# Table 2 P-values of all variables included in the final multivariable analysis, analysed by generalized linear mixed model

Sub- Group Independent variables: Outcome variables:
Positive samples/ herd (n) Median GE/μl Positive NP / herd (n) Positive GP/herd (n) Positive FP/herd (n)
Environment Season, in which sampling was performed      p = 0.033
Replacement rate/year p = 0.300   p = 0.387
Flooring in units of NP p = 0.019 p = 0.021 x p = 0.062
Flooring in units of GP p = 0.663 x x
Straw in units of NP    x p = 0.772 p = 0.048
Texture of feed for NP p = 0.183
Internal biosecurity Occupancy in units for NP    p = 0.289
Occupancy in units for GP    x
Disinfection in units of NP   p = 0.017
Average down time in units of GP p = 0.025     p = 0.237
Average down time in units of FP    p = 0.157
Age group vaccinated against Lawsonia intracellularis      x
Handling of runts    p = 0.684
Median number of pigs per pen in nursery p = 0.010 p = 0.018 p = 0.009
Use of antimicrobials at/ around weaning   p = 0.018
Use of zinc oxide at/around weaning   p = 0.027 p = 0.004
Animal related Average age at weaning    p = 0.003
Average weight at weaning p = 0.006    p = 0.020
Average daily growth in FP p = 0.209 x
Total mortality in NP p = 0.021   p = 0.187
Days between last diarrhea on farm and sampling   p = 0.218
Morbidity of NP p = 0.313 p = 0.225 p = 0.321
Morbidity of GP   p = 0.039    p = 0.407
Morbidity of FP   p = 0.286
Number of significant variables (p < 0.05) 5 (10) 6 (11)a 3 (13)a 1 (3) 2 (5)
1. NP Nursery pigs, GP Growing pigs, FP Finishing pigs, GE Genome equivalents, measured by quantitative Polymerase chain reaction out of faecal samples. Empty fields indicate no calculation in the multivariable model, due to a p-value of ≥0.05 in the univariable model. ‘x’ indicates an abort of the model after including this or a previous variable
2. aThe deviation compared to the number of significant variables in Additional file 2, is due to the exclusion of variables with a correlation of more than 60% in the present model. Bold letters indicate a p-value < 0.05. The length of lines between the sub-groups is limited to the outcome variable for which they were used. Explanations on answer characteristics of the independent variables (factor levels) can be found in Additional file 1