HKU Engineering team develops a useful framework to identify high-risk antibiotic resistance genes

A research team led by Professor Tong Zhang at the University of Hong Kong’s Department of Civil Engineering, has developed a useful framework to evaluate the risks of antibiotic resistance genes (ARGs), which have been declared a global public health threat by the World Health Organization.

ARGs are the genetic basis for antibiotic resistance. Fulfilling a long-term goal of identifying high-risk ARGs among the many thousands of presumptive ARGs, the newly-developed assessment framework evaluates the risks based on three factors, namely enrichment in human-associated environments, gene mobility, and host pathogenicity.

The framework results in a sensible risk hierarchy: ARGs that are not human-associated (Rank IV), ie. the least likely to endanger human health; human-associated but non-mobile ARGs (Rank III), ie. less likely to contribute to an emergence of new resistance in pathogens; mobile ARGs that pose the risk of contributing to new resistance in pathogens in the future (Rank II), and ARGs already present in pathogens (Rank I).

The framework marks a critical step in providing guidance to decision-making on how to tackle environmental ARGs. It offers an easy-to-implement evaluation in different scenarios, including environmental risk assessment, improvement of fecal microbiota transplant, etc., and provides a helpful approach for identifying current and future antibiotic resistance threats. The ground-breaking achievement has been published in the leading multidisciplinary science journal Nature Communications.

Professor Zhang said: “As we move into an era of heightened molecular surveillance, it is important to interpret the risk of ARGs in environments rather than simply document their presence and concentration. This study provides an easy-to-implement framework and a bioinformatic method to assess ARGs in genomes and metagenomes, and offers insights for future studies.”

This work is part of Professor Zhang’s project supported by the University Grants Committee’s Theme-based Research Scheme (TRS) aimed at supporting academic research efforts of UGC-funded universities on themes of strategic importance.

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About the research team
The first author, Dr Anni Zhang, is a former PhD student of Professor Zhang and now a Postdoctoral Fellow at MIT. Other scientists contributing to the research include a PhD student Miss Xiaole Yin and a postdoc Dr. Liguan Li in Professor Zhang’s research group, Professor James M Tiedje (Michigan State University), Dr. Edward Topp (Principal Research Scientist, Agriculture and Agri-Food Canada), Professor Eric Alm (MIT), Professor William Hanage (Harvard University), Professor Michael Gillings (Macquarie University), Professor Mark Loosdrecht (Delft University), etc.

About Professor Tong Zhang
Professor Tong Zhang led the Environmental Microbiome Engineering and Biotechnology Laboratory at HKU’s Department of Civil Engineering. His research focuses on “environmental microbiome”. He did frontier work on the emerging topic of “Environmental Dimension of Antibiotics Resistance” in the microbiome field. More information about Professor Tong Zhang and his research team can be found here: https://smile.hku.hk/

The research paper “An omics-based framework for assessing the health risk of antimicrobial resistance genes” published in Nature Communications: https://doi.org/10.1038/s41467-021-25096-3