The Campylobacter Reference Unit therefore developed and standardised a breakpoint method. While it differs from practices in some other laboratories it provides consistency within this dataset. DNA boilate preparation Boilates for use as template in PCR reactions were prepared as follows. A cell suspension of each culture was made in 125 μl phosphate buffered saline or in water (Sigma Aldrich, UK) in a 0.2 ml PCR tube. Suspensions
were vortexed and transferred to a heat GSK458 clinical trial block at 100°C for five minutes. This killed cell suspension was clarified by centrifugation at 13, 000 rpm for 10 min and stored at −20°C. PCR, Sequencing and bioinformatics DNA template arrays were created in 96-well Thermo-fast®, polypropylene plates (Abgene, UK) and seven-locus MLST was carried out in Oxford by standard methods using published primers [40, 44]. Each 25 μl PCR reaction comprised molecular grade water check details (Sigma-Aldrich, United Kingdom), 2.5 μl 10x PCR buffer (Qiagen Ltd.), 0.25 μM each of forward and reverse primer, 0.2 mM dNTP mix (Invitrogen
Ltd.), 0.025 units/μl (0.125 μl) taq polymerase (Qiagen Ltd.) and 2 μl of template DNA. The PCR thermal cycle began with a 15 min denaturation step at 95°C, followed by 35 cycles of 94°C for 30 seconds, 50°C for 30 seconds and 72°C for 1 minute, with a final extension at 72°C for 5 minutes. 5 μl of PCR products were visualised with ultraviolet transillumination following electrophoresis at 200 V (10 min) on a 1% (w/v) agarose gel in 1x TAE buffer (1 mM EDTA, 40 mM Tris-acetate). The amplification products were purified by precipitation with 20% polyethylene glycol–2.5 M NaCl [41] and stored at −20°C. Nucleotide sequencing PCRs were performed in both directions with the same primers (f or r), diluted in water. Reactions were carried out in 10 μl volumes containing 2 μl of PEG precipitated DNA resuspended in water, 1.0 μl 5x buffer, 0.02 μl BigDye Terminator v3.1 mix (Applied
Biosystems, UK) and 0.25 μM of either the forward or the Thiamine-diphosphate kinase reverse primer. Cycling parameters were as follows: 30 cycles of 96°C for 10 s, 50°C for 5 s, and 60°C for 2 min. Unincorporated dye terminators were removed by precipitation of the termination products with 95% ethanol, and the reaction products were separated and detected with an ABI Prism 3730 automated DNA sequencer (AZD1152 cell line Applied Biosyststems, UK). Forward and reverse sequences were assembled from the resultant chromatograms using the Staden suite of computer programs from the Genetics Computer Group package (Madison, WI). The consensus sequence was queried against the Campylobacter database to give an allele number. The combination of alleles for the seven housekeeping genes gave the sequence type (ST). STs are assigned into genetically related clonal complexes, based on sharing four or more alleles with the central genotype.