Real-time PCR for universal antibiotic susceptibility testing

Objectives: Determination of bacterial antimicrobial susceptibility is usually performed using phenotypic methods. In this study, we developed a universal 16S rRNA and rpoB quantitative PCR assay for susceptibility testing of bacteria commonly isolated in clinical microbiology laboratories. Methods: Antibiotic susceptibilities for 24 bacterial strains of various species were tested by real-time quantitative PCR assay and by conventional methods. Quantification of DNA copies of either the 16S RNA genes or rpoB were recorded over time in the presence or absence of antibiotics to determine the bacterial growth kinetics and the optimal testing time. Results: Molecular results for antibiotic susceptibility or resistance were in accordance with those obtained using a standard macrodilution broth assay. The method was reproducible, sensitive and rapid (2 h for Gram-negative bacilli and 4 h for Gram-positive cocci). Moreover, this assay was also able to determine the antibiotic susceptibilities of fastidious bacteria, such as mycobacteria, within 5 days. Conclusions: These results demonstrate that molecular detection of bacteria could be more rapid than phenotypic methods for antibiotic susceptibility testing.