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Kong L, Wang Y, Cui D, He W, Zhang C, Zheng C. Application of single-cell Raman-deuterium isotope probing to reveal the resistance of marine ammonia-oxidizing archaea SCM1 against common antibiotics. CHEMOSPHERE 2024; 362:142500. [PMID: 38852635 DOI: 10.1016/j.chemosphere.2024.142500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/11/2024]
Abstract
Antimicrobial resistance (AMR) in oceans poses a significant threat to human health through the seafood supply chain. Ammonia-oxidizing archaea (AOA) are important marine microorganisms and play a key role in the biogeochemical nitrogen cycle around the world. However, the AMR of marine AOA to aquicultural antibiotics is poorly explored. Here, Raman-deuterium isotope probing (Raman-DIP), a single-cell tool, was developed to reveal the AMR of a typical marine species of AOA, Nitrosopumilus maritimus (designated SCM1), against six antibiotics, including erythromycin, tetracycline, novobiocin, neomycin, bacitracin, and vancomycin. The D2O concentration (30% v/v) and culture period (9 days) were optimized for the precise detection of metabolic activity in SCM1 cells through Raman-DIP. The relative metabolic activity of SCM1 upon exposure to antibiotics was semi-quantitatively calculated based on single-cell Raman spectra. SCM1 exhibited high resistance to erythromycin, tetracycline, novobiocin, neomycin, and vancomycin, with minimum inhibitory concentration (MIC) values between 100 and 400 mg/L, while SCM1 is very sensitive to bacitracin (MIC: 0.8 mg/L). Notably, SCM1 cells were completely inactive under the metabolic activity minimum inhibitory concentration conditions (MA-MIC: 1.6-800 mg/L) for the six antibiotics. Further genomic analysis revealed the antibiotic resistance genes (ARGs) of SCM1, including 14 types categorized into 33 subtypes. This work increases our knowledge of the AMR of marine AOA by linking the resistant phenome to the genome, contributing to the risk assessment of AMR in the underexplored ocean environment. As antibiotic resistance in marine microorganisms is significantly affected by the concentration of antibiotics in coastal environments, we encourage more studies concentrating on both the phenotypic and genotypic antibiotic resistance of marine archaea. This may facilitate a comprehensive evaluation of the capacity of marine microorganisms to spread AMR and the implementation of suitable control measures to protect environmental safety and human health.
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Affiliation(s)
- Lingchao Kong
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China; Eastern Institute for Advanced Study, Eastern Institute of Technology, Ningbo, 315200, China
| | - Yi Wang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Eastern Institute for Advanced Study, Eastern Institute of Technology, Ningbo, 315200, China.
| | - Dongyu Cui
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chunmiao Zheng
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China; Eastern Institute for Advanced Study, Eastern Institute of Technology, Ningbo, 315200, China
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2
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Zhao L, Jiang Z, Wang J, Wang X, Zhang Z, Hu H, Qi X, Zeng H, Song Y. Micro-flow cell washing technique combined with single-cell Raman spectroscopy for rapid and automatic antimicrobial susceptibility test of pathogen in urine. Talanta 2024; 277:126354. [PMID: 38850804 DOI: 10.1016/j.talanta.2024.126354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
Facing the rapid spread of antimicrobial resistance, methods based on single-cell Raman spectroscopy have proven their advances in reducing the turn-around time (TAT) of antimicrobial susceptibility tests (AST). However, the Raman-based methods are still hindered by the prolonged centrifugal cell washing procedure, which may require complex labor operation and induce high mechanical stress, resulting in a pretreatment time of over 1 h as well as a high cell-loss probability. In this study, we developed a micro-flow cell washing device and corresponding Raman-compatible washing chips, which were able to automatically remove the impurities in the samples, retain the bacterial cell and perform Raman spectra acquisition in situ. Results of washing the 5- and 10-μm polymethyl methacrylate (PMMA) microspheres showed that the novel technique achieved a successful removal of 99 % impurity and an 80 % particle retention rate after 6 to 10 cycles of washing. The micro-flow cell washing technique could complete the pretreatment for urine samples in a 96-well plate within 10 min, only taking 15 % of the handling time required by centrifugation. The AST profiles of urine sample spiked with E. coli 25922, E. faecalis 29212, and S. aureus 29213 obtained by the proposed Raman-based approach were found to be 100 % consistent with the results from broth micro-dilution while reducing the TAT to 3 h from several days which is required by the latter. Our study has demonstrated the micro-flow cell washing technique is a reliable, fast and compatible approach to replace centrifuge washing for sample pretreatment of Raman-AST and could be readily applied in clinical scenarios.
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Affiliation(s)
- Luoqi Zhao
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, 215163, Jiangsu Province, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, Jiangsu Province, China
| | - Zheng Jiang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, Jiangsu Province, China
| | - Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, Jiangsu Province, China
| | - Xinyue Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, Jiangsu Province, China
| | - Zhiqiang Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, 215163, Jiangsu Province, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, Jiangsu Province, China
| | - Huijie Hu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, 215163, Jiangsu Province, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, Jiangsu Province, China
| | - Xiangdong Qi
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, Jiangsu Province, China
| | - Huan Zeng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, Jiangsu Province, China
| | - Yizhi Song
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, 215163, Jiangsu Province, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, Jiangsu Province, China.
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3
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Karlo J, Vijay A, Phaneeswar MS, Singh SP. Sensing the Bactericidal and Bacteriostatic Antimicrobial Mode of Action Using Raman Deuterium Stable Isotope Probing (DSIP) in Escherichia coli. ACS OMEGA 2024; 9:23753-23760. [PMID: 38854576 PMCID: PMC11154948 DOI: 10.1021/acsomega.4c01666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
The mode of action of antibiotics can be broadly classified as bacteriostatic and bactericidal. The bacteriostatic mode leads to the arrested growth of the cells, while the bacteriocidal mode causes cell death. In this work, we report the applicability of deuterium stable isotope probing (DSIP) in combination with Raman spectroscopy (Raman DSIP) for discriminating the mode of action of antibiotics at the community level. Escherichia coli, a well-known model microbe, was used as an organism for the study. We optimized the concentration of deuterium oxide required for metabolic activity monitoring without compromising the microbial growth. Our findings suggest that changes in the intensity of the C-D band in the high-wavenumber region could serve as a quantifiable marker for determining the antibiotic mode of action. This can be used for early identification of the antibiotic's mode of action. Our results explore the new perspective that supports the utility of deuterium-based vibrational tags in the field of clinical spectroscopy. Understanding the antibiotic's mode of action on bacterial cells in a short and objective manner can significantly enhance the clinical management abilities of infectious diseases and may also help in personalized antimicrobial therapy.
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Affiliation(s)
- Jiro Karlo
- Department of Biosciences
and Bioengineering, Indian Institute of
Technology Dharwad, Dharwad, Karnataka 580011, India
| | - Arunsree Vijay
- Department of Biosciences
and Bioengineering, Indian Institute of
Technology Dharwad, Dharwad, Karnataka 580011, India
| | - Mahamkali Sri Phaneeswar
- Department of Biosciences
and Bioengineering, Indian Institute of
Technology Dharwad, Dharwad, Karnataka 580011, India
| | - Surya Pratap Singh
- Department of Biosciences
and Bioengineering, Indian Institute of
Technology Dharwad, Dharwad, Karnataka 580011, India
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Dunnington EL, Wong BS, Fu D. Innovative Approaches for Drug Discovery: Quantifying Drug Distribution and Response with Raman Imaging. Anal Chem 2024; 96:7926-7944. [PMID: 38625100 PMCID: PMC11108735 DOI: 10.1021/acs.analchem.4c01413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Affiliation(s)
| | | | - Dan Fu
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
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Xu J, Chen H, Wang C, Ma Y, Song Y. Raman Flow Cytometry and Its Biomedical Applications. BIOSENSORS 2024; 14:171. [PMID: 38667164 PMCID: PMC11048678 DOI: 10.3390/bios14040171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024]
Abstract
Raman flow cytometry (RFC) uniquely integrates the "label-free" capability of Raman spectroscopy with the "high-throughput" attribute of traditional flow cytometry (FCM), offering exceptional performance in cell characterization and sorting. Unlike conventional FCM, RFC stands out for its elimination of the dependency on fluorescent labels, thereby reducing interference with the natural state of cells. Furthermore, it significantly enhances the detection information, providing a more comprehensive chemical fingerprint of cells. This review thoroughly discusses the fundamental principles and technological advantages of RFC and elaborates on its various applications in the biomedical field, from identifying and characterizing cancer cells for in vivo cancer detection and surveillance to sorting stem cells, paving the way for cell therapy, and identifying metabolic products of microbial cells, enabling the differentiation of microbial subgroups. Moreover, we delve into the current challenges and future directions regarding the improvement in sensitivity and throughput. This holds significant implications for the field of cell analysis, especially for the advancement of metabolomics.
