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Dieng I, Sadio BD, Gaye A, Sagne SN, Ndione MHD, Kane M, Diallo MK, Sow B, Sankhe S, Sene O, Diallo A, Dieng M, Doukanda SFM, Mbanne M, Diop SMBS, Balde D, Ndiaye M, Sow KD, Diarra M, Sam A, Mbaye A, Diallo B, Sall Y, Faye O, Diop B, Sow A, Sall AA, Loucoubar C, Dia N, Faye O, Diallo D, Fall G, Weaver SC, Barry MA, Diallo M, Diagne MM. Genomic characterization of a reemerging Chikungunya outbreak in Kedougou, Southeastern Senegal, 2023. Emerg Microbes Infect 2024; 13:2373308. [PMID: 38934257 PMCID: PMC11268258 DOI: 10.1080/22221751.2024.2373308] [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: 02/15/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
Chikungunya virus has caused millions of cases worldwide over the past 20 years, with recent outbreaks in Kedougou region in the southeastern Senegal, West Africa. Genomic characterization highlights that an ongoing epidemic in Kedougou in 2023 is not due to an introduction event but caused by the re-emergence of an endemic strain evolving linearly in a sylvatic context.
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Affiliation(s)
- Idrissa Dieng
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Alioune Gaye
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Samba Niang Sagne
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Mouhamed Kane
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mamadou Korka Diallo
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Bocar Sow
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ousseynou Sene
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Diallo
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Madeleine Dieng
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Maimouna Mbanne
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | - Mignane Ndiaye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Maryam Diarra
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Abdoulaye Sam
- Prevention Department, Ministry of Health, Dakar, Senegal
| | - Ababacar Mbaye
- Kedougou Medical Region, Ministry of Health, Kedougou, Senegal
| | - Boubacar Diallo
- Public Health Direction, Institut Pasteur de Dakar, Dakar, Senegal
| | - Yoro Sall
- Prevention Department, Ministry of Health, Dakar, Senegal
| | - Ousmane Faye
- Public Health Direction, Institut Pasteur de Dakar, Dakar, Senegal
| | - Boly Diop
- Prevention Department, Ministry of Health, Dakar, Senegal
| | - Abdourahmane Sow
- Public Health Direction, Institut Pasteur de Dakar, Dakar, Senegal
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Pharmacy and Odonto-stomatology, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | | | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Diawo Diallo
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Gamou Fall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Scott C. Weaver
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mawlouth Diallo
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar, Senegal
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2
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Levine ZC, Sene A, Mkandawire W, Deme AB, Ndiaye T, Sy M, Gaye A, Diedhiou Y, Mbaye AM, Ndiaye IM, Gomis J, Ndiop M, Sene D, Faye Paye M, MacInnis BL, Schaffner SF, Park DJ, Badiane AS, Colubri A, Ndiaye M, Sy N, Sabeti PC, Ndiaye D, Siddle KJ. Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing. Nat Commun 2024; 15:747. [PMID: 38272885 PMCID: PMC10810818 DOI: 10.1038/s41467-024-44800-7] [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: 08/22/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024] Open
Abstract
The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata in a cross-sectional study of febrile patients and healthy controls in a low malaria burden area. Using 16S and untargeted sequencing, we detected viral, bacterial, or eukaryotic pathogens in 23% (38/163) of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15.5% and 3.8% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model that can distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs (F1 score: 0.823). These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
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Affiliation(s)
- Zoë C Levine
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
- Harvard/MIT MD-PhD Program, Boston, MA, USA
| | - Aita Sene
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Winnie Mkandawire
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Awa B Deme
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Tolla Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Mouhamad Sy
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Amy Gaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Younouss Diedhiou
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Amadou M Mbaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Ibrahima M Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Jules Gomis
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Médoune Ndiop
- Programme National de lutte contre le Paludisme, Ministère de la Santé, Dakar Fann, Senegal
| | - Doudou Sene
- Programme National de lutte contre le Paludisme, Ministère de la Santé, Dakar Fann, Senegal
| | | | - Bronwyn L MacInnis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aida S Badiane
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Andres Colubri
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Mouhamadou Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Ngayo Sy
- Service de Lutte Anti Parasitaire, Thies, Senegal
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Daouda Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal.
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal.
