Gastroenteritis caused by the bacterium, Clostridium difficile, is a global healthcare problem and a common complication of antibiotic therapy. A subset of toxin-producing C. difficile strains has recently emerged to cause large nosocomial outbreaks and an ongoing C. difficile pandemic. One hypothesis to explain the emergence of pandemic strains is the overproduction of toxins and an increased ability to form environmentally-resistant spores. However, recent studies that include data from a larger set of representative isolates challenge this hypothesis and illustrate the need for novel genetic characterizations that improve the surveillance and molecular epidemiology of these pathogens. The work proposed here will provide genome sequences of a broad diversity of C. difficile isolates and test the hypothesis that certain genomic traits are significantly associated with the severity of human C. difficile infection (CDI). Isolates will be collected from symptomatic hospita inpatients as part of an ongoing C. difficile clinical study at the University of Michigan. A totalof 1,500 isolates will be genotyped using high-throughput fluorescent-PCR ribotyping and subtyped using multi-locus variable number tandem repeat analysis (MLVA). Based on these characterizations, 150 representative isolates spanning the genotypic diversity of isolates and clinical spectrum of CDI severity will be selected for genome sequencing. Isolates from an additional ~200 CDI cases in our collection are presently being sequenced as part of a parallel project. Sequence data for all isolates (~350) will be bioinformatically manipulated and analyzed with respect to clinical parameters from the patient record database. Results from this analysis will epidemiologically link C. difficile genetic diversity in the form of single nucleotide polymorphisms (SNPs) with CDI severity and response to therapy. SNP data will be used to develop a novel phylogenetically-based typing system for the rapid genomic characterization of C. difficile strains. SNP typing will be used to characterize the genomic diversity of a large collection of isolates (n=5,000) and assess the bacterial genome-based correlates of CDI severity. The completion of this research requires that the candidate complete a didactic training program designed to specifically master concepts and tools from the fields of bioinformatics, computational biology, and genomics. A combination of coursework, mentorship from leaders in the field, and experiential knowledge to be gained from in depth data analysis will ensure the success of the research and the future career of the candidate.

Public Health Relevance

This project will improve the surveillance and molecular epidemiology of pathogenic C. difficile by identifying the bacterial genomic correlates of clinical disease severit and by developing a novel genomics-based typing system for the rapid discrimination of pathogens. The combinatorial approach of C. difficile genomics and clinical data will develop a more comprehensive epidemiology of this important global disease. Relevance This project will improve the surveillance and molecular epidemiology of pathogenic C. difficile by identifying the bacterial genomic correlates of clinical disease severity and by developing a novel genomics-based typing system for the rapid discrimination of pathogens. The combinatorial approach of C. difficile genomics and clinical data will develop a more comprehensive epidemiology of this important global disease.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Scientist Development Award - Research & Training (K01)
Project #
7K01AI097281-02
Application #
8526047
Study Section
Microbiology and Infectious Diseases B Subcommittee (MID)
Program Officer
Ranallo, Ryan
Project Start
2012-05-01
Project End
2017-04-30
Budget Start
2012-08-16
Budget End
2013-04-30
Support Year
2
Fiscal Year
2012
Total Cost
$75,600
Indirect Cost
$5,600
Name
Montana State University - Bozeman
Department
Microbiology/Immun/Virology
Type
Schools of Arts and Sciences
DUNS #
625447982
City
Bozeman
State
MT
Country
United States
Zip Code
59717
Rao, Krishna; Young, Vincent B; Aronoff, David M (2015) Reply to Planche et al. Clin Infect Dis 61:1211-2
Micic, Dejan; Rao, Krishna; Trindade, Bruno Caetano et al. (2015) Serum 25-Hydroxyvitamin D Levels are not Associated with Adverse Outcomes in Clostridium Difficile Infection. Infect Dis Rep 7:5979
Rao, Krishna; Micic, Dejan; Natarajan, Mukil et al. (2015) Clostridium difficile ribotype 027: relationship to age, detectability of toxins A or B in stool with rapid testing, severe infection, and mortality. Clin Infect Dis 61:233-41
Aitken, Samuel L; Alam, M Jahangir; Khaleduzzaman, Mohammed et al. (2015) In the Endemic Setting, Clostridium difficile Ribotype 027 Is Virulent But Not Hypervirulent. Infect Control Hosp Epidemiol 36:1318-23
Martinson, Jonathan N V; Broadaway, Susan; Lohman, Egan et al. (2015) Evaluation of portability and cost of a fluorescent PCR ribotyping protocol for Clostridium difficile epidemiology. J Clin Microbiol 53:1192-7
Rao, Krishna; Erb-Downward, John R; Walk, Seth T et al. (2014) The systemic inflammatory response to Clostridium difficile infection. PLoS One 9:e92578
Walk, Seth T; Micic, Dejan; Galecki, Andrzej T et al. (2013) Reply to Walker et al. Clin Infect Dis 56:1846-7
Rao, Krishna; Berland, Daniel; Young, Carol et al. (2013) The nose knows not: poor predictive value of stool sample odor for detection of Clostridium difficile. Clin Infect Dis 56:615-6
Behroozian, Adam A; Chludzinski, Jeffrey P; Lo, Eugene S et al. (2013) Detection of mixed populations of Clostridium difficile from symptomatic patients using capillary-based polymerase chain reaction ribotyping. Infect Control Hosp Epidemiol 34:961-6
Natarajan, Mukil; Walk, Seth T; Young, Vincent B et al. (2013) A clinical and epidemiological review of non-toxigenic Clostridium difficile. Anaerobe 22:1-5

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