title: Development and validation of a resistance and virulence gene microarray targeting Escherichia coli and Salmonella enterica.
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.
authors.affiliation: Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-7040, United States. madavis@vetmed.wsu.edu
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Davis
authors.forename: Ji Youn
authors.initials: JY
authors.lastname: Lim
authors.forename: Yesim
authors.initials: Y
authors.lastname: Soyer
authors.forename: Heather
authors.initials: H
authors.lastname: Harbottle
authors.forename: Yung-Fu
authors.initials: YF
authors.lastname: Chang
authors.forename: Daniel
authors.initials: D
authors.lastname: New
authors.forename: Lisa H
authors.initials: LH
authors.lastname: Orfe
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Besser
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Call
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics*; D024901:Drug Resistance, Multiple, Bacterial; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D008826:Microbial Sensitivity Tests; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D019779:Salmonella enterica / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D037521:Virulence Factors / Q000235:genetics*
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D037521:Virulence Factors