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Pastusiak A, Reddy MR, Chen X, Hoyer I, Dorman J, Gebhardt ME, Carpi G, Norris DE, Pipas JM, Jackson EK. A metagenomic analysis of the phase 2 Anopheles gambiae 1000 genomes dataset reveals a wide diversity of cobionts associated with field collected mosquitoes. Commun Biol 2024; 7:667. [PMID: 38816486 PMCID: PMC11139907 DOI: 10.1038/s42003-024-06337-9] [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: 03/07/2023] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
The Anopheles gambiae 1000 Genomes (Ag1000G) Consortium previously utilized deep sequencing methods to catalogue genetic diversity across African An. gambiae populations. We analyzed the complete datasets of 1142 individually sequenced mosquitoes through Microsoft Premonition's Bayesian mixture model based (BMM) metagenomics pipeline. All specimens were confirmed as either An. gambiae sensu stricto (s.s.) or An. coluzzii with a high degree of confidence ( > 98% identity to reference). Homo sapiens DNA was identified in all specimens indicating contamination may have occurred either at the time of specimen collection, preparation and/or sequencing. We found evidence of vertebrate hosts in 162 specimens. 59 specimens contained validated Plasmodium falciparum reads. Human hepatitis B and primate erythroparvovirus-1 viral sequences were identified in fifteen and three mosquito specimens, respectively. 478 of the 1,142 specimens were found to contain bacterial reads and bacteriophage-related contigs were detected in 27 specimens. This analysis demonstrates the capacity of metagenomic approaches to elucidate important vector-host-pathogen interactions of epidemiological significance.
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Affiliation(s)
| | - Michael R Reddy
- Microsoft Premonition, Microsoft Research, Redmond, WA, 98052, USA.
| | - Xiaoji Chen
- Microsoft Premonition, Microsoft Research, Redmond, WA, 98052, USA
| | - Isaiah Hoyer
- Microsoft Premonition, Microsoft Research, Redmond, WA, 98052, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Mary E Gebhardt
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Douglas E Norris
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - James M Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Ethan K Jackson
- Microsoft Premonition, Microsoft Research, Redmond, WA, 98052, USA
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2
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Knight T, Sureka S. A New Paradigm for Threat Agnostic Biodetection: Biological Intelligence (BIOINT). Health Secur 2024; 22:31-38. [PMID: 38054947 PMCID: PMC10902261 DOI: 10.1089/hs.2023.0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Affiliation(s)
- Thomas Knight
- Thomas Knight, PhD, is Co-Founder and Ginkgo Fellow, Ginkgo Bioworks, Boston, MA
| | - Swati Sureka
- Swati Sureka, MSc (Oxon, Edin), is Business Operations Manager; Ginkgo Bioworks, Boston, MA
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McMinn RJ, Chacon A, Rückert C, Scorza V, Young MC, Worthington D, Lamb MM, Medrano RE, Harris EK, Arias K, Lopez MR, Asturias EJ, Foy BD, Stenglein MD, Olson D, Ebel GD. Evaluation of Vector-Enabled Xenosurveillance in Rural Guatemala. Am J Trop Med Hyg 2023; 109:1303-1310. [PMID: 37972312 DOI: 10.4269/ajtmh.22-0774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/02/2023] [Indexed: 11/19/2023] Open
Abstract
Surveillance methods that permit rapid detection of circulating pathogens in low-resource settings are desperately needed. In this study, we evaluated a mosquito bloodmeal-based surveillance method ("xenosurveillance") in rural Guatemala. Twenty households from two villages (Los Encuentros and Chiquirines) in rural southwest Guatemala were enrolled and underwent weekly prospective surveillance from August 2019 to December 2019 (16 weeks). When febrile illness was reported in a household, recently blood-fed mosquitoes were collected from within dwellings and blood samples taken from each member of the household. Mosquitoes were identified to species and blood sources identified by sequencing. Shotgun metagenomic sequencing was used to identify circulating viruses. Culex pipiens (60.9%) and Aedes aegypti (18.6%) were the most abundant mosquitoes collected. Bloodmeal sources were most commonly human (32.6%) and chicken (31.6%), with various other mammal and avian hosts detected. Several mosquito-specific viruses were detected, including Culex orthophasma virus. Human pathogens were not detected. Therefore, xenosurveillance may require more intensive sampling to detect human pathogens in Guatemala and ecologically similar localities in Central America.
