Table 1. Overview of the samples collected during sampling 1 and sampling 2 including different sampling methods and corresponding laboratory pools at stable and herd levels.

Pool name	Sampling 1	Sampling 2	Samples included in laboratory pool	Number of samples (n)
	1 stable sampled	5 stables sampled
All animals	+	-	All individual animals from sampling 1 (extraction from rectum)	n = 84
Individual animal pool pen	+	-	Pool of individual animals within each pen (extraction from rectum)	Pen 1 n = 22;pen 2 n = 20;pen 3 n = 22;pen 4 n = 20
Pen floor samples	+	+	Not pooled	Sampling 1 n = 4; sampling 2 n = 20
Pen floor pool stable	+	+	Pool of pen floor samples from pens 1–4 in each stable	Sampling 1 n = 1;sampling 2 n = 5
Pen floor pool herd	-	+	Pool of pen floor samples from each stable (1–5)	n = 1
Shoe cover samples	+	+	Not pooled	Sampling 1 n = 4;sampling 2 n = 10
Shoe cover pool stable	+	+	Pool of the shoe cover samples in each stable	Sampling 1 n = 1;sampling 2 n = 2
Shoe cover pool herd	-	+	Pool of shoe cover samples from each stable (1–5)	n = 1
Slurry tank samples	-	+	Each sample was a pool from 3 depths collected at the same spot (1m, 1.5m, and 2m)	n = 3
Pool slurry	-	+	Pool of slurry tank samples 1–3	n = 1