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Neves MM, Guerra RF, de Lima IL, Arrais TS, Guevara-Vega M, Ferreira FB, Rosa RB, Vieira MS, Fonseca BB, Sabino da Silva R, da Silva MV. Perspectives of FTIR as Promising Tool for Pathogen Diagnosis, Sanitary and Welfare Monitoring in Animal Experimentation Models: A Review Based on Pertinent Literature. Microorganisms 2024; 12:833. [PMID: 38674777 PMCID: PMC11052489 DOI: 10.3390/microorganisms12040833] [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: 03/04/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Currently, there is a wide application in the literature of the use of the Fourier Transform Infrared Spectroscopy (FTIR) technique. This basic tool has also proven to be efficient for detecting molecules associated with hosts and pathogens in infections, as well as other molecules present in humans and animals' biological samples. However, there is a crisis in science data reproducibility. This crisis can also be observed in data from experimental animal models (EAMs). When it comes to rodents, a major challenge is to carry out sanitary monitoring, which is currently expensive and requires a large volume of biological samples, generating ethical, legal, and psychological conflicts for professionals and researchers. We carried out a survey of data from the relevant literature on the use of this technique in different diagnostic protocols and combined the data with the aim of presenting the technique as a promising tool for use in EAM. Since FTIR can detect molecules associated with different diseases and has advantages such as the low volume of samples required, low cost, sustainability, and provides diagnostic tests with high specificity and sensitivity, we believe that the technique is highly promising for the sanitary and stress and the detection of molecules of interest of infectious or non-infectious origin.
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Affiliation(s)
- Matheus Morais Neves
- Biotechnology in Experimental Models Laboratory—LABME, Federal University of Uberlândia, Uberlândia 38405-330, MG, Brazil; (M.M.N.); (R.F.G.); (I.L.d.L.); (T.S.A.); (F.B.F.)
| | - Renan Faria Guerra
- Biotechnology in Experimental Models Laboratory—LABME, Federal University of Uberlândia, Uberlândia 38405-330, MG, Brazil; (M.M.N.); (R.F.G.); (I.L.d.L.); (T.S.A.); (F.B.F.)
- Rodents Animal Facilities Complex, Federal University of Uberlandia, Uberlândia 38400-902, MG, Brazil;
| | - Isabela Lemos de Lima
- Biotechnology in Experimental Models Laboratory—LABME, Federal University of Uberlândia, Uberlândia 38405-330, MG, Brazil; (M.M.N.); (R.F.G.); (I.L.d.L.); (T.S.A.); (F.B.F.)
| | - Thomas Santos Arrais
- Biotechnology in Experimental Models Laboratory—LABME, Federal University of Uberlândia, Uberlândia 38405-330, MG, Brazil; (M.M.N.); (R.F.G.); (I.L.d.L.); (T.S.A.); (F.B.F.)
| | - Marco Guevara-Vega
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlândia 38408-100, MG, Brazil; (M.G.-V.); (R.S.d.S.)
| | - Flávia Batista Ferreira
- Biotechnology in Experimental Models Laboratory—LABME, Federal University of Uberlândia, Uberlândia 38405-330, MG, Brazil; (M.M.N.); (R.F.G.); (I.L.d.L.); (T.S.A.); (F.B.F.)
| | - Rafael Borges Rosa
- Rodents Animal Facilities Complex, Federal University of Uberlandia, Uberlândia 38400-902, MG, Brazil;
| | - Mylla Spirandelli Vieira
- Faculty of Medicine, Maria Ranulfa Institute, Av. Vasconselos Costa 321, Uberlândia 38400-448, MG, Brazil;
| | | | - Robinson Sabino da Silva
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlândia 38408-100, MG, Brazil; (M.G.-V.); (R.S.d.S.)
| | - Murilo Vieira da Silva
- Biotechnology in Experimental Models Laboratory—LABME, Federal University of Uberlândia, Uberlândia 38405-330, MG, Brazil; (M.M.N.); (R.F.G.); (I.L.d.L.); (T.S.A.); (F.B.F.)
