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Applied and Environmental Microbiology, October 2009, p. 6534-6544, Vol. 75, No. 20
0099-2240/09/$08.00+0 doi:10.1128/AEM.01262-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Cryptic Lineages of the Genus Escherichia
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Seth T. Walk,1*
Elizabeth W. Alm,2
David M. Gordon,3
Jeffrey L. Ram,4
Gary A. Toranzos,5
James M. Tiedje,6 and
Thomas S. Whittam7
Department of Internal Medicine, University of Michigan Health System, 4618 Medical Science Building II, Ann Arbor, Michigan 48109,1 Department of Biology, Central Michigan University, 157 Brooks Building, Mount Pleasant, Michigan 48859,2 Research School of Biology, Australian National University, Building 116, Gould Wing, Canberra, ACT 0200, Australia,3 Department of Physiology, Wayne State University, 6112 Scott Hall, Detroit, Michigan 48202,4 Environmental Microbiology Laboratory, Department of Biology, P.O. Box 23360, University of Puerto Rico, San Juan, PR 00931-3360, Puerto Rico,5 Center for Microbial Ecology, and Departments of Crop and Soil Sciences and Microbiology and Molecular Genetics, Michigan State University, 540E Plant and Soil Science, East Lansing, Michigan 48824,6 Microbial Evolution Laboratory, National Food Safety and Toxicology Center, and Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 488247
Received 1 June 2009/ Accepted 17 August 2009
Extended multilocus sequence typing (MLST) analysis of atypical Escherichia isolates was used to identify five novel phylogenetic clades (CI to CV) among isolates from environmental, human, and animal sources. Analysis of individual housekeeping loci showed that E. coli and its sister clade, CI, remain largely indistinguishable and represent nascent evolutionary lineages. Conversely, clades of similar age (CIII and CIV) were found to be phylogenetically distinct. When all Escherichia lineages (named and unnamed) were evaluated, we found evidence that Escherichia fergusonii has evolved at an accelerated rate compared to E. coli, CI, CIII, CIV, and CV, suggesting that this species is younger than estimated by the molecular clock method. Although the five novel clades were phylogenetically distinct, we were unable to identify a discriminating biochemical marker for all but one of them (CIII) with traditional phenotypic profiling. CIII had a statistically different phenotype from E. coli that resulted from the loss of sucrose and sorbitol fermentation and lysine utilization. The lack of phenotypic distinction has likely hindered the ability to differentiate these clades from typical E. coli, and so their ecological significance and importance for applied and clinical microbiology are yet to be determined. However, our sampling suggests that CIII, CIV, and CV represent environmentally adapted Escherichia lineages that may be more abundant outside the host gastrointestinal tract.
* Corresponding author. Mailing address: Department of Internal Medicine, University of Michigan Health System, 4618 Medical Science Building II, Ann Arbor, MI 48109. Phone: (734) 763-4133. Fax: (734) 763-4168. E-mail: sethwalk{at}umich.edu
Published ahead of print on 21 August 2009.
Supplemental material for this article may be found at http://aem.asm.org/.
This work is dedicated to Thomas Whittam, now deceased, for his inspiring support and guidance throughout this project.
Applied and Environmental Microbiology, October 2009, p. 6534-6544, Vol. 75, No. 20
0099-2240/09/$08.00+0 doi:10.1128/AEM.01262-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
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