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

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 Sanchez-Cid; 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 Loosdrecht; Pedro J. J. Alvarez; Martin J. Blaser; James M. Tiedje; Edward Topp; Tong Zhang

doi:10.1021/acs.est.3c00159

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

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 Sanchez-Cid
, 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 Loosdrecht, Pedro J. J. Alvarez, Martin J. Blaser, James M. Tiedje, Edward Topp, Tong Zhang^*

^*Corresponding author for this work

The University of Hong Kong
University of New South Wales
Sun Yat-Sen University
Tsinghua University
Hong Kong Science & Technology Parks
Michigan State University
Université de Lyon
Maynooth University
Technische Universität Dresden
Wellcome Trust
McGill University
McMaster University
North West University
Universidade Federal do Rio de Janeiro
Indian Institute of Technology Delhi
Aalborg University
University of Queensland
Southern Cross University
National Research Council of Italy
University of Cyprus
Swiss Federal Institute of Aquatic Science and Technology
Delft University of Technology
Chung-Ang University
Virginia Polytechnic Institute and State University
Julius Kühn Institute - Federal Research Centre for Cultivated Plants
Agricultural Research Organization of Israel
Chinese Academy of Sciences
Newcastle University
Macquarie University
University of Exeter
Catholic University of Portugal
Rice University
Rutgers University
Agriculture and Agri-Food Canada

Research output: Contribution to journal › Journal article › Research › peer-review

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.

Original language	English
Journal	Environmental Science and Technology
Volume	57
Issue number	26
Pages (from-to)	9713-9721
Number of pages	9
ISSN	0013-936X
DOIs	https://doi.org/10.1021/acs.est.3c00159
Publication status	Published - 2023

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

One-health
Metagenomics
Long-read sequencing
ARG copy per cell
Standardization

Access to Document

10.1021/acs.est.3c00159

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Yin, X., Chen, X., Jiang, X.-T., Yang, Y., Li, B., Shum, M. H.-H., Lam, T. T. Y., Leung, G. M., Rose, J., Sanchez-Cid, C., Vogel, T. M., Walsh, F., Berendonk, T. U., Midega, J., Uchea, C., Frigon, D., Wright, G. D., Bezuidenhout, C., Picão, R. C., ... Zhang, T. (2023). Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples. Environmental Science and Technology, 57(26), 9713-9721. https://doi.org/10.1021/acs.est.3c00159

@article{9efa4446808e4620984b2f3faa439dbd,

title = "Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples",

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.",

keywords = "One-health, Metagenomics, Long-read sequencing, ARG copy per cell, Standardization",

author = "Xiaole Yin and Xi Chen and Xiao-Tao Jiang and Ying Yang and Bing Li and Shum, \{Marcus Ho-Hin\} and Lam, \{Tommy T. Y.\} and Leung, \{Gabriel M.\} and Joan Rose and Concepcion Sanchez-Cid and Vogel, \{Timothy M.\} and Fiona Walsh and Berendonk, \{Thomas U.\} and Janet Midega and Chibuzor Uchea and Dominic Frigon and Wright, \{Gerard D.\} and Carlos Bezuidenhout and Pic{\~a}o, \{Renata C.\} and Ahammad, \{Shaikh Z.\} and Nielsen, \{Per Halkj{\ae}r\} and Philip Hugenholtz and Ashbolt, \{Nicholas J.\} and Gianluca Corno and Despo Fatta-Kassinos and Helmut B{\"u}rgmann and Heike Schmitt and Chang-Jun Cha and Amy Pruden and Kornelia Smalla and Eddie Cytryn and Yu Zhang and Min Yang and Yong-Guan Zhu and Arnaud Dechesne and Smets, \{Barth F.\} and Graham, \{David W.\} and Gillings, \{Michael R.\} and Gaze, \{William H.\} and Manaia, \{C{\'e}lia M.\} and \{van Loosdrecht\}, \{Mark C. M.\} and Alvarez, \{Pedro J. J.\} and Blaser, \{Martin J.\} and Tiedje, \{James M.\} and Edward Topp and Tong Zhang",

year = "2023",

doi = "10.1021/acs.est.3c00159",

language = "English",

volume = "57",

pages = "9713--9721",

journal = "Environmental Science and Technology",

issn = "0013-936X",

publisher = "American Chemical Society",

number = "26",

}

Yin, X, Chen, X, Jiang, X-T, Yang, Y, Li, B, Shum, MH-H, Lam, TTY, Leung, GM, Rose, J, Sanchez-Cid, C, Vogel, TM, Walsh, F, Berendonk, TU, Midega, J, Uchea, C, Frigon, D, Wright, GD, Bezuidenhout, C, Picão, RC, Ahammad, SZ, Nielsen, PH, Hugenholtz, P, Ashbolt, NJ, Corno, G, Fatta-Kassinos, D, Bürgmann, H, Schmitt, H, Cha, C-J, Pruden, A, Smalla, K, Cytryn, E, Zhang, Y, Yang, M, Zhu, Y-G, Dechesne, A, Smets, BF, Graham, DW, Gillings, MR, Gaze, WH, Manaia, CM, van Loosdrecht, MCM, Alvarez, PJJ, Blaser, MJ, Tiedje, JM, Topp, E & Zhang, T 2023, 'Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples', Environmental Science and Technology, vol. 57, no. 26, pp. 9713-9721. https://doi.org/10.1021/acs.est.3c00159

TY - JOUR

T1 - Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples

AU - Yin, Xiaole

AU - Chen, Xi

AU - Jiang, Xiao-Tao

AU - Yang, Ying

AU - Li, Bing

AU - Shum, Marcus Ho-Hin

AU - Lam, Tommy T. Y.

AU - Leung, Gabriel M.

AU - Rose, Joan

AU - Sanchez-Cid, Concepcion

AU - Vogel, Timothy M.

AU - Walsh, Fiona

AU - Berendonk, Thomas U.

AU - Midega, Janet

AU - Uchea, Chibuzor

AU - Frigon, Dominic

AU - Wright, Gerard D.

AU - Bezuidenhout, Carlos

AU - Picão, Renata C.

AU - Ahammad, Shaikh Z.

AU - Nielsen, Per Halkjær

AU - Hugenholtz, Philip

AU - Ashbolt, Nicholas J.

AU - Corno, Gianluca

AU - Fatta-Kassinos, Despo

AU - Bürgmann, Helmut

AU - Schmitt, Heike

AU - Cha, Chang-Jun

AU - Pruden, Amy

AU - Smalla, Kornelia

AU - Cytryn, Eddie

AU - Zhang, Yu

AU - Yang, Min

AU - Zhu, Yong-Guan

AU - Dechesne, Arnaud

AU - Smets, Barth F.

AU - Graham, David W.

AU - Gillings, Michael R.

AU - Gaze, William H.

AU - Manaia, Célia M.

AU - van Loosdrecht, Mark C. M.

AU - Alvarez, Pedro J. J.

AU - Blaser, Martin J.

AU - Tiedje, James M.

AU - Topp, Edward

AU - Zhang, Tong

PY - 2023

Y1 - 2023

N2 - 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.

AB - 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.

KW - One-health

KW - Metagenomics

KW - Long-read sequencing

KW - ARG copy per cell

KW - Standardization

U2 - 10.1021/acs.est.3c00159

DO - 10.1021/acs.est.3c00159

M3 - Journal article

C2 - 37310875

SN - 0013-936X

VL - 57

SP - 9713

EP - 9721

JO - Environmental Science and Technology

JF - Environmental Science and Technology

IS - 26

ER -

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

Abstract

UN SDGs

Keywords

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