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Mwanga EP, Kweyamba PA, Siria DJ, Mshani IH, Mchola IS, Makala FE, Seleman G, Abbasi S, Mwinyi SH, González-Jiménez M, Waynne K, Baldini F, Babayan SA, Okumu FO. Reagent-free detection of Plasmodium falciparum malaria infections in field-collected mosquitoes using mid-infrared spectroscopy and machine learning. Sci Rep 2024; 14:12100. [PMID: 38802488 PMCID: PMC11130311 DOI: 10.1038/s41598-024-63082-z] [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: 02/19/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024] Open
Abstract
Field-derived metrics are critical for effective control of malaria, particularly in sub-Saharan Africa where the disease kills over half a million people yearly. One key metric is entomological inoculation rate, a direct measure of transmission intensities, computed as a product of human biting rates and prevalence of Plasmodium sporozoites in mosquitoes. Unfortunately, current methods for identifying infectious mosquitoes are laborious, time-consuming, and may require expensive reagents that are not always readily available. Here, we demonstrate the first field-application of mid-infrared spectroscopy and machine learning (MIRS-ML) to swiftly and accurately detect Plasmodium falciparum sporozoites in wild-caught Anopheles funestus, a major Afro-tropical malaria vector, without requiring any laboratory reagents. We collected 7178 female An. funestus from rural Tanzanian households using CDC-light traps, then desiccated and scanned their heads and thoraces using an FT-IR spectrometer. The sporozoite infections were confirmed using enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR), to establish references for training supervised algorithms. The XGBoost model was used to detect sporozoite-infectious specimen, accurately predicting ELISA and PCR outcomes with 92% and 93% accuracies respectively. These findings suggest that MIRS-ML can rapidly detect P. falciparum in field-collected mosquitoes, with potential for enhancing surveillance in malaria-endemic regions. The technique is both fast, scanning 60-100 mosquitoes per hour, and cost-efficient, requiring no biochemical reactions and therefore no reagents. Given its previously proven capability in monitoring key entomological indicators like mosquito age, human blood index, and identities of vector species, we conclude that MIRS-ML could constitute a low-cost multi-functional toolkit for monitoring malaria risk and evaluating interventions.
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Affiliation(s)
- Emmanuel P Mwanga
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania.
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Prisca A Kweyamba
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
| | - Doreen J Siria
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Issa H Mshani
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Idrisa S Mchola
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Faraja E Makala
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Godian Seleman
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Said Abbasi
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Sophia H Mwinyi
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | | | - Klaas Waynne
- School of Chemistry, The University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francesco Baldini
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Simon A Babayan
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fredros O Okumu
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania.
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
- School of Public Health, 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.
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Ferreira TN, Santos LMB, Valladares V, Flanley CM, McDowell MA, Garcia GA, Mello-Silva CC, Maciel-de-Freitas R, Genta FA. Age, sex, and mating status discrimination in the sand fly Lutzomyia longipalpis using near infra-red spectroscopy (NIRS). Parasit Vectors 2024; 17:19. [PMID: 38217054 PMCID: PMC10787389 DOI: 10.1186/s13071-023-06097-1] [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: 06/08/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Understanding aspects related to the physiology and capacity of vectors is essential for effectively controlling vector-borne diseases. The sand fly Lutzomyia longipalpis has great importance in medical entomology for disseminating Leishmania parasites, the causative agent of Leishmaniasis, one of the main neglected diseases listed by the World Health Organization (WHO). In this respect, it is necessary to evaluate the transmission potential of this species and the success of vector control interventions. Near-infrared spectroscopy (NIRS) has been used to estimate the age of mosquitoes in different conditions (laboratory, semi-field, and conservation), taxonomic analysis, and infection detection. However, no studies are using NIRS for sand flies. METHODS In this study, we developed analytic models to estimate the age of L. longipalpis adults under laboratory conditions, identify their copulation state, and evaluate their gonotrophic cycle and diet. RESULTS Sand flies were classified with an accuracy of 58-82% in 3 age groups and 82-92% when separating them into young (<8 days) or old (>8 days) insects. The classification between mated and non-mated sandflies was 98-100% accurate, while the percentage of hits of females that had already passed the first gonotrophic cycle was only 59%. CONCLUSIONS We consider the age and copula estimation results very promising, as they provide essential aspects of vector capacity assessment, which can be obtained quickly and at a lower cost with NIRS.
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Affiliation(s)
- Tainá Neves Ferreira
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Lilha M B Santos
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Vanessa Valladares
- Malacology Laboratory, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Catherine M Flanley
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - Mary Ann McDowell
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - Gabriela A Garcia
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | | | - Rafael Maciel-de-Freitas
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, Brazil
| | - Fernando Ariel Genta
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, Brazil.
