High prevalence of Brachyspira spp. in layers kept in alternative husbandry systems associated with frequent species variations from end of rearing to slaughter

Figures & data

Table 1. List of primers and probes used for qPCR detection of B. hyodysenteriae, B. pilosicoli and B. intermedia.

Name of primer/probe	Sequence (5’-3’) primer/probe	Strain specificity	Concentration used in real-time PCR
qPCR-Brachy-F	TTG CTA CTG GTT CTT GGC CTG	B. hyodysenteriae, B. pilosicoli, B. intermedia	400 nM
qPCR-Brachy-R	CTT CTA TAA GTT CAA CAC CTA T
B. hyodysenteriae probe	FAM-CGA AGG CTT AAA ACA AGA AGG A-BHQ1	B. hyodysenteriae	400 nM
B. pilosicoli probe	HEX-TGA GGG yTT AAA ACA AGA AGG T-BHQ1	B. pilosicoli	400 nM
B. intermedia probe	Cy5-AGA AGG ATT AAA ACA GGA AGG A-BHQ1	B. intermedia	200 nM

Figure 1. Significant increase of occurrence of Brachyspira spp. with age of birds.

Figure 2. Occurrence of Brachyspira spp. in different housing systems.

Table 2. Estimated probability for positive Brachyspira samples for different housing systems and sampling time points according to the logistic model.

	Sampling time points
Housing system	Peak of production	End of production
Deep litter	36.4%	60.3%
Conventional free range	46.0%	69.3%
Organic production	65.2%	83.3%

Table 3. Results of all-pairwise comparisons of means with Tukey contrasts.

Linear hypotheses	Estimate	P-value
Conventional free range–deep litter system = 0	0.40	0.6266
Organic production–deep litter system = 0	1.19	0.0338
Conventional free range–organic production = 0	−0.79	0.2765

Figure 3. Frequent change of Brachyspira spp. during the lifetime of birds. (a) end of rearing; (b) peak of production; (c) end of production.