An omics-based framework for assessing the health risk of antimicrobial resistance genes

An-Ni Zhang, Jeffry M. Gaston, Chengzhen L. Dai, Shijie Zhao, Mathilde Poyet, Mathieu Groussin, Xiaole Yin, Li-Guan Li, Mark C. M. Loosdrecht, Edward Topp, Michael R. Gillings, William P. Hanage, James M. Tiedje, Katya Moniz, Eric J. Alm and Tong Zhang ()
Additional contact information
An-Ni Zhang: The University of Hong Kong
Jeffry M. Gaston: Google
Chengzhen L. Dai: Massachusetts Institute of Technology
Shijie Zhao: Massachusetts Institute of Technology
Mathilde Poyet: Massachusetts Institute of Technology
Mathieu Groussin: Massachusetts Institute of Technology
Xiaole Yin: The University of Hong Kong
Li-Guan Li: The University of Hong Kong
Mark C. M. Loosdrecht: Delft University of Technology
Edward Topp: Agriculture and Agri-Food Canada
Michael R. Gillings: Macquarie University
William P. Hanage: Harvard TH Chan School of Public Health
James M. Tiedje: Michigan State University
Katya Moniz: Massachusetts Institute of Technology
Eric J. Alm: Massachusetts Institute of Technology
Tong Zhang: The University of Hong Kong

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: 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.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25096-3

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DOI: 10.1038/s41467-021-25096-3

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