Identification of Enterococcus, Streptococcus, and Staphylococcus by multivariate analysis of proton magnetic resonance spectroscopic data from plate cultures

Abstract

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.

FIG. 1

(A) Representative ¹H MR spectra of E. faecalis, S. milleri, S. pneumoniae, and S. pyogenes isolates. Refer to Table 2 for the identity of the major metabolites contributing to the spectra in each integration region. (B) Representative ¹H MR spectra of S. epidermidis, S. aureus, and S. agalactiae isolates. The intense betaine peaks in the spectra of S. aureus and S. epidermidis and the glycerol phosphocholine (GPC) peak of S. agalactiae have been truncated to show details of the less intense peaks. The relative intensities of the betaine and glycerol phosphocholine peaks can be seen in Fig. 2. Refer to Table 2 for the identity of the major metabolites contributing to the spectra in each integration region.

FIG. 2

Range of measured integral intensities for each species group. The means (bars) and standard deviations (error bars) are shown.

FIG. 2

Range of measured integral intensities for each species group. The means (bars) and standard deviations (error bars) are shown.