Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing
Levine, Zoë C ; Sene, Aita ; Mkandawire, Winnie ; Deme, Awa B ; Ndiaye, Tolla ; Sy, Mouhamad ; Gaye, Amy ; Diedhiou, Younouss ; Mbaye, Amadou M ; Ndiaye, Ibrahima M ... show 10 more
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Sene, Aita
Mkandawire, Winnie
Deme, Awa B
Ndiaye, Tolla
Sy, Mouhamad
Gaye, Amy
Diedhiou, Younouss
Mbaye, Amadou M
Ndiaye, Ibrahima M
Gomis, Jules
Ndiop, Médoune
Sene, Doudou
Faye Paye, Marietou
MacInnis, Bronwyn L
Schaffner, Stephen F
Park, Daniel J
Badiane, Aida S
Colubri, Andrés
Ndiaye, Mouhamadou
Sy, Ngayo
Sabeti, Pardis C
Ndiaye, Daouda
Siddle, Katherine J
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UMass Chan Affiliations
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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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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 Jan 25;15(1):747. doi: 10.1038/s41467-024-44800-7. PMID: 38272885; PMCID: PMC10810818.