A novel, magnetic bead-based extraction method for the isolation of antimicrobial resistance genes with a case study in river water in Malawi
File(s)
Published version
Author(s)
Type
Journal Article
Abstract
Aims
The environment is increasingly recognized as an important reservoir of antimicrobial resistance genes (ARGs), which can be identified using molecular platforms. Yet, environmental surveillance remains an underutilised tool as there is no agreement on the best strategy for sample processing. We aim to develop a low‐cost extraction method independent to commercial kits or reagents.
Methods and Results
We present a novel, magnetic bead‐based method for the isolation of ARGs from river water named MagnaExtract. We present this with analytic limit of detection as well as a case study in Southern Malawi. Here we compare the DNA yield from MagnaExtract with commercially available QIAGEN kits and the crude boil and spin method, using a high‐resolution melt analysis PCR panel designed for the detection of third‐generation cephalosporin and carbapenem‐resistant genes from 98 water samples.
Conclusion
The MagnaExtract method is comparable, and in some instance's superior to commercially available kits for the isolation of ARGs from river water samples.
Significance and Impact of the Study
The MagnaExtract approach offers a simple, affordable, high yielding extraction method that could be used for the detection of ARGs from river water samples in surveillance campaigns in East Africa.
The environment is increasingly recognized as an important reservoir of antimicrobial resistance genes (ARGs), which can be identified using molecular platforms. Yet, environmental surveillance remains an underutilised tool as there is no agreement on the best strategy for sample processing. We aim to develop a low‐cost extraction method independent to commercial kits or reagents.
Methods and Results
We present a novel, magnetic bead‐based method for the isolation of ARGs from river water named MagnaExtract. We present this with analytic limit of detection as well as a case study in Southern Malawi. Here we compare the DNA yield from MagnaExtract with commercially available QIAGEN kits and the crude boil and spin method, using a high‐resolution melt analysis PCR panel designed for the detection of third‐generation cephalosporin and carbapenem‐resistant genes from 98 water samples.
Conclusion
The MagnaExtract method is comparable, and in some instance's superior to commercially available kits for the isolation of ARGs from river water samples.
Significance and Impact of the Study
The MagnaExtract approach offers a simple, affordable, high yielding extraction method that could be used for the detection of ARGs from river water samples in surveillance campaigns in East Africa.
Date Issued
2022-11-01
Date Acceptance
2022-07-31
Citation
Journal of Applied Microbiology, 2022, 133 (5), pp.3191-3200
ISSN
1364-5072
Publisher
Oxford University Press (OUP)
Start Page
3191
End Page
3200
Journal / Book Title
Journal of Applied Microbiology
Volume
133
Issue
5
Copyright Statement
© 2022 The Society for Applied Microbiology This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by/4.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/35946113
Subjects
AMR
ARG
environmental surveillance
qPCR
river water
Anti-Bacterial Agents
Rivers
Genes, Bacterial
Drug Resistance, Bacterial
Malawi
Carbapenems
Cephalosporins
Magnetic Phenomena
Water
Publication Status
Published
Coverage Spatial
England
Date Publish Online
2022-11-01