- Rodents Animal Facilities Complex, Federal University of Uberlandia, Uberlândia 38400-902, MG, Brazil;
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Othman AM, Sabry YM, Khalil D, Saadany B, Bourouina T. A disposable optofluidic micro-transmission cell with tailorable length for Fourier-transform infrared spectroscopy of biological fluids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:262-268. [PMID: 38111305 DOI: 10.1039/d3ay01710a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Mid-infrared Fourier-transform infrared (FT-IR) spectroscopy of liquid biological samples is limited by the high absorption of water in this spectral range, which makes conventional transmission cuvettes unsuitable as their centimeter-scale length is already too big. The most common alternative relies on the use of attenuated total reflection (ATR) accessories, which provide a small interaction path length for light along the interface between the analyte and the expensive ATR crystals. In this work, we address this issue by proposing a disposable and low-cost micro-transmission cell. Its construction relies on a simple technique, which consists of dispersing plastic spherical microparticles in a liquid sample before dispensing it between two pieces of silicon assembled one onto the other and acting as windows for the cell. Consequently, the microparticles act as a spacer of very precise height in-between the two silicon windows. This technique allows easy construction of infrared absorption cells with near-optimum optical interaction path length just by selecting the most appropriate particle size. The concept is demonstrated by measuring the concentration of glucose in aqueous solutions using microspheres of diameter 20 μm then 40 μm and analyzing the corresponding glucose absorption peaks in the wavenumber range 950-1200 cm-1. The performance is compared to that of standard ATR spectroscopy of the same samples. This resulted in a root-mean-square error of cross-validation (RMSECV) of 58.8 mg dl-1 as obtained for transmission measurements by partial least squares (PLS) regression, which is comparable to the RMSECV of 53 mg dl-1 for single-reflection diamond ATR measurements.
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Affiliation(s)
- Ahmed M Othman
- Université Gustave Eiffel, ESYCOM CNRS UMR 9007, Noisy-le-Grand ESIEE Paris, 93162, France.
- Si-Ware Systems, 3 Khalid Ibn Al-Waleed St., Heliopolis, Cairo, Egypt
| | - Yasser M Sabry
- Si-Ware Systems, 3 Khalid Ibn Al-Waleed St., Heliopolis, Cairo, Egypt
- Faculty of Engineering, Ain-Shams University, 1 Elsarayat St. Abbassia, Cairo, Egypt
| | - Diaa Khalil
- Si-Ware Systems, 3 Khalid Ibn Al-Waleed St., Heliopolis, Cairo, Egypt
- Faculty of Engineering, Ain-Shams University, 1 Elsarayat St. Abbassia, Cairo, Egypt
| | - Bassam Saadany
- Si-Ware Systems, 3 Khalid Ibn Al-Waleed St., Heliopolis, Cairo, Egypt
| | - Tarik Bourouina
- Université Gustave Eiffel, ESYCOM CNRS UMR 9007, Noisy-le-Grand ESIEE Paris, 93162, France.
- CINTRA, IRL 3288 CNRS-NTU-THALES, Nanyang Technological University, 637553, Singapore
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3
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Girardeau A, Passot S, Meneghel J, Cenard S, Lieben P, Trelea IC, Fonseca F. Insights into lactic acid bacteria cryoresistance using FTIR microspectroscopy. Anal Bioanal Chem 2021; 414:1425-1443. [PMID: 34967915 DOI: 10.1007/s00216-021-03774-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/31/2021] [Accepted: 11/04/2021] [Indexed: 10/19/2022]
Abstract
Freezing is widely used for bacterial cell preservation. However, resistance to freezing can greatly vary depending on bacterial species or growth conditions. Our study aims at identifying cellular markers of cryoresistance based on the comparison of three lactic acid bacteria (LAB) exhibiting different tolerance to freezing: Carnobacterium maltaromaticum CNCM I-3298, Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842, and Lactobacillus delbrueckii subsp. bulgaricus CFL1. A thorough characterization of their cytoplasmic membrane properties was carried out by measuring their fatty acid composition, membrane fluidity, and lipid phase transition upon cooling from 50 to -50 °C. Vitrification temperatures of the intra- and extra-cellular compartments were also quantified by differential scanning calorimetry. Additionally, the cell biochemical characterization was carried out using a recently developed Fourier transform infrared (FTIR) micro-spectroscopic approach allowing the analysis of live bacteria in an aqueous environment. The multivariate analysis of the FTIR spectra of fresh and thawed cells enabled the discrimination of the three bacteria according to their lipid, protein, and cell wall peptidoglycan components. It also revealed freezing-induced modifications of these three cellular components and an increase in bacteria heterogeneity for the two strains of L. bulgaricus, the freeze-sensitive bacteria. No cellular damage was observed for C. maltaromaticum, the freeze-resistant bacteria. Comparison of the results obtained from the different analytical methods confirmed previously reported cryoresistance markers and suggested new ones, such as changes in the absorbance of specific infrared spectral bands. FTIR microspectroscopy could be used as a rapid and non-invasive technique to evaluate the freeze-sensitivity of LAB.
