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Umar Hussain M, Kainat K, Nawaz H, Irfan Majeed M, Akhtar N, Alshammari A, Albekairi NA, Fatima R, Amber A, Bano A, Shabbir I, Tahira M, Pallares RM. SERS characterization of biochemical changes associated with biodesulfurization of dibenzothiophene using Gordonia sp. HS126-4N. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 320:124534. [PMID: 38878718 DOI: 10.1016/j.saa.2024.124534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/08/2024] [Accepted: 05/24/2024] [Indexed: 07/08/2024]
Abstract
In this study, Gordonia sp. HS126-4N was employed for dibenzothiophene (DBT) biodesulfurization, tracked over 9 days using SERS. During the initial lag phase, no significant spectral changes were observed, but after 48 h, elevated metabolic activity was evident. At 72 h, maximal bacterial population correlated with peak spectrum variance, followed by stable spectral patterns. Despite 2-hydroxybiphenyl (2-HBP) induced enzyme suppression, DBT biodesulfurization persisted. PCA and PLS-DA analysis of the SERS spectra revealed distinctive features linked to both bacteria and DBT, showcasing successful desulfurization and bacterial growth stimulation. PLS-DA achieved a specificity of 95.5 %, sensitivity of 94.3 %, and AUC of 74 %, indicating excellent classification of bacteria exposed to DBT. SERS effectively tracked DBT biodesulfurization and bacterial metabolic changes, offering insights into biodesulfurization mechanisms and bacterial development phases. This study highlights SERS' utility in biodesulfurization research, including its use in promising advancements in the field.
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Affiliation(s)
- Muhammad Umar Hussain
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Kiran Kainat
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Nasrin Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan.
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Norah A Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Rida Fatima
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Arooj Amber
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Aqsa Bano
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Ifra Shabbir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Maryam Tahira
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Roger M Pallares
- Institute for Experimental Molecular Imaging, RWTH Aachen University Hospital, Aachen 52074, Germany
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Tahseen H, Ul Huda N, Nawaz H, Majeed MI, Alwadie N, Rashid N, Aslam MA, Zafar N, Asghar M, Anwar A, Ashraf A, Umer R. Surface-enhanced Raman spectroscopy for comparison of biochemical profile of bacteriophage sensitive and resistant methicillin-resistant Staphylococcus aureus (MRSA) strains. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123968. [PMID: 38330510 DOI: 10.1016/j.saa.2024.123968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is gram positive bacteria and leading cause of a wide variety of diseases. It is a common cause of hospitalized and community-acquired infections. Development of increasing antibiotic-resistance by methicillin-resistant S. aureus (MRSA) strains demand to develop alternate novel therapies. Bacteriophages are now widely used as antibacterial therapies against antibiotic-resistant gram-positive pathogens. So, there is an urgent need to find fast detection techniques to point out phage susceptible and resistant strains of methicillin-resistant S. aureus (MRSA) bacteria. Samples of two separate strains of bacteria, S. aureus, in form of pellets and supernatant, were used for this purpose. Strain-I was resistant to phage, while the other (strain-II) was sensitive. Surface Enhanced Raman Spectroscopy (SERS) has detected significant biochemical changes in these bacterial strains of pellets and supernatants in the form of SERS spectral features. The protein portion of these two types of strains of methicillin-resistant S. aureus (MRSA) in their relevant pellets and supernatants is major distinguishing biomolecule as shown by their representative SERS spectral features. In addition, multivariate data analysis techniques such as principal component analysis (PCA) and a partial least squares-discriminant analysis (PLS-DA) were found to be helpful in identifying and characterizing various strains of S. aureus which are sensitive and resistant to bacteriophage with 100% specificity, 100% accuracy, and 99.8% sensitivity in case of SERS spectral data sets of bacterial cell pellets. Moreover, in case of supernatant samples, the results of PLS-DA model including 95.5% specificity, 96% sensitivity, and 96.5% accuracy are obtained.
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Affiliation(s)
- Hira Tahseen
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Noor Ul Huda
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Najah Alwadie
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad Campus, Faisalabad 38000, Pakistan
| | - Muhammad Aamir Aslam
- Institute of Microbiology, Faculty of Veterinary, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Nishat Zafar
- Institute of Microbiology, Faculty of Veterinary, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Maria Asghar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Ayesha Anwar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Ayesha Ashraf
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Rabiea Umer
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
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Wang W, Wang X, Huang Y, Zhao Y, Fang X, Cong Y, Tang Z, Chen L, Zhong J, Li R, Guo Z, Zhang Y, Li S. Raman spectrum combined with deep learning for precise recognition of Carbapenem-resistant Enterobacteriaceae. Anal Bioanal Chem 2024:10.1007/s00216-024-05209-9. [PMID: 38383664 DOI: 10.1007/s00216-024-05209-9] [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: 12/31/2023] [Revised: 02/08/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) is a major pathogen that poses a serious threat to human health. Unfortunately, currently, there are no effective measures to curb its rapid development. To address this, an in-depth study on the surface-enhanced Raman spectroscopy (SERS) of 22 strains of 7 categories of CRE using a gold silver composite SERS substrate was conducted. The residual networks with an attention mechanism to classify the SERS spectrum from three perspectives (pathogenic bacteria type, enzyme-producing subtype, and sensitive antibiotic type) were performed. The results show that the SERS spectrum measured by the composite SERS substrate was repeatable and consistent. The SERS spectrum of CRE showed varying degrees of species differences, and the strain difference in the SERS spectrum of CRE was closely related to the type of enzyme-producing subtype. The introduced attention mechanism improved the classification accuracy of the residual network (ResNet) model. The accuracy of CRE classification for different strains and enzyme-producing subtypes reached 94.0% and 96.13%, respectively. The accuracy of CRE classification by pathogen sensitive antibiotic combination reached 93.9%. This study is significant for guiding antibiotic use in CRE infection, as the sensitive antibiotic used in treatment can be predicted directly by measuring CRE spectra. Our study demonstrates the potential of combining SERS with deep learning algorithms to identify CRE without culture labels and classify its sensitive antibiotics. This approach provides a new idea for rapid and accurate clinical detection of CRE and has important significance for alleviating the rapid development of resistance to CRE.
