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- Title
An omics-based framework for assessing the health risk of antimicrobial resistance genes.
- Authors
Zhang, An-Ni; Gaston, Jeffry M.; Dai, Chengzhen L.; Zhao, Shijie; Poyet, Mathilde; Groussin, Mathieu; Yin, Xiaole; Li, Li-Guan; van Loosdrecht, Mark C. M.; Topp, Edward; Gillings, Michael R.; Hanage, William P.; Tiedje, James M.; Moniz, Katya; Alm, Eric J.; Zhang, Tong
- Abstract
Antibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that are high-risk. Here, we developed an 'omics-based' framework to evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our framework classifies human-associated, mobile ARGs (3.6% of all ARGs) as the highest risk, which we further differentiate as 'current threats' (Rank I; 3%) - already present among pathogens - and 'future threats' (Rank II; 0.6%) - novel resistance emerging from non-pathogens. Our framework identified 73 'current threat' ARG families. Of these, 35 were among the 37 high-risk ARGs proposed by the World Health Organization and other literature; the remaining 38 were significantly enriched in hospital plasmids. By evaluating all pathogen genomes released since framework construction, we confirmed that ARGs that recently transferred into pathogens were significantly enriched in Rank II ('future threats'). Lastly, we applied the framework to gut microbiome genomes from fecal microbiota transplantation donors. We found that although ARGs were widespread (73% of genomes), only 8.9% of genomes contained high-risk ARGs. Our framework provides an easy-to-implement approach to identify current and future antimicrobial resistance threats, with potential clinical applications including reducing risk of microbiome-based interventions. Antibiotic resistance genes are common but not all are of high risk to human health. Here, the authors develop an omics-based framework for ranking genes by risk that incorporates level of enrichment in human associated environments, gene mobility, and host pathogenicity.
- Subjects
WORLD Health Organization; GUT microbiome; FECAL microbiota transplantation; DRUG resistance in microorganisms; GENES; DRUG resistance in bacteria; HUMAN ecology
- Publication
Nature Communications, 2021, Vol 12, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-021-25096-3