All clinical specimens were stored at −70 °C for the duration of the study. DNA from culture samples was prepared by a simple
boiling method (Merritt et al., 2006). Culture samples obtained from the diagnostic laboratory were subcultured on nutrient agar and incubated at 37 °C overnight. DNA extraction from culture samples was done as described with some modifications. A single colony from the overnight culture was picked using a flamed wire loop and suspended in 100 μL of sterile distilled water. The bacterial suspension was then boiled at 100 °C for 10 min followed by centrifugation at 13 000 g for 1 min and the supernatant containing the DNA was aliquoted and stored at −20 °C for the course of the study. Extraction of DNA from blood samples was performed according to the protocol provided with the Qiagen Blood Mini Amp Kit (Qiagen). Three sets of primers were designed, each one targeting groEL (chaperonin) (gro1 and gro2) of Burkholderia genus, mprA (serine metalloprotease) PI3K inhibitor (mpr1 and mpr2) gene of B. pseudomallei and zmpA (zinc metalloprotease) (zmp1 and zmp2) gene of B. cepacia, respectively (Table 1, Patent Ref: PI 20083144). All gene sequences were obtained from the National Centre for Biotechnology Information (NCBI) database (http://www.ncbi.nlm.nih.gov), and analyzed using the blast and clustalw programs to reveal the conserved as well
as unique regions of the targeted genes. The GenBank accession numbers for groEL, mprA and zmpA were AF287633, AF254803 and AY143552, respectively. The primers were designed with SGI-1776 solubility dmso similar melting temperatures to enable conversion of standard PCR to multiplex PCR in future. Each of the sequences was then analyzed using blast to ascertain the specificity of
the primers for the possibility of cross-reaction with other closely related organisms. The primer sequences were also analyzed for the presence of secondary structures using the oligo analyzer software. Primers that satisfactorily fulfilled the basic criteria were chosen and synthesized by Helix Biotech (Sigma Proligo, France). All PCR reactions Clomifene were set up in 0.5-μL flat cap Eppendorf microcentrifuge tubes. Optimization parameters included MgCl2 concentration, annealing temperature and the number of PCR cycles. MgCl2 concentrations were optimized using 1.0 mM, 1.5 mM and 2.5 mM and the annealing temperature was set at 52 °C (predicted, based on melting temperature of primers) and number of cycles randomly at 35. The annealing temperature was then optimized using gradient PCR at temperatures ranging from 50 to 60 °C. Finally, PCR cycles were optimized using 25, 30 and 35 cycles. The rest of the parameters were followed within the range recommended by standard PCR protocol: 1 × buffer, 0.2 μM of each of the primers, 200 μM of dNTP, 1.25 U of Taq DNA Polymerase recombinant and 5 ng μL−1 of DNA for 50 μL of final reaction volume. PCR reactions were performed using a BioRad DNA thermal cycler.