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Affiliation(s)
- Wen Wang
- Dongguan Key Laboratory of Medical Electronics and Medical Imaging Equipment, Guangdong Medical University Dongguan First Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Xin Wang
- Dongguan Key Laboratory of Medical Electronics and Medical Imaging Equipment, Guangdong Medical University Dongguan First Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Ya Huang
- Donghua Hospital Laboratory Department, Dongguan, 523808, Guangdong, China
| | - Yi Zhao
- Dongguan Key Laboratory of Environmental Medicine, School of Basic Medicine, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Xianglin Fang
- Dongguan Key Laboratory of Medical Electronics and Medical Imaging Equipment, Guangdong Medical University Dongguan First Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Yanguang Cong
- Dongguan Key Laboratory of Medical Electronics and Medical Imaging Equipment, Guangdong Medical University Dongguan First Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Zhi Tang
- Dongguan Key Laboratory of Environmental Medicine, School of Basic Medicine, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Luzhu Chen
- Dongguan Key Laboratory of Medical Electronics and Medical Imaging Equipment, Guangdong Medical University Dongguan First Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Jingyi Zhong
- Dongguan Key Laboratory of Medical Electronics and Medical Imaging Equipment, Guangdong Medical University Dongguan First Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Ruoyi Li
- Dongguan Key Laboratory of Medical Electronics and Medical Imaging Equipment, Guangdong Medical University Dongguan First Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Zhusheng Guo
- Donghua Hospital Laboratory Department, Dongguan, 523808, Guangdong, China.
| | - Yanjiao Zhang
- Dongguan Key Laboratory of Environmental Medicine, School of Basic Medicine, Guangdong Medical University, Dongguan, 523808, Guangdong, China.
| | - Shaoxin Li
- Dongguan Key Laboratory of Medical Electronics and Medical Imaging Equipment, Guangdong Medical University Dongguan First Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, 523808, Guangdong, China.
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Caliskan-Aydogan O, Alocilja EC. A Review of Carbapenem Resistance in Enterobacterales and Its Detection Techniques. Microorganisms 2023; 11:1491. [PMID: 37374993 DOI: 10.3390/microorganisms11061491] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Infectious disease outbreaks have caused thousands of deaths and hospitalizations, along with severe negative global economic impacts. Among these, infections caused by antimicrobial-resistant microorganisms are a major growing concern. The misuse and overuse of antimicrobials have resulted in the emergence of antimicrobial resistance (AMR) worldwide. Carbapenem-resistant Enterobacterales (CRE) are among the bacteria that need urgent attention globally. The emergence and spread of carbapenem-resistant bacteria are mainly due to the rapid dissemination of genes that encode carbapenemases through horizontal gene transfer (HGT). The rapid dissemination enables the development of host colonization and infection cases in humans who do not use the antibiotic (carbapenem) or those who are hospitalized but interacting with environments and hosts colonized with carbapenemase-producing (CP) bacteria. There are continuing efforts to characterize and differentiate carbapenem-resistant bacteria from susceptible bacteria to allow for the appropriate diagnosis, treatment, prevention, and control of infections. This review presents an overview of the factors that cause the emergence of AMR, particularly CRE, where they have been reported, and then, it outlines carbapenemases and how they are disseminated through humans, the environment, and food systems. Then, current and emerging techniques for the detection and surveillance of AMR, primarily CRE, and gaps in detection technologies are presented. This review can assist in developing prevention and control measures to minimize the spread of carbapenem resistance in the human ecosystem, including hospitals, food supply chains, and water treatment facilities. Furthermore, the development of rapid and affordable detection techniques is helpful in controlling the negative impact of infections caused by AMR/CRE. Since delays in diagnostics and appropriate antibiotic treatment for such infections lead to increased mortality rates and hospital costs, it is, therefore, imperative that rapid tests be a priority.
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Affiliation(s)
- Oznur Caliskan-Aydogan
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lansing, MI 48824, USA
| | - Evangelyn C Alocilja
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lansing, MI 48824, USA
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Ehsan U, Nawaz H, Irfan Majeed M, Rashid N, Ali Z, Zulfiqar A, Tariq A, Shahbaz M, Meraj L, Naheed I, Sadaf N. Surface-enhanced Raman spectroscopy of centrifuged blood serum samples of diabetic type II patients by using 50KDa filter devices. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 293:122457. [PMID: 36764165 DOI: 10.1016/j.saa.2023.122457] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Blood serum contains essential biochemical information which are used for early disease diagnosis. Blood serum consisted of higher molecular weight fractions (HMWF) and lower molecular weight fractions (LMWF). The disease biomarkers are lower molecular weight fraction proteins, and their contribution to disease diagnosis is suppressed due to higher molecular weight fraction proteins. To diagnose diabetes in early stages are difficult because of the presence of huge amount of these HMWF. In the current study, surface-enhanced Raman spectroscopy (SERS) are employed to diagnose diabetes after centrifugation of serum samples using Amicon ultra filter devices of 50 kDa which produced two fractions of whole blood serum of filtrate, low molecular weight fraction, and residue, high molecular weight fraction. Furthermore SERS is employed to study the LMW fractions of healthy and diseased samples. Some prominent SERS bands are observed at 725 cm-1, 842 cm-1, 1025 cm-1, 959 cm-1, and 1447 cm-1 due to small molecular weight proteins, and these biomarkers helped to diagnose the disease early stage. Moreover, chemometric techniques such as principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) are employed to check the potential of surface-enhanced Raman spectroscopy for the differentiation and classifications of the blood serum samples. SERS can be employed for the early diagnosis and screening of biochemical changes during type II diabetes.
