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Pourtois JD, Tallam K, Jones I, Hyde E, Chamberlin AJ, Evans MV, Ihantamalala FA, Cordier LF, Razafinjato BR, Rakotonanahary RJL, Tsirinomen'ny Aina A, Soloniaina P, Raholiarimanana SH, Razafinjato C, Bonds MH, De Leo GA, Sokolow SH, Garchitorena A. Climatic, land-use and socio-economic factors can predict malaria dynamics at fine spatial scales relevant to local health actors: Evidence from rural Madagascar. PLOS Glob Public Health 2023; 3:e0001607. [PMID: 36963091 PMCID: PMC10021226 DOI: 10.1371/journal.pgph.0001607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/23/2023] [Indexed: 02/24/2023]
Abstract
While much progress has been achieved over the last decades, malaria surveillance and control remain a challenge in countries with limited health care access and resources. High-resolution predictions of malaria incidence using routine surveillance data could represent a powerful tool to health practitioners by targeting malaria control activities where and when they are most needed. Here, we investigate the predictors of spatio-temporal malaria dynamics in rural Madagascar, estimated from facility-based passive surveillance data. Specifically, this study integrates climate, land-use, and representative household survey data to explain and predict malaria dynamics at a high spatial resolution (i.e., by Fokontany, a cluster of villages) relevant to health care practitioners. Combining generalized linear mixed models (GLMM) and path analyses, we found that socio-economic, land use and climatic variables are all important predictors of monthly malaria incidence at fine spatial scales, via both direct and indirect effects. In addition, out-of-sample predictions from our model were able to identify 58% of the Fokontany in the top quintile for malaria incidence and account for 77% of the variation in the Fokontany incidence rank. These results suggest that it is possible to build a predictive framework using environmental and social predictors that can be complementary to standard surveillance systems and help inform control strategies by field actors at local scales.
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Affiliation(s)
- Julie D Pourtois
- Biology Department, Stanford University, Stanford, CA, United States of America
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States of America
| | - Krti Tallam
- Biology Department, Stanford University, Stanford, CA, United States of America
| | - Isabel Jones
- Biology Department, Stanford University, Stanford, CA, United States of America
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States of America
| | - Elizabeth Hyde
- School of Medicine, Stanford University, Stanford, CA, United States of America
| | - Andrew J Chamberlin
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States of America
| | - Michelle V Evans
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Felana A Ihantamalala
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, United States of America
- NGO Pivot, Ifanadiana, Madagascar
| | | | | | - Rado J L Rakotonanahary
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, United States of America
- NGO Pivot, Ifanadiana, Madagascar
| | | | | | | | - Celestin Razafinjato
- Programme National de Lutte contre le Paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Matthew H Bonds
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, United States of America
- NGO Pivot, Ifanadiana, Madagascar
| | - Giulio A De Leo
- Biology Department, Stanford University, Stanford, CA, United States of America
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States of America
| | - Susanne H Sokolow
- Woods Institute for the Environment, Stanford University, Stanford, CA, United States of America
- Marine Science Institute and Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, United States of America
| | - Andres Garchitorena
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
- NGO Pivot, Ifanadiana, Madagascar
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Tallam K, Liu ZYC, Chamberlin AJ, Jones IJ, Shome P, Riveau G, Ndione RA, Bandagny L, Jouanard N, Eck PV, Ngo T, Sokolow SH, De Leo GA. Identification of Snails and Schistosoma of Medical Importance via Convolutional Neural Networks: A Proof-of-Concept Application for Human Schistosomiasis. Front Public Health 2021; 9:642895. [PMID: 34336754 PMCID: PMC8319642 DOI: 10.3389/fpubh.2021.642895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/08/2021] [Indexed: 11/21/2022] Open
Abstract