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3
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Mshani IH, Siria DJ, Mwanga EP, Sow BB, Sanou R, Opiyo M, Sikulu-Lord MT, Ferguson HM, Diabate A, Wynne K, González-Jiménez M, Baldini F, Babayan SA, Okumu F. Key considerations, target product profiles, and research gaps in the application of infrared spectroscopy and artificial intelligence for malaria surveillance and diagnosis. Malar J 2023; 22:346. [PMID: 37950315 PMCID: PMC10638832 DOI: 10.1186/s12936-023-04780-3] [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: 03/04/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Studies on the applications of infrared (IR) spectroscopy and machine learning (ML) in public health have increased greatly in recent years. These technologies show enormous potential for measuring key parameters of malaria, a disease that still causes about 250 million cases and 620,000 deaths, annually. Multiple studies have demonstrated that the combination of IR spectroscopy and machine learning (ML) can yield accurate predictions of epidemiologically relevant parameters of malaria in both laboratory and field surveys. Proven applications now include determining the age, species, and blood-feeding histories of mosquito vectors as well as detecting malaria parasite infections in both humans and mosquitoes. As the World Health Organization encourages malaria-endemic countries to improve their surveillance-response strategies, it is crucial to consider whether IR and ML techniques are likely to meet the relevant feasibility and cost-effectiveness requirements-and how best they can be deployed. This paper reviews current applications of IR spectroscopy and ML approaches for investigating malaria indicators in both field surveys and laboratory settings, and identifies key research gaps relevant to these applications. Additionally, the article suggests initial target product profiles (TPPs) that should be considered when developing or testing these technologies for use in low-income settings.
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Affiliation(s)
- Issa H Mshani
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania.
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | - Doreen J Siria
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Emmanuel P Mwanga
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Bazoumana Bd Sow
- Department of Medical Biology and Public Health, Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Roger Sanou
- Department of Medical Biology and Public Health, Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Mercy Opiyo
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Malaria Elimination Initiative (MEI), Institute for Global Health Sciences, University of California, San Francisco, USA
| | - Maggy T Sikulu-Lord
- Faculty of Science, School of the Environment, The University of Queensland, Brisbane, QLD, Australia
| | - Heather M Ferguson
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Abdoulaye Diabate
- Department of Medical Biology and Public Health, Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Klaas Wynne
- School of Chemistry, The University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mario González-Jiménez
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
- School of Chemistry, The University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francesco Baldini
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Simon A Babayan
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | - Fredros Okumu
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania.
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
- School of Life Sciences and Biotechnology, Nelson Mandela African Institution of Science and Technology, Arusha, United Republic of Tanzania.
- School of Public Health, The University of the Witwatersrand, Park Town, South Africa.
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Garcia GA, Lord AR, Santos LMB, Kariyawasam TN, David MR, Couto-Lima D, Tátila-Ferreira A, Pavan MG, Sikulu-Lord MT, Maciel-de-Freitas R. Rapid and Non-Invasive Detection of Aedes aegypti Co-Infected with Zika and Dengue Viruses Using Near Infrared Spectroscopy. Viruses 2022; 15:11. [PMID: 36680052 PMCID: PMC9863061 DOI: 10.3390/v15010011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/03/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
The transmission of dengue (DENV) and Zika (ZIKV) has been continuously increasing worldwide. An efficient arbovirus surveillance system is critical to designing early-warning systems to increase preparedness of future outbreaks in endemic countries. The Near Infrared Spectroscopy (NIRS) is a promising high throughput technique to detect arbovirus infection in Ae. aegypti with remarkable advantages such as cost and time effectiveness, reagent-free, and non-invasive nature over existing molecular tools for similar purposes, enabling timely decision making through rapid detection of potential disease. Our aim was to determine whether NIRS can differentiate Ae. aegypti females infected with either ZIKV or DENV single infection, and those coinfected with ZIKV/DENV from uninfected ones. Using 200 Ae. aegypti females reared and infected in laboratory conditions, the training model differentiated mosquitoes into the four treatments with 100% accuracy. DENV-, ZIKV-, and ZIKV/DENV-coinfected mosquitoes that were used to validate the model could be correctly classified into their actual infection group with a predictive accuracy of 100%, 84%, and 80%, respectively. When compared with mosquitoes from the uninfected group, the three infected groups were predicted as belonging to the infected group with 100%, 97%, and 100% accuracy for DENV-infected, ZIKV-infected, and the co-infected group, respectively. Preliminary lab-based results are encouraging and indicate that NIRS should be tested in field settings to evaluate its potential role to monitor natural infection in field-caught mosquitoes.
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Affiliation(s)
- Gabriela A. Garcia
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
| | - Anton R. Lord
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia
- Spectroscopy and Data Consultants Pty Ltd., Brisbane, QLD 4035, Australia
| | - Lilha M. B. Santos
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
| | | | - Mariana R. David
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
| | - Dinair Couto-Lima
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
| | - Aline Tátila-Ferreira
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
| | - Márcio G. Pavan
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
| | - Maggy T. Sikulu-Lord
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Rafael Maciel-de-Freitas
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
- Department of Arbovirology, Bernhard Nocht Institute of Tropical Medicine, 20359 Hamburg, Germany
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Somé BM, Da DF, McCabe R, Djègbè NDC, Paré LIG, Wermé K, Mouline K, Lefèvre T, Ouédraogo AG, Churcher TS, Dabiré RK. Adapting field-mosquito collection techniques in a perspective of near-infrared spectroscopy implementation. Parasit Vectors 2022; 15:338. [PMID: 36163071 PMCID: PMC9513905 DOI: 10.1186/s13071-022-05458-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/27/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Near-infrared spectroscopy (NIRS) has the potential to be a useful tool for assessing key entomological parameters of malaria-transmitting mosquitoes, including age, infectious status and species identity. However, before NIRS can be reliably used in the field at scale, methods for killing mosquitoes and conserving samples prior to NIRS scanning need to be further optimized. Historically, mosquitoes used in studies have been killed with chloroform, although this approach is not without health hazards and should not be used in human dwellings. For the application of NIRS scanning it is also unclear which mosquito preservation method to use. The aim of the study reported here was to investigate the use of pyrethrum spray, a commercially available insecticide spray in Burkina Faso, for killing mosquitoes METHODS: Laboratory-reared Anopheles gambiae and Anopheles coluzzii were killed using either a pyrethrum insecticide spray routinely used in studies involving indoor mosquito collections (Kaltox Paalga®; Saphyto, Bobo-Dioulasso, Burkina Faso) or chloroform ("gold standard"). Preservative methods were also investigated to determine their impact on NIRS accuracy in predicting the species of laboratory-reared Anopheles and wild-caught mosquito species. After analysis of fresh samples, mosquitoes were stored in 80% ethanol or in silica gel for 2 weeks and re-analyzed by NIRS. In addition, experimentally infected An. coluzzii and wild-caught An. gambiae sensu lato (s.l.) were scanned as fresh samples to determine whether they contained sporozoites, then stored in the preservatives mentioned above for 2 weeks before being re-analyzed. RESULTS The difference in the accuracy of NIRS to differentiate between laboratory-reared An. gambiae mosquitoes and An. coluzzii mosquitoes killed with either insecticide (90%) or chloroform (92%) was not substantial. NIRS had an accuracy of 90% in determining mosquito species for mosquitoes killed with chloroform and preserved in ethanol or silica gel. The accuracy was the same when the pyrethrum spray was used to kill mosquitoes followed by preservation in silica gel, but was lower when ethanol was used as a preservative (80%). Regarding infection status, NIRS was able to differentiate between infected and uninfected mosquitoes, with a slightly lower accuracy for both laboratory and wild-caught mosquitoes preserved in silica gel or ethanol. CONCLUSIONS The results show that NIRS can be used to classify An. gambiae s.l. species killed by pyrethrum spray with no loss of accuracy. This insecticide may have practical advantages over chloroform for the killing of mosquitoes in NIRS analysis.
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Affiliation(s)
- Bernard Mouonniba Somé
- Institut de Recherche en Sciences de La Santé, Direction Régionale, 399 avenue de la liberté, 01 BP 545, Bobo-Dioulasso 01, Burkina Faso
- Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Dari F. Da
- Institut de Recherche en Sciences de La Santé, Direction Régionale, 399 avenue de la liberté, 01 BP 545, Bobo-Dioulasso 01, Burkina Faso
| | - Ruth McCabe
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG UK
- Department of Statistics, University of Oxford, 24-29 St Giles, Oxford, OX1 3LB UK
- NIHR Health Research Protection Unit in Emerging and Zoonotic Infections, University of Liverpool, The Ronald Ross Building, 8 West Derby Street, Liverpool, L69 7BE UK
| | - Nicaise Denis C. Djègbè
- Institut de Recherche en Sciences de La Santé, Direction Régionale, 399 avenue de la liberté, 01 BP 545, Bobo-Dioulasso 01, Burkina Faso
- Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Lawata Inès Géraldine Paré
- Institut de Recherche en Sciences de La Santé, Direction Régionale, 399 avenue de la liberté, 01 BP 545, Bobo-Dioulasso 01, Burkina Faso
- Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Kadidia Wermé
- Institut de Recherche en Sciences de La Santé, Direction Régionale, 399 avenue de la liberté, 01 BP 545, Bobo-Dioulasso 01, Burkina Faso
| | - Karine Mouline
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), IRD, CNRS, Montpellier University, Montpellier, France
| | - Thierry Lefèvre
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), IRD, CNRS, Montpellier University, Montpellier, France
| | | | - Thomas S. Churcher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG UK
| | - Roch Kounbobr Dabiré
- Institut de Recherche en Sciences de La Santé, Direction Régionale, 399 avenue de la liberté, 01 BP 545, Bobo-Dioulasso 01, Burkina Faso
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6
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The Application of NIRS to Determine Animal Physiological Traits for Wildlife Management and Conservation. REMOTE SENSING 2021. [DOI: 10.3390/rs13183699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The ability to measure and monitor wildlife populations is important for species management and conservation. The use of near-infrared spectroscopy (NIRS) to rapidly detect physiological traits from wildlife scat and other body materials could play an important role in the conservation of species. Previous research has demonstrated the potential for NIRS to detect diseases such as the novel COVID-19 from saliva, parasites from feces, and numerous other traits from animal skin, hair, and scat, such as cortisol metabolites, diet quality, sex, and reproductive status, that may be useful for population monitoring. Models developed from NIRS data use light reflected from a sample to relate the variation in the sample’s spectra to variation in a trait, which can then be used to predict that trait in unknown samples based on their spectra. The modelling process involves calibration, validation, and evaluation. Data sampling, pre-treatments, and the selection of training and testing datasets can impact model performance. We review the use of NIRS for measuring physiological traits in animals that may be useful for wildlife management and conservation and suggest future research to advance the application of NIRS for this purpose.
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7
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Detection of Plasmodium falciparum in laboratory-reared and naturally infected wild mosquitoes using near-infrared spectroscopy. Sci Rep 2021; 11:10289. [PMID: 33986416 PMCID: PMC8119679 DOI: 10.1038/s41598-021-89715-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/21/2021] [Indexed: 11/18/2022] Open
Abstract
There is an urgent need for high throughput, affordable methods of detecting pathogens inside insect vectors to facilitate surveillance. Near-infrared spectroscopy (NIRS) has shown promise to detect arbovirus and malaria in the laboratory but has not been evaluated in field conditions. Here we investigate the ability of NIRS to identify Plasmodium falciparum in Anopheles coluzzii mosquitoes. NIRS models trained on laboratory-reared mosquitoes infected with wild malaria parasites can detect the parasite in comparable mosquitoes with moderate accuracy though fails to detect oocysts or sporozoites in naturally infected field caught mosquitoes. Models trained on field mosquitoes were unable to predict the infection status of other field mosquitoes. Restricting analyses to mosquitoes of uninfectious and highly-infectious status did improve predictions suggesting sensitivity and specificity may be better in mosquitoes with higher numbers of parasites. Detection of infection appears restricted to homogenous groups of mosquitoes diminishing NIRS utility for detecting malaria within mosquitoes.
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8
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Guissou E, Waite JL, Jones M, Bell AS, Suh E, Yameogo KB, Djègbè N, Da DF, Hien DFDS, Yerbanga RS, Ouedraogo AG, Dabiré KR, Cohuet A, Thomas MB, Lefèvre T. A non-destructive sugar-feeding assay for parasite detection and estimating the extrinsic incubation period of Plasmodium falciparum in individual mosquito vectors. Sci Rep 2021; 11:9344. [PMID: 33927245 PMCID: PMC8085177 DOI: 10.1038/s41598-021-88659-w] [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] [Received: 01/12/2021] [Accepted: 04/14/2021] [Indexed: 01/19/2023] Open
Abstract
Despite its epidemiological importance, the time Plasmodium parasites take to achieve development in the vector mosquito (the extrinsic incubation period, EIP) remains poorly characterized. A novel non-destructive assay designed to estimate EIP in single mosquitoes, and more broadly to study Plasmodium-Anopheles vectors interactions, is presented. The assay uses small pieces of cotton wool soaked in sugar solution to collect malaria sporozoites from individual mosquitoes during sugar feeding to monitor infection status over time. This technique has been tested across four natural malaria mosquito species of Africa and Asia, infected with Plasmodium falciparum (six field isolates from gametocyte-infected patients in Burkina Faso and the NF54 strain) and across a range of temperatures relevant to malaria transmission in field conditions. Monitoring individual infectious mosquitoes was feasible. The estimated median EIP of P. falciparum at 27 °C was 11 to 14 days depending on mosquito species and parasite isolate. Long-term individual tracking revealed that sporozoites transfer onto cotton wool can occur at least until day 40 post-infection. Short individual EIP were associated with short mosquito lifespan. Correlations between mosquito/parasite traits often reveal trade-offs and constraints and have important implications for understanding the evolution of parasite transmission strategies.
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Affiliation(s)
- Edwige Guissou
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso.
- MIVEGEC, Montpellier University, IRD, CNRS, Montpellier, France.
- Laboratoire mixte international sur les vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso.
- Université Nazi Boni, Bobo Dioulasso, Burkina Faso.
| | - Jessica L Waite
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, 16802, USA
- Green Mountain Antibodies, Inc. 1 Mill St. Suites 1-7, Burlington, VT, 05401, USA
| | - Matthew Jones
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Andrew S Bell
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Eunho Suh
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Nicaise Djègbè
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Dari F Da
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Domonbabele F D S Hien
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
- Laboratoire mixte international sur les vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
| | - Rakiswende S Yerbanga
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
- Laboratoire mixte international sur les vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
| | | | - Kounbobr Roch Dabiré
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
- Laboratoire mixte international sur les vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
| | - Anna Cohuet
- MIVEGEC, Montpellier University, IRD, CNRS, Montpellier, France
- Laboratoire mixte international sur les vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
| | - Matthew B Thomas
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, 16802, USA
- York Environmental Sustainability Institute and Department of Biology, University of York, York, UK
| | - Thierry Lefèvre
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
- MIVEGEC, Montpellier University, IRD, CNRS, Montpellier, France
- Laboratoire mixte international sur les vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
- Centre de Recherche en Écologie et Évolution de la Santé (CREES), Montpellier, France
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Goh B, Ching K, Soares Magalhães RJ, Ciocchetta S, Edstein MD, Maciel-de-Freitas R, Sikulu-Lord MT. The application of spectroscopy techniques for diagnosis of malaria parasites and arboviruses and surveillance of mosquito vectors: A systematic review and critical appraisal of evidence. PLoS Negl Trop Dis 2021; 15:e0009218. [PMID: 33886567 PMCID: PMC8061870 DOI: 10.1371/journal.pntd.0009218] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
CONCLUSIONS/SIGNIFICANCE The potential of RS as a surveillance tool for malaria and arbovirus vectors and MIRS for the diagnosis and surveillance of arboviruses is yet to be assessed. NIRS capacity as a surveillance tool for malaria and arbovirus vectors should be validated under field conditions, and its potential as a diagnostic tool for malaria and arboviruses needs to be evaluated. It is recommended that all 3 techniques evaluated simultaneously using multiple machine learning techniques in multiple epidemiological settings to determine the most accurate technique for each application. Prior to their field application, a standardised protocol for spectra collection and data analysis should be developed. This will harmonise their application in multiple field settings allowing easy and faster integration into existing disease control platforms. Ultimately, development of rapid and cost-effective point-of-care diagnostic tools for malaria and arboviruses based on spectroscopy techniques may help combat current and future outbreaks of these infectious diseases.
