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Sandt C. Identification and classification of proteins by FTIR microspectroscopy. A proof of concept. Biochim Biophys Acta Gen Subj 2024:130688. [PMID: 39117047 DOI: 10.1016/j.bbagen.2024.130688] [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: 02/21/2024] [Revised: 07/23/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
FTIR spectroscopy is well known for its molecule fingerprinting capability but is also able to differentiate classes in complex biological systems. This includes strain typing and species level identification of bacterial, yeast or fungal cells, as well as distinguishing between cell layers in eukaryotic tissues. However, its use for the identification of macromolecules such as proteins remains underexplored and rarely used in practice. Here we demonstrate the efficacy of FTIR microspectroscopy coupled with machine learning methods for rapid and accurate identification of proteins in their dry state within minutes, from very small quantities of material, if they are obtained in a pure aqueous solution. FTIR microspectroscopy can provide additional information beside identification: it can detect small differences among different purification batches potentially originating from post-translational modifications or distinct folding states. Moreover, it distinguishes glycoproteins and evaluate glycosylation while detecting contaminants. This methodology presents itself as a valuable quality control tool in protein purification processes or any process requiring the utilization of precisely identified, pure proteins.
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Affiliation(s)
- Christophe Sandt
- SMIS beamline, Synchrotron SOLEIL, RD128, 91190 Saint Aubin, France.
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2
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Baba H, Kanamori H, Nakayama A, Sato T, Katsumi M, Chida T, Ikeda S, Seki R, Arai T, Kamei K, Tokuda K. A cluster of Candida parapsilosis displaying fluconazole-trailing in a neonatal intensive care unit successfully contained by multiple infection-control interventions. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2024; 4:e86. [PMID: 38774118 PMCID: PMC11106732 DOI: 10.1017/ash.2024.77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 05/24/2024]
Abstract
Objective This study aimed to investigate and contain a cluster of invasive candidiasis cases caused by fluconazole-resistant Candida parapsilosis (FRC) in a neonatal intensive care unit. Methods Active surveillance was initiated. Direct observations of hand-hygiene compliance (HHC) among staff were conducted before and after the implementation of hand-hygiene (HH) education. Thirty-five environmental cultures were obtained. Phylogenetic analysis of FRC was performed using Fourier-transform infrared spectroscopy and microsatellite genotyping. Results A total of 14 patients (mean birth weight = 860 g, gestational age = 25 weeks) infected with FRC were identified using the fully automated analyzer, including 5 with clinical infection (three with catheter-related bloodstream infection, one with cutaneous infection, and one with fatal peritonitis) and 9 with colonization. The HHC rate in nurses before performing a sterile or aseptic procedure significantly improved after the HH education (P < .05). Sinks near the patients were contaminated with FRC. All FRC strains were confirmed to be susceptible to fluconazole using the CLSI method, and the microdilution procedure indicated a trailing effect. Phylogenetic analysis showed that all the fluconazole-trailing isolates from patients were clustered together and had the same genotype. Sinks were successfully decontaminated using accelerated hydrogen peroxide and drainage pipes were replaced. Ultraviolet-C decontamination was applied in the milk preparation room. No new cases were detected after the education and disinfection interventions. Conclusions Sinks are an important reservoir of C. parapsilosis. Active surveillance, environmental hygiene, and constant staff education on maintaining a high level of HHC are necessary to limit the spread of C. parapsilosis.
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Affiliation(s)
- Hiroaki Baba
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Division of Infection Control, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Hajime Kanamori
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Division of Infection Control, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Asami Nakayama
- Department of Laboratory Medicine, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Takami Sato
- Department of Laboratory Medicine, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Makoto Katsumi
- Department of Laboratory Medicine, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Takae Chida
- Division of Infection Control, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Shinobu Ikeda
- Division of Infection Control, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Rio Seki
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Teppei Arai
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Katsuhiko Kamei
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Koichi Tokuda
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Division of Infection Control, Tohoku University Hospital, Sendai, Miyagi, Japan
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Hu Y, Zhou H, Lu J, Sun Q, Liu C, Zeng Y, Zhang R. Evaluation of the IR Biotyper for Klebsiella pneumoniae typing and its potentials in hospital hygiene management. Microb Biotechnol 2021; 14:1343-1352. [PMID: 33205912 PMCID: PMC8313285 DOI: 10.1111/1751-7915.13709] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/29/2020] [Indexed: 02/02/2023] Open
Abstract
Klebsiella pneumoniae has emerged as one of the most important pathogens that frequently encounter in community-acquired or hospital-acquired infections. Timely epidemiological surveillance could greatly facilitate infection control of K. pneumoniae and many deadly pathogens alike. In this study, we evaluated the performance of the IR Biotyper, a Fourier transform infrared (FTIR) spectroscopy system for K. pneumoniae isolates typing through (i) optimizing the culture scheme and defining the cutoff value (COV) range and (ii) comparing with commonly used typing tools such as multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). We found that a non-selective and non-chromogenic medium with 24 ± 2 h incubation gives the best discriminatory power for the IR Biotyper (IRBT). COV evaluation indicated that the IRBT is a robust typing method with good reproducibility. Besides, we observed that the modified H2 O-EtOH suspensions preparation method could enhance the quality of the spectrum, especially for those hypermucoviscous strains. For the method comparison study, our data demonstrated that FTIR spectroscopy could accurately cluster K. pneumoniae strains. The typing results of the IRBT were almost entirely in concordance with those from PFGE and WGS. Together with the advantages such as low costs and short turnaround time (less than 3h), the IRBT is a promising tool for strain typing that could make real-time outbreak investigation a reality.