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
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3
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Levine ZC, Sene A, Mkandawire W, Deme AB, Ndiaye T, Sy M, Gaye A, Diedhiou Y, Mbaye AM, Ndiaye I, Gomis J, Ndiop M, Sene D, Paye MF, MacInnis B, Schaffner SF, Park DJ, Badiane AS, Colubri A, Ndiaye M, Sy N, Sabeti PC, Ndiaye D, Siddle KJ. Improving diagnosis of non-malarial fevers in Senegal: Borrelia and the contribution of tick-borne bacteria. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.24.23294564. [PMID: 37662407 PMCID: PMC10473814 DOI: 10.1101/2023.08.24.23294564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata from febrile patients and healthy controls in a low malaria burden area. Using 16S and unbiased sequencing, we detected viral, bacterial, or eukaryotic pathogens in 29% of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15% and 3.7% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model to distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs. These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
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Affiliation(s)
- Zoë C Levine
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
- Harvard/MIT MD-PhD Program, Boston, MA, 02115, USA
| | - Aita Sene
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Winnie Mkandawire
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Awa B Deme
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Tolla Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Mouhamad Sy
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Amy Gaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Amadou M Mbaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ibrahima Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jules Gomis
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Médoune Ndiop
- Programme National de Lutte contre le Paludisme (PNLP), Ministère de la Santé, Dakar Fann, Senegal
| | - Doudou Sene
- Programme National de Lutte contre le Paludisme (PNLP), Ministère de la Santé, Dakar Fann, Senegal
| | | | - Bronwyn MacInnis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aida S Badiane
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Andres Colubri
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Mouhamadou Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ngayo Sy
- Service de Lutte Anti Parasitaire, Thies, Senegal
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Daouda Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
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Kigozi BK, Kharod GA, Bukenya H, Shadomy SV, Haberling DL, Stoddard RA, Galloway RL, Tushabe P, Nankya A, Nsibambi T, Mbidde EK, Lutwama JJ, Perniciaro JL, Nicholson WL, Bower WA, Bwogi J, Blaney DD. Investigating the etiology of acute febrile illness: a prospective clinic-based study in Uganda. BMC Infect Dis 2023; 23:411. [PMID: 37328808 PMCID: PMC10276394 DOI: 10.1186/s12879-023-08335-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 05/17/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Historically, malaria has been the predominant cause of acute febrile illness (AFI) in sub-Saharan Africa. However, during the last two decades, malaria incidence has declined due to concerted public health control efforts, including the widespread use of rapid diagnostic tests leading to increased recognition of non-malarial AFI etiologies. Our understanding of non-malarial AFI is limited due to lack of laboratory diagnostic capacity. We aimed to determine the etiology of AFI in three distinct regions of Uganda. METHODS A prospective clinic-based study that enrolled participants from April 2011 to January 2013 using standard diagnostic tests. Participant recruitment was from St. Paul's Health Centre (HC) IV, Ndejje HC IV, and Adumi HC IV in the western, central and northern regions, which differ by climate, environment, and population density. A Pearson's chi-square test was used to evaluate categorical variables, while a two-sample t-test and Krukalis-Wallis test were used for continuous variables. RESULTS Of the 1281 participants, 450 (35.1%), 382 (29.8%), and 449 (35.1%) were recruited from the western, central, and northern regions, respectively. The median age (range) was 18 (2-93) years; 717 (56%) of the participants were female. At least one AFI pathogen was identified in 1054 (82.3%) participants; one or more non-malarial AFI pathogens were identified in 894 (69.8%) participants. The non-malarial AFI pathogens identified were chikungunya virus, 716 (55.9%); Spotted Fever Group rickettsia (SFGR), 336 (26.2%) and Typhus Group rickettsia (TGR), 97 (7.6%); typhoid fever (TF), 74 (5.8%); West Nile virus, 7 (0.5%); dengue virus, 10 (0.8%) and leptospirosis, 2 (0.2%) cases. No cases of brucellosis were identified. Malaria was diagnosed either concurrently or alone in 404 (31.5%) and 160 (12.5%) participants, respectively. In 227 (17.7%) participants, no cause of infection was identified. There were statistically significant differences in the occurrence and distribution of TF, TGR and SFGR, with TF and TGR observed more frequently in the western region (p = 0.001; p < 0.001) while SFGR in the northern region (p < 0.001). CONCLUSION Malaria, arboviral infections, and rickettsioses are major causes of AFI in Uganda. Development of a Multiplexed Point-of-Care test would help identify the etiology of non-malarial AFI in regions with high AFI rates.
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Affiliation(s)
- Brian K Kigozi
- Uganda Virus Research Institute, Entebbe, Uganda.
- College of Health Sciences, Clinical Epidemiology Unit, Makerere University, Kampala, Uganda.
| | - Grishma A Kharod
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | | | - Sean V Shadomy
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | - Dana L Haberling
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | - Robyn A Stoddard
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | - Renee L Galloway
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | | | - Annet Nankya
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Thomas Nsibambi
- Uganda Virus Research Institute, Entebbe, Uganda
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | | | | | | | | | - William A Bower
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | | | - David D Blaney
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
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