Label-free, rapid and quantitative phenotyping of stress response in E. coli via ramanome

Abstract

Rapid profiling of stress-response at single-cell resolution yet in a label-free, non-disruptive and mechanism-specific manner can lead to many new applications. We propose a single-cell-level biochemical fingerprinting approach named “ramanome”, which is the collection of Single-cell Raman Spectra (SCRS) from a number of cells randomly selected from an isogenic population at a given time and condition, to rapidly and quantitatively detect and characterize stress responses of cellular population. SCRS of Escherichia coli cells are sensitive to both exposure time (eight time points) and dosage (six doses) of ethanol, with detection time as early as 5 min and discrimination rate of either factor over 80%. Moreover, the ramanomes upon six chemical compounds from three categories, including antibiotics of ampicillin and kanamycin, alcohols of ethanol and n-butanol and heavy metals of Cu2+ and Cr6+, were analyzed and 31 marker Raman bands were revealed which distinguish stress-responses via cytotoxicity mechanism and variation of inter-cellular heterogeneity. Furthermore, specificity, reproducibility and mechanistic basis of ramanome were validated by tracking stress-induced dynamics of metabolites and by contrasting between cells with and without genes that convey stress resistance. Thus ramanome enables rapid prediction and mechanism-based screening of cytotoxicity and stress-response programs at single-cell resolution.

Detection and classification of Bacteria using Raman Spectroscopy Combined with Multivariate Analysis

“…Another characteristic peak for biological samples is the distinct Amide I peak which appears at 1668 cm -1 . These spectral features were found to be consistent with the earlier reported literature and have been compiled inTable 1 12,[34][35][36][37][38] . The Raman shifts for all the four strains closely resembles each other and therefore, it is quite challenging to identify strains based on merely comparing the spectral frequencies or amplitude.…”

“…The Raman shifts for all the four strains closely resembles each other and therefore, it is quite challenging to identify strains based on merely comparing the spectral frequencies or amplitude. Therefore, [12,[34][35][36][37][38] . in order to discriminate the bacteria unequivocally, one has to resort to multivariate analyses tools.…”

Raman spectral signature reflects transcriptomic features of antibiotic resistance in Escherichia coli

“…of cysteineNucleic acid, proteinNotingher et al 30 Teng et al 15 ~730A ring breath.Nucleic acidNotingher et al 30 ~752δ(C–C) TyrProtein, cytochromeNotingher et al 30 ~786C, T, U ring br., ν PO 2 groupNucleic acidNotingher et al 30 Moritz et al 9 ~818O–P–O stretch. DNA, TyrNucleic acid, proteinTeng et al 15 ~853ν(C–C) proline, ring breath. TyrProtein (glycogen, collagen)De Gelder et al 31 Notingher et al 30 ~878ν(C–C), COH ringLipid, carbohydrateNotingher et al 30 ~922R-CH 3 L-alanineDe Gelder et al 31 ~936C–O–C linkage, C–C stretch., α-helixCarbohydrate, proteinDe Gelder et al 31 ~950CholesterolTeng et al 15 Surmacki et al 29 ~972CH 2 rock., C–C stretch., α-helixProtein, lipidMoritz et al 9 ~989β-sheetProtein, histamineDe Gelder et al 31 ~1001Phe ring breath., C–C skeletal (protein)Phenylalanine, proteinNotingher et al 30 Teng et al 15 ~1030δ(CH) bend., Tyr, PheAromatic compoundDe Gelder et al 31 Notingher et al 30 .~1079PO2 str., (C–C) stretch., C–ONucleic acid, lipid, carbohydratesNotingher et al 30 ~1101Symmetric phosphate stretch.…”

Culture‐Free Detection of Crop Pathogens at the Single‐Cell Level by Micro‐Raman Spectroscopy

“…alliicola and E. chrysanthemi were grown in NB medium. Moreover, all bacterial samples were washed with distilled water immediately prior to spectrum collection to minimize background signal contributed by different culture media 23. Raman spectroscopy has been demonstrated to be effective in discriminating microorganisms either in synchronized cultures, the stationary growth phase of unsynchronized cultures, or random growth phases of unsynchronized cells 28.…”

“…In particular, surface‐enhanced Raman scattering spectroscopy is able to enhance the signal by 11 orders of magnitude, which is sufficient for single‐molecule detection 14. Therefore, micro‐Raman spectroscopy has been utilized to monitor bacterial development, probe cellular stress response, analyze functions of microbial communities, and detect clinically relevant bacteria in laboratory settings 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24. We also utilized Raman microspectroscopy to probe bacterial metabolism and interactions9, 25 and isolate single cells 26.…”