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Affiliation(s)
- Amélie Girardeau
- UMR SayFood, Université Paris-Saclay, INRAE, 78850, Thiverval-Grignon, AgroParisTech, France
| | - Stéphanie Passot
- UMR SayFood, Université Paris-Saclay, INRAE, 78850, Thiverval-Grignon, AgroParisTech, France
| | - Julie Meneghel
- UMR SayFood, Université Paris-Saclay, INRAE, 78850, Thiverval-Grignon, AgroParisTech, France
| | - Stéphanie Cenard
- UMR SayFood, Université Paris-Saclay, INRAE, 78850, Thiverval-Grignon, AgroParisTech, France
| | - Pascale Lieben
- UMR SayFood, Université Paris-Saclay, INRAE, 78850, Thiverval-Grignon, AgroParisTech, France
| | - Ioan-Cristian Trelea
- UMR SayFood, Université Paris-Saclay, INRAE, 78850, Thiverval-Grignon, AgroParisTech, France
| | - Fernanda Fonseca
- UMR SayFood, Université Paris-Saclay, INRAE, 78850, Thiverval-Grignon, AgroParisTech, France.
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Kochan K, Bedolla DE, Perez-Guaita D, Adegoke JA, Chakkumpulakkal Puthan Veettil T, Martin M, Roy S, Pebotuwa S, Heraud P, Wood BR. Infrared Spectroscopy of Blood. APPLIED SPECTROSCOPY 2021; 75:611-646. [PMID: 33331179 DOI: 10.1177/0003702820985856] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The magnitude of infectious diseases in the twenty-first century created an urgent need for point-of-care diagnostics. Critical shortages in reagents and testing kits have had a large impact on the ability to test patients with a suspected parasitic, bacteria, fungal, and viral infections. New point-of-care tests need to be highly sensitive, specific, and easy to use and provide results in rapid time. Infrared spectroscopy, coupled to multivariate and machine learning algorithms, has the potential to meet this unmet demand requiring minimal sample preparation to detect both pathogenic infectious agents and chronic disease markers in blood. This focal point article will highlight the application of Fourier transform infrared spectroscopy to detect disease markers in blood focusing principally on parasites, bacteria, viruses, cancer markers, and important analytes indicative of disease. Methodologies and state-of-the-art approaches will be reported and potential confounding variables in blood analysis identified. The article provides an up to date review of the literature on blood diagnosis using infrared spectroscopy highlighting the recent advances in this burgeoning field.
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Affiliation(s)
- Kamila Kochan
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Diana E Bedolla
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - David Perez-Guaita
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - John A Adegoke
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | | | - Miguela Martin
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Supti Roy
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Savithri Pebotuwa
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Philip Heraud
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Bayden R Wood
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
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AlMasoud N, Muhamadali H, Chisanga M, AlRabiah H, Lima CA, Goodacre R. Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing. Analyst 2021; 146:770-788. [DOI: 10.1039/d0an01482f] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review compares and contrasts MALDI-MS, FT-IR spectroscopy and Raman spectroscopy for whole organism fingerprinting and bacterial typing.
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Affiliation(s)
- Najla AlMasoud
- Department of Chemistry
- College of Science
- Princess Nourah bint Abdulrahman University
- Riyadh 11671
- Saudi Arabia
| | - Howbeer Muhamadali
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Malama Chisanga
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Haitham AlRabiah
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Cassio A. Lima
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
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FTIR micro-spectroscopy using synchrotron-based and thermal source-based radiation for probing live bacteria. Anal Bioanal Chem 2020; 412:7049-7061. [PMID: 32839857 DOI: 10.1007/s00216-020-02835-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 11/27/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy has proven to be a non-invasive tool to analyse cells without the hurdle of employing exogenous dyes or probes. Nevertheless, the study of single live bacteria in their aqueous environment has long remained a big challenge, due to the strong infrared absorption of water and the small size of bacteria compared to the micron-range infrared wavelengths of the probing photons. To record infrared spectra of bacteria in an aqueous environment, at different spatial resolutions, two setups were developed. A custom-built attenuated total reflection inverted microscope was coupled to a synchrotron-based FTIR spectrometer, using a germanium hemisphere. With such a setup, a projected spot size of 1 × 1 μm2 was achieved, which allowed spectral acquisition at the single-cell level in the 1800-1300 cm-1 region. The second setup used a demountable liquid micro-chamber with a thermal source-powered FTIR microscope, in transmission geometry, for probing clusters of a few thousands of live cells in the mid-IR region (4000-975 cm-1). Both setups were applied for studying two strains of a model lactic acid bacterium exhibiting different cryo-resistances. The two approaches allowed the discrimination of both strains and revealed population heterogeneity among bacteria at different spatial resolutions. The multivariate analysis of spectra indicated that the cryo-sensitive cells presented the highest cell heterogeneity and the highest content of proteins with the α-helix structure. Furthermore, the results from clusters of bacterial cells evidenced phosphate and peptidoglycan vibrational bands associated with the cell envelope, as potential markers of resistance to environmental conditions. Graphical Abstract.