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Affiliation(s)
- Brendon Goh
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Koek Ching
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Ricardo J Soares Magalhães
- UQ Spatial Epidemiology Laboratory, School of Veterinary Science, The University of Queensland, Brisbane, Australia
- Children's Health Research Centre, Children's Health and Environment Program, The University of Queensland, Brisbane, Australia
| | - Silvia Ciocchetta
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- UQ Spatial Epidemiology Laboratory, School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - Michael D Edstein
- Australian Defence Force, Malaria and Infectious Disease Institute, Brisbane, Australia
| | | | - Maggy T Sikulu-Lord
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia
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10
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Kading RC, Cohnstaedt LW, Fall K, Hamer GL. Emergence of Arboviruses in the United States: The Boom and Bust of Funding, Innovation, and Capacity. Trop Med Infect Dis 2020; 5:E96. [PMID: 32517268 PMCID: PMC7345222 DOI: 10.3390/tropicalmed5020096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 11/16/2022] Open
Abstract
Mosquito-borne viruses will continue to emerge and generate a significant public health burden around the globe. Here, we provide a longitudinal perspective on how the emergence of mosquito-borne viruses in the Americas has triggered reactionary funding by sponsored agencies, stimulating a number of publications, innovative development of traps, and augmented capacity. We discuss the return on investment (ROI) from the oscillation in federal funding that influences demand for surveillance and control traps and leads to innovation and research productivity.
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Affiliation(s)
- Rebekah C. Kading
- Department of Microbiology, Colorado State University, Immunology and Pathology, Fort Collins, Colorado, CO 80523, USA
| | - Lee W. Cohnstaedt
- United States Department of Agriculture, Arthropod-borne Animal Diseases Research Unit, Agricultural Research Service, Manhattan, Kansas, KS 66502, USA;
| | - Ken Fall
- BioQuip Products, Rancho Dominguez, California, CA 90220, USA;
| | - Gabriel L. Hamer
- Department of Entomology, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, TX 77843, USA;
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11
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Fedewa R, Puri R, Fleischman E, Lee J, Prabhu D, Wilson DL, Vince DG, Fleischman A. Artificial Intelligence in Intracoronary Imaging. Curr Cardiol Rep 2020; 22:46. [DOI: 10.1007/s11886-020-01299-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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12
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Ong OTW, Kho EA, Esperança PM, Freebairn C, Dowell FE, Devine GJ, Churcher TS. Ability of near-infrared spectroscopy and chemometrics to predict the age of mosquitoes reared under different conditions. Parasit Vectors 2020; 13:160. [PMID: 32228670 PMCID: PMC7106667 DOI: 10.1186/s13071-020-04031-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/24/2020] [Indexed: 01/04/2023] Open
Abstract
Background Practical, field-ready age-grading tools for mosquito vectors of disease are urgently needed because of the impact that daily survival has on vectorial capacity. Previous studies have shown that near-infrared spectroscopy (NIRS), in combination with chemometrics and predictive modeling, can forecast the age of laboratory-reared mosquitoes with moderate to high accuracy. It remains unclear whether the technique has utility for identifying shifts in the age structure of wild-caught mosquitoes. Here we investigate whether models derived from the laboratory strain of mosquitoes can be used to predict the age of mosquitoes grown from pupae collected in the field. Methods NIRS data from adult female Aedes albopictus mosquitoes reared in the laboratory (2, 5, 8, 12 and 15 days-old) were analysed against spectra from mosquitoes emerging from wild-caught pupae (1, 7 and 14 days-old). Different partial least squares (PLS) regression methods trained on spectra from laboratory mosquitoes were evaluated on their ability to predict the age of mosquitoes from more natural environments. Results Models trained on spectra from laboratory-reared material were able to predict the age of other laboratory-reared mosquitoes with moderate accuracy and successfully differentiated all day 2 and 15 mosquitoes. Models derived with laboratory mosquitoes could not differentiate between field-derived age groups, with age predictions relatively indistinguishable for day 1–14. Pre-processing of spectral data and improving the PLS regression framework to avoid overfitting can increase accuracy, but predictions of mosquitoes reared in different environments remained poor. Principal components analysis confirms substantial spectral variations between laboratory and field-derived mosquitoes despite both originating from the same island population. Conclusions Models trained on laboratory mosquitoes were able to predict ages of laboratory mosquitoes with good sensitivity and specificity though they were unable to predict age of field-derived mosquitoes. This study suggests that laboratory-reared mosquitoes do not capture enough environmental variation to accurately predict the age of the same species reared under different conditions. Further research is needed to explore alternative pre-processing methods and machine learning techniques, and to understand factors that affect absorbance in mosquitoes before field application using NIRS.![]()
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Affiliation(s)
- Oselyne T W Ong
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
| | - Elise A Kho
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
| | - Pedro M Esperança
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Chris Freebairn
- Private Contracting Entomologist, Hammond Island, Queensland, Australia
| | - Floyd E Dowell
- USDA, Centre for Grain and Animal Health Research, 1515 College Avenue, Manhattan, KS, 66502, USA
| | - Gregor J Devine
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Thomas S Churcher
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
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13
