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1. Cholera epidemic in Yemen, 2016–18: an analysis of surveillance data

Author

Katherine E. Atkins, Abdul Rahman Al-Mesbahy, Anton Camacho, Christopher Haskew, Abdulkareem Almoalmi, Caroline Seguin, Maria Jose Sagrado, Xavier de Radiguès, Marije Broekhuijsen, Reema Alyusfi, Malika Bouhenia, Lorenzo Pezzoli, Mehmet Akif Saatcioglu, Munna Abdulla Mohammed Naji, Nevio Zagaria, Mohammed Musoke, Marie Laure Quilici, Abdulhakeem Alkohlani, Abdinasir Abubakar, Marc Poncin, Klaudia Porten, Melissa McRae, Rosalind M Eggo, Andrew S. Azman, Ankur Rakesh, Francisco J. Luquero, Epicentre [Paris] [Médecins Sans Frontières], London School of Hygiene and Tropical Medicine (LSHTM), World Health Organization [Yemen], Health Authorities, Central Public Health Laboratory [Yemen], Regional Office for the Eastern Mediterranean [Cairo] (EMRO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Médecins Sans Frontières [Dubai], Médecins sans Frontières [Barcelone], Médecins sans Frontières [Genève] (MSF), Médecins Sans Frontières [Amsterdam], Médecins sans frontières [Sana'a], World Health Organisation (WHO), Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), UNICEF [Sana'a], UNICEF Headquarters, Centre National de Référence des Vibrions et du Choléra - National Reference Center Vibrios and Cholera (CNR), Institut Pasteur [Paris], Health Authorities of Yemen, WHO, and Médecins Sans Frontières., WHO - Regional Office for the Eastern Mediterranean [Cairo, Egypt] (EMRO), and Institut Pasteur [Paris] (IP)

Subjects
0301 basic medicine, medicine.medical_specialty, Yemen, Attack rate, Plague (disease), Article, Disease Outbreaks, 03 medical and health sciences, 0302 clinical medicine, Cholera, Epidemiology, Case fatality rate, medicine, Humans, 030212 general & internal medicine, Epidemics, Transmission (medicine), lcsh:Public aspects of medicine, Incidence (epidemiology), Outbreak, lcsh:RA1-1270, General Medicine, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, 030104 developmental biology, Geography, Demography
Abstract

BACKGROUND: In war-torn Yemen, reports of confirmed cholera started in late September, 2016. The disease continues to plague Yemen today in what has become the largest documented cholera epidemic of modern times. We aimed to describe the key epidemiological features of this epidemic, including the drivers of cholera transmission during the outbreak.METHODS: The Yemen Health Authorities set up a national cholera surveillance system to collect information on suspected cholera cases presenting at health facilities. Individual variables included symptom onset date, age, severity of dehydration, and rapid diagnostic test result. Suspected cholera cases were confirmed by culture, and a subset of samples had additional phenotypic and genotypic analysis. We first conducted descriptive analyses at national and governorate levels. We divided the epidemic into three time periods: the first wave (Sept 28, 2016, to April 23, 2017), the increasing phase of the second wave (April 24, 2017, to July 2, 2017), and the decreasing phase of the second wave (July 3, 2017, to March 12, 2018). We reconstructed the changes in cholera transmission over time by estimating the instantaneous reproduction number, Rt. Finally, we estimated the association between rainfall and the daily cholera incidence during the increasing phase of the second epidemic wave by fitting a spatiotemporal regression model.FINDINGS: From Sept 28, 2016, to March 12, 2018, 1 103 683 suspected cholera cases (attack rate 3·69%) and 2385 deaths (case fatality risk 0·22%) were reported countrywide. The epidemic consisted of two distinct waves with a surge in transmission in May, 2017, corresponding to a median Rt of more than 2 in 13 of 23 governorates. Microbiological analyses suggested that the same Vibrio cholerae O1 Ogawa strain circulated in both waves. We found a positive, non-linear, association between weekly rainfall and suspected cholera incidence in the following 10 days; the relative risk of cholera after a weekly rainfall of 25 mm was 1·42 (95% CI 1·31–1·55) compared with a week without rain.INTERPRETATION: Our analysis suggests that the small first cholera epidemic wave seeded cholera across Yemen during the dry season. When the rains returned in April, 2017, they triggered widespread cholera transmission that led to the large second wave. These results suggest that cholera could resurge during the ongoing 2018 rainy season if transmission remains active. Therefore, health authorities and partners should immediately enhance current control efforts to mitigate the risk of a new cholera epidemic wave in Yemen.FUNDING: Health Authorities of Yemen, WHO, and Médecins Sans Frontières.

