in Cabo Verde, an archipelago with a history of arbovirus outbreaks. The amplicon sequence data revealed 146 SNPs, including four non-synonymous polymorphisms in the vgsc gene, one in ace-1 and the 296S rdl mutation previously associated with resistance to organochlorines. The 296S rdl mutation was identified in 98% of mosquitoes screened, consistent with the past use of an organochlorine compound (e.g., DDT). Overall, our work shows that targeted amplicon sequencing is a rapid, robust, and cost-effective tool that can be used to perform high throughput monitoring of insecticide resistance.
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Affiliation(s)
- Emma L. Collins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jody E. Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Magdalena Hubner
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Monica Campos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Daniel Ward
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Holly Acford-Palmer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ana Rita Gomes
- Laboratory of Pathogen-Host Interactions (LPHI), CNRS, Montpellier University, Montpellier, France
| | - Keily Silva
- Universidade Jean Piaget (UniPiaget), Praia, Cabo Verde
| | | | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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10
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Boddé M, Makunin A, Ayala D, Bouafou L, Diabaté A, Ekpo UF, Kientega M, Le Goff G, Makanga BK, Ngangue MF, Omitola OO, Rahola N, Tripet F, Durbin R, Lawniczak MKN. High-resolution species assignment of Anopheles mosquitoes using k-mer distances on targeted sequences. eLife 2022; 11:e78775. [PMID: 36222650 PMCID: PMC9648975 DOI: 10.7554/elife.78775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/11/2022] [Indexed: 11/13/2022] Open
Abstract
The ANOSPP amplicon panel is a genus-wide targeted sequencing panel to facilitate large-scale monitoring of Anopheles species diversity. Combining information from the 62 nuclear amplicons present in the ANOSPP panel allows for a more senstive and specific species assignment than single gene (e.g. COI) barcoding, which is desirable in the light of permeable species boundaries. Here, we present NNoVAE, a method using Nearest Neighbours (NN) and Variational Autoencoders (VAE), which we apply to k-mers resulting from the ANOSPP amplicon sequences in order to hierarchically assign species identity. The NN step assigns a sample to a species-group by comparing the k-mers arising from each haplotype's amplicon sequence to a reference database. The VAE step is required to distinguish between closely related species, and also has sufficient resolution to reveal population structure within species. In tests on independent samples with over 80% amplicon coverage, NNoVAE correctly classifies to species level 98% of samples within the An. gambiae complex and 89% of samples outside the complex. We apply NNoVAE to over two thousand new samples from Burkina Faso and Gabon, identifying unexpected species in Gabon. NNoVAE presents an approach that may be of value to other targeted sequencing panels, and is a method that will be used to survey Anopheles species diversity and Plasmodium transmission patterns through space and time on a large scale, with plans to analyse half a million mosquitoes in the next five years.
