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Journal of Clinical Microbiology, April 2006, p. 1495-1501, Vol. 44, No. 4
0095-1137/06/$08.00+0     doi:10.1128/JCM.44.4.1495-1501.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Differentiation of Escherichia coli Pathotypes by Oligonucleotide Spotted Array

Raghavan U. M. Palaniappan,¹ Yu Zhang,¹ David Chiu,¹ Alfonso Torres,¹ Chobi DebRoy,² Thomas S. Whittam,³ and Yung-Fu Chang^1*

Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853,¹ Gastroenteric Disease Center, Department of Veterinary Science, The Pennsylvania State University, University Park, Pennsylvania 16802,² Microbial Evolution Laboratory, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824³

Received 27 July 2005/ Returned for modification 28 September 2005/ Accepted 11 January 2006

To accurately determine the pathotypes of Escherichia coli strains, a comprehensive assessment of each strain that targets multiple genes is required. A new approach to the identification and characterization of E. coli pathotypes was developed by constructing gene-specific probes (70-mers) for not only the virulence genes associated with each E. coli pathotype but also the O157-, CFT073-, and K-12-specific and common genes of each pathotype. Analysis of oligonucleotide probes with reference and clinical isolates of E. coli pathotypes indicated that the array could differentiate the pathotypes on the basis of their virulence and specific gene patterns. Probes targeting common genes of E. coli were present in all the reference and clinical strains. Salmonella enterica subsp. enterica-specific genes and Salmonella core genes were used as negative controls. The entire E. coli pathotype showed reactivity to only 4 of the 81 Salmonella-specific gene probes. Characterization of the genetic and virulence profiles of a single strain by using probes for virulence factors and specific and common genes in the spotted array is an ideal diagnostic tool for determination of E. coli pathotypes and could also have a significant impact on the epidemiological analysis of E. coli infections.

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* Corresponding author. Mailing address: Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853. Phone: (607) 253-3675. Fax: (607) 253-3943. E-mail: yc42{at}cornell.edu.

Supplemental material for this article may be found at http://jcm.asm.org/.

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Journal of Clinical Microbiology, April 2006, p. 1495-1501, Vol. 44, No. 4
0095-1137/06/$08.00+0     doi:10.1128/JCM.44.4.1495-1501.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

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