Identification

Title

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

Abstract

[This dataset is embargoed until April 1, 2020]. 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. Full details about this dataset can be found at https://doi.org/10.5285/e548dc5d-49e3-467d-9435-c199da40e7be

Resource type

dataset

Resource locator

Unique resource identifier

code

https://catalogue.ceh.ac.uk/id/e548dc5d-49e3-467d-9435-c199da40e7be

codeSpace

doi:

Dataset language

eng

Spatial reference system

authority code

urn:ogc:def:crs:EPSG

code identifying the spatial reference system

27700

Classification of spatial data and services

Topic category

biota

farming

Keywords

Keyword set

keyword value

Soil

Agricultural and Aquaculture Facilities

Human Health and Safety

originating controlled vocabulary

title

GEMET - INSPIRE themes, version 1.0

reference date

date type

publication

effective date

2008-06-01

Geographic location

West bounding longitude

-6.628

East bounding longitude

1.592

North bounding latitude

56.4

South bounding latitude

52.239

Temporal reference

Temporal extent

Begin position

2016-10-19

End position

2017-04-05

Dataset reference date

date type

publication

effective date

2018-08-10

Frequency of update

Quality and validity

Lineage

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.

Conformity

Data format

name of format

Comma-separated values (CSV)

version of format

unknown

Constraints related to access and use

Constraint set

Use constraints

© University of Edinburgh

Constraint set

Limitations on public access

Responsible organisations

Responsible party

organisation name

The Roslin Institute

email address

jolinda.pollock@roslin.ed.ac.uk

responsible party role

pointOfContact

Responsible party

organisation name

SRUC/The Roslin Institute

email address

jolinda.pollock@roslin.ed.ac.uk

responsible party role

author

Responsible party

organisation name

R(D)SVS/The Roslin Institute

email address

alexander.corbishley@roslin.ed.ac.uk

responsible party role

author

Responsible party

organisation name

SRUC

email address

mike.hutchings@sruc.ac.uk

responsible party role

author

Responsible party

organisation name

The Roslin Institute

email address

david.gally@roslin.ed.ac.uk

responsible party role

author

Responsible party

organisation name

NERC Environmental Information Data Centre

email address

eidc@ceh.ac.uk

responsible party role

publisher

Responsible party

organisation name

Environmental Information Data Centre

email address

eidc@ceh.ac.uk

responsible party role

custodian

Metadata on metadata

Metadata point of contact

organisation name

Environmental Information Data Centre

full postal address

Lancaster Environment Centre, Library Avenue, Bailrigg

Lancaster

LA1 4AP

UK

email address

eidc@ceh.ac.uk

responsible party role

pointOfContact

Metadata date

2019-10-24T08:11:48

Metadata language

eng