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      The impact of social and environmental extremes on cholera time varying reproduction number in Nigeria

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          Abstract

          Nigeria currently reports the second highest number of cholera cases in Africa, with numerous socioeconomic and environmental risk factors. Less investigated are the role of extreme events, despite recent work showing their potential importance. To address this gap, we used a machine learning approach to understand the risks and thresholds for cholera outbreaks and extreme events, taking into consideration pre-existing vulnerabilities. We estimated time varying reproductive number (R) from cholera incidence in Nigeria and used a machine learning approach to evaluate its association with extreme events (conflict, flood, drought) and pre-existing vulnerabilities (poverty, sanitation, healthcare). We then created a traffic-light system for cholera outbreak risk, using three hypothetical traffic-light scenarios (Red, Amber and Green) and used this to predict R. The system highlighted potential extreme events and socioeconomic thresholds for outbreaks to occur. We found that reducing poverty and increasing access to sanitation lessened vulnerability to increased cholera risk caused by extreme events (monthly conflicts and the Palmers Drought Severity Index). The main limitation is the underreporting of cholera globally and the potential number of cholera cases missed in the data used here. Increasing access to sanitation and decreasing poverty reduced the impact of extreme events in terms of cholera outbreak risk. The results here therefore add further evidence of the need for sustainable development for disaster prevention and mitigation and to improve health and quality of life.

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          Random Forests

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            Updated Global Burden of Cholera in Endemic Countries

            Background The global burden of cholera is largely unknown because the majority of cases are not reported. The low reporting can be attributed to limited capacity of epidemiological surveillance and laboratories, as well as social, political, and economic disincentives for reporting. We previously estimated 2.8 million cases and 91,000 deaths annually due to cholera in 51 endemic countries. A major limitation in our previous estimate was that the endemic and non-endemic countries were defined based on the countries’ reported cholera cases. We overcame the limitation with the use of a spatial modelling technique in defining endemic countries, and accordingly updated the estimates of the global burden of cholera. Methods/Principal Findings Countries were classified as cholera endemic, cholera non-endemic, or cholera-free based on whether a spatial regression model predicted an incidence rate over a certain threshold in at least three of five years (2008-2012). The at-risk populations were calculated for each country based on the percent of the country without sustainable access to improved sanitation facilities. Incidence rates from population-based published studies were used to calculate the estimated annual number of cases in endemic countries. The number of annual cholera deaths was calculated using inverse variance-weighted average case-fatality rate (CFRs) from literature-based CFR estimates. We found that approximately 1.3 billion people are at risk for cholera in endemic countries. An estimated 2.86 million cholera cases (uncertainty range: 1.3m-4.0m) occur annually in endemic countries. Among these cases, there are an estimated 95,000 deaths (uncertainty range: 21,000-143,000). Conclusion/Significance The global burden of cholera remains high. Sub-Saharan Africa accounts for the majority of this burden. Our findings can inform programmatic decision-making for cholera control.
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              Variable selection using random forests

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: ResourcesRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: MethodologyRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: MethodologyRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLOS Glob Public Health
                PLOS Glob Public Health
                plos
                PLOS Global Public Health
                Public Library of Science (San Francisco, CA USA )
                2767-3375
                14 December 2022
                2022
                : 2
                : 12
                : e0000869
                Affiliations
                [1 ] Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
                [2 ] MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
                [3 ] Surveillance and Epidemiology Department/IM Cholera, Nigeria Centre for Disease Control, Abuja, Nigeria
                [4 ] Institute for Risk and Disaster Reduction, University College London, London, United Kingdom
                [5 ] Institute for Global Health, University College London, London, United Kingdom
                [6 ] University of Agder, Kristiansand, Norway
                [7 ] MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gamiba
                Ecole Normale Superieure, FRANCE
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0003-2087-7822
                https://orcid.org/0000-0002-0630-7332
                Article
                PGPH-D-22-00893
                10.1371/journal.pgph.0000869
                10022205
                36962831
                4292c0a2-b9a9-44c6-9fb9-40091d4f1456
                © 2022 Charnley et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 30 May 2022
                : 10 November 2022
                Page count
                Figures: 7, Tables: 0, Pages: 20
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100000270, Natural Environment Research Council;
                Award ID: NE/S007415/1
                Award Recipient :
                This work was supported by the Natural Environmental Research Council [NE/S007415/1] ( https://www.ukri.org/councils/nerc/), and the grant was awarded to G.Charnley as part of the Science and Solutions for a Changing Planet DTP. G.Charnley also acknowledges funding from the MRC Centre for Global Infectious Disease Analysis [MR/R015600/1], jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 programme supported by the European Union. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Medicine and Health Sciences
                Medical Conditions
                Infectious Diseases
                Bacterial Diseases
                Cholera
                Medicine and Health Sciences
                Medical Conditions
                Tropical Diseases
                Neglected Tropical Diseases
                Cholera
                Medicine and Health Sciences
                Health Care
                Environmental Health
                Sanitation
                Medicine and Health Sciences
                Public and Occupational Health
                Environmental Health
                Sanitation
                Medicine and Health Sciences
                Epidemiology
                Medical Risk Factors
                Medicine and Health Sciences
                Epidemiology
                People and Places
                Geographical Locations
                Africa
                Nigeria
                Medicine and Health Sciences
                Health Care
                Socioeconomic Aspects of Health
                Medicine and Health Sciences
                Public and Occupational Health
                Socioeconomic Aspects of Health
                Computer and Information Sciences
                Artificial Intelligence
                Machine Learning
                Earth Sciences
                Hydrology
                Flooding
                Custom metadata
                All data used here are taken from public sources and referenced throughout, except the cholera data which was provided by the NCDC and contains sensitive information and is therefore not available without signing a data sharing agreement with NCDC. The data can be requested via the Nigeria Centre for Disease Control and the data here were obtained from the Surveillance and Epidemiology Department/IM Cholera. The email for NCDC is: info@ 123456ncdc.gov.ng The institutional website is: https://ncdc.gov.ng.

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