Sample Journey

We recruited pig herds across the UK to a longitudinal field sampling study, to investigate potential changes in post-weaning diarrhoea (PWD) pathogens, the microbiome and AMR over the first 12 months following removal of pharmacological ZnO supplementation from weaner diet in the herd.

Herds were visited pre-withdrawal and then at 3-, 6- and 12-months following withdrawal of ZnO from weaner diet in that herd. While herds were recruited to the study between 2022-23, over half of the herds waited until the June 2024 UK regulatory implementation date before withdrawing ZnO supplementation in their herd.

At each visit, pen-floor dung samples were collected from up to ten pens each per weaner, grower and finisher pig stages and sent to the lab for processing. A short questionnaire was also completed with the producer at each visit, to find out about the health of the pigs in the sampled pens and any veterinary or other treatments received.

The infographic below outlines the on-farm collection procedure and the sample journey onward to the lab. The photographs illustrate how samples are processed within the lab.

Diagram depicting the sample journey, starting with a sampling questionnaire and samples collected from weaners, growers, and finishers. These samples are then anonymously labelled via a unique code and transported for same day processing. Once received the samples are either frozen in glycerol for bacterial retrieval and genome sequencing or they are snap frozen for DNA extraction.

Photograph of shipping boxes showing how the samples are stored on cold block when transported from for processing.

Receipt of samples in their relevant shipping box. Samples are stored on colds blocks when sent between locations for processing.

Image credit: University of Edinburgh

On arrival at the lab, pen-pool samples are dispensed into a plain vial as a “snap-freeze” aliquot, for extraction of whole sample DNA at a later date, and into a vial containing glycerol preservative, to allow later resuscitation of live bacteria after freeze storage. Vials are stored in the Biobank freezer, at -80 degrees celsius, until required for the different project assays.

Image credit: University of Edinburgh

Photograph of the pen-pool samples being dispensed into a plain vial as a 'snap-freeze' aliquot.

Photograph compilation of the freezer where samples are stored. One image shows the freezer door open with the different freezer draws. Another image shows a freezer draw extended with the rows of vial samples stored upright. The final image shows the-80.00 degrees celcius tempearture of the freezer.

Samples are stored frozen at -80 degrees celsius to preserve the integrity of the material prior to subsequent laboratory analyses.

Image credit: SRUC

Bacterial strain isolation from glycerol frozen pen pool samples, grown on chromogenic agar plates. Escherichia coli (E. coli) grows as pink colonies on this selective agar. The plate on the left is an unselective agar (no antibiotic present in the agar) and shows widespread E. coli growth, whilst the agar in the plate on the right contains ampicillin and shows lower levels of growth with ampicillin-resistant E. coli.

Image credit: University of Edinburgh

Photograph of two agar plates illustrating the levels of growth.

Photograph of the disc diffusion method.

Antimicrobial susceptibility testing using the EUCAST disc diffusion method, for a pure E. coli strain, isolated using chromogenic agar. This strain was tested for resistance to 14 antibiotics; antimicrobial resistance is shown where there is no zone of clear lysis around the circular discs applied to the plate. This strain is resistant to a number of the antibiotics tested.

Image credit: University of Edinburgh

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