Escherichia coli Strain Diversity in Humans: Effects of Sampling Effort and Methodology

<p>Studies investigating <em>Escherichia coli</em> strain diversity and demographics in human hosts are frequently inconsistent regarding sampling effort and methodology while current strain typing methods are often expensive or laborious. To rectify these inconsistencies, sampling effort was investigated by comparing the diversity of 15-isolate collections to 100-isolate collections from 3 human subjects. Temporal variation in <em>E. coli</em> strain diversity was also studied by collecting 15 isolates once every 6 months. Additionally, strain identification and diversity collected by different sampling methods (fecal swabs vs. anal swabs collected at different times around defecation) were compared to identify any inherent biases in sampling method. This study employed pyroprinting, a new inexpensive and simple strain typing method using pyrosequencing, to generate DNA fingerprints (or pyroprints) based on the Intergenic Transcribed Spacer sequences in the ribosomal RNA operon to differentiate <em>E. coli</em> strains. Differences in strain diversity were apparent when comparing sampling efforts. The sampling effort investigation suggested that certain subjects hosted very large and highly diverse <em>E. coli</em> strain populations such that even 100 isolates may not fully represent <em>E. coli</em> strain populations in human hosts. Instead, the sampling effort required to accurately represent strain demographics may depend on strain richness and evenness within each host. The temporal investigation yielded similar or greater strain abundance and diversity compared to other typing methods in the literature suggesting pyroprinting is a similarly discriminating tool. When agglomerated over time or by subject, no significant differences in diversity were observed between subjects or between sampling methods despite visible differences in strain richness and evenness.</p>

Name thesis:degree_name

MS in Biological Sciences

Discipline thesis:degree_discipline

Biological Sciences

Year dc:date.available

2013

Author dc:creator

• Neal, Emily R.

Contributors dc:contributor

• Michael Black

• Escherichia coli
• strain diversity
• sampling effort
• Environmental Microbiology and Microbial Ecology

Identifier

10.15368/theses.2013.135

OAI identifier oai:identifier

oai:digitalcommons.calpoly.edu:theses-2062