A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
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, 2016, p. 385–392.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
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
SP - 385
EP - 392
JO - Journal of Antimicrobial Chemotherapy
JF - Journal of Antimicrobial Chemotherapy
SN - 0305-7453
ER -
ID: 192566038