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7
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Kochan K, Nethercott C, Taghavimoghaddam J, Richardson Z, Lai E, Crawford SA, Peleg AY, Wood BR, Heraud P. Rapid Approach for Detection of Antibiotic Resistance in Bacteria Using Vibrational Spectroscopy. Anal Chem 2020; 92:8235-8243. [PMID: 32407103 DOI: 10.1021/acs.analchem.0c00474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we applied vibrational spectroscopy to investigate the drug response following incubation of S. aureus with oxacillin. The main focus of this work was to identify the chemical changes caused by oxacillin over time and to determine the feasibility of the spectroscopic approach to detect antimicrobial resistance. The oxacillin-induced changes in the chemical composition of susceptible bacteria, preceding (and leading to) the inhibition of growth, included an increase in the relative content of nucleic acids, alteration in the α-helical/β-sheet protein ratio, structural changes in carbohydrates (observed via changes in the band at 1035 cm-1), and significant thickening of the cell wall. These observations enabled a dose-dependent discrimination between susceptible bacteria incubated with and without oxacillin after 120 min. In methicillin resistant strains, no spectral differences were observed between cells, regardless of drug exposure. These results pave the way for a new, rapid spectroscopic approach to detect drug resistance in pathogens, based on their early positive/negative drug response.
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Affiliation(s)
- Kamila Kochan
- Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton Campus, Clayton 3800, Victoria, Australia
| | - Cara Nethercott
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton Campus, Clayton 3800, Victoria, Australia
| | | | - Zack Richardson
- Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton Campus, Clayton 3800, Victoria, Australia
| | - Elizabeth Lai
- Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton Campus, Clayton 3800, Victoria, Australia
| | - Simon A Crawford
- The Ramaciotti Centre for Cryo Electron Microscopy, Monash University, Clayton Campus, Clayton 3800, Victoria, Australia
| | - Anton Y Peleg
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton Campus, Clayton 3800, Victoria, Australia.,Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne 3004, Victoria, Australia
| | - Bayden R Wood
- Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton Campus, Clayton 3800, Victoria, Australia.,School of Chemistry, Monash University, Clayton Campus, Clayton 3800, Victoria, Australia
| | - Philip Heraud
- Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton Campus, Clayton 3800, Victoria, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton Campus, Clayton 3800, Victoria, Australia
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8
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Novais Â, Freitas AR, Rodrigues C, Peixe L. Fourier transform infrared spectroscopy: unlocking fundamentals and prospects for bacterial strain typing. Eur J Clin Microbiol Infect Dis 2018; 38:427-448. [DOI: 10.1007/s10096-018-3431-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/11/2018] [Indexed: 01/25/2023]
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AlRabiah H, Allwood JW, Correa E, Xu Y, Goodacre R. pH plays a role in the mode of action of trimethoprim on Escherichia coli. PLoS One 2018; 13:e0200272. [PMID: 30005078 PMCID: PMC6044521 DOI: 10.1371/journal.pone.0200272] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/20/2018] [Indexed: 01/08/2023] Open
Abstract
Metabolomics-based approaches were applied to understand interactions of trimethoprim with Escherichia coli K-12 at sub-minimum inhibitory concentrations (MIC≈0.2, 0.03 and 0.003 mg L-1). Trimethoprim inhibits dihydrofolate reductase and thereby is an indirect inhibitor of nucleic acid synthesis. Due to the basicity of trimethoprim, two pH levels (5 and 7) were selected which mimicked healthy urine pH. This also allowed investigation of the effect on bacterial metabolism when trimethoprim exists in different ionization states. UHPLC-MS was employed to detect trimethoprim molecules inside the bacterial cell and this showed that at pH 7 more of the drug was recovered compared to pH 5; this correlated with classical growth curve measurements. FT-IR spectroscopy was used to establish recovery of reproducible phenotypes under all 8 conditions (3 drug levels and control in 2 pH levels) and GC-MS was used to generate global metabolic profiles. In addition to finding direct mode-of-action effects where nucleotides were decreased at pH 7 with increasing trimethoprim levels, off-target pH-related effects were observed for many amino acids. Additionally, stress-related effects were observed where the osmoprotectant trehalose was higher at increased antibiotic levels at pH 7. This correlated with glucose and fructose consumption and increase in pyruvate-related products as well as lactate and alanine. Alanine is a known regulator of sugar metabolism and this increase may be to enhance sugar consumption and thus trehalose production. These results provide a wider view of the action of trimethoprim. Metabolomics indicated alternative metabolism areas to be investigated to further understand the off-target effects of trimethoprim.
