The Use of DNA Methods to Characterize Biofilm Infection

Abstract

Because of biofilm’s fundamental properties—its polymicrobial nature (genetic diversity) and “viable but not culturable” microbial constituents—clinical cultures are wholly unsuited for evaluating chronic infections associated with biofilm. DNA-based technologies (molecular methods) have a number of advantages for evaluating human infections. Real-time PCR and sequencing technologies are particularly robust for identifying microorganisms in human environments because of development of their methods by the human microbiome project. DNA methods enjoy much higher sensitivity and specificity than cultivation methods for identifying microorganisms regardless of their phenotype. Moreover, real-time PCR can be quantitative in an absolute sense, while sequencing methods yield accurate relative quantification of all constituents of the sampled infection. All methods for microbial identification have biases, yet molecular methods suffer the least from these biases. Although DNA-based identification of microorganisms has the limitation that sensitivities to antibiotics cannot be determined in a Petri dish and must be determined by identifying mobile genetic resistance elements within the microbes, molecular methods are a significant improvement in the identification of microorganisms for human infections and are currently the only reliable technology for diagnosing biofilm infection.