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Affiliation(s)
- Yanyan Hu
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Hongwei Zhou
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Jiayue Lu
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Qiaoling Sun
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Congcong Liu
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Yu Zeng
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Rong Zhang
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
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Heidrich D, Koehler A, Ramírez-Castrillón M, Pagani DM, Ferrão MF, Scroferneker ML, Corbellini VA. Rapid classification of chromoblastomycosis agents genera by infrared spectroscopy and chemometrics supervised by sequencing of rDNA regions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 254:119647. [PMID: 33744705 DOI: 10.1016/j.saa.2021.119647] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Chromoblastomycosis (CBM) is a skin and subcutaneous infection caused by species of seven fungal genera. Identification of CBM species is performed by DNA sequencing of one or more genes, which becomes a time-consuming work. Fourier Transform Infrared Spectroscopy (FTIR) has been used for the identification of other microorganisms, however, only one CBM genus was evaluated by FTIR analysis to date. Therefore, the study is aimed to differentiate the CBM agents for identification at genera level using FTIR supervised by Internal Transcribed Spacer (ITS) rDNA region. Seventy-seven isolates of the main five CBM genera were prepared for Attenuated Total Reflection FTIR (ATR-FTIR) with a new methodology using slices of dry fungus in glass fixing-modeling proposed in this study. The algorithm Hierarchical Cluster Analysis (HCA) was used to analyze the differences and similarities between species through the spectra. Orthogonal Partial Least Square Discriminant Analysis (OPLS-DA) allowed to correctly classify all samples of five CBM genera. The ATR-FTIR/OPLS-DA models highlighted important contributions of regions attributed to NH and OH stretching, amide I of proteins, polysaccharides bands and fingerprint region for the complete differentiation of the genera investigated. Thus, FTIR can be a fast and inexpensive alternative for identification of CBM agents.
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Affiliation(s)
- Daiane Heidrich
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos, 2400, CEP: 90035-003 Porto Alegre, RS, Brazil
| | - Alessandra Koehler
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos, 2400, CEP: 90035-003 Porto Alegre, RS, Brazil
| | - Mauricio Ramírez-Castrillón
- Postgraduate Program in Molecular and Cellular Biology, Biotechnology Center, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, CEP: 91501-970 Porto Alegre, RS, Brazil.
| | - Danielle Machado Pagani
- Postgraduate Program in Agricultural and Environmental Microbiology, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, 500, CEP: 90050-170 Porto Alegre, RS, Brazil
| | - Marco Flores Ferrão
- Department of Inorganic Chemistry, Chemistry Institute, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP: 91501-970 Porto Alegre, RS, Brazil.
| | - Maria Lúcia Scroferneker
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos, 2400, CEP: 90035-003 Porto Alegre, RS, Brazil; Department of Microbiology, Immunology and Parasitology, ICBS, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, 500, CEP: 90050-170 Porto Alegre, RS, Brazil.
| | - Valeriano Antonio Corbellini
- Department of Sciences, Humanities and Education, Postgraduate Program in Health Promotion, Postgraduate Program in Environmental Technology, Universidade de Santa Cruz do Sul, Avenida Independência, 2293, CEP: 96815-900 Santa Cruz do Sul, RS, Brazil.