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Mwanga EP, Minja EG, Mrimi E, Jiménez MG, Swai JK, Abbasi S, Ngowo HS, Siria DJ, Mapua S, Stica C, Maia MF, Olotu A, Sikulu-Lord MT, Baldini F, Ferguson HM, Wynne K, Selvaraj P, Babayan SA, Okumu FO. Detection of malaria parasites in dried human blood spots using mid-infrared spectroscopy and logistic regression analysis. Malar J 2019; 18:341. [PMID: 31590669 PMCID: PMC6781347 DOI: 10.1186/s12936-019-2982-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/28/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Epidemiological surveys of malaria currently rely on microscopy, polymerase chain reaction assays (PCR) or rapid diagnostic test kits for Plasmodium infections (RDTs). This study investigated whether mid-infrared (MIR) spectroscopy coupled with supervised machine learning could constitute an alternative method for rapid malaria screening, directly from dried human blood spots. METHODS Filter papers containing dried blood spots (DBS) were obtained from a cross-sectional malaria survey in 12 wards in southeastern Tanzania in 2018/19. The DBS were scanned using attenuated total reflection-Fourier Transform Infrared (ATR-FTIR) spectrometer to obtain high-resolution MIR spectra in the range 4000 cm-1 to 500 cm-1. The spectra were cleaned to compensate for atmospheric water vapour and CO2 interference bands and used to train different classification algorithms to distinguish between malaria-positive and malaria-negative DBS papers based on PCR test results as reference. The analysis considered 296 individuals, including 123 PCR-confirmed malaria positives and 173 negatives. Model training was done using 80% of the dataset, after which the best-fitting model was optimized by bootstrapping of 80/20 train/test-stratified splits. The trained models were evaluated by predicting Plasmodium falciparum positivity in the 20% validation set of DBS. RESULTS Logistic regression was the best-performing model. Considering PCR as reference, the models attained overall accuracies of 92% for predicting P. falciparum infections (specificity = 91.7%; sensitivity = 92.8%) and 85% for predicting mixed infections of P. falciparum and Plasmodium ovale (specificity = 85%, sensitivity = 85%) in the field-collected specimen. CONCLUSION These results demonstrate that mid-infrared spectroscopy coupled with supervised machine learning (MIR-ML) could be used to screen for malaria parasites in human DBS. The approach could have potential for rapid and high-throughput screening of Plasmodium in both non-clinical settings (e.g., field surveys) and clinical settings (diagnosis to aid case management). However, before the approach can be used, we need additional field validation in other study sites with different parasite populations, and in-depth evaluation of the biological basis of the MIR signals. Improving the classification algorithms, and model training on larger datasets could also improve specificity and sensitivity. The MIR-ML spectroscopy system is physically robust, low-cost, and requires minimum maintenance.
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Affiliation(s)
- Emmanuel P Mwanga
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania.
| | - Elihaika G Minja
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Emmanuel Mrimi
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | | | - Johnson K Swai
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Said Abbasi
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Halfan S Ngowo
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Doreen J Siria
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Salum Mapua
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
- School of Life Sciences, University of Keele, Keele, Staffordshire, ST5 5BG, UK
| | - Caleb Stica
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Marta F Maia
- KEMRI Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Ally Olotu
- KEMRI Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
- Interventions and Clinical Trials Department, Ifakara Health Institute, Bagamoyo, Tanzania
| | - Maggy T Sikulu-Lord
- School of Public Health, University of Queensland, Saint Lucia, Australia
- Department of Mathematics, Statistics and Computer Science, Marquette University, Wisconsin, USA
| | - Francesco Baldini
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Heather M Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Simon A Babayan
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fredros O Okumu
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania.
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
- School of Public Health, University of Witwatersrand, Johannesburg, South Africa.
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14
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González Jiménez M, Babayan SA, Khazaeli P, Doyle M, Walton F, Reedy E, Glew T, Viana M, Ranford-Cartwright L, Niang A, Siria DJ, Okumu FO, Diabaté A, Ferguson HM, Baldini F, Wynne K. Prediction of mosquito species and population age structure using mid-infrared spectroscopy and supervised machine learning. Wellcome Open Res 2019; 4:76. [PMID: 31544155 PMCID: PMC6753605 DOI: 10.12688/wellcomeopenres.15201.3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2019] [Indexed: 11/20/2022] Open
Abstract
Despite the global efforts made in the fight against malaria, the disease is resurging. One of the main causes is the resistance that Anopheles mosquitoes, vectors of the disease, have developed to insecticides. Anopheles must survive for at least 10 days to possibly transmit malaria. Therefore, to evaluate and improve malaria vector control interventions, it is imperative to monitor and accurately estimate the age distribution of mosquito populations as well as their population sizes. Here, we demonstrate a machine-learning based approach that uses mid-infrared spectra of mosquitoes to characterise simultaneously both age and species identity of females of the African malaria vector species Anopheles gambiae and An. arabiensis, using laboratory colonies. Mid-infrared spectroscopy-based prediction of mosquito age structures was statistically indistinguishable from true modelled distributions. The accuracy of classifying mosquitoes by species was 82.6%. The method has a negligible cost per mosquito, does not require highly trained personnel, is rapid, and so can be easily applied in both laboratory and field settings. Our results indicate this method is a promising alternative to current mosquito species and age-grading approaches, with further improvements to accuracy and expansion for use with wild mosquito vectors possible through collection of larger mid-infrared spectroscopy data sets.
