Novel algorithms for PFGE bacterial typing: Number of co-migrated DNA fragments, linking PFGE to WGS results and computer simulations for evaluation of PulseNet international typing protocols

摘要: Background: Standard protocols for Pulsed-field gel electrophoresis (PFGE) were adopted and being used in a global scale surveillance of many bacterial food-borne diseases. Matched PFGE bands are considered regardless co-migration different DNA fragments. Molecular epidemiology is turning toward whole genome sequencing (WGS). Although, WGS results can be digested In-silico, data compared separately. We describe new image analysis algorithm that enables identification how fragments co-migrate during PFGE. built database compare described to in-silico obtained digestion models (from WGS). Reliability the method was assessed using novel computer simulation approach. From WGS, 1,816 model (DMs) as recommended by PulseNet international. Simulation codes designed predict profiles when DMs separated at 5% resolution addition expected levels. Results: has shown about 35% resolution. Similar result wet-lab analyzed mentioned earlier. When DMs, returned geltowgs.uofk.edu revealed reasonable relatedness DMs. In terms number typable fragments, 45,517 (representing 46.54% out 97,801). Previously (in sizes) comprised 91.24% sum nucleotides all chromosomes tested (7.24 billion bp). However, significant variations within between protocols. Conclusions: Identification levels will reveal third dimension profiles. This provide better way evaluating isolate relationships. Linking old means demonstrated here chance link millions epidemiological accumulated last 24 years era. Evaluation population dynamics pathogenic bacteria deeper through space time. Selection restriction enzymes typing have powerful evaluation tool.