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Affiliation(s)
- Usama Ehsan
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad Campus, Faisalabad 38000, Pakistan.
| | - Zain Ali
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Anam Zulfiqar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Ayesha Tariq
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Shahbaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Lubna Meraj
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Iqra Naheed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Nimra Sadaf
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
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Haq AU, Majeed MI, Nawaz H, Rashid N, Javed MR, Raza A, Shakeel M, Zahra ST, Meraj L, Perveen A, Murtaza S, Khaliq S. Surface-enhanced Raman spectroscopy for monitoring antibacterial activity of imidazole derivative (1-benzyl-3-(sec‑butyl)-1H-imidazole-3-ium bromide) against Bacillus subtilis and Escherichia coli. Photodiagnosis Photodyn Ther 2023; 42:103533. [DOI: 10.1016/j.pdpdt.2023.103533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 02/17/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023]
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Caliskan-Aydogan O, Sharief SA, Alocilja EC. Nanoparticle-Based Plasmonic Biosensor for the Unamplified Genomic Detection of Carbapenem-Resistant Bacteria. Diagnostics (Basel) 2023; 13:diagnostics13040656. [PMID: 36832142 PMCID: PMC9955743 DOI: 10.3390/diagnostics13040656] [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: 01/14/2023] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 02/12/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global public health issue, and the rise of carbapenem-resistant bacteria needs attention. While progress is being made in the rapid detection of resistant bacteria, affordability and simplicity of detection still need to be addressed. This paper presents a nanoparticle-based plasmonic biosensor for detecting the carbapenemase-producing bacteria, particularly the beta-lactam Klebsiella pneumoniae carbapenemase (blaKPC) gene. The biosensor used dextrin-coated gold nanoparticles (GNPs) and an oligonucleotide probe specific to blaKPC to detect the target DNA in the sample within 30 min. The GNP-based plasmonic biosensor was tested in 47 bacterial isolates: 14 KPC-producing target bacteria and 33 non-target bacteria. The stability of GNPs, confirmed by the maintenance of their red appearance, indicated the presence of target DNA due to probe-binding and GNP protection. The absence of target DNA was indicated by the agglomeration of GNPs, corresponding to a color change from red to blue or purple. The plasmonic detection was quantified with absorbance spectra measurements. The biosensor successfully detected and differentiated the target from non-target samples with a detection limit of 2.5 ng/μL, equivalent to ~103 CFU/mL. The diagnostic sensitivity and specificity were found to be 79% and 97%, respectively. The GNP plasmonic biosensor is simple, rapid, and cost-effective in detecting blaKPC-positive bacteria.
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Affiliation(s)
- Oznur Caliskan-Aydogan
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lansing, MI 48824, USA
| | - Saad Asadullah Sharief
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lansing, MI 48824, USA
| | - Evangelyn C. Alocilja
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lansing, MI 48824, USA
- Correspondence:
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Akram M, Majeed MI, Nawaz H, Rashid N, Javed MR, Ali MZ, Raza A, Shakeel M, Hasan HMU, Ali Z, Ehsan U, Shahid M. Surface-enhanced Raman spectroscopy for characterization of filtrate portions of blood serum samples of typhoid patients. Photodiagnosis Photodyn Ther 2022; 40:103199. [PMID: 36371020 DOI: 10.1016/j.pdpdt.2022.103199] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Surface-enhanced Raman spectroscopy (SERS) is explored to design a rapid screening method for the characterization and diagnosis of typhoid fever by employing filtrate fractions of blood serum samples obtained by centrifugal filtration with 50 KDa filters. OBJECTIVES The purpose of this study, to separate the filtrate portions of blood serum samples in this way contain proteins smaller than 50 kDa and removal of bigger size protein which allows to acquire the SERS spectral features of smaller proteins more effectively which are probably associated with typhoid disease. Disease caused by Salmonella typhi diagnose more effectively by using surface-enhanced Raman spectroscopy (SERS) and multivariate data analysis tools. METHODS SERS was used as a diagnostic tool for typhoid fever by comparison between healthy and diseased samples. For this purpose, all the samples were analyzed by comparing their SERS spectral features. Over the spectral range of 400-1800cm-1, multivariate data analysis techniques such as Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) are applied to diagnose and differentiate different filtrate fractions of blood serum samples of patients of typhoid fever and healthy ones. RESULTS By comparing SERS spectra of healthy filtrate with that of filtrate of typhoid sample, the SERS spectral features associated with disease development are identified including PCA is found to be efficient for the qualitative differentiation of all of the samples analyzed. Moreover, PLS-DA successfully identified and classified healthy and typhoid positive blood serum samples with 97 % accuracy, 99 % specificity, 91 % sensitivity and 0.78 area under the receiver operating characteristic (AUROC) curve. CONCLUSIONS Surface enhanced Raman spectroscopy using silver nanoparticles SERS substrate, is found to be useful technique for the quick identification and evaluation of filtrate fractions of the blood serum samples of healthy and typhoid samples for disease diagnosis.
