Author ORCID Identifier

0000-0003-3038-161X

Date of Graduation

8-2020

Document Type

Thesis (MS)

Program Affiliation

Microbiology and Molecular Genetics

Degree Name

Masters of Science (MS)

Advisor/Committee Chair

Charles Darkoh, Ph.D.

Committee Member

Cesar Arias, M.D., Ph.D.

Committee Member

Anne-Marie Krachler, Ph.D.

Committee Member

Steven Norris, Ph.D.

Committee Member

Shane Cunha, Ph.D.

Abstract

C. difficile is a nosocomial, opportunistic pathogen that has become more hypervirulent over the last decade. Vancomycin is currently a frontline antibiotic for the treatment of C. difficile infections. Yet, strains of C. difficile are becoming non-susceptible to vancomycin. Emergence of the vancomycin non-susceptible phenotype has led to various questions including: What resistance elements are present that might contribute to the phenotype? Are these elements located on the chromosome or a plasmid? Where did these elements originate from? To address these questions, whole genome sequence analysis was performed to survey genes that may be involved in the vancomycin non-susceptible phenotype. Bioinformatic analysis was used to answer whether putative vancomycin-resistance genes were chromosomal or plasmid based. Culture-dependent methods were used to detect enterococci from stools of patients from Texas and Kenya infected with C. difficile and this was supplemented with patient data to describe co-colonization in the gut and its effects on patients.

The sequencing analysis revealed the presence of a putative van gene cluster in all isolates tested. The presence of vancomycin-resistance elements varied among the isolates and included: vanRS, vanW, vanH, and vanZ. In silico analysis of sequences suggested that the putative vancomycin-resistance genes were chromosomal. A high prevalence of enterococci and vancomycin-resistant enterococci (VRE) was observed in the stools of C. difficile patients from both Kenya and Texas. In addition, the presence of enterococci increased the duration of CDI symptoms and this might also promote selection of non-spore forming C. difficile isolates. Finally, high proportions of VRE and non-susceptible C. difficile isolates were found in the same stools, suggesting a potential source of resistance elements.

Although rigorous functional analysis is needed to confirm the specific genes responsible for vancomycin non-susceptibility in C. difficile, the presence of vancomycin-resistance genes underlines a promising avenue for further experimentation. Knowing that the genes are likely chromosomal will help in downstream characterization of these genes. Given the correlation between vancomycin-resistant enterococci and the vancomycin non-susceptibility phenotype in C. difficile, and the shared epidemiology between the two bacteria, it is plausible that these resistance elements may have originated from Enterococci spp, however, further genetic analysis is needed to confirm this observation. Overall, this study has shed some light on the mechanism of vancomycin non-susceptibility in C. difficile and has highlighted avenues for further exploration. Moreover, the relationship between Enterococci spp. and C. difficile during infection has become clearer and might enhance future treatment strategies

Keywords

C. difficile, vancomycin resistance, enterococcus, CDI

Available for download on Tuesday, August 10, 2021

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