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: Figure 9 shows the P-values for all 36 fragments matched to the barcodes of strains CCUG 10979 and P12b. While there is a slight trend that the P-values are lower for the correct strain, the resolution in separating the two is poor. However, when using the IS threshold introduced above, a vast majority of the DNA fragments have a significantly lower P-value than for strain P12b; there is only one significant false positive.
Affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden.