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Fingerprinting and characterisation of Escherichia coli isolates using DNA arrays

Fingerprinting and characterisation of Escherichia coli isolates using DNA arrays

Van Ijperen, Antonia Cornelia (2005) Fingerprinting and characterisation of Escherichia coli isolates using DNA arrays. PhD thesis, University of Greenwich..

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Abstract

Two commercially available DNA whole genome Escherichia coli K12 arrays were compared to identify a subset of markers for typing. The arrays were identical in probe composition but different in substrate (membrane and glass slide arrays) and probe preparation (radio- and fluorescent-labelled). Labelled genomic E. coli DNA from five strains of the E. coli reference (ECOR) collection (ATCT35320 - ATCX35324) and E. coli K12 were hybridised against these arrays. A group of 1240 putative markers was identified on the membrane arrays and 649 were found on the glass slide arrays. Only a small proportion of these sequences (8%) was found through both platforms. Variability in the hybridisation signals from duplicate experiments made it difficult to identify useful markers.

In order to investigate whether this technology could be used for characterising or typing E. coli strains, an array for the detection of 29 pathogenicity markers in E. coli strains was produced. This array was used with eight reference strains, including different pathotypes, 72 strains from the ECOR collection, and 49 clinical isolates. A wide range of E. coli pathogenicity markers was detected. The pathogenicity markers that were most common include chuA and iucC, which are both involved in iron metabolism. Additionally, the clinical isolates were grouped into clusters different from groupings based on biochemical tests. This demonstrates that the use of pathogenicity array typing can complement diagnostic tests on clinical E. coli isolates.

An extended, second-generation, pathogenicity marker array containing 75 probes was made. The extended array successfully distinguished between ten closely related isolates from an outbreak of urinary tract infections, while previous tests were unable to do so. This array has the potential for providing a rapid and novel means of characterising pathogenic isolates.

Item Type: Thesis (PhD)
Uncontrolled Keywords: E. coli, microbiology, microorganisms
Subjects: Q Science > QR Microbiology
Faculty / Department / Research Group: Faculty of Engineering & Science > Department of Life & Sports Sciences
Last Modified: 03 Mar 2018 15:11
Selected for GREAT 2016: None
Selected for GREAT 2017: None
Selected for GREAT 2018: None
URI: http://gala.gre.ac.uk/id/eprint/6329

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