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Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing

Author

Listed:
  • Zoë C. Levine

    (Broad Institute of Harvard and MIT
    Harvard Graduate Program in Biological and Biomedical Science
    Harvard/MIT MD-PhD Program)

  • Aita Sene

    (Cheikh Anta Diop University Dakar
    Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire)

  • Winnie Mkandawire

    (Broad Institute of Harvard and MIT
    University of Massachusetts Medical School)

  • Awa B. Deme

    (Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire)

  • Tolla Ndiaye

    (Cheikh Anta Diop University Dakar
    Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire)

  • Mouhamad Sy

    (Cheikh Anta Diop University Dakar
    Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire)

  • Amy Gaye

    (Cheikh Anta Diop University Dakar
    Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire)

  • Younouss Diedhiou

    (Cheikh Anta Diop University Dakar
    Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire)

  • Amadou M. Mbaye

    (Cheikh Anta Diop University Dakar
    Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire)

  • Ibrahima M. Ndiaye

    (Cheikh Anta Diop University Dakar
    Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire)

  • Jules Gomis

    (Cheikh Anta Diop University Dakar
    Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire)

  • Médoune Ndiop

    (Programme National de lutte contre le Paludisme, Ministère de la Santé)

  • Doudou Sene

    (Programme National de lutte contre le Paludisme, Ministère de la Santé)

  • Marietou Faye Paye

    (Broad Institute of Harvard and MIT)

  • Bronwyn L. MacInnis

    (Broad Institute of Harvard and MIT
    Harvard T.H. Chan School of Public Health, Harvard University)

  • Stephen F. Schaffner

    (Broad Institute of Harvard and MIT
    Harvard T.H. Chan School of Public Health, Harvard University
    Harvard University)

  • Daniel J. Park

    (Broad Institute of Harvard and MIT)

  • Aida S. Badiane

    (Cheikh Anta Diop University Dakar
    Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire)

  • Andres Colubri

    (Broad Institute of Harvard and MIT
    University of Massachusetts Medical School)

  • Mouhamadou Ndiaye

    (Cheikh Anta Diop University Dakar
    Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire)

  • Ngayo Sy

    (Service de Lutte Anti Parasitaire)

  • Pardis C. Sabeti

    (Broad Institute of Harvard and MIT
    Harvard T.H. Chan School of Public Health, Harvard University
    Harvard University
    Howard Hughes Medical Institute)

  • Daouda Ndiaye

    (Cheikh Anta Diop University Dakar
    Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire)

  • Katherine J. Siddle

    (Broad Institute of Harvard and MIT
    Brown University)

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.

Suggested Citation

  • Zoë C. Levine & Aita Sene & Winnie Mkandawire & Awa B. Deme & Tolla Ndiaye & Mouhamad Sy & Amy Gaye & Younouss Diedhiou & Amadou M. Mbaye & Ibrahima M. Ndiaye & Jules Gomis & Médoune Ndiop & Doudou Se, 2024. "Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-44800-7
    DOI: 10.1038/s41467-024-44800-7
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    References listed on IDEAS

    as
    1. Friedman, Jerome H. & Hastie, Trevor & Tibshirani, Rob, 2010. "Regularization Paths for Generalized Linear Models via Coordinate Descent," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 33(i01).
    2. Judith U. Oguzie & Brittany A. Petros & Paul E. Oluniyi & Samar B. Mehta & Philomena E. Eromon & Parvathy Nair & Opeoluwa Adewale-Fasoro & Peace Damilola Ifoga & Ikponmwosa Odia & Andrzej Pastusiak & , 2023. "Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
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