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Affiliation(s)
- Maria Akram
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad Campus, Faisalabad 38000, Pakistan.
| | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Muhammad Zeeshan Ali
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Ali Raza
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Shakeel
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Hafiz Mahmood Ul Hasan
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Zain Ali
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Usama Ehsan
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Shahid
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
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Mushtaq A, Nawaz H, Irfan Majeed M, Rashid N, Tahir M, Zaman Nawaz M, Shahzad K, Dastgir G, Zaki Abdul Bari R, Ul Haq A, Saleem M, Akhtar F. Surface-enhanced Raman spectroscopy (SERS) for monitoring colistin-resistant and susceptible E. coli strains. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121315. [PMID: 35576839 DOI: 10.1016/j.saa.2022.121315] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/21/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
The emergence of drug-resistant bacteria is a precarious global health concern. In this study, surface-enhanced Raman spectroscopy (SERS) is used to characterize colistin-resistant and susceptible E. coli strains based on their distinguished SERS spectral features for the development of rapid and cost-effective detection and differentiation methods. For this purpose, three colistin-resistant and three colistin susceptible E. coli strains were analyzed by comparing their SERS spectral signatures. Moreover, multivariate data analysis techniques including Principal component analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) were used to examine the SERS spectral data of colistin-resistant and susceptible strains. PCA technique was employed for differentiating colistin susceptible and resistant E.coli strains due to alteration in biochemical compositions of the bacterial cell. PLS-DA is employed on SERS spectral data sets for discrimination of these resistant and susceptible E. coli strains with 100% specificity, 100% accuracy, 99.8% sensitivity, and 86% area under receiver operating characteristics (AUROC) curve.
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Affiliation(s)
- Aqsa Mushtaq
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad Campus, Faisalabad 38000, Pakistan.
| | - Muhammad Tahir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Zaman Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Kashif Shahzad
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Ghulam Dastgir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Rana Zaki Abdul Bari
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Anwar Ul Haq
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Mudassar Saleem
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Farwa Akhtar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
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Assessing the effect of different pH maintenance situations on bacterial SERS spectra. Anal Bioanal Chem 2022; 414:4977-4985. [PMID: 35606451 DOI: 10.1007/s00216-022-04125-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/24/2022] [Accepted: 05/10/2022] [Indexed: 11/01/2022]
Abstract
Phenotyping of bacteria with vibrational spectroscopy has caught much attention in bacteria-related research. It is known that many factors could affect this process. Among them, solution pH maintenance is crucial, yet its impact on the bacterial SERS spectra is surprisingly neglected. In this work, we focused on two situations related to pH maintenance: the effect of the same buffer on the SERS spectra of bacteria under different pH values, and the influence of different buffers on the SERS spectra of bacteria under the same pH value. Specifically, Britton-Robison (BR) buffer was used to evaluate the effect of pH value on bacteria SERS spectra thanks to its wide pH range. Four different buffers, namely BR buffer, acetate buffer, phosphate buffer, and carbonate buffer, were used to illustrate the impact of buffer types on SERS spectra of bacteria. The results showed that the intensity and number of characteristic peaks of the SERS spectra of Gram-negative (G -) bacteria changed more significantly than Gram-positive (G +) bacteria with the change of pH value. Furthermore, compared with phosphate buffer and carbonate buffer, BR buffer could bring more characteristic SERS bands with better reproducibility, but slightly inferior to acetate buffer. In conclusion, the influence of the pH and types of the buffer on the SERS spectra of bacteria are worthy of further discussion.
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Lister AP, Highmore CJ, Hanrahan N, Read J, Munro APS, Tan S, Allan RN, Faust SN, Webb JS, Mahajan S. Multi-Excitation Raman Spectroscopy for Label-Free, Strain-Level Characterization of Bacterial Pathogens in Artificial Sputum Media. Anal Chem 2022; 94:669-677. [DOI: 10.1021/acs.analchem.1c02501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Adam P. Lister
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- National Biofilms Innovation Centre (NBIC) and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Callum J. Highmore
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Niall Hanrahan
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- National Biofilms Innovation Centre (NBIC) and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - James Read
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- National Biofilms Innovation Centre (NBIC) and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Alasdair P. S. Munro
- NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Samuel Tan
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Raymond N. Allan
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- School of Pharmacy, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK
| | - Saul N. Faust
- NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- National Biofilms Innovation Centre (NBIC) and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Jeremy S. Webb
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- National Biofilms Innovation Centre (NBIC) and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Sumeet Mahajan
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- National Biofilms Innovation Centre (NBIC) and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
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12
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Machine learning analysis of SERS fingerprinting for the rapid determination of Mycobacterium tuberculosis infection and drug resistance. Comput Struct Biotechnol J 2022; 20:5364-5377. [PMID: 36212533 PMCID: PMC9526180 DOI: 10.1016/j.csbj.2022.09.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Handheld Raman spectrometer is able to generate SERS spectra with sufficient quality for Mycobacterium tuberculosis detection. It is feasible to accurately discriminate Mtb-positive sputum from Mtb-negative sputum through SERS spectrometry. Pulmonary and extra-pulmonary Mtb strains were able to be accurately distinguished via SERS spectral analysis. Profiling of antibiotic resistance of Mtb strains was successfully achieved through machine learning analysis of SERS spectra.
