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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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Soghigian J, Sither C, Justi SA, Morinaga G, Cassel BK, Vitek CJ, Livdahl T, Xia S, Gloria-Soria A, Powell JR, Zavortink T, Hardy CM, Burkett-Cadena ND, Reeves LE, Wilkerson RC, Dunn RR, Yeates DK, Sallum MA, Byrd BD, Trautwein MD, Linton YM, Reiskind MH, Wiegmann BM. Phylogenomics reveals the history of host use in mosquitoes. Nat Commun 2023; 14:6252. [PMID: 37803007 PMCID: PMC10558525 DOI: 10.1038/s41467-023-41764-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023] Open
Abstract
Mosquitoes have profoundly affected human history and continue to threaten human health through the transmission of a diverse array of pathogens. The phylogeny of mosquitoes has remained poorly characterized due to difficulty in taxonomic sampling and limited availability of genomic data beyond the most important vector species. Here, we used phylogenomic analysis of 709 single copy ortholog groups from 256 mosquito species to produce a strongly supported phylogeny that resolves the position of the major disease vector species and the major mosquito lineages. Our analyses support an origin of mosquitoes in the early Triassic (217 MYA [highest posterior density region: 188-250 MYA]), considerably older than previous estimates. Moreover, we utilize an extensive database of host associations for mosquitoes to show that mosquitoes have shifted to feeding upon the blood of mammals numerous times, and that mosquito diversification and host-use patterns within major lineages appear to coincide in earth history both with major continental drift events and with the diversification of vertebrate classes.
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Affiliation(s)
- John Soghigian
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Charles Sither
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Silvia Andrade Justi
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, USA
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, USA
| | - Gen Morinaga
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Brian K Cassel
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Christopher J Vitek
- Center for Vector-Borne Diseases, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Todd Livdahl
- Department of Biology, Clark University, Worcester, MA, USA
| | - Siyang Xia
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Andrea Gloria-Soria
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Department of Entomology, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Jeffrey R Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Thomas Zavortink
- Bohart Museum of Entomology, University of California, Davis, CA, USA
| | | | - Nathan D Burkett-Cadena
- Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, FL, USA
| | - Lawrence E Reeves
- Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, FL, USA
| | - Richard C Wilkerson
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - David K Yeates
- Australian National Insect Collection, CSIRO National Collections and Marine Infrastructure, Canberra, ACT, Australia
| | - Maria Anice Sallum
- Departamento de Epidemiologia, Faculdade de Saude Publica, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Brian D Byrd
- College of Health and Human Sciences, School of Health Sciences, Western Carolina University, Cullowhee, NC, USA
| | - Michelle D Trautwein
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, USA
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, USA
| | - Michael H Reiskind
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Brian M Wiegmann
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA.
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Meireles ACA, Rios FGF, Feitoza LHM, da Silva LR, Julião GR. Nondestructive Methods of Pathogen Detection: Importance of Mosquito Integrity in Studies of Disease Transmission and Control. Pathogens 2023; 12:816. [PMID: 37375506 DOI: 10.3390/pathogens12060816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/26/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Mosquitoes are vectors of many pathogens, including viruses, protozoans, and helminths, spreading these pathogens to humans as well as to wild and domestic animals. As the identification of species and the biological characterization of mosquito vectors are cornerstones for understanding patterns of disease transmission, and the design of control strategies, we conducted a literature review on the current use of noninvasive and nondestructive techniques for pathogen detection in mosquitoes, highlighting the importance of their taxonomic status and systematics, and some gaps in the knowledge of their vectorial capacity. Here, we summarized the alternative techniques for pathogen detection in mosquitoes based on both laboratory and field studies. Parasite infection and dissemination by mosquitoes can also be obtained via analyses of saliva- and excreta-based techniques or of the whole mosquito body, using a near-infrared spectrometry (NIRS) approach. Further research should be encouraged to seek strategies for detecting target pathogens while preserving mosquito morphology, especially in biodiversity hotspot regions, thus enabling the discovery of cryptic or new species, and the determination of more accurate taxonomic, parasitological, and epidemiological patterns.
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Affiliation(s)
- Anne Caroline Alves Meireles
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Biodiversity and Health, PhD in Sciences-Fiocruz Rondônia/Oswaldo Cruz Institute, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
| | - Flávia Geovana Fontineles Rios
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Experimental Biology-PGBIOEXP, Fiocruz Rondônia-UNIR, BR-364, Km 9.5, Porto Velho 78900-550, RO, Brazil
| | - Luiz Henrique Maciel Feitoza
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Experimental Biology-PGBIOEXP, Fiocruz Rondônia-UNIR, BR-364, Km 9.5, Porto Velho 78900-550, RO, Brazil
| | - Lucas Rosendo da Silva
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Experimental Biology-PGBIOEXP, Fiocruz Rondônia-UNIR, BR-364, Km 9.5, Porto Velho 78900-550, RO, Brazil
| | - Genimar Rebouças Julião
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Experimental Biology-PGBIOEXP, Fiocruz Rondônia-UNIR, BR-364, Km 9.5, Porto Velho 78900-550, RO, Brazil
- National Institute of Epidemiology of Western Amazônia-INCT-EpiAmO, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
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Winkler IS, Kirk-Spriggs AH, Bayless KM, Soghigian J, Meier R, Pape T, Yeates DK, Carvalho AB, Copeland RS, Wiegmann BM. Phylogenetic resolution of the fly superfamily Ephydroidea-Molecular systematics of the enigmatic and diverse relatives of Drosophilidae. PLoS One 2022; 17:e0274292. [PMID: 36197946 PMCID: PMC9534441 DOI: 10.1371/journal.pone.0274292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/26/2022] [Indexed: 11/05/2022] Open
Abstract
The schizophoran superfamily Ephydroidea (Diptera: Cyclorrhapha) includes eight families, ranging from the well-known vinegar flies (Drosophilidae) and shore flies (Ephydridae), to several small, relatively unusual groups, the phylogenetic placement of which has been particularly challenging for systematists. An extraordinary diversity in life histories, feeding habits and morphology are a hallmark of fly biology, and the Ephydroidea are no exception. Extreme specialization can lead to "orphaned" taxa with no clear evidence for their phylogenetic position. To resolve relationships among a diverse sample of Ephydroidea, including the highly modified flies in the families Braulidae and Mormotomyiidae, we conducted phylogenomic sampling. Using exon capture from Anchored Hybrid Enrichment and transcriptomics to obtain 320 orthologous nuclear genes sampled for 32 species of Ephydroidea and 11 outgroups, we evaluate a new phylogenetic hypothesis for representatives of the superfamily. These data strongly support monophyly of Ephydroidea with Ephydridae as an early branching radiation and the placement of Mormotomyiidae as a family-level lineage sister to all remaining families. We confirm placement of Cryptochetidae as sister taxon to a large clade containing both Drosophilidae and Braulidae-the latter a family of honeybee ectoparasites. Our results reaffirm that sampling of both taxa and characters is critical in hyperdiverse clades and that these factors have a major influence on phylogenomic reconstruction of the history of the schizophoran fly radiation.
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Affiliation(s)
- Isaac S. Winkler
- Department of Biology, Cornell College, Mount Vernon, Iowa, United States of America
| | | | - Keith M. Bayless
- Australian National Insect Collection, CSIRO National Research Collection, Australia (NRCA), Acton, Canberra, ACT, Australia
| | - John Soghigian
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Thomas Pape
- Natural History Museum of Denmark, Copenhagen, Denmark
| | - David K. Yeates
- Australian National Insect Collection, CSIRO National Research Collection, Australia (NRCA), Acton, Canberra, ACT, Australia
| | - A. Bernardo Carvalho
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Robert S. Copeland
- International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Brian M. Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
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Justi SA, Dale C. Designation of the neotype of Triatomadimidiata (Latreille, 1811) (Hemiptera, Reduviidae, Triatominae), with full integrated redescription including mitogenome and nuclear ITS-2 sequences. Zookeys 2022; 1076:9-24. [PMID: 34975271 PMCID: PMC8674215 DOI: 10.3897/zookeys.1076.72835] [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: 08/10/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022] Open
Abstract
The taxonomic status of Triatomadimidiata (Latreille, 1811) is, by far, the most discussed within Triatominae. Molecular studies have recovered at least three independently evolving lineages in T.dimidiata across its range. The original description of T.dimidiata (as Reduviusdimidiatus) included few taxonomic characters, and no types were assigned. To define and describe the cryptic diversity within T.dimidiata sensu lato (s.l.), a neotype must be designated. For this purpose, all 199 specimens identified as T.dimidiata from the collections of the Smithsonian Institution – National Museum of Natural History and the American Museum of Natural History, ranging from Peru to Mexico, were studied. Only one specimen (from Tumbes, Peru) matched the combination of characters as listed in the original description, and it is herein formally designated as the neotype for T.dimidiata. The neotype is morphologically described and DNA sequences of its whole mitochondrial genome and the nuclear second internal transcribed spacer region (ITS2), commonly used in triatomine molecular systematics studies, are presented and compared to other publicly available sequences of T.dimidiata s.l. in GenBank. Our results suggest that T.dimidiata sensu stricto (s.s.) is somewhat rare and, therefore, unlikely to serve as a major vector of Chagas disease.
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Affiliation(s)
- Silvia Andrade Justi
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, 4210 Silver Hill Road, Suitland, MD 20746, USA Smithsonian Institution Museum Support Center Suitland United States of America.,Entomology Branch, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA Entomology Branch, Walter Reed Army Institute of Research Silver Spring United States of America.,Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC 20560, USA Smithsonian Institution National Museum of Natural History Washington United States of America
| | - Carolina Dale
- Laboratório de Biodiversidade Entomológica, Instituto Oswaldo Cruz, Fiocruz, Av. Brasil 4365, Rio de Janeiro, RJ, 21040-900, Brazil Instituto Oswaldo Cruz Rio de Janeiro Brazil
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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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Lessard BD, Kurucz N, Rodriguez J, Carter J, Hardy CM. Detection of the Japanese encephalitis vector mosquito Culex tritaeniorhynchus in Australia using molecular diagnostics and morphology. Parasit Vectors 2021; 14:411. [PMID: 34407880 PMCID: PMC8371801 DOI: 10.1186/s13071-021-04911-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/31/2021] [Indexed: 11/30/2022] Open
Abstract
Background Culex (Culex) tritaeniorhynchus is an important vector of Japanese encephalitis virus (JEV) affecting feral pigs, native mammals and humans. The mosquito species is widely distributed throughout Southeast Asia, Africa and Europe, and thought to be absent in Australia. Methods In February and May, 2020 the Medical Entomology unit of the Northern Territory (NT) Top End Health Service collected Cx. tritaeniorhynchus female specimens (n = 19) from the Darwin and Katherine regions. Specimens were preliminarily identified morphologically as the Vishnui subgroup in subgenus Culex. Molecular identification was performed using cytochrome c oxidase subunit 1 (COI) barcoding, including sequence percentage identity using BLAST and tree-based identification using maximum likelihood analysis in the IQ-TREE software package. Once identified using COI, specimens were reanalysed for diagnostic morphological characters to inform a new taxonomic key to related species from the NT. Results Sequence percentage analysis of COI revealed that specimens from the NT shared 99.7% nucleotide identity to a haplotype of Cx. tritaeniorhynchus from Dili, Timor-Leste. The phylogenetic analysis showed that the NT specimens formed a monophyletic clade with other Cx. tritaeniorhynchus from Southeast Asia and the Middle East. We provide COI barcodes for most NT species from the Vishnui subgroup to aid future identifications, including the first genetic sequences for Culex (Culex) crinicauda and the undescribed species Culex (Culex) sp. No. 32 of Marks. Useful diagnostic morphological characters were identified and are presented in a taxonomic key to adult females to separate Cx. tritaeniorhynchus from other members of the Vishnui subgroup from the NT. Conclusions We report the detection of Cx. tritaeniorhynchus in Australia from the Darwin and Katherine regions of the NT. The vector is likely to be already established in northern Australia, given the wide geographical spread throughout the Top End of the NT. The establishment of Cx. tritaeniorhynchus in Australia is a concern to health officials as the species is an important vector of JEV and is now the sixth species from the subgenus Culex capable of vectoring JEV in Australia. We suggest that the species must now be continuously monitored during routine mosquito surveillance programmes to determine its current geographical spread and prevent the potential transmission of exotic JEV throughout Australia. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04911-2.
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Affiliation(s)
- Bryan D Lessard
- Australian National Insect Collection, National Research Collections Australia-CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia.
| | - Nina Kurucz
- Medical Entomology, NT Health-Royal Darwin Hospital, Top End Health Service, GPO Box 41326, Casuarina, NT, 0810, Australia
| | - Juanita Rodriguez
- Australian National Insect Collection, National Research Collections Australia-CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Jane Carter
- Medical Entomology, NT Health-Royal Darwin Hospital, Top End Health Service, GPO Box 41326, Casuarina, NT, 0810, Australia
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