TY - JOUR

T1 - Active antibiotic resistome in soils unraveled by single-cell isotope probing and targeted metagenomics

AU - Li, Hong Zhe

AU - Yang, Kai

AU - Liao, Hu

AU - Lassen, Simon Bo

AU - Su, Jian Qiang

AU - Zhang, Xian

AU - Cui, Li

AU - Zhu, Yong Guan

N1 - Publisher Copyright: Copyright © 2022 the Author(s). Published by PNAS.

PY - 2022

Y1 - 2022

N2 - Antimicrobial resistance (AMR) in soils represents a serious risk to human health through the food chain and human–nature contact. However, the active antibiotic-resistant bacteria (ARB) residing in soils that primarily drive AMR dissemination are poorly explored. Here, single-cell Raman-D2O coupled with targeted metagenomics is developed as a culture-independent approach to phenotypically and genotypically profiling active ARB against clinical antibiotics in a wide range of soils. This method quantifies the prevalence (contamination degree) and activity (spread potential) of soil ARB and reveals a clear elevation with increasing anthropogenic activities such as farming and the creation of pollution, thereby constituting a factor that is critical for the assessment of AMR risks. Further targeted sorting and metagenomic sequencing of the most active soil ARB uncover several uncultured genera and a pathogenic strain. Furthermore, the underlying resistance genes, virulence factor genes, and associated mobile genetic elements (including plasmids, insertion sequences, and prophages) are fully deciphered at the single-cell level. This study advances our understanding of the soil active AMR repertoire by linking the resistant phenome to the genome. It will aid in the risk assessment of environmental AMR and guide the combat under the One Health framework.

AB - Antimicrobial resistance (AMR) in soils represents a serious risk to human health through the food chain and human–nature contact. However, the active antibiotic-resistant bacteria (ARB) residing in soils that primarily drive AMR dissemination are poorly explored. Here, single-cell Raman-D2O coupled with targeted metagenomics is developed as a culture-independent approach to phenotypically and genotypically profiling active ARB against clinical antibiotics in a wide range of soils. This method quantifies the prevalence (contamination degree) and activity (spread potential) of soil ARB and reveals a clear elevation with increasing anthropogenic activities such as farming and the creation of pollution, thereby constituting a factor that is critical for the assessment of AMR risks. Further targeted sorting and metagenomic sequencing of the most active soil ARB uncover several uncultured genera and a pathogenic strain. Furthermore, the underlying resistance genes, virulence factor genes, and associated mobile genetic elements (including plasmids, insertion sequences, and prophages) are fully deciphered at the single-cell level. This study advances our understanding of the soil active AMR repertoire by linking the resistant phenome to the genome. It will aid in the risk assessment of environmental AMR and guide the combat under the One Health framework.

KW - antimicrobial resistance

KW - risk assessment

KW - single-cell Raman

KW - targeted metagenomics

U2 - 10.1073/pnas.2201473119

DO - 10.1073/pnas.2201473119

M3 - Journal article

C2 - 36161886

AN - SCOPUS:85138607891

VL - 119

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 40

M1 - e2201473119

ER -