A novel, magnetic bead-based extraction method for the isolation of antimicrobial resistance genes with a case study in river water in Malawi

Rachel L Byrne; Derek Cocker; Ghaith Alyayyoussi; Madalitso Mphasa; Mary Charles; Tamandani Mandula; Christopher T Williams; Jonathan Rigby; Jack Hearn; Nicholas Feasey; Emily R Adams; Thomas Edwards

doi:10.1111/jam.15755

A novel, magnetic bead-based extraction method for the isolation of antimicrobial resistance genes with a case study in river water in Malawi

Rachel L Byrne, Derek Cocker, Ghaith Alyayyoussi, Madalitso Mphasa, Mary Charles, Tamandani Mandula, Christopher T Williams, Jonathan Rigby, Jack Hearn, Nicholas Feasey, Emily R Adams, Thomas Edwards

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

5 Citations (Scopus)

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.

Original language	English
Pages (from-to)	3191-3200
Number of pages	10
Journal	Journal of Applied Microbiology
Volume	133
Issue number	5
Early online date	1 Nov 2022
DOIs	https://doi.org/10.1111/jam.15755
Publication status	First published - 1 Nov 2022
Externally published	Yes

Bibliographical note

Keywords

Anti-Bacterial Agents/pharmacology
Rivers
Genes, Bacterial/genetics
Drug Resistance, Bacterial/genetics
Malawi
Carbapenems
Cephalosporins
Magnetic Phenomena
Water/analysis
environmental surveillance
AMR
ARG
river water
qPCR

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10.1111/jam.15755Licence: CC BY

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Byrne, R. L., Cocker, D., Alyayyoussi, G., Mphasa, M., Charles, M., Mandula, T., Williams, C. T., Rigby, J., Hearn, J., Feasey, N., Adams, E. R., & Edwards, T. (2022). A novel, magnetic bead-based extraction method for the isolation of antimicrobial resistance genes with a case study in river water in Malawi. Journal of Applied Microbiology, 133(5), 3191-3200. Advance online publication. https://doi.org/10.1111/jam.15755

@article{8bff52abe72c4b16af1f0e3ef50cbca0,

title = "A novel, magnetic bead-based extraction method for the isolation of antimicrobial resistance genes with a case study in river water in Malawi",

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.",

keywords = "Anti-Bacterial Agents/pharmacology, Rivers, Genes, Bacterial/genetics, Drug Resistance, Bacterial/genetics, Malawi, Carbapenems, Cephalosporins, Magnetic Phenomena, Water/analysis, environmental surveillance, AMR, ARG, river water, qPCR",

author = "Byrne, {Rachel L} and Derek Cocker and Ghaith Alyayyoussi and Madalitso Mphasa and Mary Charles and Tamandani Mandula and Williams, {Christopher T} and Jonathan Rigby and Jack Hearn and Nicholas Feasey and Adams, {Emily R} and Thomas Edwards",

note = "{\textcopyright} 2022 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.",

year = "2022",

month = nov,

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doi = "10.1111/jam.15755",

language = "English",

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Byrne, RL, Cocker, D, Alyayyoussi, G, Mphasa, M, Charles, M, Mandula, T, Williams, CT, Rigby, J, Hearn, J, Feasey, N, Adams, ER & Edwards, T 2022, 'A novel, magnetic bead-based extraction method for the isolation of antimicrobial resistance genes with a case study in river water in Malawi', Journal of Applied Microbiology, vol. 133, no. 5, pp. 3191-3200. https://doi.org/10.1111/jam.15755

TY - JOUR

T1 - A novel, magnetic bead-based extraction method for the isolation of antimicrobial resistance genes with a case study in river water in Malawi

AU - Byrne, Rachel L

AU - Cocker, Derek

AU - Alyayyoussi, Ghaith

AU - Mphasa, Madalitso

AU - Charles, Mary

AU - Mandula, Tamandani

AU - Williams, Christopher T

AU - Rigby, Jonathan

AU - Hearn, Jack

AU - Feasey, Nicholas

AU - Adams, Emily R

AU - Edwards, Thomas

PY - 2022/11/1

Y1 - 2022/11/1

N2 - 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.

AB - 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.

KW - Anti-Bacterial Agents/pharmacology

KW - Rivers

KW - Genes, Bacterial/genetics

KW - Drug Resistance, Bacterial/genetics

KW - Malawi

KW - Carbapenems

KW - Cephalosporins

KW - Magnetic Phenomena

KW - Water/analysis

KW - environmental surveillance

KW - AMR

KW - ARG

KW - river water

KW - qPCR

UR - http://www.scopus.com/inward/record.url?scp=85136487662&partnerID=8YFLogxK

U2 - 10.1111/jam.15755

DO - 10.1111/jam.15755

M3 - Article

C2 - 35946113

SN - 1364-5072

VL - 133

SP - 3191

EP - 3200

JO - Journal of Applied Microbiology

JF - Journal of Applied Microbiology

IS - 5

ER -

A novel, magnetic bead-based extraction method for the isolation of antimicrobial resistance genes with a case study in river water in Malawi

Abstract

Bibliographical note

Keywords

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