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Affiliation(s)
- Marilou Boddé
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | | | - Diego Ayala
- Institut de Recherche pour le Développement, MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellier,France
| | - Lemonde Bouafou
- Institut de Recherche pour le Développement, MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellier,France
| | - Abdoulaye Diabaté
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l'OuestBobo-DioulassoBurkina Faso
| | | | - Mahamadi Kientega
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l'OuestBobo-DioulassoBurkina Faso
| | - Gilbert Le Goff
- Institut de Recherche pour le Développement, MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellier,France
| | | | - Marc F Ngangue
- Centre International de Recherches Medicales de FrancevilleFrancevilleGabon
| | | | - Nil Rahola
- Institut de Recherche pour le Développement, MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellier,France
| | - Frederic Tripet
- Centre for Applied Entomology and Parasitology, Keele UniversityNewcastleUnited Kingdom
| | - Richard Durbin
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger InstituteHinxtonUnited Kingdom
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11
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Campos M, Phelan J, Spadar A, Collins E, Gonçalves A, Pelloquin B, Vaselli NM, Meiwald A, Clark E, Stica C, Orsborne J, Sylla M, Edi C, Camara D, Mohammed AR, Afrane YA, Kristan M, Walker T, Gomez LF, Messenger LA, Clark TG, Campino S. High-throughput barcoding method for the genetic surveillance of insecticide resistance and species identification in Anopheles gambiae complex malaria vectors. Sci Rep 2022; 12:13893. [PMID: 35974073 PMCID: PMC9381500 DOI: 10.1038/s41598-022-17822-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/01/2022] [Indexed: 12/30/2022] Open
Abstract
Surveillance of malaria vector species and the monitoring of insecticide resistance are essential to inform malaria control strategies and support the reduction of infections and disease. Genetic barcoding of mosquitoes is a useful tool to assist the high-throughput surveillance of insecticide resistance, discriminate between sibling species and to detect the presence of Plasmodium infections. In this study, we combined multiplex PCR, custom designed dual indexing, and Illumina next generation sequencing for high throughput single nucleotide polymorphism (SNP)-profiling of four species from the Anopheles (An.) gambiae complex (An. gambiae sensu stricto, An. coluzzii, An. arabiensis and An. melas). By amplifying and sequencing only 14 genetic fragments (500 bp each), we were able to simultaneously detect Plasmodium infection; insecticide resistance-conferring SNPs in ace1, gste2, vgsc and rdl genes; the partial sequences of nuclear ribosomal internal transcribed spacers (ITS1 and ITS2) and intergenic spacers (IGS), Short INterspersed Elements (SINE), as well as mitochondrial genes (cox1 and nd4) for species identification and genetic diversity. Using this amplicon sequencing approach with the four selected An. gambiae complex species, we identified a total of 15 non-synonymous mutations in the insecticide target genes, including previously described mutations associated with resistance and two new mutations (F1525L in vgsc and D148E in gste2). Overall, we present a reliable and cost-effective high-throughput panel for surveillance of An. gambiae complex mosquitoes in malaria endemic regions.
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Affiliation(s)
- Monica Campos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Emma Collins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adéritow Gonçalves
- Laboratório de Entomologia Médica, Instituto Nacional de Saúde Pública, Praia, 719, Cabo Verde
| | - Bethanie Pelloquin
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, University of Nagasaki, Nagasaki, Japan
| | - Natasha Marcella Vaselli
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anne Meiwald
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Emma Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Caleb Stica
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - James Orsborne
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Moussa Sylla
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland
| | - Constant Edi
- Centre Suisse de Recherches Scientifiques en Cote d'Ivoire, Abidjan, Côte d'Ivoire
| | - Denka Camara
- Programme National de Lutte Contre le Paludisme, Ministère de la Santé, BP. 595, Conakry, Guinea
| | - Abdul Rahim Mohammed
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Yaw Asare Afrane
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Mojca Kristan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Thomas Walker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Louisa A Messenger
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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12
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Giraldo-Calderón GI, Harb OS, Kelly SA, Rund SS, Roos DS, McDowell MA. VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100860. [PMID: 34864248 PMCID: PMC9133010 DOI: 10.1016/j.cois.2021.11.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/29/2021] [Indexed: 06/12/2023]
Abstract
VectorBase (VectorBase.org) is part of the VEuPathDB Bioinformatics Resource Center, providing free online access to multi-omics and population biology data, focusing on arthropod vectors and invertebrates of importance to human health. VectorBase includes genomics and functional genomics data from bed bugs, biting midges, body lice, kissing bugs, mites, mosquitoes, sand flies, ticks, tsetse flies, stable flies, house flies, fruit flies, and a snail intermediate host. Tools include the Search Strategy system and MapVEu, enabling users to interrogate and visualize diverse 'omics and population-level data using a graphical interface (no programming experience required). Users can also analyze their own private data, such as transcriptomic sequences, exploring their results in the context of other publicly-available information in the database. Help Desk: help@vectorbase.org.