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Affiliation(s)
- Jiayang Xu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Hangzhou 310058, China;
- Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Hongyi Chen
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, China
| | - Ce Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yuting Ma
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, China
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6
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Karlo J, Dhillon AK, Siddhanta S, Singh SP. Reverse stable isotope labelling with Raman spectroscopy for microbial proteomics. JOURNAL OF BIOPHOTONICS 2024; 17:e202300341. [PMID: 38010366 DOI: 10.1002/jbio.202300341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023]
Abstract
Global proteome changes in microbes affect the survival and overall production of commercially relevant metabolites through different bioprocesses. The existing methods to monitor proteome level changes are destructive in nature. Stable isotope probing (SIP) coupled with Raman spectroscopy is a relatively new approach for proteome analysis. However, applying this approach for monitoring changes in a large culture volume is not cost-effective. In this study, for the first time we are presenting a novel method of combining reverse SIP using 13 C-glucose and Deuterium to monitor the proteome changes through Raman spectroscopy. The findings of the study revealed visible changes (blue shifts) in proteome related peaks that can be used for monitoring proteome dynamics, that is, synthesis of nascent amino acids and its turnover with time in a non-destructive, cost-effective, and label-free manner.
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Affiliation(s)
- Jiro Karlo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | | | - Soumik Siddhanta
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Surya Pratap Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
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7
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Zhang H, Wang L, Zhang Z, Lin J, Ju F. Cost-Efficient Micro-Well Array-Based Colorimetric Antibiotic Susceptibility Testing (MacAST) for Bacteria from Culture or Community. BIOSENSORS 2023; 13:1028. [PMID: 38131788 PMCID: PMC10741774 DOI: 10.3390/bios13121028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Rapid and cost-efficient antibiotic susceptibility testing (AST) is key to timely prescription-oriented diagnosis and precision treatment. However, current AST methods have limitations in throughput or cost effectiveness, and are impractical for microbial communities. Here, we developed a high-throughput micro-well array-based colorimetric AST (macAST) system equipped with a self-developed smartphone application that could efficiently test sixteen combinations of bacteria strains and antibiotics, achieving comparable AST results based on resazurin metabolism assay. For community samples, we integrated immunomagnetic separation into the macAST (imacAST) system to specifically enrich the target cells before testing, which shortened bacterial isolation time from days to only 45 min and achieved AST of the target bacteria with a low concentration (~103 CFU/mL). This proof-of-concept study developed a high-throughput AST system with an at least ten-fold reduction in cost compared with a system equipped with a microscope or Raman spectrum. Based on colorimetric readout, the antimicrobial susceptibility of the bacteria from microbial communities can be delivered within 6 h, compared to days being required based on standard procedures, bypassing the need for precise instrumentation in therapy to combat bacterial antibiotic resistance in resource-limited settings.
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Affiliation(s)
- Huilin Zhang
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310027, China
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, China
| | - Lei Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Zhiguo Zhang
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, China
| | - Jianhan Lin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou 310024, China
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8
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Pramanik A, Kolawole OP, Gates K, Kundu S, Shukla MK, Moser RD, Ucak-Astarlioglu M, Al-Ostaz A, Ray PC. 2D Fluorinated Graphene Oxide (FGO)-Polyethyleneimine (PEI) Based 3D Porous Nanoplatform for Effective Removal of Forever Toxic Chemicals, Pharmaceutical Toxins, and Waterborne Pathogens from Environmental Water Samples. ACS OMEGA 2023; 8:44942-44954. [PMID: 38046318 PMCID: PMC10688155 DOI: 10.1021/acsomega.3c06360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023]
Abstract
Although water is essential for life, as per the United Nations, around 2 billion people in this world lack access to safely managed drinking water services at home. Herein we report the development of a two-dimensional (2D) fluorinated graphene oxide (FGO) and polyethylenimine (PEI) based three-dimensional (3D) porous nanoplatform for the effective removal of polyfluoroalkyl substances (PFAS), pharmaceutical toxins, and waterborne pathogens from contaminated water. Experimental data show that the FGO-PEI based nanoplatform has an estimated adsorption capacity (qm) of ∼219 mg g-1 for perfluorononanoic acid (PFNA) and can be used for 99% removal of several short- and long-chain PFAS. A comparative PFNA capturing study using different types of nanoplatforms indicates that the qm value is in the order FGO-PEI > FGO > GO-PEI, which indicates that fluorophilic, electrostatic, and hydrophobic interactions play important roles for the removal of PFAS. Reported data show that the FGO-PEI based nanoplatform has a capability for 100% removal of moxifloxacin antibiotics with an estimated qm of ∼299 mg g-1. Furthermore, because the pore size of the nanoplatform is much smaller than the size of pathogens, it has a capability for 100% removal of Salmonella and Escherichia coli from water. Moreover, reported data show around 96% removal of PFAS, pharmaceutical toxins, and pathogens simultaneously from spiked river, lake, and tap water samples using the nanoplatform.
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Affiliation(s)
- Avijit Pramanik
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
| | - Olorunsola Praise Kolawole
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
| | - Kaelin Gates
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
| | - Sanchita Kundu
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
| | - Manoj K. Shukla
- US
Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, Mississippi 39180-6199, United States
| | - Robert D Moser
- US
Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, Mississippi 39180-6199, United States
| | - Mine Ucak-Astarlioglu
- US
Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, Mississippi 39180-6199, United States
| | - Ahmed Al-Ostaz
- Department
of Civil Engineering, University of Mississippi, University, Mississippi 38677, United States
| | - Paresh Chandra Ray
- Department
of Chemistry and Biochemistry, Jackson State
University, Jackson, Mississippi 39217, United States
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9
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Ren W, Mao Y, Li S, Gao B, Fu X, Liu X, Zhu P, Shang Y, Li Y, Ma B, Sun L, Xu J, Pang Y. Rapid Mycobacterium abscessus antimicrobial susceptibility testing based on antibiotic treatment response mapping via Raman Microspectroscopy. Ann Clin Microbiol Antimicrob 2023; 22:94. [PMID: 37904155 PMCID: PMC10617219 DOI: 10.1186/s12941-023-00644-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
OBJECTIVES Antimicrobial susceptibility tests (ASTs) are pivotal tools for detecting and combating infections caused by multidrug-resistant rapidly growing mycobacteria (RGM) but are time-consuming and labor-intensive. DESIGN We used a Mycobacterium abscessus-based RGM model to develop a rapid (24-h) AST from the beginning of the strain culture, the Clinical Antimicrobials Susceptibility Test Ramanometry for RGM (CAST-R-RGM). The ASTs obtained for 21 clarithromycin (CLA)-treated and 18 linezolid (LZD)-treated RGM isolates. RESULTS CAST-R-RGM employs D2O-probed Raman microspectroscopy to monitor RGM metabolic activity, while also revealing bacterial antimicrobial drug resistance mechanisms. The results of clarithromycin (CLA)-treated and linezolid (LZD)-treated RGM isolates exhibited 90% and 83% categorical agreement, respectively, with conventional AST results of the same isolates. Furthermore, comparisons of time- and concentration-dependent Raman results between CLA- and LZD-treated RGM strains revealed distinct metabolic profiles after 48-h and 72-h drug treatments, despite similar profiles obtained for both drugs after 24-h treatments. CONCLUSIONS Ultimately, the rapid, accurate, and low-cost CAST-R-RGM assay offers advantages over conventional culture-based ASTs that warrant its use as a tool for improving patient treatment outcomes and revealing bacterial drug resistance mechanisms.
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Affiliation(s)
- Weicong Ren
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Yuli Mao
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Bo Gao
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoting Fu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolu Liu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Zhu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao Single-Cell Biotech, Co. Ltd, Qingdao, Shandong, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Yuandong Li
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Ma
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Luyang Sun
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jian Xu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China.