Published
2018

2. Worldwide Reduction in MERS Cases and Deaths since 2016

Author

Mamun Malik, Maria D. Van Kerkhove, Christl A. Donnelly, Amgad Elkholy, Simon Cauchemez, University of Oxford [Oxford], Imperial College London, Regional Office for the Eastern Mediterranean [Cairo] (EMRO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Institut Pasteur [Paris], C.A.D. thanks the UK Medical Research Council for center funding (MR/R015600/1) and the National Institute for Health Research for funding the NIHR Health Protection Research Unit in Modelling Methodology and the Vaccine Efficacy Evaluation for Priority Emerging Diseases Epidemic Modelling Consortium (EPIDZO34). S.C. acknowledges financial support from the Investissement d’Avenir program, the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases program (grant ANR-10-LABX-62-IBEID), the Models of Infectious Disease Agent Study of the National Institute of General Medical Sciences, and the AXA Research Fund., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Medical Research Council (MRC), National Institute for Health Research, University of Oxford, WHO - Regional Office for the Eastern Mediterranean [Cairo, Egypt] (EMRO), Institut Pasteur [Paris] (IP), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiology (medical), medicine.medical_specialty, MESH: Coronavirus Infections, Epidemiology, media_common.quotation_subject, OUTBREAK, 030231 tropical medicine, Immunology, lcsh:Medicine, MESH: Global Health, medicine.disease_cause, Global Health, Microbiology, lcsh:Infectious and parasitic diseases, Disease Outbreaks, 1117 Public Health and Health Services, Worldwide Reduction in MERS Cases and Deaths since 2016, 03 medical and health sciences, 0302 clinical medicine, 1108 Medical Microbiology, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Global health, medicine, Research Letter, Humans, lcsh:RC109-216, 030212 general & internal medicine, MESH: Incidence, MESH: Disease Outbreaks, media_common, Coronavirus, Science & Technology, MESH: Humans, business.industry, Incidence (epidemiology), Incidence, lcsh:R, Outbreak, 1103 Clinical Sciences, medicine.disease, 3. Good health, Infectious Diseases, Emergency medicine, Middle East respiratory syndrome, business, Coronavirus Infections, Life Sciences & Biomedicine, Vigilance (psychology)
Abstract

International audience; Since 2012, Middle East respiratory syndrome (MERS) coronavirus has infected 2,442 persons worldwide. Case-based data analysis suggests that since 2016, as many as 1,465 cases and 293-520 deaths might have been averted. Efforts to reduce the global MERS threat are working, but countries must maintain vigilance to prevent further infections.

Published
2019
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3. Comparative Analysis of Eleven Healthcare-Associated Outbreaks of Middle East Respiratory Syndrome Coronavirus (Mers-Cov) from 2015 to 2017

Author

Sibylle Bernard-Stoecklin, Mamunur Rahman Malik, Abdullah M. Assiri, Birgit Nikolay, Maria D. Van Kerkhove, Hassan El Bushra, Moran Ki, Simon Cauchemez, Abdul Aziz Bin Saeed, Arnaud Fontanet, Peter Ben Embarek, Center for Global Health Research and Education - Centre pour la Recherche et la Formation en Santé Mondiale (CGH), Institut Pasteur [Paris]-Réseau International des Instituts Pasteur (RIIP), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Ministry of Health [Riyadh], Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), National Cancer Center Korea, Regional Office for the Eastern Mediterranean [Cairo] (EMRO), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Conservatoire National des Arts et Métiers [CNAM] (CNAM), B.N. and S.C. acknowledge financial support from the Investissement d’Avenir program, the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases program (Grant ANR-10-LABX-62-IBEID), the Models of Infectious Disease Agent Study of the National Institute of General Medical Sciences, the AXA Research Fund and the INCEPTION project (PIA/ANR-16-CONV-0005)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), Institut Pasteur [Paris] (IP)-Réseau International des Instituts Pasteur (RIIP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), WHO - Regional Office for the Eastern Mediterranean [Cairo, Egypt] (EMRO), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), and HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)

Subjects
0301 basic medicine, Male, Multivariate analysis, MESH: Coronavirus Infections, lcsh:Medicine, MESH: Infectious Disease Transmission, Professional-to-Patient, MESH: Comorbidity, Comorbidity, medicine.disease_cause, Disease Outbreaks, Infectious Disease Transmission, Professional-to-Patient, 0302 clinical medicine, Healthcare associated, MESH: Risk Factors, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Health care, Epidemiology, MESH: Disease Outbreaks, lcsh:Science, MESH: Aged, Cross Infection, Multidisciplinary, MESH: Middle Aged, Transmission (medicine), Age Factors, Middle Aged, MESH: Hospitals, Hospitals, 3. Good health, Middle East Respiratory Syndrome Coronavirus, Infectious diseases, Female, Coronavirus Infections, MESH: History, 21st Century, Adult, MESH: Republic of Korea, medicine.medical_specialty, Infectious Disease Transmission, Patient-to-Professional, Middle East respiratory syndrome coronavirus, Health Personnel, Saudi Arabia, History, 21st Century, World health, Article, 03 medical and health sciences, Environmental health, MESH: Infectious Disease Transmission, Patient-to-Professional, Republic of Korea, medicine, Humans, Aged, MESH: Age Factors, MESH: Humans, business.industry, lcsh:R, MESH: Middle East Respiratory Syndrome Coronavirus, Outbreak, MESH: Cross Infection, MESH: Adult, MESH: Male, MESH: Saudi Arabia, 030104 developmental biology, Risk factors, MESH: Health Personnel, lcsh:Q, business, MESH: Female, 030217 neurology & neurosurgery
Abstract

Since its emergence in 2012, 2,260 cases and 803 deaths due to Middle East respiratory syndrome coronavirus (MERS-CoV) have been reported to the World Health Organization. Most cases were due to transmission in healthcare settings, sometimes causing large outbreaks. We analyzed epidemiologic and clinical data of laboratory-confirmed MERS-CoV cases from eleven healthcare-associated outbreaks in the Kingdom of Saudi Arabia and the Republic of Korea between 2015–2017. We quantified key epidemiological differences between outbreaks. Twenty-five percent (n = 105/422) of MERS cases who acquired infection in a hospital setting were healthcare personnel. In multivariate analyses, age ≥65 (OR 4.8, 95%CI: 2.6–8.7) and the presence of underlying comorbidities (OR: 2.7, 95% CI: 1.3–5.7) were associated with increased mortality whereas working as healthcare personnel was protective (OR 0.07, 95% CI: 0.01–0.34). At the start of these outbreaks, the reproduction number ranged from 1.0 to 5.7; it dropped below 1 within 2 to 6 weeks. This study provides a comprehensive characterization of MERS HCA-outbreaks. Our results highlight heterogeneities in the epidemiological profile of healthcare-associated outbreaks. The limitations of our study stress the urgent need for standardized data collection for high-threat respiratory pathogens, such as MERS-CoV.

