Table 1.

Overview of samples collected during the trial.

Type of sample	Total	Frequency	Pool	Analysis	Reason
		F0; before inoculation	3 calves per pool: 1: oral 2: no challenge 3a&b: T-tracheal 4a&b: Nasal		Faecal MAP shedding before infection
Faeces	13 per calf	Week 1 F1-3 pi Week 2 F4-6 pi Week 3 F7-9 pi; Each of 3 days following weekly inoculation.	3 samples of 2 calves per pool: 1a&b: oral 2a&b: no challenge 3a, b&c: T-tracheal 4a, b&c: Nasal	Liquid MAP culture with confirmation IS900 PCR	Passive faecal MAP shedding after inoculation
		Week 6 F10 pi	3 calves per pool: 1: oral 2: no challenge 3a&b: T-tracheal 4a&b: Nasal		Faecal MAP Shedding
		Week 9 F11 pi	Individually
		Week 12 F12 pi	Individually		Faecal MAP Shedding
Dust	18; at each stall	Week 11 pi	Individually	Liquid MAP culture with confirmation IS900 PCR	Environmental contamination with MAP
Serum	2 per calf	Week 0 pi Week 12 pi	Individually	Commercial JD-ELISA	B-cell activation& seroconversion
Whole blood	1 per calf	Week 12 pi	Individually	Bovigam® interferon gamma essay	T-cell sensitisation
Tissue	18 (19*) per calf	W 12 pi	Individually	Liquid MAP culture with confirmation IS900 PCR	Tissue colonisation with MAP

Overview of the samples collected. Frequencies and time points of collection and tests used for analysis during the 12 week trial are described. Additionally, the reason for sampling is indicated. F = faecal sample, pi = post inoculation, T-tracheal = transtracheal. *an additional piece of lung was sampled from one calf.