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Journal of Clinical Microbiology, January 2007, p. 206-214, Vol. 45, No. 1
0095-1137/07/$08.00+0     doi:10.1128/JCM.01543-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Probe Hybridization Array Typing: a Binary Typing Method for Escherichia coli{triangledown}

U. Srinivasan,1 L. Zhang,1 A. M. France,1 D. Ghosh,2 W. Shalaby,1 J. Xie,1 C. F. Marrs,1 and B. Foxman1*

Department of Epidemiology,1 Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan 481092

Received 25 July 2006/ Returned for modification 11 September 2006/ Accepted 16 October 2006

The ability to distinguish between Escherichia coli strains is critical for outbreak investigations. Binary typing, based on the presence or absence of genetic material, provides a high-throughput alternative to gel- and PCR-based typing techniques that generate complex banding patterns and lack uniform interpretation criteria. We developed, validated, and determined the discriminatory power of an E. coli binary typing method, probe hybridization array typing (PHAT). In PHAT, the absence or presence of genetic material is identified by using DNA hybridization to produce a reproducible and portable fingerprint for each genome. PHAT probes were generated from genome subtractive hybridization experiments. We PHAT typed the ECOR collection of strains from a variety of geographical locations, and 33 rectal E. coli strains selected from college-aged women with urinary tract infection. In the set of 33 human rectal strains, the discriminatory power of PHAT (98%) equaled that of multilocus sequence typing (MLST) and pulsed-field gel electrophoresis. However, for ECOR strains, which include nonhuman strains, the current set of PHAT probes was less discriminating than MLST, ribotyping, and enterobacterial repetitive intergenic consensus sequence PCR (80% versus 97, 92, and 97%, respectively). When we limited the analysis to ECOR strains of B2 and D lineage, which are associated with human infection, current PHAT probes were highly discriminatory (94%). PHAT can be applied in a high-throughput format (i.e., "library on a slide"), the discriminatory ability can be varied based on the probe set, and PHAT is readily adapted to other bacterial species with high variation in genetic content.

* Corresponding author. Mailing address: Department of Epidemiology, University of Michigan, School of Public Health, 109 Observatory, Ann Arbor, MI 48109. Phone: (734) 764-5487. Fax: (734) 936-6732. E-mail: bfoxman{at}umich.edu.

{triangledown} Published ahead of print on 1 November 2006.

Journal of Clinical Microbiology, January 2007, p. 206-214, Vol. 45, No. 1
0095-1137/07/$08.00+0     doi:10.1128/JCM.01543-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



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