Development and validation of a resistance and virulence gene microarray targeting Escherichia coli and Salmonella enterica


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Davis M. A. , Lim J. Y. , Soyer Y. , Harbottle H., Chang Y., New D., ...More

JOURNAL OF MICROBIOLOGICAL METHODS, vol.82, no.1, pp.36-41, 2010 (Journal Indexed in SCI) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 82 Issue: 1
  • Publication Date: 2010
  • Doi Number: 10.1016/j.mimet.2010.03.017
  • Title of Journal : JOURNAL OF MICROBIOLOGICAL METHODS
  • Page Numbers: pp.36-41
  • Keywords: Microarray, Validation, Resistance genes, Enterobacteriaceae, DIFFERENTIALLY EXPRESSED GENES, MEDIATED QUINOLONE RESISTANCE, ANTIMICROBIAL RESISTANCE, DNA MICROARRAY, OLIGONUCLEOTIDE MICROARRAY, MOLECULAR CHARACTERIZATION, PLATFORM COMPARABILITY, BETA-LACTAMASES, GENOME SEQUENCE, QUALITY-CONTROL

Abstract

A microarray was developed to simultaneously screen Escherichia coli and Salmonella enterica for multiple genetic traits. The final array included 203 60-mer oligonucleotide probes, including 117 for resistance genes, 16 for virulence genes, 25 for replicon markers, and 45 other markers. Validity of the array was tested by assessing inter-laboratory agreement among four collaborating groups using a blinded study design. Internal validation indicated that the assay was reliable (area under the receiver-operator characteristic curve = 0.97). Inter-laboratory agreement, however, was poor when estimated using the intraclass correlation coefficient, which ranged from 0.27 (95% confidence interval 0.24, 0.29) to 0.29 (0.23, 0.34). These findings suggest that extensive testing and procedure standardization will be needed before bacterial genotyping arrays can be readily shared between laboratories. (C) 2010 Elsevier B.V. All rights reserved.