An Assessment of Potential False Positive E.coli Pyroprints in the CPLOP Database

<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>

Name thesis:degree_name

MS in Engineering - Bioengineering

Discipline thesis:degree_discipline

Biomedical and General Engineering

Year dc:date.available

2017

Author dc:creator

• Gordon, Skyler A

Contributors dc:contributor

• Trevor Cardinal

• 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

Identifier

10.15368/theses.2017.4

OAI identifier oai:identifier

oai:digitalcommons.calpoly.edu:theses-2905