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Affiliation(s)
- Haitham AlRabiah
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - J. William Allwood
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Invergowrie, Dundee, Scotland United Kingdom
| | - Elon Correa
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Yun Xu
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Royston Goodacre
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
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De Bruyne S, Speeckaert MM, Delanghe JR. Applications of mid-infrared spectroscopy in the clinical laboratory setting. Crit Rev Clin Lab Sci 2017; 55:1-20. [PMID: 29239240 DOI: 10.1080/10408363.2017.1414142] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fourier transform mid-infrared (MIR-FTIR) spectroscopy is a nondestructive, label-free, highly sensitive and specific technique that provides complete information on the chemical composition of biological samples. The technique both can offer fundamental structural information and serve as a quantitative analysis tool. Therefore, it has many potential applications in different fields of clinical laboratory science. Although considerable technological progress has been made to promote biomedical applications of this powerful analytical technique, most clinical laboratory analyses are based on spectroscopic measurements in the visible or ultraviolet (UV) spectrum and the potential role of FTIR spectroscopy still remains unexplored. In this review, we present some general principles of FTIR spectroscopy as a useful method to study molecules in specimens by MIR radiation together with a short overview of methods to interpret spectral data. We aim at illustrating the wide range of potential applications of the proposed technique in the clinical laboratory setting with a focus on its advantages and limitations and discussing the future directions. The reviewed applications of MIR spectroscopy include (1) quantification of clinical parameters in body fluids, (2) diagnosis and monitoring of cancer and other diseases by analysis of body fluids, cells, and tissues, (3) classification of clinically relevant microorganisms, and (4) analysis of kidney stones, nails, and faecal fat.
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Affiliation(s)
- Sander De Bruyne
- a Department of Clinical Chemistry , Ghent University Hospital , Ghent , Belgium
| | | | - Joris R Delanghe
- a Department of Clinical Chemistry , Ghent University Hospital , Ghent , Belgium
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11
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Quintelas C, Ferreira EC, Lopes JA, Sousa C. An Overview of the Evolution of Infrared Spectroscopy Applied to Bacterial Typing. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700449] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/18/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Cristina Quintelas
- Dr. C. Quintelas, Dr. E. C. Ferreira; CEB − Centro de Engenharia Biológica; Universidade do Minho; Braga Portugal
| | - Eugénio C. Ferreira
- Dr. C. Quintelas, Dr. E. C. Ferreira; CEB − Centro de Engenharia Biológica; Universidade do Minho; Braga Portugal
| | - João A. Lopes
- Dr. J. A. Lopes; Research Institute for Medicines (iMed.ULisboa); Faculdade de Farmácia; Universidade de Lisboa; Lisboa Portugal
| | - Clara Sousa
- Dr. C. Sousa; LAQV/REQUIMTE; Departamento de Ciências Químicas Faculdade de Farmácia; Universidade do Porto; Rua Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
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12
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AlMasoud N, Xu Y, Trivedi DK, Salivo S, Abban T, Rattray NJW, Szula E, AlRabiah H, Sayqal A, Goodacre R. Classification of Bacillus and Brevibacillus species using rapid analysis of lipids by mass spectrometry. Anal Bioanal Chem 2016; 408:7865-7878. [PMID: 27604269 PMCID: PMC5061856 DOI: 10.1007/s00216-016-9890-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 08/16/2016] [Indexed: 01/02/2023]
Abstract
Bacillus are aerobic spore-forming bacteria that are known to lead to specific diseases, such as anthrax and food poisoning. This study focuses on the characterization of these bacteria by the detection of lipids extracted from 33 well-characterized strains from the Bacillus and Brevibacillus genera, with the aim to discriminate between the different species. For the purpose of analysing the lipids extracted from these bacterial samples, two rapid physicochemical techniques were used: matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography in conjunction with mass spectrometry (LC-MS). The findings of this investigation confirmed that MALDI-TOF-MS could be used to identify different bacterial lipids and, in combination with appropriate chemometrics, allowed for the discrimination between these different bacterial species, which was supported by LC-MS. The average correct classification rates for the seven species of bacteria were 62.23 and 77.03 % based on MALDI-TOF-MS and LC-MS data, respectively. The Procrustes distance for the two datasets was 0.0699, indicating that the results from the two techniques were very similar. In addition, we also compared these bacterial lipid MALDI-TOF-MS profiles to protein profiles also collected by MALDI-TOF-MS on the same bacteria (Procrustes distance, 0.1006). The level of discrimination between lipids and proteins was equivalent, and this further indicated the potential of MALDI-TOF-MS analysis as a rapid, robust and reliable method for the classification of bacteria based on different bacterial chemical components. Graphical abstract MALDI-MS has been successfully developed for the characterization of bacteria at the subspecies level using lipids and benchmarked against HPLC.
