Resequencing microarray for rapid detection & antimicrobial resistance profiling

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DESCRIPTION (provided by applicant): 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. Drs. Andersen, Brodie and DeSantis of LBNL have created a number of microarrays e.g. the 16S rRNA PhyloChip that detects all known bacteria and archaea. Drs. Lynch and Flanagan of UCSF have previously used the PhyloChip to describe bacterial community dynamics associated with antimicrobial resistant pathogen proliferation in clinical samples from critically ill patients during antimicrobial administration. Drs. Wiener-Kronish and Miller of UCSF are physician-scientists. Drs. MacDougall and Yang of UCSF are antimicrobial pharmacists, who will obtain clinical samples for testing and validation. Dr. Foxall will bring the industrial expertise of Affymetrix, world leaders in microarray development, to make the proposed tool a clinical device based on the latest state-of-the-science technology. Dr. Segal of UCSF is a statistician and bioinformatics expert with particular expertise in microarray analysis. 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.