DNA extraction from swabs

Swabs were randomised for processing by assigning a random number generated in Microsoft Excel 2016 stratified by flock. DNA extraction was performed using a Nucleospin^® Tissue kit (Macherey–Nagel) with modifications. Swabs were thawed at room temperature, transferred to microcentrifuge tubes and lysis buffer T1 (400 μl) and proteinase K (40 μl) were added. Samples were vortexed for 5 s and incubated for 10 min at 56 °C. Post-incubation, lysis buffer B3 (400 μl) was added. Each sample was vortexed for 5 s and incubated at 70 °C for 5 min. Samples were cooled at room temperature for 5 min before being centrifuged at 12,000g for 1 min. The supernatant was added to 100% ethanol (400 μl) and centrifuged at 11,000g for 1 min and then loaded onto spin columns and centrifuged at 11,500g for 1 min. Flow-through was discarded and BW wash buffer (500 μl) was added to the spin columns and centrifuged at 11,000g for 1 min. Flow-through was discarded and B5 wash buffer (600 μl) was added to the spin columns and centrifuged at 11,000g for 1 min. Flow-through was discarded and spin columns were centrifuged for 1 min at 11,000g to dry the membrane. Spin columns were placed in microcentrifuge tubes and BE elution buffer (45 μl) heated to 70 °C was added and allowed to stand for 2 min. Tubes were spun at 11,000g for 1 min to elute DNA and extracted DNA was stored at − 20 °C.