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Affiliation(s)
- Gloria I Giraldo-Calderón
- Department of Biological Sciences, Eck Institute for Global Health, University Notre Dame, Notre Dame, IN 46556, USA; Dept. Ciencias Biológicas & Dept. Ciencias Básicas Médicas, Universidad Icesi, Calle 18 No 122-135, Cali, Colombia
| | - Omar S Harb
- Department of Biology, University of Pennsylvania, Philadelphia 19104, PA, USA
| | - Sarah A Kelly
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Samuel Sc Rund
- Department of Biological Sciences, Eck Institute for Global Health, University Notre Dame, Notre Dame, IN 46556, USA
| | - David S Roos
- Department of Biology, University of Pennsylvania, Philadelphia 19104, PA, USA
| | - Mary Ann McDowell
- Department of Biological Sciences, Eck Institute for Global Health, University Notre Dame, Notre Dame, IN 46556, USA.
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13
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Zhang C, Luo C, Yang R, Yang Y, Guo X, Deng Y, Zhou H, Zhang Y. Morphological and molecular identification reveals a high diversity of Anopheles species in the forest region of the Cambodia-Laos border. Parasit Vectors 2022; 15:94. [PMID: 35303948 PMCID: PMC8933986 DOI: 10.1186/s13071-022-05167-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/17/2022] [Indexed: 11/25/2022] Open
Abstract
Background To develop an effective malaria vector intervention method in forested international border regions within the Greater Mekong Subregion (GMS), more in-depth studies should be conducted on local Anopheles species composition and bionomic features. There is a paucity of comprehensive surveys of biodiversity integrating morphological and molecular species identification conducted within the border of Laos and Cambodia. Methods A total of 2394 adult mosquitoes were trapped in the Cambodia–Laos border region. We first performed morphological identification of Anopheles mosquitoes and subsequently performed molecular identification using 412 recombinant DNA–internal transcribed spacer 2 (rDNA-ITS2) and 391 mitochondrial DNA–cytochrome c oxidase subunit 2 (mtDNA-COII) sequences. The molecular and morphological identification results were compared, and phylogenetic analysis of rDNA-ITS2 and mtDNA-COII was conducted for the sequence divergence among species. Results Thirteen distinct species of Anopheles were molecularly identified in a 26,415 km2 border region in Siem Pang (Cambodia) and Pathoomphone (Laos). According to the comparisons of morphological and molecular identity, the interpretation of local species composition for dominant species in the Cambodia–Laos border (An. dirus, An. maculatus, An. philippinensis, An. kochi and An. sinensis) achieved the highest accuracy of morphological identification, from 98.37 to 100%. In contrast, the other species which were molecularly identified were less frequently identified correctly (0–58.3%) by morphological methods. The average rDNA-ITS2 and mtDNA-COII interspecific divergence was respectively 318 times and 15 times higher than their average intraspecific divergence. The barcoding gap ranged from 0.042 to 0.193 for rDNA-ITS2, and from 0.033 to 0.047 for mtDNA-COII. Conclusions The Cambodia–Laos border hosts a high diversity of Anopheles species. The morphological identification of Anopheles species provides higher accuracy for dominant species than for other species. Molecular methods combined with morphological analysis to determine species composition, population dynamics and bionomic characteristics can facilitate a better understanding of the factors driving malaria transmission and the effects of interventions, and can aid in achieving the goal of eliminating malaria. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05167-0.
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Affiliation(s)
- Canglin Zhang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Chunhai Luo
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Rui Yang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Yaming Yang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Xiaofang Guo
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Yan Deng
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Hongning Zhou
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China.
| | - Yilong Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China.