Over the past decades, conventional methods and molecular assays have been developed for the detection of tuberculosis (TB). However, these techniques suffer limitations in the identification of Mycobacterium tuberculosis (Mtb), such as long turnaround time and low detection sensitivity, etc., not even mentioning the difficulty in discriminating antibiotics-resistant Mtb strains that cause great challenges in TB treatment and prevention. Thus, techniques with easy implementation for rapid diagnosis of Mtb infection are in high demand for routine TB diagnosis. Due to the label-free, low-cost and non-invasive features, surface enhanced Raman spectroscopy (SERS) has been extensively investigated for its potential in bacterial pathogen identification. However, at current stage, few studies have recruited handheld Raman spectrometer to discriminate sputum samples with or without Mtb, separate pulmonary Mtb strains from extra-pulmonary Mtb strains, or profile Mtb strains with different antibiotic resistance characteristics. In this study, we recruited a set of supervised machine learning algorithms to dissect different SERS spectra generated via a handheld Raman spectrometer with a focus on deep learning algorithms, through which sputum samples with or without Mtb strains were successfully differentiated (5-fold cross-validation accuracy = 94.32%). Meanwhile, Mtb strains isolated from pulmonary and extra-pulmonary samples were effectively separated (5-fold cross-validation accuracy = 99.86%). Moreover, Mtb strains with different drug-resistant profiles were also competently distinguished (5-fold cross-validation accuracy = 99.59%). Taken together, we concluded that, with the assistance of deep learning algorithms, handheld Raman spectrometer has a high application potential for rapid point-of-care diagnosis of Mtb infections in future.
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Serebrennikova KV, Berlina AN, Sotnikov DV, Zherdev AV, Dzantiev BB. Raman Scattering-Based Biosensing: New Prospects and Opportunities. BIOSENSORS 2021; 11:512. [PMID: 34940269 PMCID: PMC8699498 DOI: 10.3390/bios11120512] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 05/02/2023]
Abstract
The growing interest in the development of new platforms for the application of Raman spectroscopy techniques in biosensor technologies is driven by the potential of these techniques in identifying chemical compounds, as well as structural and functional features of biomolecules. The effect of Raman scattering is a result of inelastic light scattering processes, which lead to the emission of scattered light with a different frequency associated with molecular vibrations of the identified molecule. Spontaneous Raman scattering is usually weak, resulting in complexities with the separation of weak inelastically scattered light and intense Rayleigh scattering. These limitations have led to the development of various techniques for enhancing Raman scattering, including resonance Raman spectroscopy (RRS) and nonlinear Raman spectroscopy (coherent anti-Stokes Raman spectroscopy and stimulated Raman spectroscopy). Furthermore, the discovery of the phenomenon of enhanced Raman scattering near metallic nanostructures gave impetus to the development of the surface-enhanced Raman spectroscopy (SERS) as well as its combination with resonance Raman spectroscopy and nonlinear Raman spectroscopic techniques. The combination of nonlinear and resonant optical effects with metal substrates or nanoparticles can be used to increase speed, spatial resolution, and signal amplification in Raman spectroscopy, making these techniques promising for the analysis and characterization of biological samples. This review provides the main provisions of the listed Raman techniques and the advantages and limitations present when applied to life sciences research. The recent advances in SERS and SERS-combined techniques are summarized, such as SERRS, SE-CARS, and SE-SRS for bioimaging and the biosensing of molecules, which form the basis for potential future applications of these techniques in biosensor technology. In addition, an overview is given of the main tools for success in the development of biosensors based on Raman spectroscopy techniques, which can be achieved by choosing one or a combination of the following approaches: (i) fabrication of a reproducible SERS substrate, (ii) synthesis of the SERS nanotag, and (iii) implementation of new platforms for on-site testing.
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Affiliation(s)
| | | | | | | | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (K.V.S.); (A.N.B.); (D.V.S.); (A.V.Z.)
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14
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Vaitiekūnaitė D, Snitka V. Differentiation of Closely Related Oak-Associated Gram-Negative Bacteria by Label-Free Surface Enhanced Raman Spectroscopy (SERS). Microorganisms 2021; 9:1969. [PMID: 34576865 PMCID: PMC8466144 DOI: 10.3390/microorganisms9091969] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 12/02/2022] Open
Abstract
Due to the harmful effects of chemical fertilizers and pesticides, the need for an eco-friendly solution to improve soil fertility has become a necessity, thus microbial biofertilizer research is on the rise. Plant endophytic bacteria inhabiting internal tissues represent a novel niche for research into new biofertilizer strains. However, the number of species and strains that need to be differentiated and identified to facilitate faster screening in future plant-bacteria interaction studies, is enormous. Surface enhanced Raman spectroscopy (SERS) may provide a platform for bacterial discrimination and identification, which, compared with the traditional methods, is relatively rapid, uncomplicated and ensures high specificity. In this study, we attempted to differentiate 18 bacterial isolates from two oaks via morphological, physiological, biochemical tests and SERS spectra analysis. Previous 16S rRNA gene fragment sequencing showed that three isolates belong to Paenibacillus, 3-to Pantoea and 12-to Pseudomonas genera. Additional tests were not able to further sort these bacteria into strain-specific groups. However, the obtained label-free SERS bacterial spectra along with the high-accuracy principal component (PCA) and discriminant function analyses (DFA) demonstrated the possibility to differentiate these bacteria into variant strains. Furthermore, we collected information about the biochemical characteristics of selected isolates. The results of this study suggest a promising application of SERS in combination with PCA/DFA as a rapid, non-expensive and sensitive method for the detection and identification of plant-associated bacteria.