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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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Pham DQ, Bryant SJ, Cheeseman S, Huang LZY, Bryant G, Dupont MF, Chapman J, Berndt CC, Vongsvivut JP, Crawford RJ, Truong VK, Ang ASM, Elbourne A. Micro- to nano-scale chemical and mechanical mapping of antimicrobial-resistant fungal biofilms. NANOSCALE 2020; 12:19888-19904. [PMID: 32985644 DOI: 10.1039/d0nr05617k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A fungal biofilm refers to the agglomeration of fungal cells surrounded by a polymeric extracellular matrix (ECM). The ECM is composed primarily of polysaccharides that facilitate strong surface adhesion, proliferation, and cellular protection from the surrounding environment. Biofilms represent the majority of known microbial communities, are ubiquitous, and are found on a multitude of natural and synthetic surfaces. The compositions, and in-turn nanomechanical properties, of fungal biofilms remain poorly understood, because these systems are complex, composed of anisotropic cellular and extracellular material, and importantly are species and environment dependent. Therefore, genomic variation, and/or mutations, as well as environmental and growth factors can change the composition of a fungal cell's biofilm. In this work, we probe the physico-mechanical and biochemical properties of two fungal species, Candida albicans (C. albicans) and Cryptococcus neoformans (C. neoformans), as well as two antifungal resistant sub-species of C. neoformans, fluconazole-resistant C. neoformans (FlucRC. neoformans) and amphotericin B-resistant C. neoformans (AmBRC. neoformans). A new experimental methodology of characterization is proposed, employing a combination of atomic force microscopy (AFM), instrumented nanoindentation, and Synchrotron ATR-FTIR measurements. This allowed the nano-mechanical and chemical characterisation of each fungal biofilm.
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Affiliation(s)
- Duy Quang Pham
- Surface Engineering for Advanced Materials (SEAM), Department of Mechanical and Production Design Engineering, Swinburne University of Technology, Hawthorn, Australia.
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Vatanshenassan M, Boekhout T, Mauder N, Robert V, Maier T, Meis JF, Berman J, Then E, Kostrzewa M, Hagen F. Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris. J Fungi (Basel) 2020; 6:jof6030146. [PMID: 32854308 PMCID: PMC7576496 DOI: 10.3390/jof6030146] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/19/2022] Open
Abstract
Candida auris is an emerging opportunistic yeast species causing nosocomial outbreaks at a global scale. A few studies have focused on the C. auris genotypic structure. Here, we compared five epidemiological typing tools using a set of 96 C. auris isolates from 14 geographical areas. Isolates were analyzed by microsatellite typing, ITS sequencing, amplified fragment length polymorphism (AFLP) fingerprint analysis, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and Fourier-transform infrared (FTIR) spectroscopy methods. Microsatellite typing grouped the isolates into four main clusters, corresponding to the four known clades in concordance with whole genome sequencing studies. The other investigated typing tools showed poor performance compared with microsatellite typing. A comparison between the five methods showed the highest agreement between microsatellite typing and ITS sequencing with 45% similarity, followed by microsatellite typing and the FTIR method with 33% similarity. The lowest agreement was observed between FTIR spectroscopy, MALDI-TOF MS, and ITS sequencing. This study indicates that microsatellite typing is the tool of choice for C. auris outbreak investigations. Additionally, FTIR spectroscopy requires further optimization and evaluation before it can be used as an epidemiological typing method, comparable with microsatellite typing, as a rapid method for tracing nosocomial fungal outbreaks.
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Affiliation(s)
- Mansoureh Vatanshenassan
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX Amsterdam, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX Amsterdam, The Netherlands
| | - Norman Mauder
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- BioAware, B-4280 Hannut, Belgium
| | - Thomas Maier
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands;
- Center of Expertise in Mycology Radboudumc, Canisius Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands
- Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, 80060-000 Curitiba, Brazil
| | - Judith Berman
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, 6997801 Tel Aviv, Israel;
| | - Euníce Then
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
- Correspondence: (M.K.); (F.H.); Tel.: +49-421-2205-1258 (M.K.); +31-30-2122-600 (F.H.)
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Correspondence: (M.K.); (F.H.); Tel.: +49-421-2205-1258 (M.K.); +31-30-2122-600 (F.H.)
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Influence of the Sample Preparation Method in Discriminating Candida spp. Using ATR-FTIR Spectroscopy. Molecules 2020; 25:molecules25071551. [PMID: 32231044 PMCID: PMC7180699 DOI: 10.3390/molecules25071551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/08/2023] Open
Abstract
Several studies have investigated the capacity of ATR-FTIR spectroscopy for fungal species discrimination. However, preparation methods vary among studies. This study aims to ascertain the effect of sample preparation on the discriminatory capacity of ATR-FTIR spectroscopy. Candida species were streaked to obtain colonies and spectra were collected from each preparation type, which included: (a) untreated colonies being directly transferred to the ATR crystal, (b) following washing and (c) following 24-h fixation in formalin. Spectra were pre-processed and principal component analysis (PCA) and K-means cluster analysis (KMC) were performed. Results showed that there was a clear discrimination between preparation types. Groups of spectra from untreated and washed isolates clustered separately due to intense protein, DNA and polysaccharide bands, whilst fixed spectra clustered separately due to intense polysaccharide bands. This signified that sample preparation had influenced the chemical composition of samples. Nevertheless, across preparation types, significant species discrimination was observed, and the polysaccharide (1200-900 cm-1) region was a common critical marker for species discrimination. However, different discriminatory marker bands were observed across preparation methods. Thus, sample preparation appears to influence the chemical composition of Candida samples; however, does not seem to significantly impact the species discrimination potential for ATR-FTIR spectroscopy.
