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 journalArticlepeer-review

1 Citation (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 languageEnglish
Pages (from-to)3191-3200
Number of pages10
JournalJournal of Applied Microbiology
Volume133
Issue number5
Early online date1 Nov 2022
DOIs
Publication statusFirst published - 1 Nov 2022
Externally publishedYes

Bibliographical note

© 2022 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.

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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