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Affiliation(s)
- Rebekah J McMinn
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Andrea Chacon
- Fundacion para la Salud Integral de los Guatemaltecos, Retalhuleu, Guatemala
| | - Claudia Rückert
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada
| | - Valeria Scorza
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Michael C Young
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Delaney Worthington
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Molly M Lamb
- Colorado School of Public Health, Aurora, Colorado
| | - Ramon E Medrano
- Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Emma K Harris
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Kareen Arias
- Center for Human Development, Retalhuleu, Guatemala
| | - Maria Renee Lopez
- Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Edwin J Asturias
- Colorado School of Public Health, Aurora, Colorado
- Center for Human Development, Retalhuleu, Guatemala
- Department of Pediatrics, Section of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado
| | - Brian D Foy
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Daniel Olson
- Colorado School of Public Health, Aurora, Colorado
- Center for Human Development, Retalhuleu, Guatemala
- Department of Pediatrics, Section of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado
| | - Gregory D Ebel
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
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4
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Integrated xenosurveillance of Loa loa, Wuchereria bancrofti, Mansonella perstans and Plasmodium falciparum using mosquito carcasses and faeces: A pilot study in Cameroon. PLoS Negl Trop Dis 2022; 16:e0010868. [PMID: 36322515 PMCID: PMC9629651 DOI: 10.1371/journal.pntd.0010868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Community presence of loiasis must be determined before mass drug administration programmes for lymphatic filariasis and onchocerciasis can be implemented. However, taking human blood samples for loiasis surveillance is invasive and operationally challenging. A xenosurveillance approach based on the molecular screening of mosquitoes and their excreta/feces (E/F) for Loa loa DNA may provide a non-invasive method for detecting the community presence of loiasis. METHODS We collected 770 wild mosquitoes during a pilot study in a known loiasis transmission area in Mbalmayo, Cameroon. Of these, 376 were preserved immediately while 394 were kept in pools to collect 36-hour E/F samples before processing. Carcasses and E/F were screened for L. loa DNA. To demonstrate this method's potential for integrated disease surveillance, the samples were further tested for Wuchereria bancrofti, Mansonella perstans, and Plasmodium falciparum. RESULTS Despite limited sample numbers, L. loa DNA was detected in eight immediately-stored mosquitoes (2.13%; 95% CI 1.08 to 4.14), one carcass stored after providing E/F (0.25%; 95% CI 0.04 to 1.42), and three E/F samples (estimated prevalence 0.77%; 95% CI 0.15 to 2.23%). M. perstans and P. falciparum DNA were also detected in carcasses and E/F samples, while W. bancrofti DNA was detected in E/F. None of the carcasses positive for filarial worm DNA came from pools that provided a positive E/F sample, supporting the theory that, in incompetent vectors, ingested parasites undergo a rapid, complete expulsion in E/F. CONCLUSIONS Mosquito xenosurveillance may provide a useful tool for the surveillance of loiasis alongside other parasitic diseases.
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Hernández-Triana LM, Garza-Hernández JA, Ortega Morales AI, Prosser SWJ, Hebert PDN, Nikolova NI, Barrero E, de Luna-Santillana EDJ, González-Alvarez VH, Mendez-López R, Chan-Chable RJ, Fooks AR, Rodríguez-Pérez MA. An Integrated Molecular Approach to Untangling Host-Vector-Pathogen Interactions in Mosquitoes (Diptera: Culicidae) From Sylvan Communities in Mexico. Front Vet Sci 2021; 7:564791. [PMID: 33778029 PMCID: PMC7988227 DOI: 10.3389/fvets.2020.564791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 12/18/2020] [Indexed: 11/23/2022] Open
Abstract
There are ~240 species of Culicidae in Mexico, of which some are vectors of arthropod-borne viruses such as Zika virus, dengue virus, chikungunya virus, and West Nile virus. Thus, the identification of mosquito feeding preferences is paramount to understanding of vector–host–pathogen interactions that, in turn, can aid the control of disease outbreaks. Typically, DNA and RNA are extracted separately for animal (insects and blood meal hosts) and viral identification, but this study demonstrates that multiple organisms can be analyzed from a single RNA extract. For the first time, residual DNA present in standard RNA extracts was analyzed by DNA barcoding in concert with Sanger and next-generation sequencing (NGS) to identify both the mosquito species and the source of their meals in blood-fed females caught in seven sylvan communities in Chiapas State, Mexico. While mosquito molecular identification involved standard barcoding methods, the sensitivity of blood meal identification was maximized by employing short primers with NGS. In total, we collected 1,634 specimens belonging to 14 genera, 25 subgenera, and 61 morphospecies of mosquitoes. Of these, four species were new records for Mexico (Aedes guatemala, Ae. insolitus, Limatus asulleptus, Trichoprosopon pallidiventer), and nine were new records for Chiapas State. DNA barcode sequences for >300 bp of the COI gene were obtained from 291 specimens, whereas 130 bp sequences were recovered from another 179 specimens. High intraspecific divergence values (>2%) suggesting cryptic species complexes were observed in nine taxa: Anopheles eiseni (5.39%), An. pseudopunctipennis (2.79%), Ae. podographicus (4.05%), Culex eastor (4.88%), Cx. erraticus (2.28%), Toxorhynchites haemorrhoidalis (4.30%), Tr. pallidiventer (4.95%), Wyeomyia adelpha/Wy. guatemala (7.30%), and Wy. pseudopecten (4.04%). The study increased the number of mosquito species known from 128 species to 138 species for Chiapas State, and 239 for Mexico as a whole. Blood meal analysis showed that Aedes angustivittatus fed on ducks and chicken, whereas Psorophora albipes fed on humans. Culex quinquefasciatus fed on diverse hosts including chicken, human, turkey, and Mexican grackle. No arbovirus RNA was detected by reverse transcriptase–polymerase chain reaction in the surveyed specimens. This study demonstrated, for the first time, that residual DNA present in RNA blood meal extracts can be used to identify host vectors, highlighting the important role of molecular approaches in both vector identification and revealing host–vector–pathogen interactions.
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Affiliation(s)
- Luis M Hernández-Triana
- Animal and Plant Health Agency, Virology Department, Rabies and Wildlife Zoonoses Research Group, Addlestone, United Kingdom
| | | | - Aldo I Ortega Morales
- Departamento de Parasitología, Universidad Autónoma Agraria Antonio Narro, Unidad Laguna, Periférico Raúl López Sánchez y Carretera a Santa Fe, Torreón, Mexico
| | - Sean W J Prosser
- Center for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Paul D N Hebert
- Center for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Nadya I Nikolova
- Center for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Elsa Barrero
- Animal and Plant Health Agency, Virology Department, Rabies and Wildlife Zoonoses Research Group, Addlestone, United Kingdom
| | | | | | - Ramón Mendez-López
- Departamento de Parasitología, Universidad Autónoma Agraria Antonio Narro, Unidad Laguna, Periférico Raúl López Sánchez y Carretera a Santa Fe, Torreón, Mexico
| | - Rahuel J Chan-Chable
- Departamento de Parasitología, Universidad Autónoma Agraria Antonio Narro, Unidad Laguna, Periférico Raúl López Sánchez y Carretera a Santa Fe, Torreón, Mexico
| | - Anthony R Fooks
- Animal and Plant Health Agency, Virology Department, Rabies and Wildlife Zoonoses Research Group, Addlestone, United Kingdom
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6
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Petrone ME, Earnest R, Lourenço J, Kraemer MUG, Paulino-Ramirez R, Grubaugh ND, Tapia L. Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic. Nat Commun 2021; 12:151. [PMID: 33420058 PMCID: PMC7794562 DOI: 10.1038/s41467-020-20391-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/27/2020] [Indexed: 12/21/2022] Open
Abstract
Mosquito-borne viruses threaten the Caribbean due to the region's tropical climate and seasonal reception of international tourists. Outbreaks of chikungunya and Zika have demonstrated the rapidity with which these viruses can spread. Concurrently, dengue fever cases have climbed over the past decade. Sustainable disease control measures are urgently needed to quell virus transmission and prevent future outbreaks. Here, to improve upon current control methods, we analyze temporal and spatial patterns of chikungunya, Zika, and dengue outbreaks reported in the Dominican Republic between 2012 and 2018. The viruses that cause these outbreaks are transmitted by Aedes mosquitoes, which are sensitive to seasonal climatological variability. We evaluate whether climate and the spatio-temporal dynamics of dengue outbreaks could explain patterns of emerging disease outbreaks. We find that emerging disease outbreaks were robust to the climatological and spatio-temporal constraints defining seasonal dengue outbreak dynamics, indicating that constant surveillance is required to prevent future health crises.
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Affiliation(s)
- Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Robert Paulino-Ramirez
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, Santo Domingo, Dominican Republic
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Leandro Tapia
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, Santo Domingo, Dominican Republic.
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7
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Drummond C, Gebhardt ME, Sáenz Robles MT, Carpi G, Hoyer I, Pastusiak A, Reddy MR, Norris DE, Pipas JM, Jackson EK. Stability and detection of nucleic acid from viruses and hosts in controlled mosquito blood feeds. PLoS One 2020; 15:e0231061. [PMID: 32525960 PMCID: PMC7289426 DOI: 10.1371/journal.pone.0231061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/23/2020] [Indexed: 12/29/2022] Open
Abstract
Monitoring the presence and spread of pathogens in the environment is of critical importance. Rapid detection of infectious disease outbreaks and prediction of their spread can facilitate early responses of health agencies and reduce the severity of outbreaks. Current sampling methods are sorely limited by available personnel and throughput. For instance, xenosurveillance utilizes captured arthropod vectors, such as mosquitoes, as sampling tools to access blood from a wide variety of vertebrate hosts. Next generation sequencing (NGS) of nucleic acid from individual blooded mosquitoes can be used to identify mosquito and host species, and microorganisms including pathogens circulating within either host. However, there are practical challenges to collecting and processing mosquitoes for xenosurveillance, such as the rapid metabolization or decay of microorganisms within the mosquito midgut. This particularly affects pathogens that do not replicate in mosquitoes, preventing their detection by NGS or other methods. Accordingly, we performed a series of experiments to establish the windows of detection for DNA or RNA from human blood and/or viruses present in mosquito blood meals. Our results will contribute to the development of xenosurveillance techniques with respect to optimal timing of sample collection and NGS processing and will also aid trap design by demonstrating the stabilizing effect of temperature control on viral genome recovery from blood-fed mosquitoes.
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Affiliation(s)
- Coyne Drummond
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mary E. Gebhardt
- Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Maria Teresa Sáenz Robles
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Isaiah Hoyer
- Health Futures, Microsoft Research, Redmond, Washington, United States of America
| | - Andrzej Pastusiak
- Health Futures, Microsoft Research, Redmond, Washington, United States of America
| | - Michael R. Reddy
- Health Futures, Microsoft Research, Redmond, Washington, United States of America
- * E-mail:
| | - Douglas E. Norris
- Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - James M. Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ethan K. Jackson
- Health Futures, Microsoft Research, Redmond, Washington, United States of America
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8
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Pilotte N, Cook DA, Pryce J, Zulch MF, Minetti C, Reimer LJ, Williams SA. Laboratory evaluation of molecular xenomonitoring using mosquito and tsetse fly excreta/feces to amplify Plasmodium, Brugia, and Trypanosoma DNA. Gates Open Res 2020; 3:1734. [PMID: 32596646 PMCID: PMC7308644 DOI: 10.12688/gatesopenres.13093.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2020] [Indexed: 11/20/2022] Open
Abstract
Background: Results from an increasing number of studies suggest that mosquito excreta/feces (E/F) testing has considerable potential to serve as a supplement for traditional molecular xenomonitoring techniques. However, as the catalogue of possible use-cases for this methodology expands, and the list of amenable pathogens grows, a number of fundamental methods-based questions remain. Answering these questions is critical to maximizing the utility of this approach and to facilitating its successful implementation as an effective tool for molecular xenomonitoring. Methods: Utilizing E/F produced by mosquitoes or tsetse flies experimentally exposed to Brugia malayi, Plasmodium falciparum, or Trypanosoma brucei brucei, factors such as limits of detection, throughput of testing, adaptability to use with competent and incompetent vector species, and effects of additional blood feedings post parasite-exposure were evaluated. Two platforms for the detection of pathogen signal (quantitative real-time PCR and digital PCR (dPCR)) were also compared, with strengths and weaknesses examined for each. Results: Experimental results indicated that high throughput testing is possible when evaluating mosquito E/F for the presence of either B. malayi or P. falciparum from both competent and incompetent vector mosquito species. Furthermore, following exposure to pathogen, providing mosquitoes with a second, uninfected bloodmeal did not expand the temporal window for E/F collection during which pathogen detection was possible. However, this collection window did appear longer in E/F collected from tsetse flies following exposure to T. b. brucei. Testing also suggested that dPCR may facilitate detection through its increased sensitivity. Unfortunately, logistical obstacles will likely make the large-scale use of dPCR impractical for this purpose. Conclusions: By examining many E/F testing variables, expansion of this technology to a field-ready platform has become increasingly feasible. However, translation of this methodology from the lab to the field will first require field-based pilot studies aimed at assessing the efficacy of E/F screening.
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Affiliation(s)
- Nils Pilotte
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts, 01003, USA
| | - Darren A.N. Cook
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Joseph Pryce
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Michael F. Zulch
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Corrado Minetti
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Lisa J. Reimer
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Steven A. Williams
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts, 01003, USA
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9
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Pilotte N, Cook DA, Pryce J, Zulch MF, Minetti C, Reimer LJ, Williams SA. Laboratory evaluation of molecular xenomonitoring using mosquito excreta/feces to amplify Plasmodium, Brugia, and Trypanosoma DNA. Gates Open Res 2019; 3:1734. [PMID: 32596646 PMCID: PMC7308644 DOI: 10.12688/gatesopenres.13093.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2019] [Indexed: 03/30/2024] Open
Abstract
Background: Results from an increasing number of studies suggest that mosquito excreta/feces (E/F) testing has considerable potential to serve as a supplement for traditional molecular xenomonitoring techniques. However, as the catalogue of possible use-cases for this methodology expands, and the list of amenable pathogens grows, a number of fundamental methods-based questions remain. Answering these questions is critical to maximizing the utility of this approach and to facilitating its successful implementation as an effective tool for molecular xenomonitoring. Methods: Utilizing E/F produced by mosquitoes or tsetse flies experimentally exposed to Brugia malayi, Plasmodium falciparum, or Trypanosoma brucei brucei, factors such as limits of detection, throughput of testing, adaptability to use with competent- and incompetent-vector species, and effects of additional blood feedings post parasite-exposure were evaluated. Two platforms for the detection of pathogen signal (quantitative real-time PCR and digital PCR [dPCR]) were also compared, with strengths and weaknesses examined for each. Results: Experimental results indicated that high throughput testing is possible when evaluating mosquito E/F for the presence of either B. malayi or P. falciparum from both competent- and incompetent-vector mosquito species. Furthermore, following exposure to pathogen, providing mosquitoes with a second, uninfected bloodmeal did not expand the temporal window for E/F collection during which pathogen detection was possible. However, this collection window did appear longer in E/F collected from tsetse flies following exposure to T. b. brucei. Testing also suggested that dPCR may facilitate detection through its increased sensitivity. Unfortunately, logistical obstacles will likely make the large-scale use of dPCR impractical for this purpose. Conclusions: By examining many E/F testing variables, expansion of this technology to a field-ready platform has become increasingly feasible. However, translation of this methodology from the lab to the field will first require the completion of field-based pilot studies aimed at assessing the efficacy of E/F screening.
