DNA Microarray for Direct Identification of Bacterial Pathogens in Human Stool Samples

Abstract

AIM: To establish and evaluate a quick and accurate DNA microarray method to detect intestinal pathogens directly from human diarrheal stool samples as an alternative to traditional culture methods. METHOD: Primers and 21 oligonucleotide probes based on sequences of the bacterial 16SrRNA gene were arrayed on microarray slides. Hybridization between probes and amplicons was performed. To determine the consistency of DNA microarray and culture method, 1,500 samples of clinical diarrheal stool and 200 samples of normal stool from healthy individuals were examined in a double-blind fashion. Basic information from patients was collected and analyzed. RESULT: Our data showed that the probes of the assay were successful in discriminating 14 genera or species of intestinal pathogens. The limit of detection was approximately 10(3) CFU/ml for one species of pathogen. Of the 1,500 clinical cases, 32.7% of the patient stools were positive for bacteria. Using stool culture as a control, gene-chip sensitivity was 100%, specificity 95.2%, and index of accurate diagnosis 0.952. CONCLUSION: Our data suggested that DNA microarray with its high efficiency and accuracy could be used as an alternative to the culture method.