GCAT-SEEKquence
The Genome Consortium for Active Teaching
NextGen Sequencing Group
NextGen Sequencing Request Form
Complete fields below, save file with your last name at the beginning of
the filename (e.g. newman-GCAT-SEEK Sequence request form.pdf) and
email to Vincent Buonaccorsi <BUONACCORSI@juniata.edu>
A. Contact Information
1. Name: Dr. Nancy Trun and Dr. Becky Morrow
2. Department: Biological Sciences
3. Institution: Duquesne University
4. Phone Number: 412-396-1853
5. Email Address: trun@duq.edu
B. Project Information
1. Title: Determining the genomic sequence of the pathogen Streptococcus equi.
2. Category: bacterial genome sequence
3. Total amount of sequence requested: complete genome (probably 4-6 million base pairs)
4. Preferred technology: To be determined in conjunction with the Core Sequencing Facility
5. Do you have funds for a partial run next Spring? no
C. Describe the background, hypotheses and specific aims (500 words max)
Hundreds of cats were rescued from a disease-ridden pseudo-sanctuary located north of Pittsburgh,
Pennsylvania. Dr. Morrow and her undergraduate students determined that over 50 cats in the population had
clinical signs highly similar to those in horses infected with Streptococcus equi (S. equi), including cervical
lymphadenitis with abscessation and acute rhinitis characterized by profuse mucopurulent nasal discharge. In
addition to the spontaneous neck abscesses and atypical upper respiratory infections, many cats exhibited septic
arthritis with total joint destruction, paw abscessation, necrotizing fasciitis, meningitis, otitis, and septic shock,
often leading to death.
After gathering medical data on over 400 cats, as well as culturing Group C Streptococcal bacteria from
several samples taken from the various regions of the cats, it was hypothesized that a single bacterial species, S.
equi, was responsible for all of these clinical signs. This would be a very unusual and interesting finding because
S. equi has not been reported to infect cats. Undergraduate students in a lab class characterized the bacteria
from the cats. After DNA isolation, amplification of the ribosomal RNA intergenic region, cloning, and
sequencing, Streptococcus canis (Group G) was consistently identified in the cats.
At this point, phenotypes indicate one bacterial species and genetics indicates a second. We would like
to sequence the genome of the infecting organism to determine which bacterium it most closely resembles. The
clinical syndromes may be explained by different Streptococcal virulence factors. Sequencing of the organism
will provide greater insight into this novel infectious agent and will help use determine if unique virulence
factors are present in the infectious strain.
The undergraduates will focus on potential virulence factor genes to develop novel PCR primers for the
feline S. equi. They will determine if these novel genes are present in the S. equi that infects horses, develop PCR
tests for the presence of the organism and other studies that bridge basic science and medicine. Dr. Morrow is
uniquely qualified for this work because she is a veterinarian and she teaches full time at Duquesne. She teaches
a lab class both fall and spring each semester and students conduct novel research in both lab classes. Dr. Trun is
a microbiologist/molecular biologist and will assist in the project as needed.
D. Describe the methods [sample prep, calculation of amount of sequence required, analysis plan]
Pure culture of the infectious feline Streptococcus has been obtained from the cats. The DNA from this strain
will be purified using a Mo Bio microbial genome purification kit. The sequencing platform, as well as the
coverage needed, will be determined in conjunction with the Core faculty conducting the sequencing. The
genome sequence will be assembled and analyzed in Dr. Morrow’s lab class.
E. Describe the role and number of undergraduates involved in the project, and how they would benefit.
Dr. Morrow teaches one section of the lab class in the fall semester and one in the spring. A total of 32 students
per year would learn how to analyze large sequencing data sets. Many of Dr. Morrow’s students do not have
time in their schedules for independent research, and this would be their main exposure to research methods
and analysis.
F. I agree to administer the GCAT-SEEK pre- and post-activity assessment test for students and to complete the
faculty post-utilization survey. __x__ yes, ____ no
G. Describe any other broader impact or intellectual merit considerations.
This project will give a large number of students who traditionally do not carry out research an opportunity to
experience novel research. Thirty-two students per year will benefit from this experience. In addition to this
main focus, the research will shed light on a unique infectious bacterium. The research will be presented at
veterinary conferences and knowledge of this Streptococcal species will of use in treating feline infections.