Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.
Bottom Line: Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold.The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains.The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.
Affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden.Show MeSH
Related in: MedlinePlus
Mentions: One potential application of optical mapping is the characterization and identification of bacterial species and strains. We extracted DNA from the E. coli strain CCUG 10979 (= ATCC 8739), using conventional methods (see the Materials and Methods section). During the extraction protocol the DNA is fragmented, and barcodes for 36 such DNA fragments, with lengths ranging from 51.7 kb to 153.4 kb, were matched to the theoretical barcode of CCUG 10979, derived from the genome sequence (RefSeq, Acc. No. NC_010468.1). Figure 6A shows the full theoretical barcode of CCUG 10979 calculated using the transfer matrix approach (see the Materials and Methods section for details and input parameters). Figure 6A also shows the location of the best fits and the associated IS for each of the 36 fragments along the genome.
Affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden.