1
|
Macharia PM, Ray N, Gitonga CW, Snow RW, Giorgi E. Combining school-catchment area models with geostatistical models for analysing school survey data from low-resource settings: Inferential benefits and limitations. SPATIAL STATISTICS 2022; 51:100679. [PMID: 35880005 PMCID: PMC7613137 DOI: 10.1016/j.spasta.2022.100679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
School-based sampling has been used to inform targeted responses for malaria and neglected tropical diseases. Standard geostatistical methods for mapping disease prevalence use the school location to model spatial correlation, which is questionable since exposure to the disease is more likely to occur in the residential location. In this paper, we propose to overcome the limitations of standard geostatistical methods by introducing a modelling framework that accounts for the uncertainty in the location of the residence of the students. By using cost distance and cost allocation models to define spatial accessibility and in absence of any information on the travel mode of students to school, we consider three school catchment area models that assume walking only, walking and bicycling and, walking and motorized transport. We illustrate the use of this approach using two case studies of malaria in Kenya and compare it with the standard approach that uses the school locations to build geostatistical models. We argue that the proposed modelling framework presents several inferential benefits, such as the ability to combine data from multiple surveys some of which may also record the residence location, and to deal with ecological bias when estimating the effects of malaria risk factors. However, our results show that invalid assumptions on the modes of travel to school can worsen the predictive performance of geostatistical models. Future research in this area should focus on collecting information on the modes of transportation to school which can then be used to better parametrize the catchment area models.
Collapse
Affiliation(s)
- Peter M. Macharia
- Centre for Health Informatics, Computing, and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW, UK
- Population Health Unit, Kenya Medical Research Institute-Wellcome Trust Research Programme, PO, Box 43640, Nairobi, Kenya
| | - Nicolas Ray
- GeoHealth group, Institute of Global Health, University of Geneva, Geneva, Switzerland
- Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
| | - Caroline W. Gitonga
- Population Health Unit, Kenya Medical Research Institute-Wellcome Trust Research Programme, PO, Box 43640, Nairobi, Kenya
| | - Robert W. Snow
- Population Health Unit, Kenya Medical Research Institute-Wellcome Trust Research Programme, PO, Box 43640, Nairobi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LG, UK
| | - Emanuele Giorgi
- Centre for Health Informatics, Computing, and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW, UK
| |
Collapse
|
2
|
Participatory mapping identifies risk areas and environmental predictors of endemic anthrax in rural Africa. Sci Rep 2022; 12:10514. [PMID: 35732674 PMCID: PMC9217952 DOI: 10.1038/s41598-022-14081-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/01/2022] [Indexed: 11/08/2022] Open
Abstract
Disease mapping reveals geographical variability in incidence, which can help to prioritise control efforts. However, in areas where this is most needed, resources to generate the required data are often lacking. Participatory mapping, which makes use of indigenous knowledge, is a potential approach to identify risk areas for endemic diseases in low- and middle-income countries. Here we combine this method with Geographical Information System-based analyses of environmental variables as a novel approach to study endemic anthrax, caused by the spore-forming bacterium Bacillus anthracis, in rural Africa. Our aims were to: (1) identify high-risk anthrax areas using community knowledge; (2) enhance our understanding of the environmental characteristics associated with these areas; and (3) make spatial predictions of anthrax risk. Community members from the Ngorongoro Conservation Area (NCA), northern Tanzania, where anthrax is highly prevalent in both animals and humans, were asked to draw areas they perceived to pose anthrax risks to their livestock on geo-referenced maps. After digitisation, random points were generated within and outside the defined areas to represent high- and low-risk areas, respectively. Regression analyses were used to identify environmental variables that may predict anthrax risk. Results were combined to predict how the probability of being a high-risk area for anthrax varies across space. Participatory mapping identified fourteen discrete high-risk areas ranging from 0.2 to 212.9 km2 in size and occupying 8.4% of the NCA. Areas that pose a high risk of anthrax were positively associated with factors that increase contact with Bacillus anthracis spores rather than those associated with the pathogen's survival: close proximity to inland water bodies, where wildlife and livestock congregate, and low organic carbon content, which may indicate an increased likelihood of animals grazing close to soil surface and ingesting spores. Predicted high-risk areas were located in the centre of the NCA, which is likely to be encountered by most herds during movements in search for resources. We demonstrate that participatory mapping combined with spatial analyses can provide novel insights into the geography of disease risk. This approach can be used to prioritise areas for control in low-resource settings, especially for diseases with environmental transmission.
