Learning and forecasting shared evolutionary pathways to multi-drug resistance across global pathogens
Aga, O.; Moyo, S.; Ferno, J.; Manyahi, J.; Kibwana, U.; Löhr, I.; Langeland, N.; Blomberg, B.; Johnston, I.
Show abstract
Infections with bacteria which have evolved multi-drug resistance (MDR) cause millions of deaths worldwide. Large-scale efforts are gathering genotypic and phenotypic data on MDR bacteria, but methods for learning the structure, diversity, and predictors of evolutionary pathways to MDR have yet to take full advantage of these data. Here, we use evolutionary accumulation modelling (EvAM), an emerging class of machine learning methods with roots in cancer progression, to infer these evolutionary pathways across ESKAPEE pathogens (seven bacterial species that dominate health burdens), using a database of over 635k genotyped phenotypic observations from around the world. We identify global patterns in MDR evolutionary pathways, remarkably shared across multiple ESKAPEE species. Species-specific deviations from these stereotypical pathways are connected with geographical and demographic covariates, facilitating predictions of future MDR evolution. We verify these predictions with several hundred new phenotypes from ESKAPEE samples spanning decades of clinical infections in sub-Saharan Africa, demonstrating the capacity to forecast future MDR evolution from these inferred shared pathways.
Matching journals
The top 3 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Rapid evolution and biogeographic spread in a colorectal cancer 94%
- Convolutional neural networks quantify antibiotic resistance in Mycobacterium tuberculosis with diagnostic grade accuracy and predict treatment response 94%
- In Vitro and Viral Evolution Convergence Reveal the Selective Pressures Driving Omicron Emergence 94%
Similar papers in this journal
- GenomegaMap: within-species genome-wide dN/dS estimation from over 10,000 genomes 96%
- Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen 95%
- From root to tips: sporulation evolution and specialization in Bacillus subtilis and the intestinal pathogen Clostridioides difficile 94%
Similar papers in this journal
- The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria 96%
- Evolutionary stability of collateral sensitivity to antibiotics in the model pathogen Pseudomonas aeruginosa 95%
- Quantifying antibiotic impact on within-host dynamics of extended-spectrum beta-lactamase resistance in hospitalized patients 94%
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.