Specific biomarker mining and rapid detection of Burkholderia cepacia complex by recombinase polymerase amplification

Objective To mine specific proteins and their protein-coding genes as suitable molecular biomarkers for the Burkholderia cepacia Complex (BCC) bacteria detection based on mega analysis of microbial proteomic genomic data comparisons to develop a real-time recombinase polymerase amplification (rt-RPA) assay rapid isothermal screening pharmaceutical personal care products. Methods We constructed an automatic framework Python compare proteomes 78 BCC strains 263 non-BCC identify BCC-specific protein sequences. In addition, gene its core DNA sequence were validated in silico with self-built genome database containing 158 thousand bacteria. The appropriate methodology using rt-RPA was evaluated by 58 pure culture 33 batches artificially contaminated Results identified SecY secY through comparison framework. virtual evaluation conserved region showed more than 99.8% specificity from database, it can distinguish all known species other phylogenetic analysis. Furthermore, limit targeting 5.6 × 10 2 CFU or 1.2 pg within 30 min. It detect <1 CFU/portion samples after pre-enrichment process. relative trueness sensitivity 100% practice compared reference methods. Conclusion biomarker mining is straightforward, universal, applicable, efficient. Based recognizing gene, we successfully established