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Alunni Cardinali M, Casagrande Pierantoni D, Caponi S, Corte L, Fioretto D, Cardinali G. Meso-Raman approach for rapid yeast cells identification. Biophys Chem 2019; 254:106249. [DOI: 10.1016/j.bpc.2019.106249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 01/28/2023]
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Taha M, Hassan M, Essa S, Tartor Y. Use of Fourier transform infrared spectroscopy (FTIR) spectroscopy for rapid and accurate identification of Yeasts isolated from human and animals. Int J Vet Sci Med 2019. [DOI: 10.1016/j.ijvsm.2013.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- M. Taha
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Cairo, Egypt
| | - M. Hassan
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Cairo, Egypt
| | - S. Essa
- Department of Microbiology, Research Institute of Animal Health, Dokki, Giza, Egypt
| | - Y. Tartor
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Cairo, Egypt
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Dalvand A, Katiraee F, Jafari Joozani R, Shokri H. Genotyping of Candida albicans isolated from animals using 25S ribosomal DNA and ALT repeats polymorphism in repetitive sequence. Curr Med Mycol 2019; 4:12-19. [PMID: 30815612 PMCID: PMC6386504 DOI: 10.18502/cmm.4.4.381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background and Purpose: Candida albicans is the most prevalent Candida species isolated from animals. Candidiasis can be systemic in animals or may affect a single organ, such as the mouth, urinary tract, and skin. The aim of the present study was to determine the genetic diversity of C. albicans isolated from different animals and investigate the presence of a relationship between host specificity and genetic typing of C. albicans. Materials and Methods: For the purpose of the study, DNA extraction was performed on 27 clinical isolates of C. albicans obtained from animals. Subsequently, they were subjected to 25S ribosomal DNA amplification and ALT repeats in repetitive sequences (RPSs). The minimum inhibitory concentrations of fluconazole, ketoconazole, clotrimazole, nystatin, amphotericin B, and caspofungin were determined using the microdilution method based on the Clinical and Laboratory Standards Institute M27-S4 standard. Results: Out of 27 C. albicans strains, 11, 6, 5, and 5 cases were recognized as genotypes A (40.8%), E (22.2%), B (18.5%), and C (18.5%), respectively, through amplification using AS-I, which revealed 17 different types of C. albicans. By combining the two typing methods, 27 C. albicans strains were finally divided into 22 genotypes. Conclusion: Different genotypes showed genetic diversity among the C. albicans strains isolated from animal sources. The results revealed no special genotype relationship according to the host, anatomical source of isolation, and antifungal susceptibility.
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Affiliation(s)
- Armina Dalvand
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Farzad Katiraee
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Raziallah Jafari Joozani
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Hojjatolah Shokri
- Department of Pathobiology, Faculty of Veterinary Medicine, Amol University of Special Modern Technologies, Amol, Iran
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Shi QY, Câmara CRS, Schlegel V. Biochemical alterations of Candida albicans during the phenotypic transition from yeast to hyphae captured by Fourier transform mid-infrared-attenuated reflectance spectroscopy. Analyst 2019; 143:5404-5416. [PMID: 30302456 DOI: 10.1039/c8an01452c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Candida albicans is an opportunistic human pathogen that can become virulent due to its ability to switch from a benign yeast to virulent hyphae phenotype. The emergence of C. albicans resistant to commonly used antifungal agents has necessitated the development of innovative treatments, which must be accompanied by an understanding of the molecular changes that occur during the phenotypic shift. For this purpose, Fourier transform mid-infrared spectroscopy in attenuated total reflectance mode (FT-mIR-ATR) was applied to monitor the structural and compositional changes in C. albicans during the yeast-to-hyphae transition. FT-mIR-ATR measurements were completed on the whole cell of C. albicans (SC5314) during hyphal formation induced by N-acetylglucosamine at 0, 1, 2, 3, 6 and 24 h. Principal component analysis separated the FT-mIR-ATR spectra into four groups that were aligned with the morphological changes captured by microscopic imaging. Spectral signatures indicating the structural and compositional modifications during the transition were identified mainly in the fatty acid region (3100-2800 cm-1), the protein and peptide region (1800-1500 cm-1), the mixed region (1500-1200 cm-1) and the polysaccharide region (1200-900 cm-1). A spectral fingerprint of the transition via a heat map was generated based on the peak shift in position. Quantitative evaluation of the spectra by curve fitting further revealed the dynamics of the cell's main components during the transition. This work provides valuable structural and functional information on the C. albicans phenotypic transition to hyphae, which has diagnostic implications.