Collapse
|
3
|
Cameron E, Young AJ, Twohig KA, Pothin E, Bhavnani D, Dismer A, Merilien JB, Hamre K, Meyer P, Le Menach A, Cohen JM, Marseille S, Lemoine JF, Telfort MA, Chang MA, Won K, Knipes A, Rogier E, Amratia P, Weiss DJ, Gething PW, Battle KE. Mapping the endemicity and seasonality of clinical malaria for intervention targeting in Haiti using routine case data. eLife 2021; 10:62122. [PMID: 34058123 PMCID: PMC8169118 DOI: 10.7554/elife.62122] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 05/15/2021] [Indexed: 01/26/2023] Open
Abstract
Towards the goal of malaria elimination on Hispaniola, the National Malaria Control Program of Haiti and its international partner organisations are conducting a campaign of interventions targeted to high-risk communities prioritised through evidence-based planning. Here we present a key piece of this planning: an up-to-date, fine-scale endemicity map and seasonality profile for Haiti informed by monthly case counts from 771 health facilities reporting from across the country throughout the 6-year period from January 2014 to December 2019. To this end, a novel hierarchical Bayesian modelling framework was developed in which a latent, pixel-level incidence surface with spatio-temporal innovations is linked to the observed case data via a flexible catchment sub-model designed to account for the absence of data on case household locations. These maps have focussed the delivery of indoor residual spraying and focal mass drug administration in the Grand’Anse Department in South-Western Haiti.
Collapse
Affiliation(s)
- Ewan Cameron
- Curtin University, Perth, Australia.,Telethon Kids Institute, Perth Children's Hospital, Perth, Australia
| | - Alyssa J Young
- Clinton Health Access Initiative, Boston, United States.,Tulane University School of Public Health and Tropical Medicine, New Orleans, United States
| | - Katherine A Twohig
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Emilie Pothin
- Clinton Health Access Initiative, Boston, United States.,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Amber Dismer
- Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, United States
| | | | - Karen Hamre
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, United States
| | - Phoebe Meyer
- Clinton Health Access Initiative, Boston, United States
| | | | | | - Samson Marseille
- Programme National de Contrôle de la Malaria/MSPP, Port-au-Prince, Haiti.,Direction d'Epidémiologie de Laboratoire et de la Recherche, Port-au-Prince, Haiti
| | | | | | - Michelle A Chang
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, United States
| | - Kimberly Won
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, United States
| | - Alaine Knipes
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, United States
| | - Eric Rogier
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, United States
| | - Punam Amratia
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Daniel J Weiss
- Curtin University, Perth, Australia.,Telethon Kids Institute, Perth Children's Hospital, Perth, Australia
| | - Peter W Gething
- Curtin University, Perth, Australia.,Telethon Kids Institute, Perth Children's Hospital, Perth, Australia
| | | |
Collapse
|
4
|
Mmbando AS, Kaindoa EW, Ngowo HS, Swai JK, Matowo NS, Kilalangongono M, Lingamba GP, Mgando JP, Namango IH, Okumu FO, Nelli L. Fine-scale distribution of malaria mosquitoes biting or resting outside human dwellings in three low-altitude Tanzanian villages. PLoS One 2021; 16:e0245750. [PMID: 33507908 PMCID: PMC7842886 DOI: 10.1371/journal.pone.0245750] [Citation(s) in RCA: 3] [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: 06/02/2020] [Accepted: 01/06/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND While malaria transmission in Africa still happens primarily inside houses, there is a substantial proportion of Anopheles mosquitoes that bite or rest outdoors. This situation may compromise the performance of indoor insecticidal interventions such as insecticide-treated nets (ITNs). This study investigated the distribution of malaria mosquitoes biting or resting outside dwellings in three low-altitude villages in south-eastern Tanzania. The likelihood of malaria infections outdoors was also assessed. METHODS Nightly trapping was done outdoors for 12 months to collect resting mosquitoes (using resting bucket traps) and host-seeking mosquitoes (using odour-baited Suna® traps). The mosquitoes were sorted by species and physiological states. Pooled samples of Anopheles were tested to estimate proportions infected with Plasmodium falciparum parasites, estimate proportions carrying human blood as opposed to other vertebrate blood and identify sibling species in the Anopheles gambiae complex and An. funestus group. Environmental and anthropogenic factors were observed and recorded within 100 meters from each trapping positions. Generalised additive models were used to investigate relationships between these variables and vector densities, produce predictive maps of expected abundance and