Resequencing Microarray for Rapid Detection and Antimicrobial Resistance Profiling

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Investigator: Susan Lynch, PhD
Sponsor: NIH National Institute of Allergy and Infectious Disease

Location(s): United States

Description

The long-term objective of this application is to create and validate a diagnostic tool (a resequencing microarray), that will permit rapid detection of nosocomial pathogens, Clostridium difficile, Pseudomonas aeruginosa, Acinetobacterspp., Enterobacterspp., Klebsiella spp., Serratia marcescens, Proteus mirabilis and Stenotrophomonas maltophila as well as their antibiotic resistance gene polymorphisms within 8 hours. The team of investigators involved in this application represents a multidisciplinary group of scientists involved in the molecular detection of bacteria in environmental and clinical samples.  The proposed process involves selection of regions of genetic variation in biomarkers and antibiotic resistance determinants for pathogen identification and antibiotic resistance phenotype prediction; design and fabrication of an Affymetrix platform resequencing microarray, to be named the Bacterial Antibiotic Resistance GeneChip or BARChip which will interrogate each nucleotide position at the discriminatory loci selected; optimization of target preparation and hybridization processes to decrease time to result; clinical sample collection for final resequencing array validation in a CLIA certified laboratory followed by blinded validation of the BARChip with these prospectively collected clinical samples in the final year of the proposed project. This application would lead to the development of a diagnostic test that could rapidly determine whether a patient has a bacterial infection. The test would permit physicians to rapidly choose appropriate antibiotic(s) to treat the bacterial infection; this tool will also identify the strain of bacteria infecting patients, so outbreaks of infection could be rapidly identified and controlled.