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Affiliation(s)
| | - Simon A. Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Pegah Khazaeli
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Margaret Doyle
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Finlay Walton
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Elliott Reedy
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Thomas Glew
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mafalda Viana
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Lisa Ranford-Cartwright
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Abdoulaye Niang
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Doreen J. Siria
- Environmental Health & Ecological Sciences Department, Ifakara Health Institute, Off Mlabani Passage, PO Box 53, Ifakara, Tanzania
| | - Fredros O. Okumu
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- Environmental Health & Ecological Sciences Department, Ifakara Health Institute, Off Mlabani Passage, PO Box 53, Ifakara, Tanzania
| | - Abdoulaye Diabaté
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Heather M. Ferguson
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francesco Baldini
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
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15
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González Jiménez M, Babayan SA, Khazaeli P, Doyle M, Walton F, Reedy E, Glew T, Viana M, Ranford-Cartwright L, Niang A, Siria DJ, Okumu FO, Diabaté A, Ferguson HM, Baldini F, Wynne K. Prediction of mosquito species and population age structure using mid-infrared spectroscopy and supervised machine learning. Wellcome Open Res 2019; 4:76. [PMID: 31544155 PMCID: PMC6753605 DOI: 10.12688/wellcomeopenres.15201.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2019] [Indexed: 01/14/2023] Open
Abstract
Despite the global efforts made in the fight against malaria, the disease is resurging. One of the main causes is the resistance that Anopheles mosquitoes, vectors of the disease, have developed to insecticides. Anopheles must survive for at least 10 days to possibly transmit malaria. Therefore, to evaluate and improve malaria vector control interventions, it is imperative to monitor and accurately estimate the age distribution of mosquito populations as well as their population sizes. Here, we demonstrate a machine-learning based approach that uses mid-infrared spectra of mosquitoes to characterise simultaneously both age and species identity of females of the African malaria vector species Anopheles gambiae and An. arabiensis, using laboratory colonies. Mid-infrared spectroscopy-based prediction of mosquito age structures was statistically indistinguishable from true modelled distributions. The accuracy of classifying mosquitoes by species was 82.6%. The method has a negligible cost per mosquito, does not require highly trained personnel, is rapid, and so can be easily applied in both laboratory and field settings. Our results indicate this method is a promising alternative to current mosquito species and age-grading approaches, with further improvements to accuracy and expansion for use with wild mosquito vectors possible through collection of larger mid-infrared spectroscopy data sets.
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Affiliation(s)
| | - Simon A. Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Pegah Khazaeli
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Margaret Doyle
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Finlay Walton
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Elliott Reedy
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Thomas Glew
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mafalda Viana
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Lisa Ranford-Cartwright
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Abdoulaye Niang
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Doreen J. Siria
- Environmental Health & Ecological Sciences Department, Ifakara Health Institute, Off Mlabani Passage, PO Box 53, Ifakara, Tanzania
| | - Fredros O. Okumu
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- Environmental Health & Ecological Sciences Department, Ifakara Health Institute, Off Mlabani Passage, PO Box 53, Ifakara, Tanzania
| | - Abdoulaye Diabaté
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Heather M. Ferguson
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francesco Baldini
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
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16
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Mwanga EP, Mapua SA, Siria DJ, Ngowo HS, Nangacha F, Mgando J, Baldini F, González Jiménez M, Ferguson HM, Wynne K, Selvaraj P, Babayan SA, Okumu FO. Using mid-infrared spectroscopy and supervised machine-learning to identify vertebrate blood meals in the malaria vector, Anopheles arabiensis. Malar J 2019; 18:187. [PMID: 31146762 PMCID: PMC6543689 DOI: 10.1186/s12936-019-2822-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/25/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The propensity of different Anopheles mosquitoes to bite humans instead of other vertebrates influences their capacity to transmit pathogens to humans. Unfortunately, determining proportions of mosquitoes that have fed on humans, i.e. Human Blood Index (HBI), currently requires expensive and time-consuming laboratory procedures involving enzyme-linked immunosorbent assays (ELISA) or polymerase chain reactions (PCR). Here, mid-infrared (MIR) spectroscopy and supervised machine learning are used to accurately distinguish between vertebrate blood meals in guts of malaria mosquitoes, without any molecular techniques. METHODS Laboratory-reared Anopheles arabiensis females were fed on humans, chickens, goats or bovines, then held for 6 to 8 h, after which they were killed and preserved in silica. The sample size was 2000 mosquitoes (500 per host species). Five individuals of each host species were enrolled to ensure genotype variability, and 100 mosquitoes fed on each. Dried mosquito abdomens were individually scanned using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectrometer to obtain high-resolution MIR spectra (4000 cm-1 to 400 cm-1). The spectral data were cleaned to compensate atmospheric water and CO2 interference bands using Bruker-OPUS software, then transferred to Python™ for supervised machine-learning to predict host species. Seven classification algorithms were trained using 90% of the spectra through several combinations of 75-25% data splits. The best performing model was used to predict identities of the remaining 10% validation spectra, which had not been used for model training or testing. RESULTS The logistic regression (LR) model achieved the highest accuracy, correctly predicting true vertebrate blood meal sources with overall accuracy of 98.4%. The model correctly identified 96% goat blood meals, 97% of bovine blood meals, 100% of chicken blood meals and 100% of human blood meals. Three percent of bovine blood meals were misclassified as goat, and 2% of goat blood meals misclassified as human. CONCLUSION Mid-infrared spectroscopy coupled with supervised machine learning can accurately identify multiple vertebrate blood meals in malaria vectors, thus potentially enabling rapid assessment of mosquito blood-feeding histories and vectorial capacities. The technique is cost-effective, fast, simple, and requires no reagents other than desiccants. However, scaling it up will require field validation of the findings and boosting relevant technical capacity in affected countries.
