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

• DOI: 10.1021/acs.est.3c00159
• Publication Date: 2023-06-13T16:56:20Z
• Authors: Xiaole Yin; Xi Chen; Xiao-Tao Jiang; Ying Yang; Bing Li; Marcus Ho-Hin Shum; Tommy T. Y. Lam; Gabriel M. Leung; Joan Rose; Concepcion Sanche...; Timothy M. Vogel; Fiona Walsh; Thomas U. Berendonk; Janet Midega; Chibuzor Uchea; Dominic Frigon; Gerard D. Wright; Carlos Bezuidenhout; Renata C. Picão; Shaikh Z. Ahammad; Per Halkjær Nielsen; Philip Hugenholtz; Nicholas J. Ashbolt; Gianluca Corno; Despo Fatta-Kassinos; Helmut Bürgmann; Heike Schmitt; Chang-Jun Cha; Amy Pruden; Kornelia Smalla; Eddie Cytryn; Yu Zhang; Min Yang; Yong-Guan Zhu; Arnaud Dechesne; Barth F. Smets; David W. Graham; Michael R. Gillings; William H. Gaze; Célia M. Manaia; Mark C. M. van Lo...; Pedro J. J. Alvarez; Martin J. Blaser; James M. Tiedje; Edward Topp; Tong Zhang
• Keywords: standardization; 020; 570; metagenomics; ARG copy per cell; Drug Resistance, Microbial; Standardization; Anti-Bacterial Agents; one-health; Genes, Bacterial; RNA, Ribosomal, 16S; [SDE]Environmental Sciences; long-read sequencing; Animals; Humans; Metagenomics; Long-read sequencing; One-health

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.