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Affiliation(s)
- Qin-Yin Shi
- Department of Food Science and Technology, 1901 N 21st St, Food Innovation Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-6205, USA.
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Chien YC, Yang TC, Hung KC, Li CC, Xu JW, Wu JH. Effects of heat treatment on the chemical compositions and thermal decomposition kinetics of Japanese cedar and beech wood. Polym Degrad Stab 2018. [DOI: 10.1016/j.polymdegradstab.2018.11.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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Lasch P, Stämmler M, Zhang M, Baranska M, Bosch A, Majzner K. FT-IR Hyperspectral Imaging and Artificial Neural Network Analysis for Identification of Pathogenic Bacteria. Anal Chem 2018; 90:8896-8904. [DOI: 10.1021/acs.analchem.8b01024] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter Lasch
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Maren Stämmler
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Miao Zhang
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-060 Krakow, Poland
| | - Alejandra Bosch
- CINDEFI,
CONICET-CCT
La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 1900 La Plata, Buenos Aires, Argentina
| | - Katarzyna Majzner
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-060 Krakow, Poland
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15
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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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16
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Colabella C, Corte L, Roscini L, Shapaval V, Kohler A, Tafintseva V, Tascini C, Cardinali G. Merging FT-IR and NGS for simultaneous phenotypic and genotypic identification of pathogenic Candida species. PLoS One 2017; 12:e0188104. [PMID: 29206226 PMCID: PMC5714347 DOI: 10.1371/journal.pone.0188104] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/18/2017] [Indexed: 01/27/2023] Open
Abstract
The rapid and accurate identification of pathogen yeast species is crucial for clinical diagnosis due to the high level of mortality and morbidity induced, even after antifungal therapy. For this purpose, new rapid, high-throughput and reliable identification methods are required. In this work we described a combined approach based on two high-throughput techniques in order to improve the identification of pathogenic yeast strains. Next Generation Sequencing (NGS) of ITS and D1/D2 LSU marker regions together with FTIR spectroscopy were applied to identify 256 strains belonging to Candida genus isolated in nosocomial environments. Multivariate data analysis (MVA) was carried out on NGS and FT-IR data-sets, separately. Strains of Candida albicans, C. parapsilosis, C. glabrata and C. tropicalis, were identified with high-throughput NGS sequencing of ITS and LSU markers and then with FTIR. Inter- and intra-species variability was investigated by consensus principal component analysis (CPCA) which combines high-dimensional data of the two complementary analytical approaches in concatenated PCA blocks normalized to the same weight. The total percentage of correct identification reached around 97.4% for C. albicans and 74% for C. parapsilosis while the other two species showed lower identification rates. Results suggested that the identification success increases with the increasing number of strains actually used in the PLS analysis. The absence of reliable FT-IR libraries in the current scenario is the major limitation in FTIR-based identification of strains, although this metabolomics fingerprint represents a valid and affordable aid to rapid and high-throughput to clinical diagnosis. According to our data, FT-IR libraries should include some tens of certified strains per species, possibly over 50, deriving from diverse sources and collected over an extensive time period. This implies a multidisciplinary effort of specialists working in strain isolation and maintenance, molecular taxonomy, FT-IR technique and chemo-metrics, data management and data basing.
