Abstract
The global threat of antimicrobial resistance has driven the use of high-throughput sequencing techniques to monitor the profile of resistance genes, known as the resistome, in microbial populations. The human oral cavity contains a poorly explored reservoir of these genes. Here we analyse and compare the resistome profiles of 788 oral cavities worldwide with paired stool metagenomes. We find country and body site-specific differences in the prevalence of antimicrobial resistance genes, classes and mechanisms in oral and stool samples. Within individuals, the highest abundances of antimicrobial resistance genes are found in the oral cavity, but the oral cavity contains a lower diversity of resistance genes compared to the gut. Additionally, co-occurrence analysis shows contrasting ARG-species associations between saliva and stool samples. Maintenance and persistence of antimicrobial resistance is likely to vary across different body sites. Thus, we highlight the importance of characterising the resistome across body sites to uncover the antimicrobial resistance potential in the human body.
Highlights
The global threat of antimicrobial resistance has driven the use of high-throughput sequencing techniques to monitor the profile of resistance genes, known as the resistome, in microbial populations
The erythromycin resistance mefA and mefE genes have been found on the MEGA mobile genetic element associated with Tn916-like conjugative transposons, and this has been implicated in conjugative transfer between viridans group streptococci (VGS) and other streptococci[21]
To establish the incidence of antimicrobial resistance genes (ARGs) in oral as well as stool metagenomes collected from various regions, metagenomes were mapped and quantified against the Comprehensive Antibiotic Resistance Database (CARD)[29]
Summary
The global threat of antimicrobial resistance has driven the use of high-throughput sequencing techniques to monitor the profile of resistance genes, known as the resistome, in microbial populations. We made up to 415 comparisons of oral resistomes with paired gut resistomes derived from stool shotgun metagenomes from the same individuals, showing the oral resistome contains the highest and lowest abundances of ARGs, but a lower diversity of ARGs than the gut resistome. Overall, these results demonstrate the requirement for wider AMR surveillance studies at different body sites, including the oral cavity, to understand the composition of the resistome across different human microbial habitats
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