Additionally, in the five conventional check details herds, 86 environmental swabs of pig pens (either empty or with animals) and
50 feed samples were collected. The swabbed surface area was measured each time. Sample processing and experimental conditions All samples were examined within four hours after sampling for Campylobacter spp. quantification by conventional culture and for species-identification by the PCR described by Denis et al. (1999)  as well as for species-specific quantification by real-time PCR assays. All animals of this study were housed and treated in accordance with the regulations of the local veterinary office (Direction des Services Vétérinaires des Côtes d’Armor, Selleck Rigosertib France). The animal experimention was carried out following the international recognized guidelines. All the animals were reared in isolation rooms with controlled air flow . DNA preparation for real-time PCR-based quantification DNA isolation from
the faecal, feed, and environmental samples was performed using a modified extraction protocol of the Nucleospin® Tissue mini-kit (Macherey Nagel, Hoerdt, France) with a preliminary step of boiling to remove inhibitors of the Taq polymerase . Five grams of sample (faeces or feed) were diluted in 5 mL of sterile water (for smaller amounts, an equivalent quantity of sterile water (w/w) was added). The environmental swabs, placed into sterile bags, were stomached for 2 min with 10 mL of sterile water. The sample solutions of faeces, feed, and swabs were boiled for 10 min, chilled on ice, Veliparib molecular weight and centrifuged (8000 g, 5 min). For each sample, 250 μL of supernatant was extracted using the Nucleospin® Tissue mini-kit according to the manufacturer’s
instructions. Finally, DNA preparations, eluted in 100 μL of elution buffer purchased in the kit, were stored at +4°C prior to use. Control of PCR inhibition To test the presence of PCR inhibitors in the Histone demethylase DNA isolated from the samples, a fixed amount of the bacterium Yersinia ruckeri was added to each sample before the DNA extraction. This internal bacterial amplification and extraction control was quantified in a separate well using a real-time PCR test described in a previous work . Samples with PCR inhibition were then removed for the rest of the study. Enumeration of Campylobacter spp. and species identification Ten grams of fresh faeces, ten grams of feed, and the environmental swabs were vortexed in 90 mL of Preston broth (Oxoid, Dardilly, France) with a Preston antibiotic supplement (Oxoid, Dardilly, France) (for rectal swabs, 9 mL of Preston broth was added to one gram of faeces). For Campylobacter numeration, 100 μL of a ten-fold dilution serie (10-1 to 10-5) were plated both on Karmali agar (Oxoid, Dardilly, France) and on Butzler agar (Oxoid, Dardilly, France) and incubated for 24 to 72 h at 41.5°C in microaerobic conditions.