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Affiliation(s)
- Claudia Colabella
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Laura Corte
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Luca Roscini
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Volha Shapaval
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Achim Kohler
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Valeria Tafintseva
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Carlo Tascini
- Azienda Ospedaliera dei Colli—Ospedale Cotugno, Napoli, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials—Department of Chemistry, Biology and Biotechnology—University of Perugia, Perugia, Italy
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17
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Wohlmeister D, Vianna DRB, Helfer VE, Calil LN, Buffon A, Fuentefria AM, Corbellini VA, Pilger DA. Differentiation of Candida albicans , Candida glabrata , and Candida krusei by FT-IR and chemometrics by CHROMagar™ Candida. J Microbiol Methods 2017; 141:121-125. [DOI: 10.1016/j.mimet.2017.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 10/19/2022]
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18
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Shapaval V, Møretrø T, Wold Åsli A, Suso H, Schmitt J, Lillehaug D, Kohler A. A novel library-independent approach based on high-throughput cultivation in Bioscreen and fingerprinting by FTIR spectroscopy for microbial source tracking in food industry. Lett Appl Microbiol 2017; 64:335-342. [DOI: 10.1111/lam.12691] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/28/2016] [Accepted: 10/23/2016] [Indexed: 12/01/2022]
Affiliation(s)
- V. Shapaval
- Faculty of Science and Technology; Norwegian University of Life Sciences; Ås Norway
- Nofima AS; Ås Norway
| | | | | | | | | | | | - A. Kohler
- Faculty of Science and Technology; Norwegian University of Life Sciences; Ås Norway
- Nofima AS; Ås Norway
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19
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Forfang K, Zimmermann B, Kosa G, Kohler A, Shapaval V. FTIR Spectroscopy for Evaluation and Monitoring of Lipid Extraction Efficiency for Oleaginous Fungi. PLoS One 2017; 12:e0170611. [PMID: 28118388 PMCID: PMC5261814 DOI: 10.1371/journal.pone.0170611] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/06/2017] [Indexed: 11/19/2022] Open
Abstract
To assess whether Fourier Transform Infrared (FTIR) spectroscopy could be used to evaluate and monitor lipid extraction processes, the extraction methods of Folch, Bligh and Lewis were used. Biomass of the oleaginous fungi Mucor circinelloides and Mortierella alpina were employed as lipid-rich material for the lipid extraction. The presence of lipids was determined by recording infrared spectra of all components in the lipid extraction procedure, such as the biomass before and after extraction, the water and extract phases. Infrared spectra revealed the incomplete extraction after all three extraction methods applied to M.circinelloides and it was shown that mechanical disruption using bead beating and HCl treatment were necessary to complete the extraction in this species. FTIR spectroscopy was used to identify components, such as polyphosphates, that may have negatively affected the extraction process and resulted in differences in extraction efficiency between M.circinelloides and M.alpina. Residual lipids could not be detected in the infrared spectra of M.alpina biomass after extraction using the Folch and Lewis methods, indicating their complete lipid extraction in this species. Bligh extraction underestimated the fatty acid content of both M.circinelloides and M.alpina biomass and an increase in the initial solvent-to-sample ratio (from 3:1 to 20:1) was needed to achieve complete extraction and a lipid-free IR spectrum. In accordance with previous studies, the gravimetric lipid yield was shown to overestimate the potential of the SCO producers and FAME quantification in GC-FID was found to be the best-suited method for lipid quantification. We conclude that FTIR spectroscopy can serve as a tool for evaluating the lipid extraction efficiency, in addition to identifying components that may affect lipid extraction processes.
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Affiliation(s)
- Kristin Forfang
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
- Nofima AS, Ås, Norway
- * E-mail:
| | - Boris Zimmermann
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Gergely Kosa
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
- Nofima AS, Ås, Norway
| | - Achim Kohler
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Volha Shapaval
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
- Nofima AS, Ås, Norway
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20
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Wang P, Liu H, Zhao Y, Gu Y, Chen W, Wang L, Li L, Zhao X, Lei W, Hu Y, Zheng Z. Electromagnetic Attenuation Characteristics of Microbial Materials in the Infrared Band. APPLIED SPECTROSCOPY 2016; 70:1456-1463. [PMID: 27581361 DOI: 10.1177/0003702816662599] [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: 07/09/2015] [Accepted: 01/07/2016] [Indexed: 06/06/2023]
Abstract
In this study, seven microbial materials (entomogenous fungi Bb3088 mycelia, entomogenous fungi Bb3088 spores, entomogenous fungi Ma2677 mycelia, entomogenous fungi Ma2677 spores, Bacillus subtilis 8204, Staphylococcus aureus 6725, and Saccharomyces cerevisiae 1025) were used to measure electromagnetic (EM) signal extinction. They were subjected to light absorption and reflection measurements in the range of 4000-400 cm(-1) (2.5-25 µm) using Fourier transform infrared spectroscopy. The specular reflection spectrum method was used to calculate the real (n) and imaginary (k) parts of the complex refractive index. The complex refractive index with real part n and imaginary part k in the infrared band satisfies the following conditions n ≥ 1 and k ≥ 0. The mass extinction coefficient was calculated based on Mie theory. Entomogenous fungi Ma2677 spores and entomogenous fungi Bb3088 spores were selected as EM signal extinction materials in the smoke box test. The transmittances of entomogenous fungi Bb3088 spores and entomogenous fungi Ma2677 spores were 11.63% and 5.42%, and the mass extinction coefficients were 1.8337 m(2)/g and 1.227 m(2)/g. These results showed that entomogenous fungi Bb3088 spores and entomogenous fungi Ma2677 spores have higher extinction characteristics than other microbial materials.
