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Bi X, Wang J, Xue B, He C, Liu F, Chen H, Lin LL, Dong B, Li B, Jin C, Pan J, Xue W, Ye J. SERSomes for metabolic phenotyping and prostate cancer diagnosis. Cell Rep Med 2024; 5:101579. [PMID: 38776910 PMCID: PMC11228451 DOI: 10.1016/j.xcrm.2024.101579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
Molecular phenotypic variations in metabolites offer the promise of rapid profiling of physiological and pathological states for diagnosis, monitoring, and prognosis. Since present methods are expensive, time-consuming, and still not sensitive enough, there is an urgent need for approaches that can interrogate complex biological fluids at a system-wide level. Here, we introduce hyperspectral surface-enhanced Raman spectroscopy (SERS) to profile microliters of biofluidic metabolite extraction in 15 min with a spectral set, SERSome, that can be used to describe the structures and functions of various molecules produced in the biofluid at a specific time via SERS characteristics. The metabolite differences of various biofluids, including cell culture medium and human serum, are successfully profiled, showing a diagnosis accuracy of 80.8% on the internal test set and 73% on the external validation set for prostate cancer, discovering potential biomarkers, and predicting the tissue-level pathological aggressiveness. SERSomes offer a promising methodology for metabolic phenotyping.
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Affiliation(s)
- Xinyuan Bi
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Jiayi Wang
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Bingsen Xue
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China; Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Chang He
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Fugang Liu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Haoran Chen
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Linley Li Lin
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Baijun Dong
- Department of Urology, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Science, Shanghai, P.R. China
| | - Butang Li
- Department of Urology, Ningbo Hangzhou Bay Hospital, Ningbo, Zhejiang, P.R. China
| | - Cheng Jin
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China; Shanghai Artificial Intelligence Laboratory, Shanghai, China; Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, P.R. China.
| | - Jiahua Pan
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China.
| | - Wei Xue
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China.
| | - Jian Ye
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China; Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, P.R. China; Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China.
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Frempong SB, Salbreiter M, Mostafapour S, Pistiki A, Bocklitz TW, Rösch P, Popp J. Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms. Molecules 2024; 29:1077. [PMID: 38474589 DOI: 10.3390/molecules29051077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
Raman spectroscopy is an emerging method for the identification of bacteria. Nevertheless, a lot of different parameters need to be considered to establish a reliable database capable of identifying real-world samples such as medical or environmental probes. In this review, the establishment of such reliable databases with the proper design in microbiological Raman studies is demonstrated, shining a light into all the parts that require attention. Aspects such as the strain selection, sample preparation and isolation requirements, the phenotypic influence, measurement strategies, as well as the statistical approaches for discrimination of bacteria, are presented. Furthermore, the influence of these aspects on spectra quality, result accuracy, and read-out are discussed. The aim of this review is to serve as a guide for the design of microbiological Raman studies that can support the establishment of this method in different fields.
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Affiliation(s)
- Sandra Baaba Frempong
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Markus Salbreiter
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Sara Mostafapour
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Aikaterini Pistiki
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Thomas W Bocklitz
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
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Jeon Y, Lee S, Vu NT, Kim H, Hwang IS, Oh CS, You J. Label-Free Surface-Enhanced Raman Scattering Detection of Fire Blight Pathogen Using a Pathogen-Specific Bacteriophage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2374-2380. [PMID: 38247141 DOI: 10.1021/acs.jafc.3c08217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Fire blight is one of the most devastating plant diseases, causing severe social and economic problems. Herein, we report a novel method based on label-free surface-enhanced Raman scattering (SERS) combined with an Erwinia amylovora-specific bacteriophage that allows detecting efficiently fire blight bacteria E. amylovora for the first time. To achieve the highest SERS signals for E. amylovora, we synthesized and compared plasmonic nanoparticles (PNPs) with different sizes, i.e., bimetallic gold core-silver shell nanoparticles (Au@AgNPs) and monometallic gold nanoparticles (AuNPs) and utilized the coffee-ring effect for the self-assembly of PNPs and enrichment of fire blight bacteria. Furthermore, we investigated the changes in the SERS spectra of E. amylovora after incubation with an E. amylovora-specific bacteriophage, and we found considerable differences in the SERS signals as a function of the bacteriophage incubation time. The results indicate that our bacteriophage-based label-free SERS analysis can specifically detect E. amylovora without the need for peak assignment on the SERS spectra but simply by monitoring the changes in the SERS signals over time. Therefore, our facile method holds great potential for the label-free detection of pathogenic bacteria and the investigation of viral-bacterial interactions.
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Affiliation(s)
- Youngho Jeon
- Department of Plant & Environmental New Resources and Institute of Graduate School of Green-Bio Science, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Suji Lee
- Department of Plant & Environmental New Resources and Institute of Graduate School of Green-Bio Science, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Nguyen Trung Vu
- Research Institute of Agriculture and Life Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Hyeongsoon Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - In Sun Hwang
- Research Institute of Agriculture and Life Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Chang-Sik Oh
- Research Institute of Agriculture and Life Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jungmok You
- Department of Plant & Environmental New Resources and Institute of Graduate School of Green-Bio Science, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, South Korea
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Wang W, Vikesland PJ. Metabolite-Mediated Bacterial Antibiotic Resistance Revealed by Surface-Enhanced Raman Spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13375-13383. [PMID: 37624741 DOI: 10.1021/acs.est.3c04001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
A prompt on-site, real-time method to detect bacterial antibiotic resistance is crucial for controlling the spread of resistance. Herein, we report the use of surface-enhanced Raman spectroscopy (SERS) for the monitoring of bioactive metabolites produced by ampicillin-resistant Pseudomonas aeruginosa strains and identification of mechanisms underlying antibiotic resistance. The results indicate that the blue-green pigment pyocyanin (PYO) dominates the metabolite signals and is significantly enhanced upon exposure to subminimal inhibitory concentrations of ampicillin. PYO accumulates during exponential growth and subsequently either diffuses into the culture medium or is consumed in response to nutrient deprivation. The SERS spectra further reveal that the production of some intermediate substances such as polysaccharides and amino acids is minimally impacted and that nutrient consumption remains consistent. Moreover, the intensity changes and peak shifts observed in the SERS spectra of non-PYO-producing ampicillin-susceptible Escherichia coli demonstrate that exogenously added PYO enhances E. coli tolerance to ampicillin to some extent. These results indicate that PYO mediates antibiotic resistance not only in the parent species but also in cocultured bacterial strains. The metabolic SERS signal provides new insight regarding antibiotic resistance with promising applications for both environmental monitoring and rapid clinical detection.
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Affiliation(s)
- Wei Wang
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia Tech Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia Tech Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
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