@article {12308, title = {A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds}, journal = {Journal of Antimicrobial Chemotherapy}, volume = {72}, number = {2}, year = {2017}, note = {Munk, Patrick Andersen, Vibe Dalhoff de Knegt, Leonardo Jensen, Marie Stengaard Knudsen, Berith Elkaer Lukjancenko, Oksana Mordhorst, Hanne Clasen, Julie Agerso, Yvonne Folkesson, Anders Pamp, Sunje Johanna Vigre, Hakan Aarestrup, Frank Moller
Munk, Patrick/0000-0001-8813-4019; Pamp, Sunje Johanna/0000-0002-6236-1763; Folkesson, Anders/0000-0002-2175-830X
1460-2091}, month = {Feb}, pages = {385-392}, 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.

}, isbn = {0305-7453}, author = {Munk, P. and Andersen, V. D. and de Knegt, L. and Jensen, M. S. and Knudsen, B. E. and Lukjancenko, O. and Mordhorst, H. and Clasen, J. and Agerso, Y. and Folkesson, A. and Pamp, S. J. and Vigre, H. and Aarestrup, F. M.} }