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

被引：76

作者：

Yin, Xiaole ^{[1
]}

Chen, Xi ^{[1
]}

Jiang, Xiao-Tao ^{[2
]}

Yang, Ying ^{[3
]}

Li, Bing ^{[4
]}

Shum, Marcus Ho-Hin ^{[5
]}

Lam, Tommy T. Y. ^{[5
]}

Leung, Gabriel M. ^{[6
]}

Rose, Joan ^{[7
]}

Sanchez-Cid, Concepcion ^{[8
]}

Vogel, Timothy M. ^{[8
]}

Walsh, Fiona ^{[9
]}

Berendonk, Thomas U. ^{[10
]}

Midega, Janet ^{[11
]}

Uchea, Chibuzor ^{[11
]}

Frigon, Dominic ^{[12
]}

Wright, Gerard D. ^{[13
]}

Bezuidenhout, Carlos ^{[14
]}

Picao, Renata C. ^{[15
]}

Ahammad, Shaikh Z. ^{[16
]}

Nielsen, Per Halkjaer ^{[17
]}

Hugenholtz, Philip ^{[18
]}

Ashbolt, Nicholas J. ^{[19
]}

Corno, Gianluca ^{[20
]}

Fatta-Kassinos, Despo ^{[21
,22
]}

Buergmann, Helmut ^{[23
]}

Schmitt, Heike ^{[24
,25
]}

Cha, Chang-Jun ^{[26
,27
]}

Pruden, Amy ^{[28
]}

Smalla, Kornelia ^{[29
]}

Cytryn, Eddie ^{[30
]}

Zhang, Yu ^{[31
]}

Yang, Min ^{[31
]}

Zhu, Yong-Guan ^{[32
]}

Dechesne, Arnaud ^{[33
]}

Smets, Barth F. ^{[33
]}

Graham, David W. ^{[34
]}

Gillings, Michael R. ^{[35
,36
]}

Gaze, William H. ^{[37
]}

Manaia, Celia M. ^{[38
]}

van Loosdrecht, Mark C. M. ^{[39
]}

Alvarez, Pedro J. J. ^{[40
]}

Blaser, Martin J. ^{[41
]}

Tiedje, James M. ^{[42
]}

Topp, Edward ^{[43
]}

Zhang, Tong ^{[1
]}

机构：

[1] Univ Hong Kong, Ctr Environm Engn Res, Dept Civil Engn, Environm Microbiome Engn & Biotechnol Lab,Pokfula, Hong Kong 99077, Peoples R China

[2] Univ New South Wales, Microbiome Res Ctr, St George & Sutherland Clin Sch, Sydney 2052, Australia

[3] Sun Yat Sen Univ, Sch Marine Sci, Zhuhai 519082, Peoples R China

[4] Tsinghua Univ, Tsinghua Shenzhen Int Grad Sch, State Environm Protect Key Lab Microorganism Appl, Shenzhen, Peoples R China

[5] Univ Hong Kong, Sch Publ Hlth, State Key Lab Emerging Infect Dis, Pokfulam, Hong Kong 999077, Peoples R China

[6] Lab Data Discovery Hlth, Hong Kong Sci & Technol Pk, Hong Kong, Peoples R China

[7] Michigan State Univ, Dept Fisheries & Wildlife, E Lansing, MI 48824 USA

[8] Univ Lyon, Univ Claude Bernard Lyon 1, CNRS UMR 5005 Lab Ampere, Ecole Cent Lyon,Environm Microbial Genom, F-69130 Ecully, France

[9] Maynooth Univ, Dept Biol, Maynooth R51, Kildare, Ireland

[10] Tech Univ Dresden, Inst Hydrobiol, Fac Environm Sci, D-01217 Dresden, Germany

[11] Wellcome Trust Res Labs, London NW1 2BE, England

[12] McGill Univ, Dept Civil Engn & Appl Mech, 817 Sherbrooke St West, Montreal, PQ H3A 0C3, Canada

[13] McMaster Univ, Michael G DeGroote Inst Infect Dis Res, Hamilton, ON L8N 3Z5, Canada

[14] North West Univ, Unit Environm Sci & Management UESM Microbiol, ZA-2531 Potchefstroom, South Africa

[15] Univ Fed Rio de Janeiro, Med Microbiol Dept, Paulo de Goes Microbiol Inst, BR-21941902 Rio De Janeiro, Brazil

[16] Indian Inst Technol Delhi, Dept Biochem Engn & Biotechnol, New Delhi 110016, India