Published
2019

4. Genomic insights into the 2016–2017 cholera epidemic in Yemen

Author

Dhirendra Kumar, Abdullah M. Assiri, Naresh Chand Sharma, Joseph F. Wamala, Samuel Kariuki, Caroline Seguin, Thérèse E. Malliavin, Abdullrahman A. Almesbahi, Nicholas R. Thomson, Samuel M. C. Njoroge, Thandavarayan Ramamurthy, Mona Naji, Daryl Domman, Elisabeth Njamkepo, Samar Saeed Nasher, Jane Y. Carter, Abdinasir Abubakar, Bita Bakhshi, Jean Rauzier, Andrew S. Azman, Christiane Bouchier, John Kiiru, Francisco J. Luquero, François-Xavier Weill, Hayder H.N. Abulmaali, Marie Laure Quilici, Mohammad Reza Pourshafie, Ankur Rakesh, Mamunur Rahman Malik, Bactéries pathogènes entériques (BPE), Institut Pasteur [Paris] (IP), The Wellcome Trust Sanger Institute [Cambridge], Los Alamos National Laboratory (LANL), Ministry of Public Health [Yemen], Epicentre [Paris] [Médecins Sans Frontières], Ministry of Health [Saudi Arabia], Kenya Medical Research Institute (KEMRI), Institut Pasteur d'Iran, Réseau International des Instituts Pasteur (RIIP), WHO - Regional Office for the Eastern Mediterranean [Cairo, Egypt] (EMRO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Amref Health Africa [Kenya], African Medical and Research Foundation (AMREF), Médecins Sans Frontières [Dubai], Génomique (Plate-Forme) - Genomics Platform, Bioinformatique structurale - Structural Bioinformatics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Tarbiat Modares University [Tehran], Ministry of Health [Iraq], Maharishi Valmiki Hospital, Translational Health Science and Technology Institute [Faridabad] (THSTI), Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), London School of Hygiene and Tropical Medicine (LSHTM), This study was supported by the Institut Pasteur, Santé publique France, the French government’s Investissement d’Avenir programme, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), the Wellcome Trust through grant 098051 to the Sanger Institute and the Department of Biotechnology of India. The Institut Pasteur Genomics Platform is a member of the France Génomique consortium (ANR10-INBS-09-08)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris], Regional Office for the Eastern Mediterranean [Cairo] (EMRO), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Serotype, Yemen, 030106 microbiology, Context (language use), Biology, medicine.disease_cause, El Tor, 03 medical and health sciences, Antibiotic resistance, Cholera, Pandemic, medicine, Humans, Vibrio cholerae, Phylogeny, Multidisciplinary, Outbreak, Genomics, biology.organism_classification, medicine.disease, Virology, 3. Good health, 030104 developmental biology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Genome, Bacterial
Abstract

International audience; Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor2-4. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic1-the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)-are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype.

Published
2019

5. Mapping the burden of cholera in sub-Saharan Africa and implications for control: an analysis of data across geographical scales

Author

Lessler, Justin, Moore, Sean M, Luquero, Francisco J, McKay, Heather S, Grais, Rebecca, Henkens, Myriam, Mengel, Martin, Dunoyer, Jessica, M'bangombe, Maurice, Lee, Elizabeth C, Djingarey, Mamoudou Harouna, Sudre, Bertrand, Bompangue, Didier, Fraser, Robert S M, Abubakar, Abdinasir, Perea, William, Legros, Dominique, Azman, Andrew S, Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), Epicentre [Paris] [Médecins Sans Frontières], Médecins Sans Frontières Belgique, Agence de Médecine Préventive, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Service de Microbiologie [Kinshasa, République Démocratique du Congo], Faculté de Médecine [Kinshasa, République Démocratique du Congo], Université Libre de Kinshasa (ULK)-Université Libre de Kinshasa (ULK), Regional Office for the Eastern Mediterranean [Cairo] (EMRO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Centre de Mathématiques Appliquées (CMA), MINES ParisTech - École nationale supérieure des mines de Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)

Subjects
Population Density, Cholera, Incidence, Vaccination, [SDE]Environmental Sciences, Humans, Sanitation, Mass Vaccination, Article, Africa South of the Sahara, Markov Chains, ComputingMilieux_MISCELLANEOUS, Demography
Abstract