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Chen C, Wang Y, Wu F, Hong W. Rapid Antifungal Susceptibility Testing Based on Single-Cell Metabolism Analysis Using Stimulated Raman Scattering Imaging. Anal Chem 2023; 95:15556-15565. [PMID: 37815933 DOI: 10.1021/acs.analchem.3c02243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Rapid antifungal susceptibility testing (AFST) is urgently needed in clinics to treat invasive fungal infections with the appropriate antifungal drugs and to slow the emergence of antifungal resistance. However, current AFST methods are time-consuming (24-48 h) due to the slow growth of fungal cells and the methods not being able to work directly for clinical samples. Here, we demonstrate rapid AFST by measuring the metabolism in single fungal cells using stimulated Raman scattering imaging and deuterium probing. Distinct metabolic responses were observed in Candida albicans to different classes of antifungal drugs: while the metabolism was inhibited by amphotericin B, it was stimulated by azoles (fluconazole and voriconazole) and micafungin. Accordingly, we propose metabolism change as a biomarker for rapid AFST. The results were obtained in 4 h with 100% categorical agreement with the gold standard broth microdilution test. In addition, a protocol was developed for direct AFST from positive blood cultures. This method overcomes the limitation of slow growth in conventional methods and has the potential for the rapid diagnosis of candidemia and other clinical fungal infections.
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Affiliation(s)
- Chen Chen
- School of Biological Science and Medical Engineering, Beihang University; Beijing 100083, China
| | - Yi Wang
- Department of Clinical Laboratory, Beijing Bo'ai Hospital, China Rehabilitation Research Center, Capital Medical University, Beijing 100068, China
| | - Fan Wu
- School of Biological Science and Medical Engineering, Beihang University; Beijing 100083, China
| | - Weili Hong
- School of Biological Science and Medical Engineering, Beihang University; Beijing 100083, China
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11
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Xiao Z, Qu L, Chen H, Liu W, Zhan Y, Ling J, Shen H, Yang L, Chen D. Raman-Based Antimicrobial Susceptibility Testing on Antibiotics of Last Resort. Infect Drug Resist 2023; 16:5485-5500. [PMID: 37638072 PMCID: PMC10456006 DOI: 10.2147/idr.s404732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 06/28/2023] [Indexed: 08/29/2023] Open
Abstract
Background Antibiotic resistance represents a serious global health challenge, particularly with the emergence of strains resistant to last-resort antibiotics such as tigecycline, polymyxin B, and vancomycin. Urgent measures are required to alleviate this situation. To facilitate the judicious use of antibiotics, rapid and precise antimicrobial susceptibility testing (AST) is essential. Heavy water (deuterium oxide, D2O)-labeled Raman spectroscopy has emerged as a promising time-saving tool for microbiological testing. Methods Deuterium incorporation and experimental conditions were examined to develop and apply a Raman-based AST method to evaluate the efficacy of last-resort antibiotics, including tigecycline, polymyxin B, and vancomycin, against Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterococcus faecium. Essential agreement and categorical agreement were used to assess the metabolism inactivation concentration based on Raman spectroscopy (R-MIC)-a new metric developed in this study-and minimum inhibitory concentration (MIC) determined via the traditional microdilution broth method. Spearman's rank correlation coefficient was employed to measure the association between R-MIC and MIC values. Results The Raman-based AST method achieved a 100% categorical agreement (92/92) with the traditional microdilution broth method within five hours, while the traditional method required approximately 24 h. The R-MIC values shared 68.5% (63/92) consistency with the MIC values. In addition, the R-MIC and MIC values were highly correlated (Spearman's r=0.96), resulting in an essential agreement of 100%. Conclusion Our optimized experimental method and conditions indicate that Raman-based AST holds great promise as a solution to overcome the time-consuming challenges of traditional AST methods.
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Affiliation(s)
- Zhirou Xiao
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People’s Republic of China
| | - Liping Qu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People’s Republic of China
| | - Haijun Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People’s Republic of China
| | - Wanting Liu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People’s Republic of China
| | - Yi Zhan
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People’s Republic of China
| | - Jiahui Ling
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People’s Republic of China
| | - Hongwei Shen
- Department of Clinical Laboratory, Shenzhen Hospital of Southern Medical University, Guangzhou, Guangdong, People’s Republic of China
| | - Ling Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People’s Republic of China
| | - Dingqiang Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People’s Republic of China
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12
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Baranova AA, Tyurin AP, Korshun VA, Alferova VA. Sensing of Antibiotic-Bacteria Interactions. Antibiotics (Basel) 2023; 12:1340. [PMID: 37627760 PMCID: PMC10451291 DOI: 10.3390/antibiotics12081340] [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: 07/05/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Sensing of antibiotic-bacteria interactions is an important area of research that has gained significant attention in recent years. Antibiotic resistance is a major public health concern, and it is essential to develop new strategies for detecting and monitoring bacterial responses to antibiotics in order to maintain effective antibiotic development and antibacterial treatment. This review summarizes recent advances in sensing strategies for antibiotic-bacteria interactions, which are divided into two main parts: studies on the mechanism of action for sensitive bacteria and interrogation of the defense mechanisms for resistant ones. In conclusion, this review provides an overview of the present research landscape concerning antibiotic-bacteria interactions, emphasizing the potential for method adaptation and the integration of machine learning techniques in data analysis, which could potentially lead to a transformative impact on mechanistic studies within the field.
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Affiliation(s)
| | | | | | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (A.P.T.); (V.A.K.)
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13
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Zhang J, Ren L, Zhang L, Gong Y, Xu T, Wang X, Guo C, Zhai L, Yu X, Li Y, Zhu P, Chen R, Jing X, Jing G, Zhou S, Xu M, Wang C, Niu C, Ge Y, Ma B, Shang G, Cui Y, Yao S, Xu J. Single-cell rapid identification, in situ viability and vitality profiling, and genome-based source-tracking for probiotics products. IMETA 2023; 2:e117. [PMID: 38867931 PMCID: PMC10989769 DOI: 10.1002/imt2.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/22/2023] [Accepted: 05/07/2023] [Indexed: 06/14/2024]
Abstract
Rapid expansion of the probiotics industry demands fast, sensitive, comprehensive, and low-cost strategies for quality assessment. Here, we introduce a culture-free, one-cell-resolution, phenome-genome-combined strategy called Single-Cell Identification, Viability and Vitality tests, and Source-tracking (SCIVVS). For each cell directly extracted from the product, the fingerprint region of D2O-probed single-cell Raman spectrum (SCRS) enables species-level identification with 93% accuracy, based on a reference SCRS database from 21 statutory probiotic species, whereas the C-D band accurately quantifies viability, metabolic vitality plus their intercellular heterogeneity. For source-tracking, single-cell Raman-activated Cell Sorting and Sequencing can proceed, producing indexed, precisely one-cell-based genome assemblies that can reach ~99.40% genome-wide coverage. Finally, we validated an integrated SCIVVS workflow with automated SCRS acquisition where the whole process except sequencing takes just 5 h. As it is >20-fold faster, >10-time cheaper, vitality-revealing, heterogeneity-resolving, and automation-prone, SCIVVS is a new technological and data framework for quality assessment of live-cell products.
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Affiliation(s)
- Jia Zhang
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lihui Ren
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
- College of Information Science & EngineeringOcean University of ChinaQingdaoShandongChina
| | - Lei Zhang
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
- Qingdao Branch of China United Network Communications Co., Ltd.QingdaoShandongChina
| | - Yanhai Gong
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Teng Xu
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaohang Wang
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Cheng Guo
- Eastsea Pharma Co., Ltd.QingdaoShandongChina
| | - Lei Zhai
- China National Research Institute of Food and Fermentation Industries Co., Ltd., China Center of Industrial Culture CollectionBeijingChina
| | - Xuejian Yu
- China National Research Institute of Food and Fermentation Industries Co., Ltd., China Center of Industrial Culture CollectionBeijingChina
| | - Ying Li
- Qingdao Single‐Cell Biotech. Co., Ltd.QingdaoShandongChina
| | - Pengfei Zhu
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Qingdao Single‐Cell Biotech. Co., Ltd.QingdaoShandongChina
| | - Rongze Chen
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoyan Jing
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Gongchao Jing
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shiqi Zhou
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
| | - Mingyue Xu
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
| | - Chen Wang
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
| | | | - Yuanyuan Ge
- China National Research Institute of Food and Fermentation Industries Co., Ltd., China Center of Industrial Culture CollectionBeijingChina
| | - Bo Ma
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Yunlong Cui
- Eastsea Pharma Co., Ltd.QingdaoShandongChina
| | - Su Yao
- China National Research Institute of Food and Fermentation Industries Co., Ltd., China Center of Industrial Culture CollectionBeijingChina
| | - Jian Xu
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoShandongChina
- Shandong Energy InstituteQingdaoShandongChina
- Qingdao New Energy Shandong LaboratoryQingdaoShandongChina
- University of Chinese Academy of SciencesBeijingChina
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14
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Lv S, Wang C, Xue K, Wang J, Xiao M, Sun Z, Han L, Shi L, Zhu C. Activated alkyne-enabled turn-on click bioconjugation with cascade signal amplification for ultrafast and high-throughput antibiotic screening. Proc Natl Acad Sci U S A 2023; 120:e2302367120. [PMID: 37364107 PMCID: PMC10318996 DOI: 10.1073/pnas.2302367120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/27/2023] [Indexed: 06/28/2023] Open
Abstract
Antimicrobial susceptibility testing plays a pivotal role in the discovery of new antibiotics. However, the development of simple, sensitive, and rapid assessment approaches remains challenging. Herein, we report an activated alkyne-based cascade signal amplification strategy for ultrafast and high-throughput antibiotic screening. First of all, a novel water-soluble aggregation-induced emission (AIE) luminogen is synthesized, which contains an activated alkyne group to enable fluorescence turn-on and metal-free click bioconjugation under physiological conditions. Taking advantage of the in-house established method for bacterial lysis, a number of clickable biological substances (i.e., bacterial solutes and debris) are released from the bacterial bodies, which remarkably increases the quantity of analytes. By means of the activated alkyne-mediated turn-on click bioconjugation, the system fluorescence signal is significantly amplified due to the increased labeling sites as well as the AIE effect. Such a cascade signal amplification strategy efficiently improves the detection sensitivity and thus enables ultrafast antimicrobial susceptibility assessment. By integration with a microplate reader, this approach is further applied to high-throughput antibiotic screening.