[17] Aalborg Univ, Ctr Microbial Communities, Dept Chem & Biosci, DK-9210 Aalborg, Denmark

[18] Univ Queensland, Australian Ctr Ecogen, Sch Chem & Mol Biosci, Brisbane, Qld 4072, Australia

[19] Southern Cross Univ, Fac Sci & Engn, Bilinga, Qld 4225, Australia

[20] Natl Res Council Italy CNR IRSA, Water Res Inst, Mol Ecol Grp MEG, I-28922 Verbania, Italy

[21] Univ Cyprus, Dept Civil & Environm Engn, CY-1678 Nicosia, Cyprus

[22] Univ Cyprus, Nireas Int Water Res Ctr, CY-1678 Nicosia, Cyprus

[23] Eawag Swiss Fed Inst Aquat Sci & Technol, CH-6047 Kastanienbaum, Switzerland

[24] Natl Inst Publ Hlth & Environm RIVM, Ctr Zoonoses & Environm Microbiol, Ctr Infect Dis Control, NL-3721 Bilthoven, Netherlands

[25] Delft Univ Technol, Dept Biotechnol, NL-2628 Delft, Netherlands

[26] Chung Ang Univ, Dept Syst Biotechnol, Anseong 17546, South Korea

[27] Chung Ang Univ, Ctr Antibiot Resistome, Anseong 17546, South Korea

[28] Virginia Tech, Charles Edward Via Jr Dept Civil & Environm Engn, Blacksburg, VA 24060 USA

[29] Fed Res Ctr Cultivated Plants, Inst Epidemiol & Pathogen Diagnost, Julius Kuhn Inst JKI, D-38104 Braunschweig, Germany

[30] Agr Res Org, Inst Soil Water & Environm Sci, Volcani Inst, Dept Soil Chem Plant Nutr & Microbiol, IL-7528809 Rishon Leziyyon, Israel

[31] Chinese Acad Sci, Res Ctr Ecoenvironm Sci, State Key Lab Environm Aquat Chem, Beijing 100085, Peoples R China

[32] Chinese Acad Sci, Inst Urban Environm, Key Lab Urban Environm & Hlth, Xiamen 361021, Peoples R China

[33] Tech Univ Denmark, Dept Environm & Resource Engn, DK-2800 Lyngby, Denmark

[34] Newcastle Univ, Sch Engn, Newcastle Upon Tyne NE1 7RU, England

[35] Macquarie Univ, Sch Nat Sci, Sydney, NSW 2109, Australia

[36] Macquarie Univ, ARC Ctr Excellence Synthet Biol, Sydney, NSW 2109, Australia

[37] Univ Exeter, Univ Exeter Med Sch, Environm & Sustainabil Inst, Exeter TR10 9FE, Cornwall, England

[38] Univ Catolica Portuguesa, CBQF Ctr Biotecnol & Quim Fina Lab Associado, Escola Super Biotecnol, P-4169005 Porto, Portugal

[39] Delft Univ Technol, Dept Biotechnol, NL-2629 HZ Delft, Netherlands

[40] Rice Univ, Dept Civil & Environm Engn, Houston, TX 77005 USA

[41] Rutgers State Univ, Ctr Adv Biotechnol & Med, Piscataway, NJ 08854 USA

[42] Michigan State Univ, Dept Plant Soil & Microbial Sci, E Lansing, MI 48824 USA

[43] Agr & Agri Food Canada, London Res & Dev Ctr LRDC, London, ON N5V 4T3, Canada

来源：

ENVIRONMENTAL SCIENCE & TECHNOLOGY | 2023年 / 57卷 / 26期

基金：

英国工程与自然科学研究理事会;

关键词：

one-health; metagenomics; long-read sequencing; ARG copy per cell; standardization; RESISTOME;

D O I：

10.1021/acs.est.3c00159

中图分类号：

X [环境科学、安全科学];

学科分类号：

08 ; 0830 ;

摘要：

Surveillance of antibiotic resistance genes (ARGs) hasbeen increasinglyconducted in environmental sectors to complement the surveys in humanand animal sectors under the "One-Health" framework.However, there are substantial challenges in comparing and synthesizingthe results of multiple studies that employ different test methodsand approaches in bioinformatic analysis. In this article, we considerthe commonly used quantification units (ARG copy per cell, ARG copyper genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage,PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copyper cell) for reporting such biological measurements of samples andimproving the comparability of different surveillance efforts. By comparing commonly used quantificationunits for environmentalARG surveillance, this study suggests a universal unit as a step towardstandardization.

引用

页码：9713 / 9721

页数：9

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