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Fingerprinting of Campylobacter jejuni by using resolution-optimized binary gene targets derived from comparative genome hybridization studies

Price, Erin P., Huygens, Flavia and Giffard, Philip M. (2006). Fingerprinting of Campylobacter jejuni by using resolution-optimized binary gene targets derived from comparative genome hybridization studies. Applied and Environmental Microbiology,72(12):7793-7803.

Document type: Journal Article
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IRMA ID 10603xPUB47
Title Fingerprinting of Campylobacter jejuni by using resolution-optimized binary gene targets derived from comparative genome hybridization studies
Author Price, Erin P.
Huygens, Flavia
Giffard, Philip M.
Journal Name Applied and Environmental Microbiology
Publication Date 2006
Volume Number 72
Issue Number 12
ISSN 0099-2240   (check CDU catalogue open catalogue search in new window)
Start Page 7793
End Page 7803
Total Pages 11
Place of Publication Washington, United States
Publisher American Society for Microbiology
Field of Research 0604 - Genetics
0799 - Other Agricultural and Veterinary Sciences
1099 - Other Technology
HERDC Category C1 - Journal Article (DEST)
Abstract The aim of this investigation was to exploit the vast comparative data generated by comparative genome hybridization (CGH) studies of Campylobacter jejuni in developing a genotyping method. We examined genes in C. jejuni that exhibit binary status (present or absent between strains) within known plasticity regions, in order to identify a minimal subset of gene targets that provide high resolution genetic fingerprints. Using CGH data from three studies as input, binary gene sets were identified with "Minimum SNPs" software. "Minimum SNPs" selects for the minimum number of targets required to obtain a predefined resolution, based on Simpson's Index of Diversity (D). After implementing stringent criteria for gene presence/absence, eight binary genes were found that provided 100% resolution (D=1) of 20 C. jejuni strains. A real-time PCR assay was developed and tested on 181 C. jejuni and Campylobacter coli isolates, a subset of which have been previously characterised by multilocus sequence typing (MLST), flaA short variable region sequencing and pulsed-field gel electrophoresis (PFGE). In addition to the binary gene real-time PCR assay, we refined the seven-member single nucleotide polymorphism (SNP) real-time PCR assay previously described for C. jejuni and C. coli. By normalising the SNP assay with the respective C. jejuni and C. coli ubiquitous genes, mapA and ceuE, the polymorphisms at each SNP could be determined without separate reactions for every polymorphism. We have developed and refined a rapid, highly discriminatory genotyping method for C. jejuni and C. coli that uses generic technology and which is amenable to high-throughput analyses.
Keywords Campylobacter jejuni
DOI http://dx.doi.org/10.1128/AEM.01338-06   (check subscription with CDU E-Gateway service for CDU Staff and Students  check subscription with CDU E-Gateway in new window)


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