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Oral and plasma microbiome in the context of acute febrile illness

Mouhamad Sy1,2, Tolla Ndiaye2,3, Ritika Thakur1

  • 1Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.

Medrxiv : the Preprint Server for Health Sciences
|May 4, 2026
PubMed

Insights

Emerging infectious diseases and antimicrobial resistance (AMR) pose significant public health risks. This study analyzed febrile illness in Senegal, revealing pathogens and AMR genes in oral and plasma samples, highlighting the need for integrated surveillance.

Area of Science:

  • Microbiology
  • Genomics
  • Public Health

Background:

  • Emerging infectious diseases and antimicrobial resistance (AMR) are critical global health challenges.
  • Integrated surveillance systems are needed to detect both pathogens and AMR simultaneously.
  • Next-generation sequencing technologies enable concurrent detection of pathogens and AMR.

Purpose of the Study:

  • To analyze oral and plasma microbiomes in febrile individuals in Senegal using advanced sequencing techniques.
  • To identify pathogens, viruses, and antimicrobial resistance genes (ARGs) in paired samples.
  • To understand the relationship between microbiome composition, fever, and the presence of ARGs.

Main Methods:

  • Utilized short-read metatranscriptomics and long-read 16S rRNA metagenomic sequencing.
  • Analyzed paired oral and plasma samples from febrile individuals in two Senegalese locations.
  • Investigated microbiome diversity, pathogen detection, viral presence, and ARG profiling.

Main Results:

  • Oral microbiome composition varied between locations, with reduced diversity linked to high fever.
  • Pathogens, including *Borrelia crocidurae*, were detected in 15.33% of samples.
  • Antimicrobial resistance genes (ARGs) and virulence factor genes were prevalent, with beta-lactam resistance being most common.

Conclusions:

  • Provides crucial data on oral and plasma microbiomes during acute febrile illness in Senegal.
  • Demonstrates the feasibility of simultaneous pathogen and AMR detection using multi-omics approaches.
  • Highlights the significant burden of ARGs in the studied population, informing public health strategies.

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