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Affiliation(s)
- Emmanuel P Mwanga
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania.
| | - Salum A Mapua
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania
| | - Doreen J Siria
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania
| | - Halfan S Ngowo
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francis Nangacha
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania
| | - Joseph Mgando
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania
| | - Francesco Baldini
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Heather M Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Simon A Babayan
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fredros O Okumu
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- School of Public Health, University of Witwatersrand, Johannesburg, South Africa
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17
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González Jiménez M, Babayan SA, Khazaeli P, Doyle M, Walton F, Reedy E, Glew T, Viana M, Ranford-Cartwright L, Niang A, Siria DJ, Okumu FO, Diabaté A, Ferguson HM, Baldini F, Wynne K. Prediction of mosquito species and population age structure using mid-infrared spectroscopy and supervised machine learning. Wellcome Open Res 2019; 4:76. [PMID: 31544155 PMCID: PMC6753605 DOI: 10.12688/wellcomeopenres.15201.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2019] [Indexed: 01/17/2023] Open
Abstract
Despite the global efforts made in the fight against malaria, the disease is resurging. One of the main causes is the resistance that Anopheles mosquitoes, vectors of the disease, have developed to insecticides. Anopheles must survive for at least 10 days to possibly transmit malaria. Therefore, to evaluate and improve malaria vector control interventions, it is imperative to monitor and accurately estimate the age distribution of mosquito populations as well as their population sizes. Here, we demonstrate a machine-learning based approach that uses mid-infrared spectra of mosquitoes to characterise simultaneously both age and species identity of females of the African malaria vector species Anopheles gambiae and An. arabiensis. mid-infrared spectroscopy-based prediction of mosquito age structures was statistically indistinguishable from true modelled distributions. The accuracy of classifying mosquitoes by species was 82.6%. The method has a negligible cost per mosquito, does not require highly trained personnel, is rapid, and so can be easily applied in both laboratory and field settings. Our results indicate this method is a promising alternative to current mosquito species and age-grading approaches, with further improvements to accuracy and expansion for use with other mosquito vectors possible through collection of larger mid-infrared spectroscopy data sets.
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Affiliation(s)
| | - Simon A. Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Pegah Khazaeli
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Margaret Doyle
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Finlay Walton
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Elliott Reedy
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Thomas Glew
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mafalda Viana
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Lisa Ranford-Cartwright
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Abdoulaye Niang
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Doreen J. Siria
- Environmental Health & Ecological Sciences Department, Ifakara Health Institute, Off Mlabani Passage, PO Box 53, Ifakara, Tanzania
| | - Fredros O. Okumu
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- Environmental Health & Ecological Sciences Department, Ifakara Health Institute, Off Mlabani Passage, PO Box 53, Ifakara, Tanzania
| | - Abdoulaye Diabaté
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Heather M. Ferguson
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francesco Baldini
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
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Maia MF, Kapulu M, Muthui M, Wagah MG, Ferguson HM, Dowell FE, Baldini F, Ranford-Cartwright L. Detection of Plasmodium falciparum infected Anopheles gambiae using near-infrared spectroscopy. Malar J 2019; 18:85. [PMID: 30890179 PMCID: PMC6423776 DOI: 10.1186/s12936-019-2719-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Large-scale surveillance of mosquito populations is crucial to assess the intensity of vector-borne disease transmission and the impact of control interventions. However, there is a lack of accurate, cost-effective and high-throughput tools for mass-screening of vectors. METHODS A total of 750 Anopheles gambiae (Keele strain) mosquitoes were fed Plasmodium falciparum NF54 gametocytes through standard membrane feeding assay (SMFA) and afterwards maintained in insectary conditions to allow for oocyst (8 days) and sporozoite development (14 days). Thereupon, each mosquito was scanned using near infra-red spectroscopy (NIRS) and processed by quantitative polymerase chain reaction (qPCR) to determine the presence of infection and infection load. The spectra collected were randomly assigned to either a training dataset, used to develop calibrations for predicting oocyst- or sporozoite-infection through partial least square regressions (PLS); or to a test dataset, used for validating the calibration's prediction accuracy. RESULTS NIRS detected oocyst- and sporozoite-stage P. falciparum infections with 88% and 95% accuracy, respectively. This study demonstrates proof-of-concept that NIRS is capable of rapidly identifying laboratory strains of human malaria infection in African mosquito vectors. CONCLUSIONS Accurate, low-cost, reagent-free screening of mosquito populations enabled by NIRS could revolutionize surveillance and elimination strategies for the most important human malaria parasite in its primary African vector species. Further research is needed to evaluate how the method performs in the field following adjustments in the training datasets to include data from wild-caught infected and uninfected mosquitoes.
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Affiliation(s)
- Marta F Maia
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4020, Basel, Switzerland.
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland.
- KEMRI Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus Roosevelt Drive, Oxford, OX3 7FZ, UK.
| | - Melissa Kapulu
- KEMRI Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Michelle Muthui
- KEMRI Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
| | - Martin G Wagah
- KEMRI Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
- Department of Public Health, School of Human and Health Sciences, Pwani University, Kilifi, Kenya
| | - Heather M Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
| | - Floyd E Dowell
- USDA, Agricultural Research Service, Center for Grain and Animal Health Research, 1515 College Avenue, Manhattan, KS, 66502, USA
| | - Francesco Baldini
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
| | - Lisa Ranford-Cartwright
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
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