The advent of new molecular technologies in genomics and proteomics is shifting traditional techniques for bacterial classification, identification, and characterization in the 21st century toward methods based on the elucidation of specific gene sequences or molecular components of a cell. We discuss current genotypic and proteomics technologies for bacterial identification and characterization, and present an overview of how these new technologies complement conventional approaches. The new methods can be rapid, offer high throughput, and produce unprecedented levels of discrimination among strains of bacteria and archaea. Remaining challenges include developing appropriate standards and methods for these techniques' routine application and establishing integrated databases that can handle the large amounts of data that they generate. We conclude by discussing the impacts of rapid bacterial identification on the environment and public health, as well as directions for future development in this field.
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