A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds

Patrick Munk, Vibe Dalhoff Andersen, Leonardo de Knegt, Marie Stengaard Jensen, Berith Elkær Knudsen, Oksana Lukjancenko, Hanne Mordhorst, Julie Clasen, Yvonne Agersø, Anders Folkesson, Sünje Johanna Pamp, Håkan Vigre, Frank Møller Aarestrup

Research output: Contribution to journalJournal articleResearchpeer-review

198 Downloads (Pure)

Abstract

Objectives
Reliable methods for monitoring antimicrobial resistance (AMR) in livestock and other reservoirs are essential to understand the trends, transmission and importance of agricultural resistance. Quantification of AMR is mostly done using culture-based techniques, but metagenomic read mapping shows promise for quantitative resistance monitoring.
Methods
We evaluated the ability of: (i) MIC determination for Escherichia coli; (ii) cfu counting of E. coli; (iii) cfu counting of aerobic bacteria; and (iv) metagenomic shotgun sequencing to predict expected tetracycline resistance based on known antimicrobial consumption in 10 Danish integrated slaughter pig herds. In addition, we evaluated whether fresh or manure floor samples constitute suitable proxies for intestinal sampling, using cfu counting, qPCR and metagenomic shotgun sequencing.
Results
Metagenomic read-mapping outperformed cultivation-based techniques in terms of predicting expected tetracycline resistance based on antimicrobial consumption. Our metagenomic approach had sufficient resolution to detect antimicrobial-induced changes to individual resistance gene abundances. Pen floor manure samples were found to represent rectal samples well when analysed using metagenomics, as they contain the same DNA with the exception of a few contaminating taxa that proliferate in the extraintestinal environment.
Conclusions
We present a workflow, from sampling to interpretation, showing how resistance monitoring can be carried out in swine herds using a metagenomic approach. We propose metagenomic sequencing should be part of routine livestock resistance monitoring programmes and potentially of integrated One Health monitoring in all reservoirs.
Original languageEnglish
Article numberdkw415
JournalJournal of Antimicrobial Chemotherapy
Volume72
Pages (from-to)385-392
Number of pages8
ISSN0305-7453
DOIs
Publication statusPublished - 2016

Cite this

@article{1ba6cd0179224a36b0c4082ab821cee5,
title = "A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds",
abstract = "ObjectivesReliable methods for monitoring antimicrobial resistance (AMR) in livestock and other reservoirs are essential to understand the trends, transmission and importance of agricultural resistance. Quantification of AMR is mostly done using culture-based techniques, but metagenomic read mapping shows promise for quantitative resistance monitoring.MethodsWe evaluated the ability of: (i) MIC determination for Escherichia coli; (ii) cfu counting of E. coli; (iii) cfu counting of aerobic bacteria; and (iv) metagenomic shotgun sequencing to predict expected tetracycline resistance based on known antimicrobial consumption in 10 Danish integrated slaughter pig herds. In addition, we evaluated whether fresh or manure floor samples constitute suitable proxies for intestinal sampling, using cfu counting, qPCR and metagenomic shotgun sequencing.ResultsMetagenomic read-mapping outperformed cultivation-based techniques in terms of predicting expected tetracycline resistance based on antimicrobial consumption. Our metagenomic approach had sufficient resolution to detect antimicrobial-induced changes to individual resistance gene abundances. Pen floor manure samples were found to represent rectal samples well when analysed using metagenomics, as they contain the same DNA with the exception of a few contaminating taxa that proliferate in the extraintestinal environment.ConclusionsWe present a workflow, from sampling to interpretation, showing how resistance monitoring can be carried out in swine herds using a metagenomic approach. We propose metagenomic sequencing should be part of routine livestock resistance monitoring programmes and potentially of integrated One Health monitoring in all reservoirs.",
author = "Patrick Munk and {Dalhoff Andersen}, Vibe and {de Knegt}, Leonardo and Jensen, {Marie Stengaard} and Knudsen, {Berith Elk{\ae}r} and Oksana Lukjancenko and Hanne Mordhorst and Julie Clasen and Yvonne Agers{\o} and Anders Folkesson and Pamp, {S{\"u}nje Johanna} and H{\aa}kan Vigre and Aarestrup, {Frank M{\o}ller}",
year = "2016",
doi = "10.1093/jac/dkw415",
language = "English",
volume = "72",
pages = "385--392",
journal = "Journal of Antimicrobial Chemotherapy",
issn = "0305-7453",
publisher = "Oxford University Press",

}

A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds. / Munk, Patrick; Dalhoff Andersen, Vibe; de Knegt, Leonardo; Jensen, Marie Stengaard; Knudsen, Berith Elkær; Lukjancenko, Oksana; Mordhorst, Hanne; Clasen, Julie; Agersø, Yvonne; Folkesson, Anders; Pamp, Sünje Johanna; Vigre, Håkan; Aarestrup, Frank Møller.