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Affiliation(s)
- Shuyi Lv
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Chao Wang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Ke Xue
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Jiaxin Wang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Minghui Xiao
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Zhencheng Sun
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Lei Han
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, Shandong266109, China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Chunlei Zhu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
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15
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Guo Z, Bai Y, Zhang M, Lan L, Cheng JX. High-Throughput Antimicrobial Susceptibility Testing of Escherichia coli by Wide-Field Mid-Infrared Photothermal Imaging of Protein Synthesis. Anal Chem 2023; 95:2238-2244. [PMID: 36651850 DOI: 10.1021/acs.analchem.2c03683] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Antimicrobial resistance poses great threats to global health and economics. Current gold-standard antimicrobial susceptibility testing (AST) requires extensive culture time (36-72 h) to determine susceptibility. There is an urgent need for rapid AST methods to slow down antimicrobial resistance. Here, we present a rapid AST method based on wide-field mid-infrared photothermal imaging of protein synthesis from 13C-glucose in Escherichia coli. Our wide-field approach achieved metabolic imaging for hundreds of bacteria at the single-cell resolution within seconds. The perturbed microbial protein synthesis can be probed within 1 h after antibiotic treatment in E. coli cells. The susceptibility of antibiotics with various mechanisms of action has been probed through monitoring protein synthesis, which promises great potential of the proposed platform toward clinical translation.
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Affiliation(s)
- Zhongyue Guo
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States.,Photonics Center, Boston University, Boston, Massachusetts 02215, United States
| | - Yeran Bai
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.,Photonics Center, Boston University, Boston, Massachusetts 02215, United States
| | - Meng Zhang
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.,Photonics Center, Boston University, Boston, Massachusetts 02215, United States
| | - Lu Lan
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.,Photonics Center, Boston University, Boston, Massachusetts 02215, United States
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States.,Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.,Photonics Center, Boston University, Boston, Massachusetts 02215, United States
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16
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Liu Z, Xue Y, Yang C, Li B, Zhang Y. Rapid identification and drug resistance screening of respiratory pathogens based on single-cell Raman spectroscopy. Front Microbiol 2023; 14:1065173. [PMID: 36778844 PMCID: PMC9909742 DOI: 10.3389/fmicb.2023.1065173] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023] Open
Abstract
Respiratory infections rank fourth in the global economic burden of disease. Lower respiratory tract infections are the leading cause of death in low-income countries. The rapid identification of pathogens causing lower respiratory tract infections to help guide the use of antibiotics can reduce the mortality of patients with lower respiratory tract infections. Single-cell Raman spectroscopy is a "whole biological fingerprint" technique that can be used to identify microbial samples. It has the advantages of no marking and fast and non-destructive testing. In this study, single-cell Raman spectroscopy was used to collect spectral data of six respiratory tract pathogen isolates. The T-distributed stochastic neighbor embedding (t-SNE) isolation analysis algorithm was used to compare the differences between the six respiratory tract pathogens. The eXtreme Gradient Boosting (XGBoost) algorithm was used to establish a Raman phenotype database model. The classification accuracy of the isolated samples was 93-100%, and the classification accuracy of the clinical samples was more than 80%. Combined with heavy water labeling technology, the drug resistance of respiratory tract pathogens was determined. The study showed that single-cell Raman spectroscopy-D2O (SCRS-D2O) labeling could rapidly identify the drug resistance of respiratory tract pathogens within 2 h.
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Affiliation(s)
- Ziyu Liu
- Department of Pediatric Respiratory, The First Hospital of Jilin University, Changchun, China,School of Life Science, Jilin University, Changchun, China
| | - Ying Xue
- HOOKE Instruments Ltd., Changchun, China
| | - Chun Yang
- Department of Laboratory Medicine, First Hospital of Jilin University, Changchun, Jilin, China
| | - Bei Li
- HOOKE Instruments Ltd., Changchun, China,The State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences (CAS), Changchun, China
| | - Ying Zhang
- Department of Pediatric Respiratory, The First Hospital of Jilin University, Changchun, China,*Correspondence: Ying Zhang ✉
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17
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Wang J, Meng S, Lin K, Yi X, Sun Y, Xu X, He N, Zhang Z, Hu H, Qie X, Zhang D, Tang Y, Huang WE, He J, Song Y. Leveraging single-cell Raman spectroscopy and single-cell sorting for the detection and identification of yeast infections. Anal Chim Acta 2023; 1239:340658. [PMID: 36628751 DOI: 10.1016/j.aca.2022.340658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022]
Abstract
Invasive fungal infection serves as a great threat to human health. Discrimination between fungal and bacterial infections at the earliest stage is vital for effective clinic practice; however, traditional culture-dependent microscopic diagnosis of fungal infection usually requires several days, meanwhile, culture-independent immunological and molecular methods are limited by the detectable type of pathogens and the issues with high false-positive rates. In this study, we proposed a novel culture-independent phenotyping method based on single-cell Raman spectroscopy for the rapid discrimination between fungal and bacterial infections. Three Raman biomarkers, including cytochrome c, peptidoglycan, and nucleic acid, were identified through hierarchical clustering analysis of Raman spectra across 12 types of most common yeast and bacterial pathogens. Compared to those of bacterial pathogens, the single cells of yeast pathogens demonstrated significantly stronger Raman peaks for cytochrome c, but weaker signals for peptidoglycan and nucleic acid. A two-step protocol combining the three biomarkers was established and able to differentiate fungal infections from bacterial infections with an overall accuracy of 94.9%. Our approach was also used to detect ten raw urinary tract infection samples. Successful identification of fungi was achieved within half an hour after sample obtainment. We further demonstrated the accurate fungal species taxonomy achieved with Raman-assisted cell ejection. Our findings demonstrate that Raman-based fungal identification is a novel, facile, reliable, and with a breadth of coverage approach, that has a great potential to be adopted in routine clinical practice to reduce the turn-around time of invasive fungal disease (IFD) diagnostics.
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Affiliation(s)
- Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Kaicheng Lin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Xiaofei Yi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 20040, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yixiang Sun
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 20040, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Na He
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhiqiang Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Huijie Hu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China
| | - Xingwang Qie
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130021, PR China
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Jian He
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China.
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18
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Bai Y, Guo Z, Pereira FC, Wagner M, Cheng JX. Mid-Infrared Photothermal-Fluorescence In Situ Hybridization for Functional Analysis and Genetic Identification of Single Cells. Anal Chem 2023; 95:2398-2405. [PMID: 36652555 PMCID: PMC9893215 DOI: 10.1021/acs.analchem.2c04474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Simultaneous identification and metabolic analysis of microbes with single-cell resolution and high throughput are necessary to answer the question of "who eats what, when, and where" in complex microbial communities. Here, we present a mid-infrared photothermal-fluorescence in situ hybridization (MIP-FISH) platform that enables direct bridging of genotype and phenotype. Through multiple improvements of MIP imaging, the sensitive detection of isotopically labeled compounds incorporated into proteins of individual bacterial cells became possible, while simultaneous detection of FISH labeling with rRNA-targeted probes enabled the identification of the analyzed cells. In proof-of-concept experiments, we showed that the clear spectral red shift in the protein amide I region due to incorporation of 13C atoms originating from 13C-labeled glucose can be exploited by MIP-FISH to discriminate and identify 13C-labeled bacterial cells within a complex human gut microbiome sample. The presented methods open new opportunities for single-cell structure-function analyses for microbiology.