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Affiliation(s)
- Dorotėja Vaitiekūnaitė
- Laboratory of Forest Plant Biotechnology, Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania
| | - Valentinas Snitka
- Research Center for Microsystems and Nanotechnology, Kaunas University of Technology, Studentu Str. 65, 51369 Kaunas, Lithuania;
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15
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Bashir S, Nawaz H, Irfan Majeed M, Mohsin M, Nawaz A, Rashid N, Batool F, Akbar S, Abubakar M, Ahmad S, Ali S, Kashif M. Surface-enhanced Raman spectroscopy for the identification of tigecycline-resistant E. coli strains. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 258:119831. [PMID: 33957452 DOI: 10.1016/j.saa.2021.119831] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
Tigecycline (TGC) is recognised as last resort of drugs against several antibiotic-resistant bacteria. Bacterial resistance to tigecycline due to presence of plasmid-mediated mobile TGC resistance genes (tet X3/X4) has broken another defense line. Therefore, rapid and reproducible detection of tigecycline-resistant E. coli (TREC) is required. The current study is designed for the identification and differentiation of TREC from tigecycline-sensitive E. coli (TSEC) by employing SERS by using Ag NPs as a SERS substrate. The SERS spectral fingerprints of E. coli strains associated directly or indirectly with the development of resistance against tigecycline have been distinguished by comparing SERS spectral data of TSEC strains with each TREC strain. Moreover, the statistical analysis including Principal Component Analysis (PCA), Hierarchical Cluster Analysis (HCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) were employed to check the diagnostic potential of SERS for the differentiation among TREC and TSEC strains. The qualitative identification and differentiation between resistant and sensitive strains and among individual strains have been efficiently done by performing both PCA and HCA. The successful discrimination among TREC and TSEC at the strain level is performed by PLS-DA with 98% area under ROC curve, 100% sensitivity, 98.7% specificity and 100% accuracy.
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Affiliation(s)
- Saba Bashir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan.
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan.
| | - Ali Nawaz
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Nosheen Rashid
- Department of Chemistry, University of Central Punjab, Faisalabad Campus, Faisalabad, Pakistan
| | - Fatima Batool
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Saba Akbar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Muhammad Abubakar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Shamsheer Ahmad
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Saqib Ali
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Muhammad Kashif
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
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Surface-enhanced Raman spectroscopy for comparison of serum samples of typhoid and tuberculosis patients of different stages. Photodiagnosis Photodyn Ther 2021; 35:102426. [PMID: 34217869 DOI: 10.1016/j.pdpdt.2021.102426] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Surface-enhanced Raman spectroscopy (SERS) is a reliable tool for the identification and differentiation of two different human pathological conditions sharing the same symptomology, typhoid and tuberculosis (TB). OBJECTIVES To explore the potential of surface-enhanced Raman spectroscopy for differentiation of two different diseases showing the same symptoms and analysis by principal component analysis (PCA) and partial least square discriminate analysis (PLS-DA). METHODS Serum samples of clinically diagnosed typhoid and tuberculosis infected individuals were analyzed and differentiated by SERS using silver nanoparticles (Ag NPs) as a SERS substrate. For this purpose, the collected serum samples were analyzed under the SERS instrument and unique SERS spectra of typhoid and tuberculosis were compared showing notable spectral differences in protein, lipid and carbohydrates features. Different stages of the diseased class of typhoid (Early acute and late acute stage) and tuberculosis (Pulmonary and extra-pulmonary stage) were compared with each other and with healthy human serum samples, which were significantly separated. Moreover, SERS data was analyzed using multivariate data analysis techniques including principal component analysis (PCA) and partial least square discriminate analysis (PLS-DA) and differences were so prominent to observe. RESULTS SERS Spectral data of typhoid and tuberculosis showed clear differences and were significantly separated using PCA. SERS spectral data of both stages of typhoid and tuberculosis were separated according to 1st principle component. Moreover, by analyzing data using partial least square discriminate analysis, differentiation of two disease classes were considered more valid with a 100% value of sensitivity, specificity and accuracy. CONCLUSION SERS can be employed for identification and comparison of two different human pathological conditions sharing same symptomology.
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17
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Bashir S, Nawaz H, Majeed MI, Mohsin M, Abdullah S, Ali S, Rashid N, Kashif M, Batool F, Abubakar M, Ahmad S, Abdulraheem A. Rapid and sensitive discrimination among carbapenem resistant and susceptible E. coli strains using Surface Enhanced Raman Spectroscopy combined with chemometric tools. Photodiagnosis Photodyn Ther 2021; 34:102280. [PMID: 33823284 DOI: 10.1016/j.pdpdt.2021.102280] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/08/2021] [Accepted: 03/29/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND Raman spectroscopy is a powerful technique for the robust, reliable and rapid detection and discrimination of bacteria. OBJECTIVES To develop a rapid and sensitive technique based on surface-enhanced Raman spectroscopy (SERS) with multivariate data analysis tools for discrimination among carbapenem resistant and susceptible E. coli strains. METHODS SERS was employed to differentiate different strains of carbapenem resistant and susceptible E. coli by using silver nanoparticles (Ag NPs) as a SERS substrate. For this purpose, four strains of carbapenem resistant and three strains of carbapenem susceptible E. coli were analyzed by comparing their SERS spectral signatures. Furthermore, multivariate data analysis techniques including Principal Component Analysis (PCA), Hierarchical Cluster Analysis (HCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) were performed over the spectral range of 400-1800 cm-1 (fingerprint region) for the identification and differentiation of different E. coli strains. RESULTS The SERS spectral features associated with resistant development against carbapenem antibiotics were separated by comparing each spectrum of susceptible strains with each resistant strain. PCA and HCA were found effective for the qualitative differentiation of all the strains analysed. PLS-DA successfully discriminated the carbapenem resistant and susceptible E. coli pellets on the strain level with 99.8 % sensitivity, 100 % specificity, 100 % accuracy and 86 % area under receiver operating characteristic (AUROC) curve. CONCLUSION SERS can be employed for the rapid discrimination among carbapenem resistant and susceptible strains of E. coil.
