Table 4 Overview of results generated by high-throughput qPCR of samples collected during the main study (farm B).

Month	Sample type	Group	PRV-3 median Ct	No. of positive	Ca.. B. cysticola median Ct	No. of positive	Ca. P. salmonis median Ct	No. of positive	Y. ruckeri median Cts	No. of positive
March	H + S + K	CA	19.4	4	24.0	2	No Ct	0	23.3	1
	H + S + K	CH	14.1	5	21.9	5	No Ct	0	No Ct	0
	Gill	CA	19.9	2	20.9	5	21.0	1	No Ct	0
	Gill	CH	18.0	5	19.7	5	No Ct	0	No Ct	0
	Water		24.6	2 of 3*	21.7	3 of 3	29.4	1 of 3*	23.1	2 of 3*
April	H + S + K	CA	13.3	5	21.5	5	No Ct	0	14.3	4
	H + S + K	CH	17.8	5	23.1	4	No Ct	0	No Ct	0
	Gill	CA	18.3	5	16.5	5	No Ct	0	15.1	4
	Gill	CH	21.8	3	16.6	5	No Ct	0	No Ct	0
	Water		39.9	1 of 3*	18.6	3 of 3	28.9	2 of 3*	22.4	3 of 3
May	H + S + K	CA	16.8	5	19.8	5	No Ct	0	No Ct	0
	H + S + K	CH	18.6	5	25.5	4	No Ct	0	No Ct	0
	Gill	CA	23.4	5	11.9	5	No Ct	0	No Ct	0
	Gill	CH	22.2	4	13.3	5	No Ct	0	19.5	1
	Water		No Ct	0 of 3	17.7	3 of 3	29.5	1 of 3*	20.8	3 of 3
June	H + S + K	CA	18.9	5	22.6	4	No Ct	0	34.3	1
	H + S + K	CH	19.3	5	23.4	5	No Ct	0	30.2	1
	Gill	CA	24.4	4	12.1	5	No Ct	0	23.9	2
	Gill	CH	24.5	4	13.0	5	No Ct	0	No Ct	0
	Water		23.3	1 of 3*	17.3	3 of 3	26.1	3 of 3	21.2	3 of 3
July	H + S + K	CA	23.7	4	21.8	5	22.9	1	15.8	2
	H + S + K	CH	22.4	5	23.2	3	23.3	1	No Ct	0
	Gill	CA	22.9	5	10.8	5	14.0	5	16.1	2
	Gill	CH	24.4	3	16.1	5	14.9	5	No Ct	0
	Water		39.5	1 of 3*	18.1	3 of 3	16.5	3 of 3	22.1	3 of 3
August	H + S + K	CA	22.9	5	25.8	4	26.3	1	No Ct	0
	H + S + K	CH	22.9	5	23.2	3	26.2	1	No Ct	0
	Gill	CA	24.7	4	15.7	5	12.2	5	No Ct	0
	Gill	CH	24.5	3	16.1	5	12.9	5	No Ct	0
	Water		No Ct	0 of 3	21.4	3 of 3	15.0	3 of 3	23.8	2 of 3*
September	H + S + K	CA	22.0	4	23.1	2	23.9	1	No Ct	0
	H + S + K	CH	23.5	5	22.4	1	No Ct	0	No Ct	0
	Gill	CA	30.1	2	16.7	5	16.2	5	No Ct	0
	Gill	CH	25.3	1	14.8	5	14.7	5	No Ct	0
	Water		24.9	1 of 3*	18.1	3 of 3	17.7	3 of 3	22.8	3 of 3

For each of the pathogens detected by the HT-qPCR method (PRV-3, Ca. B. cysticola, Ca. P. salmonis and Y. ruckeri, respectively), the median Ct value is listed for a pool of heart, spleen and kidney (H + S + K), gills and water. For tissue samples (heart, spleen and kidney, and gill), number of positive refer to number of positive samples with Ct below 25. For water samples, number of positive refers to number of replicates with a Ct value (n = 3). If less than three replicates are positive, the sample is considered negative (marked with *). Additionally, Ct above 25 is considered negative. CA Clinically affected (n = 5), CH Clinically healthy (n = 5).

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