NGS-based estimation of quality of selective pre-amplification of bacterial RRN operon using Phi29

Rapid identification of bacteria in blood is important for the early identification of infection and emergence of resistance to therapy. There is no wishful, fast and simple, technological solution for this quest. Some of infections are life-threatening and requires fast and focused drug treatment as soon as possible. The present approach is to use empirical therapy and wait for culture results (if positive) to modify treatment, i.e. to remove unaffected drugs and add/increase drugs which will attenuate identified pathogen. The sequence of bacterial 16S ribosomal RNA (rRNA) is strain specific and can be used for bacterial identification, thus, better guiding therapy. Current methods of sequencing are not sensitive enough to detect minimal amounts of bacterial 16S rRNA in samples containing an excess of human DNA. We developed a protocol to selectively amplify signals form any type of bacteria from blood and permit fast downstream molecular identification (using nucleic acid-based methods).

Jinchu Vijay
Faculty Supervisor: 
Alan Spatz
Partner University: