The genetic information found in each species of organism is unique, and can be used as a tool to differentiate at the molecular level. This has caused rapid genotyping methods to become the cornerstone of a new area of research dependent on reading the genome as a form of identification. One of these specific identification methods, known as pyroprinting, relies on the small variation of DNA sequences within the same species to develop a unique, reproducible fingerprint. By simultaneously pyrosequencing multiple polymorphic loci within the ribosomal operons known as the intergenic transcribed spacers, a reproducible output is obtained, known as a pyroprint, which can be used like a fingerprint to identify that organism. This section of the genome not only differs between species but also between isolated bacteria within that species, allowing for the differentiation of species subtypes, referred to as strains. While this is a viable method for generating reproducible fingerprints from individual strains it may be possible to obtain identical fingerprints from non-identical organisms. The following report uses direct sequence comparison and in silico pyrosequencing of E. coli isolates housed in the Center for Applications in Biotechnology at California Polytechnic State University, San Luis Obispo that have matching pyroprints to show that it is possible to receive near identical pyroprints from non-identical sequences of intergenic transcribed spacers. Although the exact likelihood and cause of this false positive result remains undetermined due to limitations in the sequencing method, its existence questions the accuracy of using pyroprints of the ITS regions as a method of strain classification.
","abstract_html":"<p>The genetic information found in each species of organism is unique, and can be used as a tool to differentiate at the molecular level. This has caused rapid genotyping methods to become the cornerstone of a new area of research dependent on reading the genome as a form of identification. One of these specific identification methods, known as pyroprinting, relies on the small variation of DNA sequences within the same species to develop a unique, reproducible fingerprint. By simultaneously pyrosequencing multiple polymorphic loci within the ribosomal operons known as the intergenic transcribed spacers, a reproducible output is obtained, known as a pyroprint, which can be used like a fingerprint to identify that organism. This section of the genome not only differs between species but also between isolated bacteria within that species, allowing for the differentiation of species subtypes, referred to as strains. While this is a viable method for generating reproducible fingerprints from individual strains it may be possible to obtain identical fingerprints from non-identical organisms. The following report uses direct sequence comparison and <em>in silico </em>pyrosequencing of <em>E. coli </em>isolates housed in the Center for Applications in Biotechnology at California Polytechnic State University, San Luis Obispo that have matching pyroprints to show that it is<strong> </strong>possible to receive near identical pyroprints from non-identical sequences of intergenic transcribed spacers. Although the exact likelihood and cause of this false positive result remains undetermined due to limitations in the sequencing method, its existence questions the accuracy of using pyroprints of the ITS regions as a method of strain classification.</p>","abstract_has_math":false,"creators":["Gordon, Skyler A"],"institution":null,"degree_name":"MS in Engineering - Bioengineering","degree_level":null,"degree_discipline":"Biomedical and General Engineering","degree_department":null,"school":null,"contributors":["Trevor Cardinal"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2017,"date_issued":"2017-02-01T08:00:00Z","date_published":"2017-02-01T08:00:00Z","updated_at":"2026-07-24T01:31:49Z","subjects":["Pyroprint Pyrosequence CPLOP Flase Positive","Bioinformatics","Biotechnology","Environmental Microbiology and Microbial Ecology","Genomics","Molecular Biology","Molecular Genetics","Other Biochemistry, Biophysics, and Structural Biology","Population Biology","Terrestrial and Aquatic Ecology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["10.15368/theses.2017.4"],"render_values":[{"text":"10.15368/theses.2017.4","href":"https://doi.org/10.15368/theses.2017.4","code":true}]}]},"links":{"outbound_url":"https://digitalcommons.calpoly.edu/theses/1730","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Trevor Cardinal"]},{"key":"dc:creator","label":"Author","values":["Gordon, Skyler A"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2017-02-03T08:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biomedical and General Engineering"]},{"key":"thesis:degree_name","label":"Degree Name","values":["MS in Engineering - Bioengineering"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Pyroprint Pyrosequence CPLOP Flase Positive","Bioinformatics","Biotechnology","Environmental Microbiology and Microbial Ecology","Genomics","Molecular Biology","Molecular Genetics","Other Biochemistry, Biophysics, and Structural Biology","Population Biology","Terrestrial and Aquatic Ecology"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://digitalcommons.calpoly.edu/theses/1730","10.15368/theses.2017.4"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The genetic information found in each species of organism is unique, and can be used as a tool to differentiate at the molecular level. This has caused rapid genotyping methods to become the cornerstone of a new area of research dependent on reading the genome as a form of identification. One of these specific identification methods, known as pyroprinting, relies on the small variation of DNA sequences within the same species to develop a unique, reproducible fingerprint. By simultaneously pyrosequencing multiple polymorphic loci within the ribosomal operons known as the intergenic transcribed spacers, a reproducible output is obtained, known as a pyroprint, which can be used like a fingerprint to identify that organism. This section of the genome not only differs between species but also between isolated bacteria within that species, allowing for the differentiation of species subtypes, referred to as strains. While this is a viable method for generating reproducible fingerprints from individual strains it may be possible to obtain identical fingerprints from non-identical organisms. The following report uses direct sequence comparison and in silico pyrosequencing of E. coli isolates housed in the Center for Applications in Biotechnology at California Polytechnic State University, San Luis Obispo that have matching pyroprints to show that it is possible to receive near identical pyroprints from non-identical sequences of intergenic transcribed spacers. Although the exact likelihood and cause of this false positive result remains undetermined due to limitations in the sequencing method, its existence questions the accuracy of using pyroprints of the ITS regions as a method of strain classification.
"]},{"key":"dc:title","label":"Title","values":["An Assessment of Potential False Positive E.coli Pyroprints in the CPLOP Database"]}]}],"canonical_facts":{"dc:contributor":["Trevor Cardinal"],"dc:creator":["Gordon, Skyler A"],"dc:date.available":["2017-02-03T08:00:00Z"],"dc:description.abstract":["The genetic information found in each species of organism is unique, and can be used as a tool to differentiate at the molecular level. This has caused rapid genotyping methods to become the cornerstone of a new area of research dependent on reading the genome as a form of identification. One of these specific identification methods, known as pyroprinting, relies on the small variation of DNA sequences within the same species to develop a unique, reproducible fingerprint. By simultaneously pyrosequencing multiple polymorphic loci within the ribosomal operons known as the intergenic transcribed spacers, a reproducible output is obtained, known as a pyroprint, which can be used like a fingerprint to identify that organism. This section of the genome not only differs between species but also between isolated bacteria within that species, allowing for the differentiation of species subtypes, referred to as strains. While this is a viable method for generating reproducible fingerprints from individual strains it may be possible to obtain identical fingerprints from non-identical organisms. The following report uses direct sequence comparison and in silico pyrosequencing of E. coli isolates housed in the Center for Applications in Biotechnology at California Polytechnic State University, San Luis Obispo that have matching pyroprints to show that it is possible to receive near identical pyroprints from non-identical sequences of intergenic transcribed spacers. Although the exact likelihood and cause of this false positive result remains undetermined due to limitations in the sequencing method, its existence questions the accuracy of using pyroprints of the ITS regions as a method of strain classification.
"],"dc:identifier":["https://digitalcommons.calpoly.edu/theses/1730","10.15368/theses.2017.4"],"dc:subject":["Pyroprint Pyrosequence CPLOP Flase Positive","Bioinformatics","Biotechnology","Environmental Microbiology and Microbial Ecology","Genomics","Molecular Biology","Molecular Genetics","Other Biochemistry, Biophysics, and Structural Biology","Population Biology","Terrestrial and Aquatic Ecology"],"dc:title":["An Assessment of Potential False Positive E.coli Pyroprints in the CPLOP Database"],"thesis:degree_discipline":["Biomedical and General Engineering"],"thesis:degree_name":["MS in Engineering - Bioengineering"]},"updated_at":"2026-07-24T01:31:49Z"}