A new fingerprinting technique with the potential for rapid identification of bacteria was developed by combining proton magnetic resonance spectroscopy ( 1 H MRS) with multivariate statistical analysis. This resulted in an objective identification strategy for common clinical isolates belonging to the bacterial species Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus agalactiae, and the Streptococcus milleri group. Duplicate cultures of 104 different isolates were examined one or more times using 1 H MRS. A total of 312 cultures were examined. An optimized classifier was developed using a bootstrapping process and a seven-group linear discriminant analysis to provide objective classification of the spectra. Identification of isolates was based on consistent high-probability classification of spectra from duplicate cultures and achieved 92% agreement with conventional methods of identification. Fewer than 1% of isolates were identified incorrectly. Identification of the remaining 7% of isolates was defined as indeterminate.In both clinical and industrial laboratories, methods for identification of microorganisms have historically been based on multiple phenotypic characters, including morphological features and a range of biochemical reactions. These tests are often time-consuming and/or relatively expensive in their application, and some are imprecise. Recently, alternative methods have been investigated in an attempt to develop a single, rapid method for characterization and identification of microorganisms. These have included Fourier transform infrared spectroscopy (11,14), pyrolysis mass spectrometry (12), electrospray ionization mass spectrometry (7), UV resonance Raman spectroscopy (15), and protein electrophoresis (16). While reports of these techniques suggest the possibility of rapid and reliable identification of some groups of microorganisms, most have been tested with small data sets. With the exception of Fourier transform infrared spectroscopy, they are destructive techniques which analyze cellular decomposition products. All have the limitation that they do not directly yield information about the biochemistry of the intact viable organism.In contrast, magnetic resonance spectroscopy (MRS) of viable cells can provide information on a large range of metabolites. Biological applications of MRS most commonly exploit the noninvasive nature of the technique to study aspects of cellular biochemistry in living systems (6). However, not all applications of MRS require or include identification of the metabolites contributing to the MR spectrum. Pattern recognition techniques, which detect gross spectral characteristics associated with a priori-defined classes (such as pathological conditions), have been successfully applied to MRS of both tissues and body fluids. Accurate and reliable classifiers based on multivariate analyses of 1 H MR spectroscopic data have been developed and validated for objective diagnosis of t...