Title: Genomic Diversity of Escherichia Isolates from Diverse Habitats

Abstract

Our understanding of the Escherichia genus is heavily biased toward pathogenic or commensal isolates from human or animal hosts. Recent studies have recovered Escherichia isolates that persist, and even grow, outside these hosts. Although the environmental isolates are typically phylogenetically distinct, they are highly related to and phenotypically indistinguishable from their human counterparts, including for the coliform test. To gain insights into the genomic diversity of Escherichia isolates from diverse habitats, including freshwater, soil, animal, and human sources, we carried out comparative DNA-DNA hybridizations using a multi-genome E. coli DNA microarray. The microarray was validated based on hybridizations with selected strains whose genome sequences were available and used to assess the frequency of microarray false positive and negative signals. Our results showed that human fecal isolates share two sets of genes (n>90) that are rarely found among environmental isolates, including genes presumably important for evading host immune mechanisms (e.g., a multi-drug transporter for acids and antimicrobials) and adhering to epithelial cells (e.g., hemolysin E and fimbrial-like adhesin protein). These results imply that environmental isolates are characterized by decreased ability to colonize host cells relative to human isolates. Our study also provides gene markers that can distinguish human isolates from thosemore » of warm-blooded animal and environmental origins, and thus can be used to more reliably assess fecal contamination in natural ecosystems.« less

Authors:

Oh, Seungdae ^[1]; Buddenborg, Sarah ^[2]; Yoder-Himes, Deborah R. ^[2]; Tiedje, James M. ^[2]; Konstantinidis, Konstantinos T. ^[3]

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+ Show Author Affiliations

1. Georgia Institute of Technology, Atlanta, GA (United States); Michigan State University, East Lansing, MI (United States)
2. Michigan State University, East Lansing, MI (United States)
3. Georgia Institute of Technology, Atlanta, GA (United States)

Publication Date:

Mon Oct 08 00:00:00 EDT 2012

Research Org.:

Michigan State Univ., East Lansing, MI (United States); Georgia Institute of Technology, Atlanta, GA (United States)

Sponsoring Org.:

USDOE Office of Science (SC); National Science Foundation (NSF)

OSTI Identifier:

1904625

Grant/Contract Number:  

FG02-07ER64389; DEB-0516252

Resource Type:

Accepted Manuscript

Journal Name:

PLoS ONE

Additional Journal Information:

Journal Volume: 7; Journal Issue: 10; Journal ID: ISSN 1932-6203

Publisher:

Public Library of Science

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; microarrays; Escherichia; genomics; Escherichia coli; genomic signal processing; animal phylogenetics; evolutionary genetics; human genomics