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Affiliation(s)
- Najla AlMasoud
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yun Xu
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Drupad K Trivedi
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Simona Salivo
- Shimadzu, Kratos Analytical Ltd. Wharfside, Trafford Wharf Road, Manchester, M17 1GP, UK
| | - Tom Abban
- Shimadzu, Kratos Analytical Ltd. Wharfside, Trafford Wharf Road, Manchester, M17 1GP, UK
| | - Nicholas J W Rattray
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Ewa Szula
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Haitham AlRabiah
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - Ali Sayqal
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Royston Goodacre
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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13
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Palama TL, Canard I, Rautureau GJP, Mirande C, Chatellier S, Elena-Herrmann B. Identification of bacterial species by untargeted NMR spectroscopy of the exo-metabolome. Analyst 2016; 141:4558-61. [PMID: 27349704 DOI: 10.1039/c6an00393a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Identification of bacterial species is a crucial bottleneck for clinical diagnosis of infectious diseases. Quick and reliable identification is a key factor to provide suitable antibiotherapies and avoid the development of multiple-drug resistance. We propose a novel nuclear magnetic resonance (NMR)-based metabolomics strategy for rapid discrimination and identification of several bacterial species that relies on untargeted metabolic profiling of supernatants from bacterial culture media. We show that six bacterial species (Gram negative: Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis; Gram positive: Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus saprophyticus) can be well discriminated from multivariate statistical analysis, opening new prospects for NMR applications to microbial clinical diagnosis.
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Affiliation(s)
- T L Palama
- Université de Lyon, Institut des Sciences Analytiques (CNRS/ENS Lyon/UCB Lyon1), Centre de RMN à Très Hauts Champs, 69100 Villeurbanne, France.
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14
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Ren Y, Palusiak A, Wang W, Wang Y, Li X, Wei H, Kong Q, Rozalski A, Yao Z, Wang Q. A High-resolution Typing Assay for Uropathogenic Escherichia coli Based on Fimbrial Diversity. Front Microbiol 2016; 7:623. [PMID: 27199951 PMCID: PMC4850163 DOI: 10.3389/fmicb.2016.00623] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/15/2016] [Indexed: 02/02/2023] Open
Abstract
Urinary tract infections (UTIs) are one of the most common bacterial infections in humans, causing cystitis, pyelonephritis, and renal failure. Uropathogenic Escherichia coli (UPEC) is the leading cause of UTIs. Accurate and rapid discrimination of UPEC lineages is useful for epidemiological surveillance. Fimbriae are necessary for the adherence of UPEC strains to host uroepithelia, and seem to be abundant and diverse in UPEC strains. By analyzing all the possible fimbrial operons in UPEC strains, we found that closely related strains had similar types of chaperone-usher fimbriae, and the diversity of fimbrial genes was higher than that of multilocus sequence typing (MLST) genes. A typing assay based on the polymorphism of four gene sequences (three fimbrial genes and one housekeeping gene) and the diversity of fimbriae present was developed. By comparison with the MLST, whole-genome sequence (WGS) and fumC/fimH typing methods, this was shown to be accurate and have high resolution, and it was also relatively inexpensive and easy to perform. The assay can supply more discriminatory information for UPEC lineages, and have the potential to be applied in epidemiological surveillance of UPEC isolates.
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Affiliation(s)
- Yi Ren
- Department of Immunology, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Educational Ministry of China, School of Basic Medical Sciences, Tianjin Medical UniversityTianjin, China
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd.Shanghai, China
| | - Agata Palusiak
- Department of General Microbiology, Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of LodzLodz, Poland
| | - Wei Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education – Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai UniversityTianjin, China
| | - Yi Wang
- Department of Immunology, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Educational Ministry of China, School of Basic Medical Sciences, Tianjin Medical UniversityTianjin, China
| | - Xiao Li
- Department of Immunology, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Educational Ministry of China, School of Basic Medical Sciences, Tianjin Medical UniversityTianjin, China
| | - Huiting Wei
- Department of Immunology, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Educational Ministry of China, School of Basic Medical Sciences, Tianjin Medical UniversityTianjin, China
| | - Qingke Kong
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Antoni Rozalski
- Department of General Microbiology, Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of LodzLodz, Poland
| | - Zhi Yao
- Department of Immunology, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Educational Ministry of China, School of Basic Medical Sciences, Tianjin Medical UniversityTianjin, China
| | - Quan Wang
- Department of Immunology, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Educational Ministry of China, School of Basic Medical Sciences, Tianjin Medical UniversityTianjin, China
