Methods of identifying an organism
This disclosure features methods of identifying an organism. In certain embodiments, the invention provides methods of distinguishing virulent and non-virulent strains of organisms, such as E. coli.
1. A method of analyzing an unknown strain of an organism, the method comprising:
obtaining a nucleic acid from an unknown strain of an organism;
preparing an optical map from the nucleic acid;
comparing the optical map of the unknown strain to at least one optical map of a known strain of the organism to identify conserved and non-conserved regions in the optical map of the unknown strain; and
determining the sequence of the non-conserved regions of the unknown strain using primers that hybridize to conserved regions flanking said non-conserved regions.
2. The method according to claim 1 , wherein the organism is E. coli.
3. The method according to claim 1 , wherein the determining step comprises sequencing by synthesis.
4. The method according to claim 1 , wherein the organism is obtained from at least one sample type selected from the group consisting of a food sample, an environmental sample, a mammalian tissue and a body fluid sample.
5. The method according to claim 4 , wherein the environmental sample is selected from the group consisting of water, soil, sewage, and vegetable matter.
6. A method for analyzing an organism, the method comprising:
obtaining a nucleic acid from an organism in a sample;
preparing an optical map from the nucleic acid;
comparing the optical map to at least one reference optical map to identify conserved and non-conserved regions in the optical map of the organism; and
designing primers that flank the non-conserved regions of the organism, to thereby determine the sequence of the non-conserved regions of the organism.
7. The method according to claim 6 , wherein the sequence of the non-conserved regions of the organism is determined using sequencing by synthesis.
8. The method according to claim 6 , wherein the sample is selected from the group consisting of: a food sample, an environmental sample, a mammalian tissue and a body fluid sample.
9. The method according to claim 8 , wherein the environmental sample is selected from the group consisting of water, soil, sewage, and vegetable matter.