Probe Hybridization Array Typing: a Binary Typing Method for Escherichia coli

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 uni...

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Bibliographic Details
Published in:Journal of Clinical Microbiology 2007-01, Vol.45 (1), p.206-214
Main Authors: Srinivasan, U, Zhang, L, France, A.M, Ghosh, D, Shalaby, W, Xie, J, Marrs, C.F, Foxman, B
Format: Article
Language:English
Subjects:
Adolescent
Adult
Bacterial Typing Techniques
Bacteriology
Biological and medical sciences
DNA Probes
DNA, Bacterial - analysis
DNA, Bacterial - genetics
Electrophoresis, Gel, Pulsed-Field
Epidemiology
Escherichia coli
Escherichia coli - classification
Escherichia coli - genetics
Escherichia coli - isolation & purification
Escherichia coli Infections - epidemiology
Escherichia coli Infections - microbiology
Female
Fundamental and applied biological sciences. Psychology
Humans
Infectious diseases
Medical sciences
Microbiology
Miscellaneous
Nucleic Acid Hybridization - methods
Polymerase Chain Reaction
Rectum - microbiology
Reference Standards
Sequence Analysis, DNA
Urinary Tract Infections - epidemiology
Urinary Tract Infections - microbiology
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Summary: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.
ISSN:0095-1137
1098-660X
1098-5530
DOI:10.1128/JCM.01543-06