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; Heike Schmitt; Chang Jun Cha; Mark C.M. Van Loosdrecht; More Authors

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
, Heike Schmitt
, Chang Jun Cha
, Mark C.M. Van Loosdrecht
, More Authors

BT/Environmental Biotechnology

Research output: Contribution to journal › Article › Scientific › peer-review

153 Citations (Scopus)

140 Downloads (Pure)

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

Bibliographical note

Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.

UN SDGs

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

SDG 3 Good Health and Well-being

Keywords

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

Access to Document

10.1021/acs.est.3c00159

acs.est.3c00159Final published version, 1.89 MB

Cite this

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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 = "ARG copy per cell, long-read sequencing, metagenomics, one-health, standardization",

author = "Xiaole Yin and Xi Chen and Jiang, \{Xiao Tao\} and Ying Yang and Bing Li and Shum, \{Marcus Ho Hin\} and Heike Schmitt and Cha, \{Chang Jun\} and \{Van Loosdrecht\}, \{Mark C.M.\} and \{More Authors\}",

note = "Green Open Access added to TU Delft Institutional Repository {\textquoteleft}You share, we take care!{\textquoteright} – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.",

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 (ACS)",

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}

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 - Schmitt, Heike

AU - Cha, Chang Jun

AU - Van Loosdrecht, Mark C.M.

AU - More Authors, null

N1 - Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.

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 - ARG copy per cell

KW - long-read sequencing

KW - metagenomics

KW - one-health

KW - standardization

UR - https://www.scopus.com/pages/publications/85163874675

U2 - 10.1021/acs.est.3c00159

DO - 10.1021/acs.est.3c00159

M3 - Article

C2 - 37310875

AN - SCOPUS:85163874675

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

Bibliographical note

UN SDGs

Keywords

Access to Document

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