- State Key Laboratory of Medicinal Chemical Biology, NanKai UniversityTianjin, China
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15
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Passot S, Gautier J, Jamme F, Cenard S, Dumas P, Fonseca F. Understanding the cryotolerance of lactic acid bacteria using combined synchrotron infrared and fluorescence microscopies. Analyst 2015. [PMID: 26212688 DOI: 10.1039/c5an00654f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Freezing is widely used for preserving different types of cells. Frozen concentrates of lactic acid bacteria (LAB) are extensively used for manufacturing food, probiotic products and for green chemistry and medical applications. However, the freezing and thawing processes cause cell injuries that result in significant cell death. Producing homogeneous bacterial populations with high cryotolerance remains a real challenge. Our objective was to investigate the biochemical and physiological changes in a LAB model at the cell scale following fermentation and freezing in order to identify cellular biomarkers of cryotolerance. Infrared spectra of individual bacteria produced by applying different fermentation and freezing conditions were acquired using synchrotron radiation-based Fourier-transform infrared (SR-FTIR) microspectroscopy to achieve sub-cellular spatial resolution. Fluorescent microscopy was concomitantly assessed, thus making possible to simultaneously analyse the biochemistry and physiological state of a single cell for the first time. Principal component analysis was used to evaluate changes in cell composition, with particular focus on lipids, proteins and polysaccharides. SR-FTIR results indicated that before freezing, freeze-resistant cells grown in a rich medium presented a high content of CH3 groups from lipid chains, of cell proteins in an α-helix secondary structure and of charged polymers such as teichoic and lipoteichoic acids that constitute the Gram-positive bacterial wall. Moreover, SR-FTIR microspectroscopy made it possible to reveal cell heterogeneity within the cluster of resistant cells, which was ascribed to the diversity of potential substrates in the growth medium. Freezing and thawing processes induced losses of membrane integrity and cell viability in more than 90% of the freeze-sensitive bacterial population. These damages leading to cell death were ascribed to biochemical modification of cell membrane phospholipids, in particular a rigidification of the cytoplasmic membrane following freezing. Furthermore the freeze-resistant cells remained viable after freezing and thawing but a modification of protein secondary structure was detected by SR-FTIR analysis. These results highlighted the potential application of bimodal analysis by SR-FTIR and fluorescence microscopy to increase our knowledge about mechanisms related to cell damage.
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Gromski PS, Muhamadali H, Ellis DI, Xu Y, Correa E, Turner ML, Goodacre R. A tutorial review: Metabolomics and partial least squares-discriminant analysis – a marriage of convenience or a shotgun wedding. Anal Chim Acta 2015; 879:10-23. [DOI: 10.1016/j.aca.2015.02.012] [Citation(s) in RCA: 509] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 02/03/2015] [Accepted: 02/06/2015] [Indexed: 01/14/2023]
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Metabolic Profiling of Geobacter sulfurreducens during Industrial Bioprocess Scale-Up. Appl Environ Microbiol 2015; 81:3288-98. [PMID: 25746987 DOI: 10.1128/aem.00294-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/24/2015] [Indexed: 11/20/2022] Open
Abstract
During the industrial scale-up of bioprocesses it is important to establish that the biological system has not changed significantly when moving from small laboratory-scale shake flasks or culturing bottles to an industrially relevant production level. Therefore, during upscaling of biomass production for a range of metal transformations, including the production of biogenic magnetite nanoparticles by Geobacter sulfurreducens, from 100-ml bench-scale to 5-liter fermentors, we applied Fourier transform infrared (FTIR) spectroscopy as a metabolic fingerprinting approach followed by the analysis of bacterial cell extracts by gas chromatography-mass spectrometry (GC-MS) for metabolic profiling. FTIR results clearly differentiated between the phenotypic changes associated with different growth phases as well as the two culturing conditions. Furthermore, the clustering patterns displayed by multivariate analysis were in agreement with the turbidimetric measurements, which displayed an extended lag phase for cells grown in a 5-liter bioreactor (24 h) compared to those grown in 100-ml serum bottles (6 h). GC-MS analysis of the cell extracts demonstrated an overall accumulation of fumarate during the lag phase under both culturing conditions, coinciding with the detected concentrations of oxaloacetate, pyruvate, nicotinamide, and glycerol-3-phosphate being at their lowest levels compared to other growth phases. These metabolites were overlaid onto a metabolic network of G. sulfurreducens, and taking into account the levels of these metabolites throughout the fermentation process, the limited availability of oxaloacetate and nicotinamide would seem to be the main metabolic bottleneck resulting from this scale-up process. Additional metabolite-feeding experiments were carried out to validate the above hypothesis. Nicotinamide supplementation (1 mM) did not display any significant effects on the lag phase of G. sulfurreducens cells grown in the 100-ml serum bottles. However, it significantly improved the growth behavior of cells grown in the 5-liter bioreactor by reducing the lag phase from 24 h to 6 h, while providing higher yield than in the 100-ml serum bottles.