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Affiliation(s)
- Nils Pilotte
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts, 01003, USA
| | - Darren A.N. Cook
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Joseph Pryce
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Michael F. Zulch
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Corrado Minetti
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Lisa J. Reimer
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Steven A. Williams
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts, 01003, USA
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10
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Nelli L, Ferguson HM, Matthiopoulos J. Achieving explanatory depth and spatial breadth in infectious disease modelling: Integrating active and passive case surveillance. Stat Methods Med Res 2019; 29:1273-1287. [PMID: 31213191 DOI: 10.1177/0962280219856380] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ideally, the data used for robust spatial prediction of disease distribution should be both high-resolution and spatially expansive. However, such in-depth and geographically broad data are rarely available in practice. Instead, researchers usually acquire either detailed epidemiological data with high resolution at a small number of active sampling sites, or more broad-ranging but less precise data from passive case surveillance. We propose a novel inferential framework, capable of simultaneously drawing insights from both passive and active data types. We developed a Bayesian latent point process approach, combining active data collection in a limited set of points, where in-depth covariates are measured, with passive case detection, where error-prone, large-scale disease data are accompanied only by coarse or remotely-sensed covariate layers. Using the example of malaria, we tested our method's efficiency under several hypothetical scenarios of reported incidence in different combinations of imperfect detection and spatial complexity of the environmental variables. We provide a simple solution to a widespread problem in spatial epidemiology, combining latent process modelling and spatially autoregressive modelling. By using active sampling and passive case detection in a complementary way, we achieved the best-of-both-worlds, in effect, a formal calibration of spatially extensive, error-prone data by localised, high-quality data.
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Affiliation(s)
- Luca Nelli
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Heather M Ferguson
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Jason Matthiopoulos
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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11
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Kęsik-Maliszewska J, Larska M, Collins ÁB, Rola J. Post-Epidemic Distribution of Schmallenberg Virus in Culicoides Arbovirus Vectors in Poland. Viruses 2019; 11:v11050447. [PMID: 31100887 PMCID: PMC6563501 DOI: 10.3390/v11050447] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/06/2019] [Accepted: 05/14/2019] [Indexed: 12/12/2022] Open
Abstract
Pooled samples of female and male Culicoides midges (5146 and 332 pools, respectively) that corresponded to a total number of 124,957 specimens were collected between 2013-2017 in the vicinity of cattle barns that were distributed throughout Poland were analyzed for the presence of Schmallenberg virus (SBV) RNA. Sixty-six pools tested positive (1.2%) with mean Ct value of 34.95. The maximum likelihood estimated infection rate (MLE) was calculated at 0.53 per 1000 individuals; however, it peaked in 2016 with MLE of 3.7. Viral RNA was detected in C. obsoletus/scoticus complex, C. punctatus, and C. pulicaris pools. Moreover, viral material was present in nulliparous (virgin) Culicoides females (MLE 0.27) and for the first time reported in males (MLE 0.34), which suggests the possibility of transovarial route of SBV or virus RNA transmission, as both do not fed on host blood. The accuracy of targeted versus random SBV surveillance in Culicoides vectors was compared. The relationship between infection rate (expressed as minimum infection rate; MIR), in addition to MLE, was compared with the density of virus infected midges (DIM). In conclusion, the SBV infection rate in the vector was significantly higher in 2016 as compared to other surveillance years; this is consistent with the simultaneous increase in SBV seroprevalence (seroconversion) in ruminants during the same year.
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Affiliation(s)
| | - Magdalena Larska
- Department of Virology, National Veterinary Institute, 24-100 Puławy, Poland.
| | - Áine B Collins
- Department of Agriculture Food and the Marine, C/o Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine University College Dublin, Belfield, D04 W6F6 Dublin 4, Ireland.
| | - Jerzy Rola
- Department of Virology, National Veterinary Institute, 24-100 Puławy, Poland.
