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

Davis, Margaret A.
Lim, Ji Youn
Soyer, Yeşim
Harbottle, Heather
Chang, Yung-Fu
New, Daniel
Orfe, Lisa H.
Besser, Thomas E.
Call, Douglas R.
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.