In recent decades, computer vision has proven remarkably effective in addressing diverse issues in public health, from determining the diagnosis, prognosis, and treatment of diseases in humans to predicting infectious disease outbreaks. Here, we investigate whether convolutional neural networks (CNNs) can also demonstrate effectiveness in classifying the environmental stages of parasites of public health importance and their invertebrate hosts. We used schistosomiasis as a reference model. Schistosomiasis is a debilitating parasitic disease transmitted to humans via snail intermediate hosts. The parasite affects more than 200 million people in tropical and subtropical regions. We trained our CNN, a feed-forward neural network, on a limited dataset of 5,500 images of snails and 5,100 images of cercariae obtained from schistosomiasis transmission sites in the Senegal River Basin, a region in western Africa that is hyper-endemic for the disease. The image set included both images of two snail genera that are relevant to schistosomiasis transmission – that is, Bulinus spp. and Biomphalaria pfeifferi – as well as snail images that are non-component hosts for human schistosomiasis. Cercariae shed from Bi. pfeifferi and Bulinus spp. snails were classified into 11 categories, of which only two, S. haematobium and S. mansoni, are major etiological agents of human schistosomiasis. The algorithms, trained on 80% of the snail and parasite dataset, achieved 99% and 91% accuracy for snail and parasite classification, respectively, when used on the hold-out validation dataset – a performance comparable to that of experienced parasitologists. The promising results of this proof-of-concept study suggests that this CNN model, and potentially similar replicable models, have the potential to support the classification of snails and parasite of medical importance. In remote field settings where machine learning algorithms can be deployed on cost-effective and widely used mobile devices, such as smartphones, these models can be a valuable complement to laboratory identification by trained technicians. Future efforts must be dedicated to increasing dataset sizes for model training and validation, as well as testing these algorithms in diverse transmission settings and geographies.
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Affiliation(s)
- Krti Tallam
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States
| | - Zac Yung-Chun Liu
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States
| | - Andrew J Chamberlin
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States
| | - Isabel J Jones
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States
| | - Pretom Shome
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States
| | - Gilles Riveau
- Centre de Recherche Biomédicale Espoir pour la Santé, Saint-Louis, Senegal.,Univ Lille, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Raphael A Ndione
- Centre de Recherche Biomédicale Espoir pour la Santé, Saint-Louis, Senegal
| | - Lydie Bandagny
- Centre de Recherche Biomédicale Espoir pour la Santé, Saint-Louis, Senegal
| | - Nicolas Jouanard
- Centre de Recherche Biomédicale Espoir pour la Santé, Saint-Louis, Senegal.,Station d'Innovation Aquacole (SIA), à Université Gaston Berger, Saint-Louis, Senegal
| | - Paul Van Eck
- International Business Machines Corporation (IBM) Silicon Valley Lab, San Jose, CA, United States
| | - Ton Ngo
- International Business Machines Corporation (IBM) Silicon Valley Lab, San Jose, CA, United States
| | - Susanne H Sokolow
- International Business Machines Corporation (IBM) Silicon Valley Lab, San Jose, CA, United States.,Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Giulio A De Leo
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States.,Woods Institute for the Environment, Stanford University, Pacific Grove, CA, United States
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Getz WM, Salter R, Muellerklein O, Yoon HS, Tallam K. Modeling epidemics: A primer and Numerus Model Builder implementation. Epidemics 2018; 25:9-19. [PMID: 30017895 DOI: 10.1016/j.epidem.2018.06.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 01/09/2023] Open
Abstract
Epidemiological models are dominated by compartmental models, of which SIR formulations are the most commonly used. These formulations can be continuous or discrete (in either the state-variable values or time), deterministic or stochastic, or spatially homogeneous or heterogeneous, the latter often embracing a network formulation. Here we review the continuous and discrete deterministic and discrete stochastic formulations of the SIR dynamical systems models, and we outline how they can be easily and rapidly constructed using Numerus Model Builder, a graphically-driven coding platform. We also demonstrate how to extend these models to a metapopulation setting using NMB network and mapping tools.
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Affiliation(s)
- Wayne M Getz
- Dept. ESPM, UC Berkeley, CA 94720-3114, USA; School of Mathematical Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa; Numerus, 850 Iron Point Rd., Folsom, CA 95630, USA.
| | - Richard Salter
- Numerus, 850 Iron Point Rd., Folsom, CA 95630, USA; Computer Science Dept., Oberlin College, Oberlin, OH 44074, USA
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