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Affiliation(s)
- Yeran Bai
- Department
of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States,Photonics
Center, Boston University, Boston, Massachusetts 02215, United States
| | - Zhongyue Guo
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States,Photonics
Center, Boston University, Boston, Massachusetts 02215, United States
| | - Fátima C. Pereira
- Centre
for Microbiology and Environmental Systems Science, Department of
Microbiology and Ecosystem Science, University
of Vienna, Vienna 1030, Austria
| | - Michael Wagner
- Centre
for Microbiology and Environmental Systems Science, Department of
Microbiology and Ecosystem Science, University
of Vienna, Vienna 1030, Austria,Department
of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark,
| | - Ji-Xin Cheng
- Department
of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States,Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States,Photonics
Center, Boston University, Boston, Massachusetts 02215, United States,
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19
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Lu W, Li H, Qiu H, Wang L, Feng J, Fu YV. Identification of pathogens and detection of antibiotic susceptibility at single-cell resolution by Raman spectroscopy combined with machine learning. Front Microbiol 2023; 13:1076965. [PMID: 36687641 PMCID: PMC9846160 DOI: 10.3389/fmicb.2022.1076965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/06/2022] [Indexed: 01/05/2023] Open
Abstract
Rapid, accurate, and label-free detection of pathogenic bacteria and antibiotic resistance at single-cell resolution is a technological challenge for clinical diagnosis. Overcoming the cumbersome culture process of pathogenic bacteria and time-consuming antibiotic susceptibility assays will significantly benefit early diagnosis and optimize the use of antibiotics in clinics. Raman spectroscopy can collect molecular fingerprints of pathogenic bacteria in a label-free and culture-independent manner, which is suitable for pathogen diagnosis at single-cell resolution. Here, we report a method based on Raman spectroscopy combined with machine learning to rapidly and accurately identify pathogenic bacteria and detect antibiotic resistance at single-cell resolution. Our results show that the average accuracy of identification of 12 species of common pathogenic bacteria by the machine learning method is 90.73 ± 9.72%. Antibiotic-sensitive and antibiotic-resistant strains of Acinetobacter baumannii isolated from hospital patients were distinguished with 99.92 ± 0.06% accuracy using the machine learning model. Meanwhile, we found that sensitive strains had a higher nucleic acid/protein ratio and antibiotic-resistant strains possessed abundant amide II structures in proteins. This study suggests that Raman spectroscopy is a promising method for rapidly identifying pathogens and detecting their antibiotic susceptibility.
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Affiliation(s)
- Weilai Lu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haifei Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haoning Qiu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lu Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu Vincent Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Yu Vincent Fu,
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20
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Dina NE, Tahir MA, Bajwa SZ, Amin I, Valev VK, Zhang L. SERS-based antibiotic susceptibility testing: Towards point-of-care clinical diagnosis. Biosens Bioelectron 2023; 219:114843. [PMID: 36327563 DOI: 10.1016/j.bios.2022.114843] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 08/09/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Emerging antibiotic resistant bacteria constitute one of the biggest threats to public health. Surface-enhanced Raman scattering (SERS) is highly promising for detecting such bacteria and for antibiotic susceptibility testing (AST). SERS is fast, non-destructive (can probe living cells) and it is technologically flexible (readily integrated with robotics and machine learning algorithms). However, in order to integrate into efficient point-of-care (PoC) devices and to effectively replace the current culture-based methods, it needs to overcome the challenges of reliability, cost and complexity. Recently, significant progress has been made with the emergence of both new questions and new promising directions of research and technological development. This article brings together insights from several representative SERS-based AST studies and approaches oriented towards clinical PoC biosensing. It aims to serve as a reference source that can guide progress towards PoC routines for identifying antibiotic resistant pathogens. In turn, such identification would help to trace the origin of sporadic infections, in order to prevent outbreaks and to design effective medical treatment and preventive procedures.
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Affiliation(s)
- Nicoleta Elena Dina
- Department of Molecular and Biomolecular Department, National Institute for Research and Development of Isotopic and Molecular Technologies, 400293, Cluj-Napoca, Romania.
| | - Muhammad Ali Tahir
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, People's Republic of China
| | - Sadia Z Bajwa
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, 38000, Faisalabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, 38000, Faisalabad, Pakistan
| | - Ventsislav K Valev
- Centre for Photonics and Photonic Materials, Department of Physics, University of Bath, Bath, BA2 7AY, United Kingdom; Centre for Therapeutic Innovation, University of Bath, Bath, United Kingdom; Centre for Nanoscience and Nanotechnology, University of Bath, Bath, United Kingdom.
| | - Liwu Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, People's Republic of China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, People's Republic of China.
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21
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Wang J, Kong K, Guo C, Yin G, Meng S, Lan L, Luo L, Song Y. Cultureless enumeration of live bacteria in urinary tract infection by single-cell Raman spectroscopy. Front Microbiol 2023; 14:1144607. [PMID: 37032883 PMCID: PMC10076591 DOI: 10.3389/fmicb.2023.1144607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Urinary tract infections (UTIs) are the most common outpatient infections. Obtaining the concentration of live pathogens in the sample is crucial for the treatment. Still, the enumeration depends on urine culture and plate counting, which requires days of turn-around time (TAT). Single-cell Raman spectra combined with deuterium isotope probing (Raman-DIP) has been proven to identify the metabolic-active bacteria with high accuracy but is not able to reveal the number of live pathogens due to bacteria replication during the Raman-DIP process. In this study, we established a new approach of using sodium acetate to inhibit the replication of the pathogen and applying Raman-DIP to identify the active single cells. By combining microscopic image stitching and recognition, we could further improve the efficiency of the new method. Validation of the new method on nine artificial urine samples indicated that the exact number of live pathogens obtained with Raman-DIP is consistent with plate-counting while shortening the TAT from 18 h to within 3 h, and the potential of applying Raman-DIP for pathogen enumeration in clinics is promising.
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Affiliation(s)
- Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Kang Kong
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Chen Guo
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, China
| | - Guangyao Yin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Lu Lan
- VibroniX, Inc., Suzhou, China
| | - Liqiang Luo
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, China
- Chongqing Guoke Medical Technology Development Co., Ltd., Chongqing, China
- *Correspondence: Yizhi Song,
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22
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Novikov A, Sayfutdinova A, Botchkova E, Kopitsyn D, Fakhrullin R. Antibiotic Susceptibility Testing with Raman Biosensing. Antibiotics (Basel) 2022; 11:antibiotics11121812. [PMID: 36551469 PMCID: PMC9774239 DOI: 10.3390/antibiotics11121812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
Antibiotics guard us against bacterial infections and are among the most commonly used medicines. The immediate consequence of their large-scale production and prescription is the development of antibiotic resistance. Therefore, rapid detection of antibiotic susceptibility is required for efficient antimicrobial therapy. One of the promising methods for rapid antibiotic susceptibility testing is Raman spectroscopy. Raman spectroscopy combines fast and contactless acquisition of spectra with good selectivity towards bacterial cells. The antibiotic-induced changes in bacterial cell physiology are detected as distinct features in Raman spectra and can be associated with antibiotic susceptibility. Therefore, the Raman-based approach may be beneficial in designing therapy against multidrug-resistant infections. The surface-enhanced Raman spectroscopy (SERS) and resonance Raman spectroscopy (RRS) additionally provide excellent sensitivity. In this review, we present an analysis of the Raman spectroscopy-based optical biosensing approaches aimed at antibiotic susceptibility testing.
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Affiliation(s)
- Andrei Novikov
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
- Correspondence: (A.N.); (R.F.)
| | - Adeliya Sayfutdinova
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Ekaterina Botchkova
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Dmitry Kopitsyn
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Rawil Fakhrullin
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Republic of Tatarstan, Russia
- Correspondence: (A.N.); (R.F.)