Summary Background Cholera remains a persistent health problem in sub-Saharan Africa and worldwide. Cholera can be controlled through appropriate water and sanitation, or by oral cholera vaccination, which provides transient (∼3 years) protection, although vaccine supplies remain scarce. We aimed to map cholera burden in sub-Saharan Africa and assess how geographical targeting could lead to more efficient interventions. Methods We combined information on cholera incidence in sub-Saharan Africa (excluding Djibouti and Eritrea) from 2010 to 2016 from datasets from WHO, Médecins Sans Frontières, ProMED, ReliefWeb, ministries of health, and the scientific literature. We divided the study region into 20 km × 20 km grid cells and modelled annual cholera incidence in each grid cell assuming a Poisson process adjusted for covariates and spatially correlated random effects. We combined these findings with data on population distribution to estimate the number of people living in areas of high cholera incidence (>1 case per 1000 people per year). We further estimated the reduction in cholera incidence that could be achieved by targeting cholera prevention and control interventions at areas of high cholera incidence. Findings We included 279 datasets covering 2283 locations in our analyses. In sub-Saharan Africa (excluding Djibouti and Eritrea), a mean of 141 918 cholera cases (95% credible interval [CrI] 141 538–146 505) were reported per year. 4·0% (95% CrI 1·7–16·8) of districts, home to 87·2 million people (95% CrI 60·3 million to 118·9 million), have high cholera incidence. By focusing on the highest incidence districts first, effective targeted interventions could eliminate 50% of the region's cholera by covering 35·3 million people (95% CrI 26·3 million to 62·0 million), which is less than 4% of the total population. Interpretation Although cholera occurs throughout sub-Saharan Africa, its highest incidence is concentrated in a small proportion of the continent. Prioritising high-risk areas could substantially increase the efficiency of cholera control programmes. Funding The Bill & Melinda Gates Foundation.

Published
2018

6. Cholera Epidemic in South Sudan and Uganda and Need for International Collaboration in Cholera Control

Author

Abdinasir Abubakar, Malika Bouhenia, Stephen Martin, Jean Rauzier, Lise Grout, Atek Kagirita, Francisco J. Luquero, Godfrey Bwire, Joseph F. Wamala, John Rumunu, Christopher Garimoi Orach, Andrew S. Azman, Lul Deng, Marie Laure Quilici, Regional Office for the Eastern Mediterranean [Cairo] (EMRO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Uganda Ministry of Health, Médecins sans Frontières [Genève] (MSF), Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), Epicentre [Paris] [Médecins Sans Frontières], Republic of South Sudan Ministry of Health, Institut Pasteur [Paris], Makerere University [Kampala, Ouganda] (MAK), This work was funded by Institut Pasteur, Santé Publique France. A.S.A. received funding from the Bill and Melinda Gates Foundation (OPP1089243 and OPP153556)., WHO - Regional Office for the Eastern Mediterranean [Cairo, Egypt] (EMRO), and Institut Pasteur [Paris] (IP)

Subjects
0301 basic medicine, Microbiology (medical), Cholera Epidemic in South Sudan and Uganda and Need for International Collaboration in Cholera Control, Time Factors, Epidemiology, International Cooperation, 030106 microbiology, 030231 tropical medicine, epidemiological data, lcsh:Medicine, cholera, medicine.disease_cause, epidemic, lcsh:Infectious and parasitic diseases, Line list, 03 medical and health sciences, 0302 clinical medicine, Molecular microbiology, parasitic diseases, medicine, Infection control, Humans, lcsh:RC109-216, Uganda, Epidemics, bacteria, South Sudan, multilocus variable number tandem repeat, enteric infections, lcsh:R, Dispatch, Outbreak, medicine.disease, Virology, Cholera, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Molecular analysis, Vibrio cholera, Infectious Diseases, Geography, Vibrio cholerae, molecular microbiology, Africa
Abstract

International audience; Combining the official cholera line list data and outbreak investigation reports from the ministries of health in Uganda and South Sudan with molecular analysis of Vibrio cholerae strains revealed the interrelatedness of the epidemics in both countries in 2014. These results highlight the need for collaboration to control cross-border outbreaks.