In: Journal of Antimicrobial Chemotherapy, Vol. 72, dkw415, 2016, p. 385-392.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds

AU - Munk, Patrick

AU - Dalhoff Andersen, Vibe

AU - de Knegt, Leonardo

AU - Jensen, Marie Stengaard

AU - Knudsen, Berith Elkær

AU - Lukjancenko, Oksana

AU - Mordhorst, Hanne

AU - Clasen, Julie

AU - Agersø, Yvonne

AU - Folkesson, Anders

AU - Pamp, Sünje Johanna

AU - Vigre, Håkan

AU - Aarestrup, Frank Møller

PY - 2016

Y1 - 2016

N2 - ObjectivesReliable methods for monitoring antimicrobial resistance (AMR) in livestock and other reservoirs are essential to understand the trends, transmission and importance of agricultural resistance. Quantification of AMR is mostly done using culture-based techniques, but metagenomic read mapping shows promise for quantitative resistance monitoring.MethodsWe evaluated the ability of: (i) MIC determination for Escherichia coli; (ii) cfu counting of E. coli; (iii) cfu counting of aerobic bacteria; and (iv) metagenomic shotgun sequencing to predict expected tetracycline resistance based on known antimicrobial consumption in 10 Danish integrated slaughter pig herds. In addition, we evaluated whether fresh or manure floor samples constitute suitable proxies for intestinal sampling, using cfu counting, qPCR and metagenomic shotgun sequencing.ResultsMetagenomic read-mapping outperformed cultivation-based techniques in terms of predicting expected tetracycline resistance based on antimicrobial consumption. Our metagenomic approach had sufficient resolution to detect antimicrobial-induced changes to individual resistance gene abundances. Pen floor manure samples were found to represent rectal samples well when analysed using metagenomics, as they contain the same DNA with the exception of a few contaminating taxa that proliferate in the extraintestinal environment.ConclusionsWe present a workflow, from sampling to interpretation, showing how resistance monitoring can be carried out in swine herds using a metagenomic approach. We propose metagenomic sequencing should be part of routine livestock resistance monitoring programmes and potentially of integrated One Health monitoring in all reservoirs.

AB - ObjectivesReliable methods for monitoring antimicrobial resistance (AMR) in livestock and other reservoirs are essential to understand the trends, transmission and importance of agricultural resistance. Quantification of AMR is mostly done using culture-based techniques, but metagenomic read mapping shows promise for quantitative resistance monitoring.MethodsWe evaluated the ability of: (i) MIC determination for Escherichia coli; (ii) cfu counting of E. coli; (iii) cfu counting of aerobic bacteria; and (iv) metagenomic shotgun sequencing to predict expected tetracycline resistance based on known antimicrobial consumption in 10 Danish integrated slaughter pig herds. In addition, we evaluated whether fresh or manure floor samples constitute suitable proxies for intestinal sampling, using cfu counting, qPCR and metagenomic shotgun sequencing.ResultsMetagenomic read-mapping outperformed cultivation-based techniques in terms of predicting expected tetracycline resistance based on antimicrobial consumption. Our metagenomic approach had sufficient resolution to detect antimicrobial-induced changes to individual resistance gene abundances. Pen floor manure samples were found to represent rectal samples well when analysed using metagenomics, as they contain the same DNA with the exception of a few contaminating taxa that proliferate in the extraintestinal environment.ConclusionsWe present a workflow, from sampling to interpretation, showing how resistance monitoring can be carried out in swine herds using a metagenomic approach. We propose metagenomic sequencing should be part of routine livestock resistance monitoring programmes and potentially of integrated One Health monitoring in all reservoirs.

U2 - 10.1093/jac/dkw415

DO - 10.1093/jac/dkw415

M3 - Journal article

VL - 72

SP - 385

EP - 392

JO - Journal of Antimicrobial Chemotherapy

JF - Journal of Antimicrobial Chemotherapy

SN - 0305-7453

M1 - dkw415

ER -