A MICROARRAY-BASED DIAGNOSTIC ASSAY FOR THE IDENTIFICATION OF CIPROFLOXACIN-RESISTANT YERSINIA PESTIS

Abstract

The potential use of Yersinia pestis as a biological threat agent and the emergence of antibiotic resistance increase public health concerns. The goal of this project was to develop a microarray-based assay for the simultaneous detection of a variety of single nucleotide polymorphisms (SNPs) that confer resistance to the drug ciprofloxacin. The CombiMatrix SNP detection platform was chosen for its post-hybridization extension and ligation steps which increase assay stringency. The 5' nucleotide of the hybridization probe discriminates between the SNP or wild-type base. In the presence of a complementary base, ligation occurs. Ligation fails if a mismatch is present. Although correct base calls were made for the wild-type and one mutant strain, the SNPs present in four other strains were not correctly identified every time. While microarray technology addresses the challenge of simultaneous SNP detection, the variable performance of the CombiMatrix platform makes it unsuitable for this application.