Metatranscriptomics reveals potential pathogens, widespread antimicrobial resistance and reduced oral microbiome diversity in acutely febrile individuals from Senegal.

Microbial infections elicit a range of clinical outcomes and overlapping symptoms, like acute fever, complicate diagnosis. Infecting microbes interact with resident microbiome communities, potentially driving dysbiosis and exchanging genetic material. There is thus a need to understand both the microbes associated with disease and the broader microbial context. To investigate these dynamics, we used metatranscriptomic sequencing of oral and plasma samples from febrile individuals in Senegal. Known pathogens were detected in 35% of individuals, with Borrelia crocidurae the most common. Viruses were present in oral (10/72) and plasma (09/78) samples, including the recently described species redondovirus, and 8 individuals had viral-bacterial co-infections. Fever was associated with reduced oral microbiome diversity and richness. Finally, a high frequency of samples expressed known virulence (24%) and resistance (10%) genes. This study sheds light on the oral microbiome in Senegal and demonstrates the utility of metatranscriptomics for integrated pathogen and resistance surveillance.