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Affiliation(s)
- Saba Bashir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan.
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan.
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan.
| | - Sabahat Abdullah
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Saqib Ali
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Nosheen Rashid
- Department of Chemistry, University of Central Punjab, Faisalabad Campus, Faisalabad, Pakistan
| | - Muhammad Kashif
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Fatima Batool
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Muhammad Abubakar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Shamsheer Ahmad
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Aliza Abdulraheem
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
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18
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Lin T, Song YL, Liao J, Liu F, Zeng TT. Applications of surface-enhanced Raman spectroscopy in detection fields. Nanomedicine (Lond) 2020; 15:2971-2989. [PMID: 33140686 DOI: 10.2217/nnm-2020-0361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Surface-enhanced Raman spectroscopy (SERS) is a Raman spectroscopy technique that has been widely used in food safety, environmental monitoring, medical diagnosis and treatment and drug monitoring because of its high selectivity, sensitivity, rapidness, simplicity and specificity in identifying molecular structures. This review introduces the detection mechanism of SERS and summarizes the most recent progress concerning the use of SERS for the detection and characterization of molecules, providing references for the later research of SERS in detection fields.
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Affiliation(s)
- Ting Lin
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Ya-Li Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Juan Liao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Fang Liu
- Department of Laboratory Pathology, Xijing Hospital, Fourth Military Medical University, Xian, 710054, PR China
| | - Ting-Ting Zeng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, PR China
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Jabłońska A, Jaworska A, Kasztelan M, Berbeć S, Pałys B. Graphene and Graphene Oxide Applications for SERS Sensing and Imaging. Curr Med Chem 2020; 26:6878-6895. [PMID: 30289065 DOI: 10.2174/0929867325666181004152247] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 11/22/2022]
Abstract
Surface Enhanced Raman Spectroscopy (SERS) has a long history as an ultrasensitive platform for the detection of biological species from small aromatic molecules to complex biological systems as circulating tumor cells. Thanks to unique properties of graphene, the range of SERS applications has largely expanded. Graphene is efficient fluorescence quencher improving quality of Raman spectra. It contributes also to the SERS enhancement factor through the chemical mechanism. In turn, the chemical flexibility of Reduced Graphene Oxide (RGO) enables tunable adsorption of molecules or cells on SERS active surfaces. Graphene oxide composites with SERS active nanoparticles have been also applied for Raman imaging of cells. This review presents a survey of SERS assays employing graphene or RGO emphasizing the improvement of SERS enhancement brought by graphene or RGO. The structure and physical properties of graphene and RGO will be discussed too.
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Affiliation(s)
- Anna Jabłońska
- Chemical and Biological Research Centre, University of Warsaw, Zwirki i Wigury str. 101, Warsaw, PL-02- 089, Poland
| | - Aleksandra Jaworska
- Faculty of Chemistry, University of Warsaw, Pasteur str. 1, Warsaw, PL-02-093, Poland
| | - Mateusz Kasztelan
- Faculty of Chemistry, University of Warsaw, Pasteur str. 1, Warsaw, PL-02-093, Poland
| | - Sylwia Berbeć
- Faculty of Chemistry, University of Warsaw, Pasteur str. 1, Warsaw, PL-02-093, Poland
| | - Barbara Pałys
- Chemical and Biological Research Centre, University of Warsaw, Zwirki i Wigury str. 101, Warsaw, PL-02- 089, Poland
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Boschetto F, Adachi T, Horiguchi S, Marin E, Paccotti N, Asai T, Zhu W, McEntire BJ, Yamamoto T, Kanamura N, Mazda O, Ohgitani E, Pezzotti G. In situ molecular vibration insights into the antibacterial behavior of silicon nitride bioceramic versus gram-negative Escherichia coli. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 223:117299. [PMID: 31277027 DOI: 10.1016/j.saa.2019.117299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/11/2019] [Accepted: 06/20/2019] [Indexed: 06/09/2023]
Abstract
Gram-negative bacteria represent a substantial fraction of pathogens responsible for periprosthetic infections. Given the increasing resistance of such bacteria to antibiotics, significant efforts are nowadays paid in developing new biomaterial surfaces, which offer resistance against bacterial adhesion and/or possess inherent antibacterial effects. Non-oxide silicon nitride (Si3N4) bioceramic in its polycrystalline form is a biomaterial with inherent antibacterial properties. Building upon previous phenomenological findings, the present study focuses on vibrational analyses of the metabolic response of Escherichia coli at the molecular level. A time-lapse study is conducted upon exposing the bacteria in vitro to Si3N4 bioceramic surfaces. A comparison is carried out with the as-cultured bacterial strain and with bacteria exposed to other commercially available biomaterials, namely, Ti-alloy (Ti6Al4V-ELI) and zirconia-toughened alumina (ZTA) oxide bioceramic tested under exactly the same experimental conditions. The metabolic pathways before and after exposure to different substrates were monitored by means of Raman and FTIR spectroscopies. Results indicated the development of significant osmotic stress in the bacterial strain and constant concentration decreases of its cellular compounds markers over time upon exposure to Si3N4. This ultimately led to bacterial lysis (also confirmed by conventional fluorescence microscopy assays). The main antibacterial effect was of chemical origin and driven by the elution of nitrogen ions from the Si3N4 surface, successively converted into ammonia (NH3) or ammonium (NH4)+ in aqueous solution, depending on environmental pH. The presence of these nitrogen species created osmotic stress in the cytoplasmic space. In answer to the osmotic stress, metabolic rates changed rapidly, the bacterial membrane was damaged, and lysis occurred almost completely within 48 h exposure. The antibacterial behavior exerted by the Si3N4 substrate on E. coli was more effective than that observed on the biomedical Ti6Al4V alloy. Conversely, no lysis but bacterial proliferation was recorded for E. coli exposed to ZTA bioceramic oxide substrates.
