# Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics

## TL;DR

Swiss expatriates in Africa showed similar gut microbes but more antibiotic resistance genes compared to those in Europe, suggesting environmental influence.

## Contribution

This study uses Nanopore metagenomics to compare gut microbiota and resistomes of expatriates in Africa and Europe.

## Key findings

- Microbiota composition was similar between African and European expatriates.
- Higher prevalence of tetracycline and folate pathway antagonist ARGs was found in African residents.
- Plasmid-borne ARGs in Gram-negative and -positive bacteria suggest potential for resistance gene spread.

## Abstract

The gut microbiota and resistome may change upon exposure to environments with high prevalence of multidrug-resistant pathogens, potentially impacting health and contributing to the spread of antimicrobial resistance genes (ARGs). In this context, expatriates may acquire endemic microbial communities and ARGs while living abroad. In this work, we investigated the microbiota and resistome of Swiss expatriates living in African countries using Nanopore shotgun metagenomics (SMS).

Stool samples from expatriates residing in African and European countries (n = 33 and n = 39, respectively) were sequenced using Nanopore V14 chemistry. Taxonomic and resistome profiling was performed with Kraken2 and ResFinder, respectively. Diversity metrics (e.g., Shannon, Simpson) assessed microbial composition. ARG and bacteria associations were determined using GTDB-Tk on metagenome-assembled genomes (MAGs). Plasmid-borne ARGs were characterized with PlasmidFinder.

Our results indicated that microbiota composition did not differ between expatriates in African and European countries. However, resistome analysis revealed a higher prevalence of tetracycline (tet) and folate pathway antagonist (dfr, sul) ARGs in those residing in Africa, suggesting adaptation to the local microbial environment or antibiotic policy. Unique plasmid families were also identified in Gram-negative (IncF) and -positive (repUS43) bacteria across African and European cohorts, indicating the potential for ARG dissemination via mobile genetic elements. Overall, Nanopore-based SMS may provide an alternative approach to monitor microbiota and resistome dynamics, and thus assisting early epidemiological surveys.

The online version contains supplementary material available at 10.1038/s41598-026-38302-3.