2209. Epigenomic Landscape of Clostridium difficile: Largely Neglected Complexity and Opportunity Learned from 45 Hospital Isolates
Session: Poster Abstract Session: Microbial Pathogenesis
Saturday, October 29, 2016
Room: Poster Hall
Background: Clostridium difficile infection (CDI) is a major concern in healthcare settings worldwide. It is critical to understand microbial factors that govern susceptibility to infection and disease. While significant insights have been obtained into genetic factors, epigenetic factors (specifically DNA methylations) have largely been ignored. Recent studies have found that DNA methylations play important roles in the regulation of virulence, antibiotic resistance and host-pathogen interactions, in a variety of bacterial pathogens. This motivated us to chart the epigenomic landscape of C. diff.

Methods: 45 clonal C. diff isolates from CDI fecal samples were obtained using protocols developed in an ongoing Pathogen Surveillance Program. Single-molecule Real-time sequencing were used for long read genome sequencing at high depth (mean read length >8,000bp; >100x coverage). An integrated pipeline was used for de novo genome assembly. Custom scripts were used for 1) methylation motif discovery; 2) characterization of cell-to-cell epigenetic heterogeneity; 3) comparative epigenomic analyses; 4) epigenetic regulators that controls methylation are identified and integrated into a functional genomic analysis.

Results: 54 high quality methylation motifs were discovered across the 45 isolates. On average, each isolate has 3.2 methylation motifs. A Type IIG methyltransferase (MTase) is the regulator of a methylation motif highly prevalent across the 45 isolates. This MTase does not have a cognate restriction enzyme, a feature that is often associated with epigenetic regulation of gene expression and pathogenicity. An integrative functional genomic analysis found that this MTase is essential for spore formation. The comparative epigenomic analyses suggest epigenetic regulation of several genes related to sporulation and pathogenicity. Cell-to-cell epigenetic heterogeneity was observed in multiple clonal isolates.

Conclusion: C. diff epigenome has high diversity, complexity and cell-to-cell heterogeneity. Multiple evidences suggest possible epigenetic regulation of sporulation and pathogenicity. Our innovative study and ongoing efforts will shed new light on the largely neglected epigenomic landscape of C. diff and open new possibilities for more the effective diagnosis, treatment and prevention of CDI.

Alex Kim, BS1, Shijia Zhu, PhD1, John Beaulaurier, MS1, Gintaras Deikus, PhD1, Theodore Pak, AB1, Martha Lewis, BS1, Deena Altman, MD2, Elizabeth Webster, BS1, Ali Bashir, PhD1, Camille Hamula, PhD3, Shirish Huprikar, MD4, Eric Schadt, PhD1, Robert Sebra, Ph.D.1, Harm Van Bakel, PhD1, Andrew Kasarskis, PhD1 and Gang Fang, PhD1, (1)Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, (2)Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, (3)Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, (4)Division of Infectious Diseases, Department of Medicine, Mount Sinai Hospital, New York, NY


A. Kim, None

S. Zhu, None

J. Beaulaurier, None

G. Deikus, None

T. Pak, None

M. Lewis, None

D. Altman, None

E. Webster, None

A. Bashir, None

C. Hamula, None

S. Huprikar, None

E. Schadt, None

R. Sebra, None

H. Van Bakel, None

A. Kasarskis, None

G. Fang, None

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