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Affiliation(s)
- Peng Wang
- Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui, P. R. China
| | - Hongxia Liu
- Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui, P. R. China Jujube Scientific Research and Applied Center, Luoyang Normal University, Luoyang, P. R. China
| | - Yizheng Zhao
- State Key Laboratory of Pulsed Power Laser Technology, Hefei, Anhui, P. R. China
| | - Youlin Gu
- State Key Laboratory of Pulsed Power Laser Technology, Hefei, Anhui, P. R. China
| | - Wei Chen
- State Key Laboratory of Pulsed Power Laser Technology, Hefei, Anhui, P. R. China
| | - Li Wang
- Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui, P. R. China
| | - Le Li
- State Key Laboratory of Pulsed Power Laser Technology, Hefei, Anhui, P. R. China
| | - Xinying Zhao
- State Key Laboratory of Pulsed Power Laser Technology, Hefei, Anhui, P. R. China
| | - Wuhu Lei
- State Key Laboratory of Pulsed Power Laser Technology, Hefei, Anhui, P. R. China
| | - Yihua Hu
- State Key Laboratory of Pulsed Power Laser Technology, Hefei, Anhui, P. R. China
| | - Zhiming Zheng
- Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui, P. R. China
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Mohammed YF, Salem EZ, Shahin IMI, Abdo HM, Emam HE, Fawzy M, Abdel Salam MF. Applicability of Fourier transform infrared (FTIR) spectroscopy in rapid identification of some Candida and dermatophyte species infections in humans. Int J Dermatol 2016; 55:1164-71. [PMID: 27337493 DOI: 10.1111/ijd.4957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2009] [Revised: 08/15/2010] [Accepted: 09/23/2010] [Indexed: 11/26/2022]
Abstract
Traditional systems of identifying yeasts and dermatophytes have many disadvantages. Preliminary data on a radically different approach based on optical spectroscopic techniques suggest that these techniques may offer some advantages. We conducted a trial to verify the practical applicability of Fourier transform infrared (FTIR) spectroscopy in the identification of some yeast and dermatophyte species, in which samples from 50 patients with superficial fungal infections were cultured on Sabouraud dextrose agar with chloramphenicol and cycloheximide (actidione) and studied using FTIR microspectroscopy. Spectra of the same species were identical, whereas spectra of different species did not show similarity. This study showed that FTIR microspectroscopy is promising and can be used to obtain, with a single measurement, a "molecular fingerprint" of Candida and dermatophyte species. It can be improved further in terms of reliability.
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Affiliation(s)
- Yaser F Mohammed
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt.
| | - Elsayed Z Salem
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Ibrahim M I Shahin
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Hamed M Abdo
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Hanaa E Emam
- Department of Dermatology and Venereology, National Research Center, Cairo, Egypt
| | - Mahmoud Fawzy
- Department of Dermatology and Venereology, National Research Center, Cairo, Egypt
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22
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Silva S, Tobaldini-Valerio F, Costa-de-Oliveira S, Henriques M, Azeredo J, Ferreira EC, Lopes JA, Sousa C. Discrimination of clinically relevant Candida species by Fourier-transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR). RSC Adv 2016. [DOI: 10.1039/c6ra16769a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Accurate Candida species identification remains a challenge due to their phenotypic and genotypic similarity.
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Affiliation(s)
- Sónia Silva
- CEB-Centro de Engenharia Biológica
- Universidade do Minho
- Braga
- Portugal
| | - Flávia Tobaldini-Valerio
- CEB-Centro de Engenharia Biológica
- Universidade do Minho
- Braga
- Portugal
- Departamento de Análises Clínicas e Biomedicina
| | | | - Mariana Henriques
- CEB-Centro de Engenharia Biológica
- Universidade do Minho
- Braga
- Portugal
| | - Joana Azeredo
- CEB-Centro de Engenharia Biológica
- Universidade do Minho
- Braga
- Portugal
| | | | - João A. Lopes
- Research Institute for Medicines (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- Lisboa
- Portugal
| | - Clara Sousa
- LAQV/REQUIMTE
- Departamento de Ciências Químicas
- Faculdade de Farmácia
- Universidade do Porto
- 4050-313 Porto
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23
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Zimkus A, Misiūnas A, Ramanavičius A, Chaustova L. Evaluation of Competence Phenomenon of Yeast Saccharomyces cerevisiae by Lipophilic Cations Accumulation and FT-IR Spectroscopy. Relation of Competence to Cell Cycle. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10142-2_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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Cardellini F, Tiecco M, Germani R, Cardinali G, Corte L, Roscini L, Spreti N. Novel zwitterionic deep eutectic solvents from trimethylglycine and carboxylic acids: characterization of their properties and their toxicity. RSC Adv 2014. [DOI: 10.1039/c4ra10628h] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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25