Published
2018

7. Current and future distribution of Aedes aegypti and Aedes albopictus (Diptera : Culicidae) in WHO Eastern Mediterranean Region

Author

Johannes Charlier, Ward Bryssinckx, Valérie De Waele, Frédéric Simard, Evans Buliva, Abdulhafid Hussain, Nhu Nguyen Tran Minh, Muhammad Mukhtar, David Roiz, Nabil Haddad, Ali Bouattour, Guy Hendrickx, Els Ducheyne, Osama Mahmoud, Mamunur Rahman Malik, Avia-GIS [Zoersel], WHO - Regional Office for the Eastern Mediterranean [Cairo, Egypt] (EMRO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Université Libanaise, Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Ministry of Health Oman, Directorate of Malaria Control [Islamabad] (DoMC), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP), Ministry of Health and Human Services [Somalia], Vector Control Group (MIVEGEC-VCG), This work was supported by the WHO Regional Office for the Eastern Mediterranean. The work was supported partially by the project InvaCosts (ANR-14-CE02-0021-01). Field work in Lebanon was supported by the WHO National Bureau (LEB1409860)., We thank the numerous entomologists and health officers of the EMR who shared data with the WHO Regional Office for the Eastern Mediterranean. Ms. Barwa and Dr. Zayed are gratefully acknowledged for their technical assistance. We gratefully acknowledge the valuable input of the anonymous reviewers on the first version of this paper., ANR-14-CE02-0021,InvaCosts,Insectes envahissants et leurs couts pour la biodiversité, l'économie et la santé humaine(2014), and Regional Office for the Eastern Mediterranean [Cairo] (EMRO)

Subjects
0301 basic medicine, Species distribution, Distribution (economics), Geographic Mapping, Distribution, medicine.disease_cause, Population density, MESH: Mosquito Vectors, MESH: Yellow Fever/diagnosis, Dengue fever, Dengue, MESH: Aedes, 0302 clinical medicine, Aedes aegypti, Aedes, MESH: Animals, Chikungunya, MESH: Dengue/diagnosis, Surveillance, biology, Mediterranean Region, Aedes albopictus, Geography, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Yellow Fever/epidemiology, lcsh:R858-859.7, Yellow fever, Cartography, MESH: Forecasting, General Computer Science, 030231 tropical medicine, MESH: Dengue/epidemiology, Mosquito Vectors, lcsh:Computer applications to medicine. Medical informatics, World Health Organization, MESH: Mediterranean Region/epidemiology, 03 medical and health sciences, Zika, MESH: World Health Organization, Species Specificity, MESH: Geographic Mapping, Yellow Fever, medicine, MESH: Species Specificity, Animals, Humans, MESH: Humans, business.industry, Research, Public Health, Environmental and Occupational Health, 15. Life on land, medicine.disease, biology.organism_classification, General Business, Management and Accounting, Spatial model, 030104 developmental biology, Culicidae, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, MESH: Culicidae, Forecasting
Abstract

Background Aedes-borne diseases as dengue, zika, chikungunya and yellow fever are an emerging problem worldwide, being transmitted by Aedes aegypti and Aedes albopictus. Lack of up to date information about the distribution of Aedes species hampers surveillance and control. Global databases have been compiled but these did not capture data in the WHO Eastern Mediterranean Region (EMR), and any models built using these datasets fail to identify highly suitable areas where one or both species may occur. The first objective of this study was therefore to update the existing Ae. aegypti (Linnaeus, 1762) and Ae. albopictus (Skuse, 1895) compendia and the second objective was to generate species distribution models targeted to the EMR. A final objective was to engage the WHO points of contacts within the region to provide feedback and hence validate all model outputs. Methods The Ae. aegypti and Ae. albopictus compendia provided by Kraemer et al. (Sci Data 2:150035, 2015; Dryad Digit Repos, 2015) were used as starting points. These datasets were extended with more recent species and disease data. In the next step, these sets were filtered using the Köppen–Geiger classification and the Mahalanobis distance. The occurrence data were supplemented with pseudo-absence data as input to Random Forests. The resulting suitability and maximum risk of establishment maps were combined into hard-classified maps per country for expert validation. Results The EMR datasets consisted of 1995 presence locations for Ae. aegypti and 2868 presence locations for Ae. albopictus. The resulting suitability maps indicated that there exist areas with high suitability and/or maximum risk of establishment for these disease vectors in contrast with previous model output. Precipitation and host availability, expressed as population density and night-time lights, were the most important variables for Ae. aegypti. Host availability was the most important predictor in case of Ae. albopictus. Internal validation was assessed geographically. External validation showed high agreement between the predicted maps and the experts’ extensive knowledge of the terrain. Conclusion Maps of distribution and maximum risk of establishment were created for Ae. aegypti and Ae. albopictus for the WHO EMR. These region-specific maps highlighted data gaps and these gaps will be filled using targeted monitoring and surveillance. This will increase the awareness and preparedness of the different countries for Aedes borne diseases. Electronic supplementary material The online version of this article (10.1186/s12942-018-0125-0) contains supplementary material, which is available to authorized users.