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12
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Fauver JR, Akter S, Morales AIO, Black WC, Rodriguez AD, Stenglein MD, Ebel GD, Weger-Lucarelli J. A reverse-transcription/RNase H based protocol for depletion of mosquito ribosomal RNA facilitates viral intrahost evolution analysis, transcriptomics and pathogen discovery. Virology 2018; 528:181-197. [PMID: 30616207 DOI: 10.1016/j.virol.2018.12.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/28/2018] [Accepted: 12/28/2018] [Indexed: 11/17/2022]
Abstract
Identifying novel viruses or assessing viral variation by NGS requires high sequencing coverage. More than 90% of total RNA is ribosomal (rRNA), making variant calling, virus discovery or transcriptomic profiling difficult. Current methods to increase informative reads suffer from drawbacks, either they cannot be used for some viruses, are optimized for a single species, or introduce bias. We describe a two-part approach combining reverse-transcription to create RNA/DNA hybrids which are then degraded with RNaseH/DNase sequentially that works for three medically relevant mosquito genera; Aedes, Anopheles, and Culex. We demonstrate depletion of rRNA from different samples, including whole mosquitoes and midgut contents from FTA cards. We describe novel insect-specific virus genomes from field collected mosquitoes. The protocol requires only common laboratory reagents and small oligonucleotides specific to rRNA. This approach can be adapted for other organisms, aiding virus diversity analyses, virus discovery and transcriptomics in both laboratory and field samples.
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Affiliation(s)
- Joseph R Fauver
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Shamima Akter
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, 360 W Campus Drive, Blacksburg, VA, USA
| | - Aldo Ivan Ortega Morales
- Departamento de Parasitología, Universidad Autónoma Agraria Antonio Narro, Torreón, Coahuila, Mexico
| | - William C Black
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Americo D Rodriguez
- Centro Regional de Investigación en Salud Publica, Instituto Nacional de Salud Pública, Tapachula, Chiapas, Mexico
| | - Mark D Stenglein
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - James Weger-Lucarelli
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
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13
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Nascimento J, Sampaio VS, Karl S, Kuehn A, Almeida A, Vitor-Silva S, de Melo GC, Baia da Silva DC, C. P. Lopes S, Fé NF, Lima JBP, Guerra MGB, Pimenta PFP, Bassat Q, Mueller I, Lacerda MVG, Monteiro WM. Use of anthropophilic culicid-based xenosurveillance as a proxy for Plasmodium vivax malaria burden and transmission hotspots identification. PLoS Negl Trop Dis 2018; 12:e0006909. [PMID: 30418971 PMCID: PMC6258424 DOI: 10.1371/journal.pntd.0006909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/26/2018] [Accepted: 10/08/2018] [Indexed: 12/14/2022] Open
Abstract
Vector-borne diseases account for more than 17% of all infectious diseases, causing more than one million deaths annually. Malaria remains one of the most important public health problems worldwide. These vectors are bloodsucking insects, which can transmit disease-producing microorganisms during a blood meal. The contact of culicids with human populations living in malaria-endemic areas suggests that the identification of Plasmodium genetic material in the blood present in the gut of these mosquitoes may be possible. The process of assessing the blood meal for the presence of pathogens is termed 'xenosurveillance'. In view of this, the present work investigated the relationship between the frequency with which Plasmodium DNA is found in culicids and the frequency with which individuals are found to be carrying malaria parasites. A cross-sectional study was performed in a peri-urban area of Manaus, in the Western Brazilian Amazon, by simultaneously collecting human blood samples and trapping culicids from households. A total of 875 individuals were included in the study and a total of 13,374mosquito specimens were captured. Malaria prevalence in the study area was 7.7%. The frequency of households with at least one culicid specimen carrying Plasmodium DNA was 6.4%. Plasmodium infection incidence was significantly related to whether any Plasmodium positive blood-fed culicid was found in the same household [IRR 3.49 (CI95% 1.38-8.84); p = 0.008] and for indoor-collected culicids [IRR 4.07 (CI95%1.25-13.24); p = 0.020]. Furthermore, the number of infected people in the house at the time of mosquito collection was related to whether there were any positive blood-fed culicid mosquitoes in that household for collection methods combined [IRR 4.48 (CI95%2.22-9.05); p<0.001] or only for indoor-collected culicids [IRR 4.88 (CI95%2.01-11.82); p<0.001]. Our results suggest that xenosurveillance can be used in endemic tropical regions in order to estimate the malaria burden and identify transmission foci in areas where Plasmodium vivax is predominant.
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Affiliation(s)
- Joabi Nascimento
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Vanderson S. Sampaio
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Stephan Karl
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Australia
- Entomology Section, Vector-borne Diseases Unit, Papua New Guinea Institute of Medical Research, Papua, New Guinea
- Department of Medical Biology, University of Melbourne, Australia
| | - Andrea Kuehn
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
| | - Anne Almeida
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Sheila Vitor-Silva
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Gisely Cardoso de Melo
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Djane C. Baia da Silva
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
| | | | - Nelson F. Fé
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
| | - José B. Pereira Lima
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Maria G. Barbosa Guerra
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Paulo F. P. Pimenta
- Laboratório de Entomologia Médica, Centro de Pesquisas René Rachou (Fiocruz), Belo Horizonte, MG, Brazil
| | - Quique Bassat
- ISGlobal, Hospital Clínic—Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ICREA, Barcelona, Spain
- Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain
| | - Ivo Mueller
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Australia
- Parasites & Hosts Unit, Institut Pasteur, Paris, France
| | - Marcus V. G. Lacerda
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Instituto Leônidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, AM, Brazil
| | - Wuelton M. Monteiro
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, AM, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil
- * E-mail:
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14
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Gutiérrez-Bugallo G, Rodríguez-Roche R, Díaz G, Pérez M, Mendizábal ME, Peraza I, Vázquez AA, Alvarez M, Rodríguez M, Bisset JA, Guzmán MG. Spatio-temporal distribution of vertically transmitted dengue viruses byAedes aegypti(Diptera: Culicidae) from Arroyo Naranjo, Havana, Cuba. Trop Med Int Health 2018; 23:1342-1349. [DOI: 10.1111/tmi.13162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Gladys Gutiérrez-Bugallo
- Department of Vector Control; Center for Research; Diagnostic and Reference; Institute of Tropical Medicine Pedro Kourí; PAHO-WHO Collaborating Center for Dengue and its Control; Havana Cuba
| | | | - Gisell Díaz
- Department of Virology; Center for Research; Diagnostic and Reference; Institute of Tropical Medicine Pedro Kourí; PAHO-WHO Collaborating Center for Dengue and its Control; Havana Cuba
| | - Magaly Pérez
- Unidad Provincial de Vigilancia y Lucha Antivectorial; Centro Provincial de Higiene y Epidemiología; Havana Cuba
| | - María Elena Mendizábal
- Unidad Provincial de Vigilancia y Lucha Antivectorial; Centro Provincial de Higiene y Epidemiología; Havana Cuba
| | - Iris Peraza
- Unidad Provincial de Vigilancia y Lucha Antivectorial; Centro Provincial de Higiene y Epidemiología; Havana Cuba
| | - Antonio A. Vázquez
- Department of Vector Control; Center for Research; Diagnostic and Reference; Institute of Tropical Medicine Pedro Kourí; PAHO-WHO Collaborating Center for Dengue and its Control; Havana Cuba
| | - Mayling Alvarez
- Department of Virology; Center for Research; Diagnostic and Reference; Institute of Tropical Medicine Pedro Kourí; PAHO-WHO Collaborating Center for Dengue and its Control; Havana Cuba
| | - Magdalena Rodríguez
- Department of Vector Control; Center for Research; Diagnostic and Reference; Institute of Tropical Medicine Pedro Kourí; PAHO-WHO Collaborating Center for Dengue and its Control; Havana Cuba
| | - Juan A. Bisset
- Department of Vector Control; Center for Research; Diagnostic and Reference; Institute of Tropical Medicine Pedro Kourí; PAHO-WHO Collaborating Center for Dengue and its Control; Havana Cuba
| | - María G. Guzmán
- Department of Virology; Center for Research; Diagnostic and Reference; Institute of Tropical Medicine Pedro Kourí; PAHO-WHO Collaborating Center for Dengue and its Control; Havana Cuba
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