Oral microbiome diversity reduced in febrile individuals with high fever in SenegalFever and oral bacteria changes seen in Senegal study

medRxiv Published April 21, 2026 Study authors: Sy, M.; Ndiaye, T.; Thakur, R.; Gaye, A.; Levine, Z. C.; Ngom, B.; Bellavia, K. L.; Firer, D.; Toure… DOI ↗ Editorial oversight: Dr. Amelia Tan, PhD · Internal Medicine & Chronic Disease

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Key Takeaway

Note that oral microbiome diversity was reduced and pathogens detected in febrile individuals in this Senegal cohort study.

This cohort study enrolled 150 febrile individuals across two locations in Senegal to characterize the oral microbiome and detect pathogens. The primary outcome assessed oral microbiome community composition, while secondary outcomes included diversity, richness, and pathogen detection.

Oral microbiome community composition differed between the two study locations. Oral microbiome diversity and richness were significantly associated with high fever. At least one known pathogen was identified in 23 of 150 (15.33%) samples, with Borrelia crocidurae being the most frequently detected pathogen. Pathogenic and non-pathogenic viruses were detected in 10 of 72 oral samples and 09 of 78 plasma samples.

Samples expressing at least one antimicrobial resistance (AMR) gene were found at a high frequency of 10%. Samples expressing virulence factor genes were found at a high frequency of 24%. Resistance to beta-lactam antibiotics was the most prevalent resistance mechanism observed. No specific adverse events or discontinuations were reported in the safety data.

As an observational cohort study, this research cannot establish causal relationships between fever, microbiome changes, or pathogen detection. The findings describe associations and prevalence in a specific setting but require further investigation to determine clinical implications for febrile illness management.

A research team examined the oral microbiomes of 150 individuals experiencing acute febrile illness. The study took place across two different locations in Senegal. Scientists analyzed samples to understand how fever and location affected the community of bacteria in the mouth.

The results showed that oral microbiome composition differed between the two locations. Additionally, the diversity and richness of these oral bacteria were significantly reduced in people with high fever. The team also detected at least one known pathogen in 23 of the 150 samples, with Borrelia crocidurae being the most frequently identified. Viruses, both pathogenic and non-pathogenic, were found in oral samples from 10 of 72 participants and in plasma samples from 9 of 78 participants.

The study also noted a high frequency of samples expressing antibiotic resistance genes, with resistance to beta-lactam antibiotics being the most prevalent type. Another 24% of samples expressed virulence factor genes. While these findings highlight the complexity of infections in this population, the study is observational. Readers should understand that these results describe links between fever and oral bacteria but do not establish a direct cause-and-effect relationship. More research is needed to determine if these changes are harmful or how they develop.

What this means for you:

Study links fever to reduced oral bacteria diversity in Senegal; findings are observational and do not prove cause.

Study Details

Study typeCohort

EvidenceLevel 3

PublishedApr 2026

View Original Abstract ↓

Emerging infectious diseases and antimicrobial resistance (AMR) have surfaced as two major public health threats over the past two decades. Consequently, integrative surveillance systems capable of detecting both emerging pathogens and resistance-carrying bacteria are crucial. With advances in next-generation sequencing, simultaneous detection of pathogens and AMR is increasingly feasible. In this study, we used short-read metatranscriptomics complemented by total 16S rRNA metagenomic long-read sequencing to analyze paired oral and plasma samples from a cohort of febrile individuals at two locations in Senegal. Oral microbiomes differed in community composition between locations, and reduced diversity and richness were significantly associated with high fever. We identified at least one known pathogen in 15.33 % (23/150) of samples, with Borrelia crocidurae as the most frequently detected pathogen. We detected both pathogenic and non-pathogenic viruses in oral (10/72) and plasma (09/78) samples. Finally, we observed a high frequency of genes associated with resistance and virulence: 10% of samples expressed at least one AMR gene (ARG), and 24% expressed virulence factor genes. Resistance to widely used beta-lactam antibiotics was the most prevalent. Our findings provide critical data on oral and plasma microbiomes in the context of acute febrile illness in Senegal while expanding understanding of circulating ARGs.

Oral microbiome diversity reduced in febrile individuals with high fever in SenegalFever and oral bacteria changes seen in Senegal study

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Oral microbiome diversity reduced in febrile individuals with high fever in SenegalFever and oral bacteria changes seen in Senegal study

Study Details

Intrawound tobramycin plus vancomycin did not reduce deep infection risk compared with vancomycin alone in high-risk tibial fractures

Adding Antibiotics to Bone Surgery Didn't Lower Infection Risk

Clinical research that matters. Delivered to your inbox.

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