Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes
Artikel i vetenskaplig tidskrift, 2025
The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aim to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. We used a phylogenetic method to identify instances of horizontal ARG transfer in similar to 1 million bacterial genomes. This data was then integrated with >20,000 metagenomes representing animal, human, soil, water, and wastewater microbiomes to develop random forest models that can reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increases the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns are observed. This study provides data-driven ways to predict the spread of ARGs and provides insights into the mechanisms governing this evolutionary process.
Författare
David Lund
Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik
Göteborgs universitet
Marcos Parras Moltó
Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik
Göteborgs universitet
Juan Salvador Inda Diaz
Göteborgs universitet
Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik
Stefan Ebmeyer
Göteborgs universitet
Chalmers, Life sciences, Systembiologi
D. G. Joakim Larsson
Göteborgs universitet
Anna Johnning
Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik
Göteborgs universitet
Stiftelsen Fraunhofer-Chalmers Centrum för Industrimatematik
Erik Kristiansson
Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik
Göteborgs universitet
Nature Communications
2041-1723 (ISSN) 20411723 (eISSN)
Vol. 16 1 2595Miljöns roll för utveckling och spridning av antibiotikaresistens
Vetenskapsrådet (VR) (2018-05771), 2019-01-01 -- 2024-12-31.
Nya resistensgener mot antibiotika och deras spridning i miljön
Vetenskapsrådet (VR) (2019-03482), 2020-01-01 -- 2023-12-31.
Ämneskategorier (SSIF 2025)
Bioinformatik (beräkningsbiologi)
Mikrobiologi
Evolutionsbiologi
DOI
10.1038/s41467-025-57825-3
PubMed
40090954
Relaterade dataset
Results from "Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes" by Lund et al. [dataset]
URI: https://doi.org/10.5281/zenodo.14901409