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23
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Wang J, Hui P, Zhang X, Cai X, Lian J, Liu X, Lu X, Chen W. Rapid Antimicrobial Susceptibility Testing Based on a Bio-Inspired Chemiluminescence Sensor. Anal Chem 2022; 94:17240-17247. [PMID: 36459659 DOI: 10.1021/acs.analchem.2c04020] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Indiscriminate usage of antibiotics has caused accelerating growth and global expansion of antimicrobial resistance. Therefore, rapid antimicrobial susceptibility testing (AST) for guiding antibiotic prescription and preventing the spread of antimicrobial resistance is in urgent need. Phenotypic AST is the clinical gold standard method; however, no phenotypic AST has realized a colony-to-answer at about 1 h by utilizing the chemiluminescence sensor to detect the enzyme expressed by bacteria. Inspired by the bubble formation in the mixture of Escherichia coli and H2O2, we demonstrate a strategy based on the chemiluminescence sensor for rapid AST. Compared with the gold standard methods, the values of AUC are 0.960 for E. coli and 0.950 for Staphylococcus aureus, close to 1, indicating superb diagnostic performance as an AST method. The whole process from colonies to answer is 55 min for E. coli and 70 min for S. aureus. The chemiluminescence readout is based on the common equipment in the laboratory of the hospital, which is conducive to follow-up clinical promotion. Our sensor promises great potential in rapid AST, facilitating antimicrobial stewardship.
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Affiliation(s)
- Jidong Wang
- Medical Research Center, Huazhong University of Science and Technology Union Shenzhen Hospital, the 6th Affiliated Hospital, Shenzhen University Health Science Center, Shenzhen 518052, P. R. China
| | - Ping Hui
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
| | - Xinyu Zhang
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
| | - Xiaoqing Cai
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
| | - Jie Lian
- Medical Research Center, Huazhong University of Science and Technology Union Shenzhen Hospital, the 6th Affiliated Hospital, Shenzhen University Health Science Center, Shenzhen 518052, P. R. China
| | - Xiaolei Liu
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
| | - Xi Lu
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
| | - Wenwen Chen
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
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24
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Hu H, Wang J, Yi X, Lin K, Meng S, Zhang X, Jiang C, Tang Y, Wang M, He J, Xu X, Song Y. Stain-free Gram staining classification of pathogens via single-cell Raman spectroscopy combined with machine learning. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4014-4020. [PMID: 36196964 DOI: 10.1039/d2ay01056a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Gram staining (GS) is one of the routine microbiological operations to classify bacteria based on the cell wall structure. Accurate GS classification of pathogens is of great significance since it helps correct administration of antimicrobial treatment. The laborious procedure and low sensitivity results related to conventional GS have resulted in reluctance among clinicians. In this study, we integrate confocal Raman spectroscopy and machine learning techniques to distinguish Gram-negative (GN) or Gram-positive (GP) bacteria. A single-cell Raman database including seven most common clinical pathogens (three GP strains and four GN strains) was constructed. Machine learning algorithms including the support-vector machine (SVM), k-nearest neighbors' algorithm (k-NN), gradient boosting machine (GBM), linear discriminant analysis (LDA), and t-distributed stochastic neighbor embedding (t-SNE) were trained to achieve the binary classification for GS. With such a relatively small database, the SVM model achieved the highest accuracy of 98.1%. The molecular signatures of GN and GP embedded in their Raman fingerprints were identified with hierarchical cluster analysis (HCA). The results indicated that Raman peaks for peptidoglycan and teichoic acid were the most significant factors that contributed to accurate classification. The Raman machine learning approach could greatly enhance the diagnosis of pathogenic infections.
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Affiliation(s)
- Huijie Hu
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, PR China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Xiaofei Yi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, PR China.
| | - Kaicheng Lin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Xin Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
- Chongqing Guoke Medical Technology Development Co., Ltd, Chongqing 400799, PR China
| | - Chenyu Jiang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
- Jinan Guoke Medical Technology Development Co., Ltd, Jinan 250102, PR China
| | - Yuguo Tang
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, PR China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, PR China.
| | - Jian He
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China.
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, PR China.
| | - Yizhi Song
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, PR China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
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25
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Li X, Liu X, Yu Z, Luo Y, Hu Q, Xu Z, Dai J, Wu N, Shen F. Combinatorial screening SlipChip for rapid phenotypic antimicrobial susceptibility testing. LAB ON A CHIP 2022; 22:3952-3960. [PMID: 36106408 DOI: 10.1039/d2lc00661h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Antimicrobial resistance (AMR) by bacteria is a serious global threat, and a rapid, high-throughput, and easy-to-use phenotypic antimicrobial susceptibility testing (AST) method is essential for making timely treatment decisions and controlling the spread of antibiotic resistant micro-organisms. Traditional culture-based methods are time-consuming, and their capability to screen against a large number of different conditions is limited; meanwhile genotypic based methods, including sequencing and PCR based methods, are constrained by rarely identified resistance genes and complicated resistance mechanisms. Here, a combinatorial-screening SlipChip (cs-SlipChip) containing 192 nanoliter-sized compartments is developed which can perform high-throughput phenotypic AST within three hours by monitoring the bacterial growth within nanoliter-sized droplets with bright-field imaging and analyzing the changes in bacterial number and morphology. The minimum inhibitory concentration (MIC) of Escherichia coli ATCC 25922 against four antibiotics (ampicillin, ciprofloxacin, ceftazidime, and nitrofurantoin) can be measured in one chip within 3 hours. Furthermore, five antibiotic-resistant E. coli strains were isolated from patients diagnosed with urinary tract infections (UTIs), and an individual isolate was tested using four antibiotics and eleven antibiotic combinations simultaneously with three different concentrations of each. The results from the cs-SlipChip agree with those of a VITEK 2 automated system. This cs-SlipChip provides a practical high-throughput and rapid phenotypic method for AST and can also be used to screen different chemicals and antibiotic combinations for the treatment of multiple antibiotic-resistant bacteria.
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Affiliation(s)
- Xiang Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Xu Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Ziqing Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Yang Luo
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Qixin Hu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Zhenye Xu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Jia Dai
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Nannan Wu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
- CreatiPhage Biotechnology Co., Ltd, Shanghai, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
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26
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Deuterium Raman imaging for lipid analysis. Curr Opin Chem Biol 2022; 70:102181. [DOI: 10.1016/j.cbpa.2022.102181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/18/2022]
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27
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Tang JW, Qiao R, Xiong XS, Tang BX, He YW, Yang YY, Ju P, Wen PB, Zhang X, Wang L. Rapid discrimination of glycogen particles originated from different eukaryotic organisms. Int J Biol Macromol 2022; 222:1027-1036. [PMID: 36181881 DOI: 10.1016/j.ijbiomac.2022.09.233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022]
Abstract
There are many commercially available glycogen particles in the market due to their bioactive functions as food additive, drug carrier and natural moisturizer, etc. It would be beneficial to rapidly determine the origins of commercially-available glycogen particles, which could facilitate the establishment of quality control methodology for glycogen-containing products. With its non-destructive, label-free and low-cost features, surface enhanced Raman spectroscopy (SERS) is an attractive technique with high potential to discriminate chemical compounds in a rapid mode. In this study, we applied the combination of SERS technique and machine leaning algorithms on glycogen analysis, which successfully predicted the origins of glycogen particles from a variety of organisms with convolutional neural network (CNN) algorithm plus attention mechanism having the best computational performance (5-fold cross validation accuracy = 96.97 %). In sum, this is the first study focusing on the discrimination of commercial glycogen particles originated from different organisms, which holds the application potential in quality control of glycogen-containing products.
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Affiliation(s)
- Jia-Wei Tang
- Department of Intelligent Medical Engineering, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Rui Qiao
- Deparment of Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xue-Song Xiong
- Laboratory Medicine, The Fifth People's Hospital of Huai'an, Huai'an, Jiangsu Province, China
| | - Bing-Xin Tang
- Department of Laboratory Medicine, Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - You-Wei He
- School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Ying-Ying Yang
- School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Pei Ju
- School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Peng-Bo Wen
- Department of Intelligent Medical Engineering, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China.
| | - Xiao Zhang
- Department of Intelligent Medical Engineering, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China.
| | - Liang Wang
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China.
