Bacterial Identification Based on Universal Gene Amplification and Sequencing

Abstract

Accurate identification of bacterial isolates is one of the fundamental tasks in clinical microbiology laboratories. This is critical in providing a microbiological diagnosis to an infectious disease and guiding appropriate antibiotic treatment as well as infection control measures. On the population scale, accurate bacterial identification is important for defining epidemiology of infectious diseases. Traditionally, identification of bacteria in clinical microbiology laboratories is performed using conventional phenotypic tests, including Gram smear, cultural requirements, growth characteristics, and biochemical tests. These tests are relatively inexpensive and accurate for most commonly encountered bacteria in clinical laboratories. However, in certain circumstances, these phenotypic tests may fail to work and more sophisticated methods may be required. For example, accurate identification of anaerobic bacteria and mycobacteria may require special equipment and expertise such as gas chromatography–mass spectrometry. Moreover, phenotypic methods often fail to identify rare bacteria or bacteria which exhibit variable expression of certain traits, and are associated with ambiguity in determining end point reactions. As phenotypic methods rely on the availability of pure culture for the study of growth characteristics and biochemical profiles, it also takes considerable time for slow-growing bacteria to be identified. Furthermore, these methods are not applicable for noncultivable bacteria and in culture-negative infections.