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18
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Tan C, Smith RP, Tsai MC, Schwartz R, You L. Phenotypic signatures arising from unbalanced bacterial growth. PLoS Comput Biol 2014; 10:e1003751. [PMID: 25101949 PMCID: PMC4125075 DOI: 10.1371/journal.pcbi.1003751] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 06/12/2014] [Indexed: 11/24/2022] Open
Abstract
Fluctuations in the growth rate of a bacterial culture during unbalanced growth are generally considered undesirable in quantitative studies of bacterial physiology. Under well-controlled experimental conditions, however, these fluctuations are not random but instead reflect the interplay between intra-cellular networks underlying bacterial growth and the growth environment. Therefore, these fluctuations could be considered quantitative phenotypes of the bacteria under a specific growth condition. Here, we present a method to identify “phenotypic signatures” by time-frequency analysis of unbalanced growth curves measured with high temporal resolution. The signatures are then applied to differentiate amongst different bacterial strains or the same strain under different growth conditions, and to identify the essential architecture of the gene network underlying the observed growth dynamics. Our method has implications for both basic understanding of bacterial physiology and for the classification of bacterial strains. The measurement of bacterial growth in batch cultures is a routine practice in microbiology. In these cultures, bacterial growth rates drastically fluctuate over time due to the continuously changing growth environment: changing population size, accumulation of waste products, and depletion of nutrients. Such “unbalanced” growth is normally considered undesirable, which has led to the design of methods to achieve balanced growth environments (i.e., chemostats). However, we have discovered that unbalanced growth dynamics contain rich information that can be exploited to deduce regulatory functions or to classify cell strains or growth conditions. We further show that this approach is generally applicable to temporal gene expression data. Taken together, our method and results have broad implications for system identification, experimental design, and the study of cellular growth.
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Affiliation(s)
- Cheemeng Tan
- Lane Center of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Biomedical Engineering, University of California Davis, Davis, California, United States of America
| | - Robert Phillip Smith
- Division of Mathematics, Science and Technology, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Ming-Chi Tsai
- Lane Center of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Russell Schwartz
- Lane Center of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (RS); (LY)
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
- * E-mail: (RS); (LY)
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Dawson SE, Gibreel T, Nicolaou N, AlRabiah H, Xu Y, Goodacre R, Upton M. Implementation of Fourier transform infrared spectroscopy for the rapid typing of uropathogenic Escherichia coli. Eur J Clin Microbiol Infect Dis 2014; 33:983-8. [DOI: 10.1007/s10096-013-2036-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 12/10/2013] [Indexed: 10/25/2022]
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20
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AlRabiah H, Xu Y, Rattray NJW, Vaughan AA, Gibreel T, Sayqal A, Upton M, Allwood JW, Goodacre R. Multiple metabolomics of uropathogenic E. coli reveal different information content in terms of metabolic potential compared to virulence factors. Analyst 2014; 139:4193-9. [DOI: 10.1039/c4an00176a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
No single analytical method can cover the whole metabolome and the choice of which platform to use may inadvertently introduce chemical selectivity.
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Affiliation(s)
- Haitham AlRabiah
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- 131 Princess Street
- Manchester, UK
| | - Yun Xu
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- 131 Princess Street
- Manchester, UK
| | - Nicholas J. W. Rattray
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- 131 Princess Street
- Manchester, UK
| | - Andrew A. Vaughan
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- 131 Princess Street
- Manchester, UK
| | - Tarek Gibreel
- School of Medicine
- University of Manchester
- Manchester, UK
| | - Ali Sayqal
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- 131 Princess Street
- Manchester, UK
| | - Mathew Upton
- School of Medicine
- University of Manchester
- Manchester, UK
| | - J. William Allwood
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- 131 Princess Street
- Manchester, UK
| | - Royston Goodacre
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- 131 Princess Street
- Manchester, UK
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21
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Diverse high-risk B2 and D Escherichia coli clones depicted by Fourier Transform Infrared Spectroscopy. Sci Rep 2013; 3:3278. [PMID: 24252832 PMCID: PMC3834554 DOI: 10.1038/srep03278] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 11/01/2013] [Indexed: 12/28/2022] Open
Abstract
We aimed to develop a reliable method based on Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR) to discriminate Escherichia coli clones from B2(n = 9) and D(n = 13) phylogenetic groups. Eighty-eight E. coli isolates belonging to phylogenetic groups B2(n = 39) and D(n = 49), including particularly widespread high risk clones or clonal complexes (HiRCC) ST131, ST69, ST393 and ST405 were studied. Spectra were analysed by unsupervised (hierarchical cluster analysis-HCA) and supervised methods (soft independent modelling of class analogy-SIMCA and partial least square discriminant analysis-PLSDA). B2-ST131 isolates were discriminated from B2 non-ST131 and D phylogroup isolates (ST69, ST393, ST405) by HCA, SIMCA and PLSDA. D-ST69, D-ST393 and D-ST405 isolates were also distinguished from each other and from other STs from phylogroup D by the three methods. We demonstrate that FTIR-ATR coupled with chemometrics is a reliable and alternative method to accurately discriminate particular E. coli clones. Its validation towards an application at a routine basis could revolutionize high-throughput bacterial typing.
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