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14
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Hancock PA, Lynd A, Wiebe A, Devine M, Essandoh J, Wat'senga F, Manzambi EZ, Agossa F, Donnelly MJ, Weetman D, Moyes CL. Modelling spatiotemporal trends in the frequency of genetic mutations conferring insecticide target-site resistance in African mosquito malaria vector species. BMC Biol 2022; 20:46. [PMID: 35164747 PMCID: PMC8845222 DOI: 10.1186/s12915-022-01242-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/28/2022] [Indexed: 12/16/2022] Open
Abstract
Background Resistance in malaria vectors to pyrethroids, the most widely used class of insecticides for malaria vector control, threatens the continued efficacy of vector control tools. Target-site resistance is an important genetic resistance mechanism caused by mutations in the voltage-gated sodium channel (Vgsc) gene that encodes the pyrethroid target-site. Understanding the geographic distribution of target-site resistance, and temporal trends across different vector species, can inform strategic deployment of vector control tools. Results We develop a Bayesian statistical spatiotemporal model to interpret species-specific trends in the frequency of the most common resistance mutations, Vgsc-995S and Vgsc-995F, in three major malaria vector species Anopheles gambiae, An. coluzzii, and An. arabiensis over the period 2005–2017. The models are informed by 2418 observations of the frequency of each mutation in field sampled mosquitoes collected from 27 countries spanning western and eastern regions of Africa. For nine selected countries, we develop annual predictive maps which reveal geographically structured patterns of spread of each mutation at regional and continental scales. The results show associations, as well as stark differences, in spread dynamics of the two mutations across the three vector species. The coverage of ITNs was an influential predictor of Vgsc allele frequencies, with modelled relationships between ITN coverage and allele frequencies varying across species and geographic regions. We found that our mapped Vgsc allele frequencies are a significant partial predictor of phenotypic resistance to the pyrethroid deltamethrin in An. gambiae complex populations. Conclusions Our predictive maps show how spatiotemporal trends in insecticide target-site resistance mechanisms in African An. gambiae vary across individual vector species and geographic regions. Molecular surveillance of resistance mechanisms will help to predict resistance phenotypes and track their spread. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01242-1.
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Affiliation(s)
| | - Amy Lynd
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
| | | | - Maria Devine
- Big Data Institute, University of Oxford, Oxford, OX3 7LF, UK
| | - John Essandoh
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
| | - Francis Wat'senga
- Institut National de Recherche Biomédicale, PO Box 1192, Kinshasa, Democratic Republic of Congo
| | - Emile Z Manzambi
- Institut National de Recherche Biomédicale, PO Box 1192, Kinshasa, Democratic Republic of Congo
| | - Fiacre Agossa
- USAID President's Malaria Initiative, VectorLink Project, Abt Associates, 6130 Executive Blvd 16, Rockville, MD, 20852, USA
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
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15
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Korlević P, McAlister E, Mayho M, Makunin A, Flicek P, Lawniczak MKN. A Minimally Morphologically Destructive Approach for DNA Retrieval and Whole-Genome Shotgun Sequencing of Pinned Historic Dipteran Vector Species. Genome Biol Evol 2021; 13:evab226. [PMID: 34599327 PMCID: PMC8536546 DOI: 10.1093/gbe/evab226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2021] [Indexed: 01/08/2023] Open
Abstract
Museum collections contain enormous quantities of insect specimens collected over the past century, covering a period of increased and varied insecticide usage. These historic collections are therefore incredibly valuable as genomic snapshots of organisms before, during, and after exposure to novel selective pressures. However, these samples come with their own challenges compared with present-day collections, as they are fragile and retrievable DNA is low yield and fragmented. In this article, we tested several DNA extraction procedures across pinned historic Diptera specimens from four disease vector genera: Anopheles, Aedes, Culex, and Glossina. We identify an approach that minimizes morphological damage while maximizing DNA retrieval for Illumina library preparation and sequencing that can accommodate the fragmented and low yield nature of historic DNA. We identify several key points in retrieving sufficient DNA while keeping morphological damage to a minimum: an initial rehydration step, a short incubation without agitation in a modified low salt Proteinase K buffer (referred to as "lysis buffer C" throughout), and critical point drying of samples post-extraction to prevent tissue collapse caused by air drying. The suggested method presented here provides a solid foundation for exploring the genomes and morphology of historic Diptera collections.
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Affiliation(s)
- Petra Korlević
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Erica McAlister
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Matthew Mayho
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alex Makunin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mara K N Lawniczak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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