Abstract
Decreasing turnaround time is a paramount objective in clinical diagnosis. We evaluated the discrimination power of Raman spectroscopy when analyzing colonies from 80 strains belonging to nine bacterial and one yeast species directly on solid culture medium after 24-h (macrocolonies) and 6-h (microcolonies) incubation. This approach, that minimizes sample preparation and culture time, would allow resuming culture after identification to perform downstream antibiotic susceptibility testing. Correct identification rates measured for macrocolonies and microcolonies reached 94.1% and 91.5%, respectively, in a leave-one-strain-out cross-validation mode without any correction for possible medium interference. Large spectral differences were observed between macrocolonies and microcolonies, that were attributed to true biological differences. Our results, conducted on a very diversified panel of species and strains, were obtained by using simple and robust sample preparation and preprocessing procedures, while still confirming published results obtained by using more complex elaborated protocols. Instrumentation is simplified by the use of 532-nm laser excitation yielding a Raman signal in the visible range. It is, to our knowledge, the first side-by-side full classification study of microorganisms in the exponential and stationary phases confirming the excellent performance of Raman spectroscopy for early species-level identification of microorganisms directly from an agar culture.
Highlights
In vitro microbiological diagnostics are still heavily relying on time-consuming cultivation of microorganisms to identify infectious agents and to prescribe therapeutic antibiotics against the diseases they cause
Raman spectroscopy is a technology with strong assets for the use in in vitro diagnostic (IVD) applications as it is a sensitive technique amenable to automation,[1] nonintrusive and possibly nondestructive assuming a proper selection of acquisition parameters
It is commonly accepted that the higher fluorescence level observed at shorter wavelength should decrease the Raman signal-to-noise ratios (SNRs) and the classification performance, we demonstrated a good classification at 532 nm
Summary
In vitro microbiological diagnostics are still heavily relying on time-consuming cultivation of microorganisms to identify infectious agents and to prescribe therapeutic antibiotics against the diseases they cause. Because of long turnaround time (TAT), clinicians prescribe broad-spectrum antibiotics prior to the availability of a more precise diagnosis facilitating a more targeted therapy. This phenomenon added to the fact that fewer new antibiotics are being discovered constitutes a major public health problem. Raman spectroscopy is a technology with strong assets for the use in in vitro diagnostic (IVD) applications as it is a sensitive technique amenable to automation,[1] nonintrusive and possibly nondestructive assuming a proper selection of acquisition parameters.
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