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Affiliation(s)
- Francesco Boschetto
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, 606-8585 Kyoto, Japan; Department of Immunology, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Tetsuya Adachi
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Satoshi Horiguchi
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, 606-8585 Kyoto, Japan; Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Niccolò Paccotti
- Department of Applied Science and Technology, Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129 Turin, Italy
| | - Tenma Asai
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, 606-8585 Kyoto, Japan
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, 606-8585 Kyoto, Japan
| | - Bryan J McEntire
- SINTX, Technologies, Co. 1885 West 2100 South, Salt Lake City, UT 84119, USA
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Osam Mazda
- Department of Immunology, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Eriko Ohgitani
- Department of Immunology, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, 606-8585 Kyoto, Japan; Department of Immunology, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, 160-0023 Tokyo, Japan; The Center for Advanced Medical Engineering and Informatics, Osaka University, Yamadaoka, Suita, 565-0871 Osaka, Japan.
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Li J, Wang C, Shi L, Shao L, Fu P, Wang K, Xiao R, Wang S, Gu B. Rapid identification and antibiotic susceptibility test of pathogens in blood based on magnetic separation and surface-enhanced Raman scattering. Mikrochim Acta 2019; 186:475. [PMID: 31250223 DOI: 10.1007/s00604-019-3571-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/02/2019] [Indexed: 12/22/2022]
Abstract
An effective surface-enhanced Raman scattering (SERS) method is presented for the rapid identification and drug sensitivity analysis of pathogens in blood. In a first step, polyethyleneimine-modified magnetic microspheres (Fe3O4@PEI) were used to enrich bacteria from blood samples. Next, the Fe3O4@PEI@bacteria complex was cultured on both ordinary and drug-sensitive plates. Lastly, the SERS spectra of single colonies were acquired in order to identify different pathogens and their resistant strains by comparison with established standardized bacterial SERS spectras and orthogonal partial least squares discriminant analysis (OPLS-DA) method. Staphylococcus aureus, Acinetobacter baumannii, Pseudomonas aeruginosa and their resistant strains were used to evaluate the performance of the SERS method. The results demonstrate that the method can accurately detect and identify all the tested sensitive and drug-resistant strains of bacteria, including 77 clinical blood infection samples. The method provides a way for rapid identification and susceptibility test of pathogens, and has great potential to replace currently used time-consuming methods. Graphical abstract Schematic presentation of a method for the rapid identification and drug sensitivity analysis of pathogens in blood. It is based on a combination of magnetic separation, SERS fingerprint analysis and orthogonal partial least squares discriminant analysis (OPLS-DA).
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Affiliation(s)
- Jia Li
- Medical Technology Institute of Xuzhou Medical University, Xuzhou, 221004, People's Republic of China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221004, People's Republic of China
| | - Chongwen Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China. .,College of Life Sciences, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
| | - Luoluo Shi
- Medical Technology Institute of Xuzhou Medical University, Xuzhou, 221004, People's Republic of China
| | - Liting Shao
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Peiwen Fu
- Medical Technology Institute of Xuzhou Medical University, Xuzhou, 221004, People's Republic of China
| | - Keli Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Rui Xiao
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China.
| | - Shengqi Wang
- Medical Technology Institute of Xuzhou Medical University, Xuzhou, 221004, People's Republic of China. .,Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China.
| | - Bing Gu
- Medical Technology Institute of Xuzhou Medical University, Xuzhou, 221004, People's Republic of China. .,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221004, People's Republic of China.
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Wang K, Li S, Petersen M, Wang S, Lu X. Detection and Characterization of Antibiotic-Resistant Bacteria Using Surface-Enhanced Raman Spectroscopy. NANOMATERIALS (BASEL, SWITZERLAND) 2018; 8:E762. [PMID: 30261660 PMCID: PMC6215266 DOI: 10.3390/nano8100762] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 09/12/2018] [Accepted: 09/23/2018] [Indexed: 12/17/2022]
Abstract
This mini-review summarizes the most recent progress concerning the use of surface-enhanced Raman spectroscopy (SERS) for the detection and characterization of antibiotic-resistant bacteria. We first discussed the design and synthesis of various types of nanomaterials that can be used as the SERS-active substrates for biosensing trace levels of antibiotic-resistant bacteria. We then reviewed the tandem-SERS strategy of integrating a separation element/platform with SERS sensing to achieve the detection of antibiotic-resistant bacteria in the environmental, agri-food, and clinical samples. Finally, we demonstrated the application of using SERS to investigate bacterial antibiotic resistance and susceptibility as well as the working mechanism of antibiotics based on spectral fingerprinting of the whole cells.
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Affiliation(s)
- Kaidi Wang
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T1Z4, Canada.
| | - Shenmiao Li
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T1Z4, Canada.
| | - Marlen Petersen
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T1Z4, Canada.
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300371, China.
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T1Z4, Canada.
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