Next to sequencing the most powerfull new technique is MaldiTof identification, using peptide fragments.

read for example Article MALDI-TOF mass spectrometry: An emerging technology for micr...

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The analytical profile index or API is a classification of bacteria based on experiments, allowing fast identification. This system is developed for quick identification of clinically relevant bacteria. Because of this, only known bacteria can be identified.

The API 20E/NE fast identification system combines some conventional tests and allows the identification of a limited number of Gram-negative Enterobacteriaceae or non-Enterobacteriaceae. The test systems are stored in 20 small reaction tubes, which include the substrates. An identification is only possible with microbiological culture. To guarantee a comparability of different samples, follow the instructions of the manufacturer.

Concerning identification of medical relevant bacteria state-of-the-art is MALDI-ToF (with a few exceptions). MALDI provides results within minutes and has a high discriminatory power for most bacteria. Sequencing requires special expertise and equipment. 16S rDNA sequencing will give you a comparable discriminatory power as MALDI-ToF. Whole genome sequencing, however, provides not only the identification but resistance markers, virulence factors and typing loci as well. Both techniques, however, are of high cost. In MALDI the initial investment is pretty high (while the single measurement is than cheap) while for WGS the equipment is of medium cost but each run is costly and requires bioinformatics expertise.

Biochemical characterization is still the standard in many labs around the globe. Miniaturized systems are available for manual work (API) or (semi-)automated processing (Vitek, Phoenix, ...).

API is an affordable technique which works quite well (no initial investment) with a discriminatory power comparable to other biochemical tests like VITEK or Phoenix (which are associated with high instrument cost, while the cost per test is usually comparable or higher to that of an API strip).