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28
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Zhu P, Ren L, Zhu Y, Dai J, Liu H, Mao Y, Li Y, He Y, Zheng X, Chen R, Fu X, Zhang L, Sun L, Zhu Y, Ji Y, Ma B, Xu Y, Xu J, Yang Q. Rapid, automated, and reliable antimicrobial susceptibility test from positive blood culture by CAST-R. MLIFE 2022; 1:329-340. [PMID: 38818218 PMCID: PMC10989881 DOI: 10.1002/mlf2.12019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/12/2022] [Accepted: 03/13/2022] [Indexed: 06/01/2024]
Abstract
Antimicrobial susceptibility tests (ASTs) are pivotal in combating multidrug resistant pathogens, yet they can be time-consuming, labor-intensive, and unstable. Using the AST of tigecycline for sepsis as the main model, here we establish an automated system of Clinical Antimicrobials Susceptibility Test Ramanometry (CAST-R), based on D2O-probed Raman microspectroscopy. Featuring a liquid robot for sample pretreatment and a machine learning-based control scheme for data acquisition and quality control, the 3-h, automated CAST-R process accelerates AST by >10-fold, processes 96 paralleled antibiotic-exposure reactions, and produces high-quality Raman spectra. The Expedited Minimal Inhibitory Concentration via Metabolic Activity is proposed as a quantitative and broadly applicable parameter for metabolism-based AST, which shows 99% essential agreement and 93% categorical agreement with the broth microdilution method (BMD) when tested on 100 Acinetobacter baumannii isolates. Further tests on 26 clinically positive blood samples for eight antimicrobials, including tigecycline, meropenem, ceftazidime, ampicillin/sulbactam, oxacillin, clindamycin, vancomycin, and levofloxacin reveal 93% categorical agreement with BMD-based results. The automation, speed, reliability, and general applicability of CAST-R suggest its potential utility for guiding the clinical administration of antimicrobials.
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Affiliation(s)
- Pengfei Zhu
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lihui Ren
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- College of Information Science & EngineeringOcean University of ChinaQingdaoChina
| | - Ying Zhu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Graduate School, Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
| | - Jing Dai
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Huijie Liu
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuli Mao
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuandong Li
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuehui He
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoshan Zheng
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Rongze Chen
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoting Fu
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lili Zhang
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lijun Sun
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuanqi Zhu
- Department of Clinical Laboratory, Affiliated Hospital of Qingdao UniversityQingdao UniversityQingdaoChina
| | - Yuetong Ji
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Qingdao Single‐Cell Biotechnology, Co., Ltd.QingdaoChina
| | - Bo Ma
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
| | - Jian Xu
- Single‐Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- The Bioland LaboratoryGuangzhouChina
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
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Zhang W, Sun H, He S, Chen X, Yao L, Zhou L, Wang Y, Wang P, Hong W. Compound Raman microscopy for rapid diagnosis and antimicrobial susceptibility testing of pathogenic bacteria in urine. Front Microbiol 2022; 13:874966. [PMID: 36090077 PMCID: PMC9449455 DOI: 10.3389/fmicb.2022.874966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
Rapid identification and antimicrobial susceptibility testing (AST) of bacteria are key interventions to curb the spread and emergence of antimicrobial resistance. The current gold standard identification and AST methods provide comprehensive diagnostic information but often take 3 to 5 days. Here, a compound Raman microscopy (CRM), which integrates Raman spectroscopy and stimulated Raman scattering microscopy in one system, is presented and demonstrated for rapid identification and AST of pathogens in urine. We generated an extensive bacterial Raman spectral dataset and applied deep learning to identify common clinical bacterial pathogens. In addition, we employed stimulated Raman scattering microscopy to quantify bacterial metabolic activity to determine their antimicrobial susceptibility. For proof-of-concept, we demonstrated an integrated assay to diagnose urinary tract infection pathogens, S. aureus and E. coli. Notably, the CRM system has the unique ability to provide Gram-staining classification and AST results within ~3 h directly from urine samples and shows great potential for clinical applications.
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Affiliation(s)
- Weifeng Zhang
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Hongyi Sun
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Shipei He
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Xun Chen
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- School of Engineering Medicine, Beihang University, Beijing, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital, Beijing, China
- Lin Yao,
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Yi Wang
- Department of Clinical Laboratory, China Rehabilitation Research Center, Capital Medical University, Beijing, China
| | - Pu Wang
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- *Correspondence: Pu Wang,
| | - Weili Hong
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- Weili Hong,
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Bandeliuk O, Assaf A, Bittel M, Durand MJ, Thouand G. Development and Automation of a Bacterial Biosensor to the Targeting of the Pollutants Toxic Effects by Portable Raman Spectrometer. SENSORS 2022; 22:s22124352. [PMID: 35746134 PMCID: PMC9228378 DOI: 10.3390/s22124352] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 02/04/2023]
Abstract
Water quality monitoring requires a rapid and sensitive method that can detect multiple hazardous pollutants at trace levels. This study aims to develop a new generation of biosensors using a low-cost fiber-optic Raman device. An automatic measurement system was thus conceived, built and successfully tested with toxic substances of three different types: antibiotics, heavy metals and herbicides. Raman spectroscopy provides a multiparametric view of metabolic responses of biological organisms to these toxic agents through their spectral fingerprints. Spectral analysis identified the most susceptible macromolecules in an E. coli model strain, providing a way to determine specific toxic effects in microorganisms. The automation of Raman analysis reduces the number of spectra required per sample and the measurement time: for four samples, time was cut from 3 h to 35 min by using a multi-well sample holder without intervention from an operator. The correct classifications were, respectively, 99%, 82% and 93% for the different concentrations of norfloxacin, while the results were 85%, 93% and 81% for copper and 92%, 90% and 96% for 3,5-dichlorophenol at the three tested concentrations. The work initiated here advances the technology needed to use Raman spectroscopy coupled with bioassays so that together, they can advance field toxicological testing.
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Affiliation(s)
- Oleksandra Bandeliuk
- Nantes Université, ONIRIS, CNRS, GEPEA, UMR 6144, 85000 La Roche-sur-Yon, France; (O.B.); (A.A.); (M.-J.D.)
- Tronico-Tame-Water, 26 Rue du Bocage, 85660 Saint-Philbert-de-Bouaine, France;
| | - Ali Assaf
- Nantes Université, ONIRIS, CNRS, GEPEA, UMR 6144, 85000 La Roche-sur-Yon, France; (O.B.); (A.A.); (M.-J.D.)
| | - Marine Bittel
- Tronico-Tame-Water, 26 Rue du Bocage, 85660 Saint-Philbert-de-Bouaine, France;
| | - Marie-Jose Durand
- Nantes Université, ONIRIS, CNRS, GEPEA, UMR 6144, 85000 La Roche-sur-Yon, France; (O.B.); (A.A.); (M.-J.D.)
| | - Gérald Thouand
- Nantes Université, ONIRIS, CNRS, GEPEA, UMR 6144, 85000 La Roche-sur-Yon, France; (O.B.); (A.A.); (M.-J.D.)
- Correspondence:
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31
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Yuan S, Chen Y, Lin K, Zou L, Lu X, He N, Liu R, Zhang S, Shen D, Song Z, Tong C, Song Y, Zhang W, Chen L, Sun G. Single Cell Raman Spectroscopy Deuterium Isotope Probing for Rapid Antimicrobial Susceptibility Test of Elizabethkingia spp. Front Microbiol 2022; 13:876925. [PMID: 35591987 PMCID: PMC9113537 DOI: 10.3389/fmicb.2022.876925] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Nosocomial infection by multi-drug resistance Elizabethkingia spp. is an emerging concern with severe clinical consequences, particularly in immunocompromised individuals and infants. Efficient control of this infection requires quick and reliable methods to determine the appropriate drugs for treatment. In this study, a total of 31 Elizabethkingia spp., including two standard strains (ATCC 13253 and FMS-007) and 29 clinical isolates obtained from hospitals in China were subjected to single cell Raman spectroscopy analysis coupled with deuterium probing (single cell Raman-DIP). The results demonstrated that single cell Raman-DIP could determine antimicrobial susceptibility of Elizabethkingia spp. in 4 h, only one third of the time required by standard broth microdilution method. The method could be integrated into current clinical protocol for sepsis and halve the report time. The study also confirmed that minocycline and levofloxacin are the first-line antimicrobials for Elizabethkingia spp. infection.
