Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Xiaole Yin - , The University of Hong Kong (Author)
  • Xi Chen - , The University of Hong Kong (Author)
  • Xiao Tao Jiang - , University of New South Wales (Author)
  • Ying Yang - , Sun Yat-Sen University (Author)
  • Bing Li - , Tsinghua University (Author)
  • Marcus Ho Hin Shum - , The University of Hong Kong (Author)
  • Tommy T.Y. Lam - , The University of Hong Kong (Author)
  • Gabriel M. Leung - , The University of Hong Kong (Author)
  • Joan Rose - , Michigan State University (Author)
  • Concepcion Sanchez-Cid - , Universite Claude Bernard Lyon 1 (Author)
  • Timothy M. Vogel - , Universite Claude Bernard Lyon 1 (Author)
  • Fiona Walsh - , National University of Ireland Maynooth (Author)
  • Thomas U. Berendonk - , Chair of Limnology (Author)
  • Janet Midega - , Wellcome Trust (Author)
  • Chibuzor Uchea - , Wellcome Trust (Author)
  • Dominic Frigon - , McGill University (Author)
  • Gerard D. Wright - , McMaster University (Author)
  • Carlos Bezuidenhout - , North West University (Author)
  • Renata C. Picão - , Universidade Federal do Rio de Janeiro (Author)
  • Shaikh Z. Ahammad - , Indian Institute of Technology Delhi (IITD) (Author)
  • Per Halkjær Nielsen - , Aalborg University (Author)
  • Philip Hugenholtz - , University of Queensland (Author)
  • Nicholas J. Ashbolt - , Southern Cross University (Author)
  • Gianluca Corno - , National Research Council of Italy (CNR) (Author)
  • Despo Fatta-Kassinos - , University of Cyprus (Author)
  • Helmut Bürgmann - , Swiss Federal Institute of Aquatic Science and Technology (Author)
  • Heike Schmitt - , National Institute of Public Health and the Environment, Delft University of Technology (Author)
  • Chang Jun Cha - , Chung-Ang University (Author)
  • Amy Pruden - , Virginia Polytechnic Institute and State University (Author)
  • Kornelia Smalla - , Julius Kühn Institute - Federal Research Centre for Cultivated Plants (Author)
  • Eddie Cytryn - , Agricultural Research Organization of Israel (Author)
  • Yu Zhang - , CAS - Research Center for Eco-Environmental Sciences (Author)
  • Min Yang - , CAS - Research Center for Eco-Environmental Sciences (Author)
  • Yong Guan Zhu - , CAS - Chinese Academy of Sciences (Author)
  • Arnaud Dechesne - , Technical University of Denmark (Author)
  • Barth F. Smets - , Technical University of Denmark (Author)
  • David W. Graham - , Newcastle University (Author)
  • Michael R. Gillings - , Macquarie University (Author)
  • William H. Gaze - , University of Exeter (Author)
  • Célia M. Manaia - , Catholic University of Portugal (Author)
  • Mark C.M. Van Loosdrecht - , Delft University of Technology (Author)
  • Pedro J.J. Alvarez - , Rice University (Author)
  • Martin J. Blaser - , Rutgers - The State University of New Jersey, New Brunswick (Author)
  • James M. Tiedje - , Michigan State University (Author)
  • Edward Topp - , Agriculture and Agri-Food Canada (Author)
  • Tong Zhang - , The University of Hong Kong (Author)

Abstract

Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health"framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.

Details

Original languageEnglish
Pages (from-to)9713–9721
Number of pages9
JournalEnvironmental Science and Technology
Volume57
Issue number26
Early online date13 Jun 2023
Publication statusPublished - 4 Jul 2023
Peer-reviewedYes

External IDs

PubMed 37310875
WOS 001008704300001
ORCID /0000-0002-9301-1803/work/161409833

Keywords

Sustainable Development Goals

Keywords

  • ARG copy per cell, long-read sequencing, metagenomics, one-health, standardization, Metagenomics, One-health, Standardization, Long-read sequencing, Genes, Bacterial, Humans, RNA, Ribosomal, 16S/genetics, Anti-Bacterial Agents/pharmacology, Metagenomics/methods, Animals, Drug Resistance, Microbial/genetics