DNA Microarray-based Detection of Bacteria in Samples Containing Antibiotics: Effect of Antibiotics on the Performance of Pathogen Detection Assays

In pathogen diagnostics, conventional culture-based assays remain the gold-standard; however, they are time-consuming, and shows the low positivity rate. Prior treatment with antibiotics is one of the major factors lowering the culture positivity rate. It is therefore important to evaluate the effects of prior antibiotic treatment on established detection methods and to develop sensitive and specific methods for detecting pathogens. Here, we report the detection of bacteria in samples containing antibiotics. Escherichia coli and Klebsiella pneumoniae were chosen as model and they were independently inoculated into culture flasks along with ceftriaxone (0.5× MIC, 1× MIC, 2× MIC). After 0, 2, 4, 6, 12, and 24 h, samples were collected from each flask and divided into two for evaluation using microarray or BacT/Alert culture-based systems. The newly designed probes showed a detection limit of 101 CFU for E. coli and 102 CFU for K. pneumoniae with high specificities. DNA microarray obtained true positive results at approximately 4 to 24 h after antimicrobial treatment, in which the culture-based method failed to detect the pathogenic bacteria. The DNA microarray-based assay could be useful for efficient detection of pathogenic bacteria in a clinical setting, allowing for appropriate administration of antibiotics in infected patients.