compare outcomes within and between villages. RESULTS A high degree of fine-scale heterogeneity in Anopheles densities was observed between and within villages. Water bodies covered with vegetation were associated with 22% higher densities of An. arabiensis and 51% lower densities of An. funestus. Increasing densities of houses and people outdoors were both associated with reduced densities of An. arabiensis and An. funestus. Vector densities were highest around the end of the rainy season and beginning of the dry seasons. More than half (14) 58.3% of blood-fed An. arabiensis had bovine blood, (6) 25% had human blood. None of the Anopheles mosquitoes caught outdoors was found infected with malaria parasites. CONCLUSION Outdoor densities of both host-seeking and resting Anopheles mosquitoes had significant heterogeneities between and within villages, and were influenced by multiple environmental and anthropogenic factors. Despite the high Anopheles densities outside dwellings, the substantial proportion of non-human blood-meals and absence of malaria-infected mosquitoes after 12 months of nightly trapping suggests very low-levels of outdoor malaria transmission in these villages.
Collapse
Affiliation(s)
- Arnold S. Mmbando
- Environmental Health and Ecological Sciences, Ifakara Health Institute, Ifakara, Tanzania
| | - Emmanuel W. Kaindoa
- Environmental Health and Ecological Sciences, Ifakara Health Institute, Ifakara, Tanzania
- Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Parktown, Republic of South Africa
| | - Halfan S. Ngowo
- Environmental Health and Ecological Sciences, Ifakara Health Institute, Ifakara, Tanzania
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Johnson K. Swai
- Environmental Health and Ecological Sciences, Ifakara Health Institute, Ifakara, Tanzania
| | - Nancy S. Matowo
- Environmental Health and Ecological Sciences, Ifakara Health Institute, Ifakara, Tanzania
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Masoud Kilalangongono
- Environmental Health and Ecological Sciences, Ifakara Health Institute, Ifakara, Tanzania
| | - Godfrey P. Lingamba
- Environmental Health and Ecological Sciences, Ifakara Health Institute, Ifakara, Tanzania
| | - Joseph P. Mgando
- Environmental Health and Ecological Sciences, Ifakara Health Institute, Ifakara, Tanzania
| | - Isaac H. Namango
- Environmental Health and Ecological Sciences, Ifakara Health Institute, Ifakara, Tanzania
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Fredros O. Okumu
- Environmental Health and Ecological Sciences, Ifakara Health Institute, Ifakara, Tanzania
- Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Parktown, Republic of South Africa
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- School of Life Science and Bioengineering, Nelson Mandela African Institution of Science & Technology, Arusha, Tanzania
| | - Luca Nelli
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
5
|
Gong M, Liu L, Sun X, Yang Y, Wang S, Zhu H. Cloud-Based System for Effective Surveillance and Control of COVID-19: Useful Experiences From Hubei, China. J Med Internet Res 2020; 22:e18948. [PMID: 32287040 PMCID: PMC7179239 DOI: 10.2196/18948] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 02/05/2023] Open
Abstract
Background Coronavirus disease (COVID-19) has been an unprecedented challenge to the global health care system. Tools that can improve the focus of surveillance efforts and clinical decision support are of paramount importance. Objective The aim of this study was to illustrate how new medical informatics technologies may enable effective control of the pandemic through the development and successful 72-hour deployment of the Honghu Hybrid System (HHS) for COVID-19 in the city of Honghu in Hubei, China. Methods The HHS was designed for the collection, integration, standardization, and analysis of COVID-19-related data from multiple sources, which includes a case reporting system, diagnostic labs, electronic medical records, and social media on mobile devices. Results HHS supports four main features: syndromic surveillance on mobile devices, policy-making decision support, clinical decision support and prioritization of resources, and follow-up of discharged patients. The syndromic surveillance component in HHS covered over 95% of the population of over 900,000 people and provided near real time evidence for the control of epidemic emergencies. The clinical decision support component in HHS was also provided to improve patient care and prioritize the limited medical resources. However, the statistical methods still require further evaluations to confirm clinical effectiveness and appropriateness of disposition assigned in this study, which warrants further investigation. Conclusions The facilitating factors and challenges are discussed to provide useful insights to other cities to build suitable solutions based on cloud technologies. The HHS for COVID-19 was shown to be feasible and effective in this real-world field study, and has the potential to be migrated.
