Pollock, J.; Corbishley, A.; Hutchings, M.R.; Gally, D.L.

Quantification of selected antimicrobial resistance genes in pig faeces on a British commercial pig farm during a typical production cycle

The data presented in pigAMRgenecounts.csv are quantitative polymerase chain reaction (qPCR) read outs from antimicrobial resistance gene (AMRG) assays and associated metadata from this project. In this dataset, the mean gene copy numbers per microlitre of DNA extract are shown.

The data were collected from faecal and environmental samples which were obtained from a single British commercial pig unit. The former were collected from the sow housing barn, pig growing houses and slurry tanks within the farm unit and the latter were obtained through random stratified sampling of the farm and the surrounding land. These samples were taken from what will be referred to as the 'main study'. A further study was carried out to obtain samples after a partial depopulation which took place on this farm. Faecal samples were obtained from the sow housing barn, pig growing houses and slurry tanks and will be referred to as the 'depopulation (depop) study'.

For the main study, the samples were collected between October 19th 2016 and April 5th 2017. For the depop study, the samples were collected between 19th June 2017 and 13th November 2017. The data associated with all samples were generated between August 1st 2017 and May 1st 2018.

Publication date: 2018-08-10

Get the data

This dataset will be available under the terms of the Open Government Licence

Format of the dataset : Comma-separated values (CSV)

You must cite: Pollock, J.; Corbishley, A.; Hutchings, M.R.; Gally, D.L. (2018). Quantification of selected antimicrobial resistance genes in pig faeces on a British commercial pig farm during a typical production cycle. NERC Environmental Information Data Centre. https://doi.org/10.5285/e548dc5d-49e3-467d-9435-c199da40e7be

 

© University of Edinburgh

Where/When

Study area
Temporal extent
2016-10-19    to    2017-04-05

Provenance & quality

Faecal and soil samples were collected from the study farm weekly using spooned universal tubes and were stored at -20°C, batch transported on dry ice to the laboratory where they were stored at -80°C until DNA extraction was carried out. DNA extracts were quantified and assessed using a NanoDrop spectrophotometer and split into aliquots for storage. DNA extracts were then screened in triplicate by qPCR and the number of gene copies assessed through the use of a standard curve generated by the inclusion of standards with known copy numbers of each target gene. Non-template controls were also included to ensure that non-specific binding or contamination were not occurring. The qPCR machine software (i.e. MxPro) was then used to calculate the number of gene copies in each of the collected samples and the mean was calculated using the three replicates. These values are included in the data set provided.

Correspondence/contact details

Dr. Jolinda Pollock
The Roslin Institute
Easter Bush Campus
Midlothian
EH25 9RG
UK
jolinda.pollock@roslin.ed.ac.uk

Authors

Pollock, J.
SRUC/The Roslin Institute
Corbishley, A.
R(D)SVS/The Roslin Institute
Hutchings, M.R.
SRUC
Gally, D.L.
The Roslin Institute

Other contacts

Custodian
Environmental Information Data Centre
eidc@ceh.ac.uk
Publisher
NERC Environmental Information Data Centre
eidc@ceh.ac.uk

Spatial

Spatial representation type
Tabular (text)
Spatial reference system
OSGB 1936 / British National Grid

Tags

Topic categories
Biota , Farming
INSPIRE Theme
Agricultural and Aquaculture Facilities
Human Health and Safety
Soil