BLAST analysis of urease gene confirms its specificity for identifying Helicobacter pylori in qPCR assays

Selecting the gene target for quantitative polymerase chain reaction (qPCR) holds critical importance to the success of the microbial identification task and assay. Such a gene target should ideally be specific to the microbe in question, but few genes fit this criterion given the high level of conservation of functions and gene sequence for genes across different microbial species. But, on rare occasions, particular microbe may have specific genes useful for its unique identification. One such example is urease gene in Helicobacter pylori. This work outlines an approach where BLAST analysis could be utilized to confirm the specificity of a target gene for identifying a microbe using qPCR assay. Results reveal that BLAST analysis was easy to use and helped in validating that all urease genes in H. pylori (ureD, ureG, ureF, ureE, ureI, ureB, and ureA) could be used in specific identification of the bacterium with 100% specificity. Overall, BLAST analysis can be utilized to help validate the specificity of a target gene in identifying microbial species via qPCR assay, and the example illustrated in this work highlights the specificity of different urease gene in identifying H. pylori. Such results lend a window and opens up new areas of inquiry examining the evolutionary forces that shape the emergence of urease gene, and more important, why another microbe did not co-opt or independently evolve the urease function.