Collapse
Affiliation(s)
- Mengchun Gong
- Institute of Health Management, Southern Medical University, Guangzhou, China
| | - Li Liu
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xin Sun
- Chinese Evidence-Based Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Yang
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shuang Wang
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Zhu
- Institute of Health Management, Southern Medical University, Guangzhou, China.,Nanfang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|
6
|
Nelli L, Guelbeogo M, Ferguson HM, Ouattara D, Tiono A, N'Fale S, Matthiopoulos J. Distance sampling for epidemiology: an interactive tool for estimating under-reporting of cases from clinic data. Int J Health Geogr 2020; 19:16. [PMID: 32312266 PMCID: PMC7171748 DOI: 10.1186/s12942-020-00209-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 04/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Distance sampling methods are widely used in ecology to estimate and map the abundance of animal and plant populations from spatial survey data. The key underlying concept in distance sampling is the detection function, the probability of detecting the occurrence of an event as a function of its distance from the observer, as well as other covariates that may influence detection. In epidemiology, the burden and distribution of infectious disease is often inferred from cases that are reported at clinics and hospitals. In areas with few public health facilities and low accessibility, the probability of detecting a case is also a function of the distance between an infected person and the "observer" (e.g. a health centre). While the problem of distance-related under-reporting is acknowledged in public health; there are few quantitative methods for assessing and correcting for this bias when mapping disease incidence. Here, we develop a modified version of distance sampling for prediction of infectious disease incidence by relaxing some of the framework's fundamental assumptions. We illustrate the utility of this approach using as our example malaria distribution in rural Burkina Faso, where there is a large population at risk but relatively low accessibility of health facilities. RESULTS The modified distance-sampling framework was used to predict the probability of reporting malaria infection at 8 rural clinics, based on road-travel distances from villages. The rate at which reporting probability dropped with distance varied between clinics, depending on road and clinic positions. The probability of case detection was estimated as 0.3-1 in the immediate vicinity of the clinic, dropping to 0.1-0.6 at a travel distance of 10 km, and effectively zero at distances > 30-40 km. CONCLUSIONS To enhance the method's strategic impact, we provide an interactive mapping tool (as a self-contained R Shiny app) that can be used by non-specialists to interrogate model outputs and visualize how the overall probability of under-reporting and the catchment area of each clinic is influenced by changing the number and spatial allocation of health centres.
Collapse
Affiliation(s)
- Luca Nelli
- University of Glasgow, Institute of Biodiversity Animal Health and Comparative Medicine, Glasgow, UK.
| | - Moussa Guelbeogo
- Centre National De Recherche et Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Heather M Ferguson
- University of Glasgow, Institute of Biodiversity Animal Health and Comparative Medicine, Glasgow, UK
| | - Daouda Ouattara
- Centre National De Recherche et Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Alfred Tiono
- Centre National De Recherche et Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Sagnon N'Fale
- Centre National De Recherche et Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Jason Matthiopoulos
- University of Glasgow, Institute of Biodiversity Animal Health and Comparative Medicine, Glasgow, UK
| |
Collapse
|