Published
2018

8. Evidence for the existence of two distinct species: Psammomys obesus and Psammomys vexillaris within the sand rats (Rodentia, Gerbillinae), reservoirs of cutaneous leishmaniasis in Tunisia

Author

Ben Ismail Riadh, Frigui Sabeh, Ben Hamou Mostafa, Ben Abderrazak Souha, Chatti Noureddine, Laboratoire d'Epidémiologie et d'Ecologie parasitaire, Institut Pasteur de Tunis, Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Faculté de Médecine Dentaire de Monastir [Tunisie] (FMDM), Regional Office for the Eastern Mediterranean [Cairo] (EMRO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), This study was supported by the Avicenne Programme of the European Commission, AVI CT92/0018, by the UNPD/World Bank/WHO Special Programme for Research and Training in Tropical Diseases I.D. 990443 and by the MRSTDC, Tunisia, within the frame of research program contracts., and We thank M. Ben Fadhel for technical help. We also thank G. Dobigny and I. Guizani for comments on the manuscript.

Subjects
0106 biological sciences, Microbiology (medical), Species complex, Tunisia, MESH: Leishmania, [SDV]Life Sciences [q-bio], Population, Karyotype, Leishmaniasis, Cutaneous, Zoology, 010603 evolutionary biology, 01 natural sciences, Microbiology, 03 medical and health sciences, Cutaneous leishmaniasis, Zoonoses, Genetics, medicine, Animals, Leishmania major, MESH: Animals, MESH: Gerbillinae, Psammomys vexillaris, education, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Disease Reservoirs, 030304 developmental biology, Leishmania, 0303 health sciences, education.field_of_study, MESH: Disease Reservoirs, biology, Psammomys, Cytochrome b, Morphometry, Zoonotic Cutaneous Leishmaniasis, biology.organism_classification, medicine.disease, Mitochondrial cytochrome b gene, MESH: Leishmaniasis, Cutaneous, Isoenzyme, Infectious Diseases, Genetic distance, Gerbillinae, MESH: Tunisia, MESH: Zoonoses
Abstract

International audience; A thorough taxonomic knowledge about putative animal reservoirs of transmissible diseases is an absolute prerequisite to any ecological investigation and epidemiological survey of zoonoses. Indeed, accurate identification of these reservoirs is essential for predicting species-specific population outbreaks and therefore to develop accurate ecological control strategies. The systematic status of sand rats (genus Psammomys) remains unclear despite the pivotal role of these rodents in the epidemiology of Zoonotic Cutaneous Leishmaniasis (ZCL) disease as sand rats are the main known reservoir hosts of the protozoan parasite Leishmania major. In the present work, we expose morphological, biochemical, genetic and cytogenetic evidence supporting the identification of at least two cryptic species within the genus Psammomys in Tunisia. First, significant morphometric differences were observed and were correlated associated with external features and biogeographic origins. Second, differences in patterns of two isoenzymic systems (Glutamate Oxaloacetate Transaminase (GOT) and 6-PhosphoGluconate Dehydrogenase (6PGD)) were found, which makes it possible to amount these isoenzyme characters to two diagnostic loci. Third, based on the mitochondrial cytochrome b (cyt b) gene, a high magnitude of genetic distance (13.89%) was also observed. Fourth, cytogenetic analysis showed that these two populations groups differ in their diploid chromosome numbers, i.e. 2N=46 versus 2N=48. We consider that all these variations are enough important to be considered as demonstrative and we propose that these two lineages should be considered as two distinct species that we refer to the fat sand rat Psammomys obesus Cretzschmar, 1828 and the thin sand rat Psammomys vexillaris Thomas, 1925. Implications of such results on the eco-epidemiology of ZCL in Tunisia are discussed.

Published
2006

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