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Affiliation(s)
- Shuying Yuan
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yanwen Chen
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Kaicheng Lin
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Lin Zou
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xinrong Lu
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Na He
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Ruijie Liu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Shaoxing Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Danfeng Shen
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhenju Song
- Department of Emergency Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chaoyang Tong
- Department of Emergency Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yizhi Song
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Li Chen
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Guiqin Sun
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
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32
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Gao X, Li M, Zhao M, Wang X, Wang S, Liu Y. Metabolism-Triggered Colorimetric Sensor Array for Fingerprinting and Antibiotic Susceptibility Testing of Bacteria. Anal Chem 2022; 94:6957-6966. [PMID: 35500293 DOI: 10.1021/acs.analchem.1c05006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rapid identification and antibiotic susceptibility testing (AST) of bacteria would help us to accurately identify the infectious sources as well as guide the use of antibiotics, which are crucial for improving the survival rate and antimicrobial resistance. Herein, a colorimetric sensor array for bacteria fingerprinting was constructed with d-amino acid (d-AA)-modified gold nanoparticles (AuNPs) as probes (Au/d-AA). Bacteria can metabolize the d-AA, triggering the aggregation of AuNPs. Making use of different metabolic capabilities of bacteria toward different d-AA, eight kinds of bacteria including antibiotic-resistant bacteria and strains of the same bacterial species are successfully differentiated via learning the response patterns. Meanwhile, the sensor array also performs well in quantitative analysis of single bacterium and differentiation of bacteria mixtures. More interestingly, a rapid colorimetric AST approach has been developed based on the Au/d-AA nanoprobes by monitoring the d-AA metabolic activity of bacteria toward various antibiotic treatments. In this regard, the outlined work here would promote clinical practicability and facilitate antibiotic stewardship.
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Affiliation(s)
- Xia Gao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Miaomiao Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Minyang Zhao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Xinke Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Yaqing Liu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
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33
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A Review of Raman-Based Technologies for Bacterial Identification and Antimicrobial Susceptibility Testing. PHOTONICS 2022. [DOI: 10.3390/photonics9030133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Antimicrobial resistance (AMR) is a global medical threat that seriously endangers human health. Rapid bacterial identification and antimicrobial susceptibility testing (AST) are key interventions to combat the spread and emergence of AMR. Although current clinical bacterial identification and AST provide comprehensive information, they are labor-intensive, complex, inaccurate, and slow (requiring several days, depending on the growth of pathogenic bacteria). Recently, Raman-based identification and AST technologies have played an increasingly important role in fighting AMR. This review summarizes major Raman-based techniques for bacterial identification and AST, including spontaneous Raman scattering, surface-enhanced Raman scattering (SERS), and coherent Raman scattering (CRS) imaging. Then, we discuss recent developments in rapid identification and AST methods based on Raman technology. Finally, we highlight the major challenges and potential future efforts to improve clinical outcomes through rapid bacterial identification and AST.
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34
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Xu J, Yi X, Jin G, Peng D, Fan G, Xu X, Chen X, Yin H, Cooper JM, Huang WE. High-Speed Diagnosis of Bacterial Pathogens at the Single Cell Level by Raman Microspectroscopy with Machine Learning Filters and Denoising Autoencoders. ACS Chem Biol 2022; 17:376-385. [PMID: 35026119 DOI: 10.1021/acschembio.1c00834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate and rapid identification of infectious bacteria is important in medicine. Raman microspectroscopy holds great promise in performing label-free identification at the single-cell level. However, due to the naturally weak Raman signal, it is a challenge to build extensive databases and achieve both accurate and fast identification. Here, we used signal-to-noise ratio (SNR) as a standard indicator for Raman data quality and performed bacterial identification using 11, 141 single-cell Raman spectra from nine bacterial strains. Subsequently, using two machine learning methods, a simple filter, and a neural network-based denoising autoencoder (DAE), we demonstrated 92% (simple filter using 1 s/cell spectra) and 84% (DAE using 0.1 s/cell spectra) identification accuracy. Our machine learning-aided Raman analysis paves the way for high-speed Raman microspectroscopic clinical diagnostics.
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Affiliation(s)
- Jiabao Xu
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, U.K
| | - Xiaofei Yi
- Shanghai Hesen Biotechnology Co., Ltd, Shanghai 201802, China
- Shanghai D-band Medical Instrument Co., Ltd, Shanghai 201802, China
| | - Guilan Jin
- Shanghai Hesen Biotechnology Co., Ltd, Shanghai 201802, China
- Shanghai D-band Medical Instrument Co., Ltd, Shanghai 201802, China
| | - Di Peng
- Shanghai Hesen Biotechnology Co., Ltd, Shanghai 201802, China
- Shanghai D-band Medical Instrument Co., Ltd, Shanghai 201802, China
| | - Gaoya Fan
- Shanghai Hesen Biotechnology Co., Ltd, Shanghai 201802, China
- Shanghai D-band Medical Instrument Co., Ltd, Shanghai 201802, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xin Chen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Huabing Yin
- James Watt School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - Jonathan M. Cooper
- James Watt School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, U.K
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35
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36
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El-Mashtoly SF, Gerwert K. Diagnostics and Therapy Assessment Using Label-Free Raman Imaging. Anal Chem 2021; 94:120-142. [PMID: 34852454 DOI: 10.1021/acs.analchem.1c04483] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Samir F El-Mashtoly
- Center for Protein Diagnostics, Ruhr University Bochum, 44801 Bochum, Germany.,Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Klaus Gerwert
- Center for Protein Diagnostics, Ruhr University Bochum, 44801 Bochum, Germany.,Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
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37
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Hare PJ, LaGree TJ, Byrd BA, DeMarco AM, Mok WWK. Single-Cell Technologies to Study Phenotypic Heterogeneity and Bacterial Persisters. Microorganisms 2021; 9:2277. [PMID: 34835403 PMCID: PMC8620850 DOI: 10.3390/microorganisms9112277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotic persistence is a phenomenon in which rare cells of a clonal bacterial population can survive antibiotic doses that kill their kin, even though the entire population is genetically susceptible. With antibiotic treatment failure on the rise, there is growing interest in understanding the molecular mechanisms underlying bacterial phenotypic heterogeneity and antibiotic persistence. However, elucidating these rare cell states can be technically challenging. The advent of single-cell techniques has enabled us to observe and quantitatively investigate individual cells in complex, phenotypically heterogeneous populations. In this review, we will discuss current technologies for studying persister phenotypes, including fluorescent tags and biosensors used to elucidate cellular processes; advances in flow cytometry, mass spectrometry, Raman spectroscopy, and microfluidics that contribute high-throughput and high-content information; and next-generation sequencing for powerful insights into genetic and transcriptomic programs. We will further discuss existing knowledge gaps, cutting-edge technologies that can address them, and how advances in single-cell microbiology can potentially improve infectious disease treatment outcomes.
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Affiliation(s)
- Patricia J. Hare
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
- School of Dental Medicine, University of Connecticut, Farmington, CT 06032, USA
| | - Travis J. LaGree
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
| | - Brandon A. Byrd
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
- School of Medicine, University of Connecticut, Farmington, CT 06032, USA
| | - Angela M. DeMarco
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
| | - Wendy W. K. Mok
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
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38
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Cui L, Li HZ, Yang K, Zhu LJ, Xu F, Zhu YG. Raman biosensor and molecular tools for integrated monitoring of pathogens and antimicrobial resistance in wastewater. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116415] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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39
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Wang J, Lin K, Hu H, Qie X, Huang WE, Cui Z, Gong Y, Song Y. In Vitro Anticancer Drug Sensitivity Sensing through Single-Cell Raman Spectroscopy. BIOSENSORS-BASEL 2021; 11:bios11080286. [PMID: 34436088 PMCID: PMC8392728 DOI: 10.3390/bios11080286] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 11/20/2022]
Abstract
Traditional in vitro anticancer drug sensitivity testing at the population level suffers from lengthy procedures and high false positive rates. To overcome these defects, we built a confocal Raman microscopy sensing system and proposed a single-cell approach via Raman-deuterium isotope probing (Raman-DIP) as a rapid and reliable in vitro drug efficacy evaluation method. Raman-DIP detected the incorporation of deuterium into the cell, which correlated with the metabolic activity of the cell. The human non-small cell lung cancer cell line HCC827 and human breast cancer cell line MCF-7 were tested against eight different anticancer drugs. The metabolic activity of cancer cells could be detected as early as 12 h, independent of cell growth. Incubation of cells in 30% heavy water (D2O) did not show any negative effect on cell viability. Compared with traditional methods, Raman-DIP could accurately determine the drug effect, meanwhile, it could reduce the testing period from 72–144 h to 48 h. Moreover, the heterogeneity of cells responding to anticancer drugs was observed at the single-cell level. This proof-of-concept study demonstrated the potential of Raman-DIP to be a reliable tool for cancer drug discovery and drug susceptibility testing.
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Affiliation(s)
- Jingkai Wang
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Kaicheng Lin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Huijie Hu
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Xingwang Qie
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Zhisong Cui
- Marine Bioresources and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Yan Gong
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
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