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Schabauer L, Wenning M, Huber I, Ehling-Schulz M. Novel physico-chemical diagnostic tools for high throughput identification of bovine mastitis associated gram-positive, catalase-negative cocci. BMC Vet Res 2014; 10:156. [PMID: 25015262 PMCID: PMC4105049 DOI: 10.1186/1746-6148-10-156] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 07/03/2014] [Indexed: 01/14/2023] Open
Abstract
Background The routine diagnosis of Streptococcus spp. and other mastitis associated gram-positive, catalase-negative cocci is still based upon biochemical tests and serological methods, which frequently provide ambiguous identification results. We therefore aimed to establish an accurate identification system for differential diagnosis of mastitis associated Streptococcus spp. and related species using biophysical techniques such as Fourier-transform infrared (FTIR) spectroscopy and MALDI – TOF/MS. Results Based on a panel of 210 isolates from cases of bovine mastitis, an unsupervised FTIR spectral reference library was established and an artificial neural network (ANN) - assisted identification system was developed. All bacterial isolates were previously identified by species-specific PCR and/or 16S rRNA gene sequence analysis. An overall identification rate of 100% at species level for 173 strains unknown to the ANN and the library was achieved by combining ANN and the spectral database, thus demonstrating the suitability of our FTIR identification system for routine diagnosis. In addition, we investigated the potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of mastitis associated Streptococcus spp. and related bacteria. Using the Microflex LT System, MALDI Biotyper software™ (V3.3) we achieved an accuracy rate of 95.2%. A blind study, including 21 clinical samples from dairy cows, revealed a 100% correct species identification rate for FTIR and 90.5% for MALDI-TOF MS, indicating that these techniques are valuable tools for diagnosis. Conclusions This study clearly demonstrates that FTIR spectroscopy as well as MALDI-TOF MS can significantly improve and facilitate the identification and differentiation of mastitis associated Streptococcus spp. and related species. Although the FTIR identification system turned out being slightly superior to MALDI-TOF MS in terms of identification on species level, both methods offer interesting alternatives to conventional methods currently used in mastitis diagnosis as both of them provide high accuracy at low operating costs once the instrument is acquired.
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Affiliation(s)
| | | | | | - Monika Ehling-Schulz
- Functional Microbiology, IBMH, Department of Pathobiology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
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Wenning M, Breitenwieser F, Konrad R, Huber I, Busch U, Scherer S. Identification and differentiation of food-related bacteria: A comparison of FTIR spectroscopy and MALDI-TOF mass spectrometry. J Microbiol Methods 2014; 103:44-52. [PMID: 24878140 DOI: 10.1016/j.mimet.2014.05.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 11/17/2022]
Abstract
The food industry requires easy, accurate, and cost-effective techniques for microbial identification to ensure safe products and identify microbial contaminations. In this work, FTIR spectroscopy and MALDI-TOF mass spectrometry were assessed for their suitability and applicability for routine microbial diagnostics of food-related microorganisms by analyzing their robustness according to changes in incubation time and medium, identification accuracy and their ability to differentiate isolates down to the strain level. Changes in the protocol lead to a significantly impaired performance of FTIR spectroscopy, whereas they had only little effects on MALDI-TOF MS. Identification accuracy was tested using 174 food-related bacteria (93 species) from an in-house strain collection and 40 fresh isolates from routine food analyses. For MALDI-TOF MS, weaknesses in the identification of bacilli and pseudomonads were observed; FTIR spectroscopy had most difficulties in identifying pseudomonads and enterobacteria. In general, MALDI-TOF MS obtained better results (52-85% correct at species level), since the analysis of mainly ribosomal proteins is more robust and seems to be more reliable. FTIR spectroscopy suffers from the fact that it generates a whole-cell fingerprint and intraspecies diversity may lead to overlapping species borders which complicates identification. In the present study values between 56% and 67% correct species identification were obtained. On the opposite, this high sensitivity offers the opportunity of typing below the species level which was not possible using MALDI-TOF MS. Using fresh isolates from routine diagnostics, both techniques performed well with 88% (MALDI-TOF) and 75% (FTIR) correct identifications at species level, respectively.
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Affiliation(s)
- Mareike Wenning
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs-und Lebensmittelforschung (ZIEL), Technische Universität München, Weihenstephaner Berg 3, 85350 Freising, Germany.
| | - Franziska Breitenwieser
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs-und Lebensmittelforschung (ZIEL), Technische Universität München, Weihenstephaner Berg 3, 85350 Freising, Germany; Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Veterinärstraße 2, 85764 Oberschleißheim, Germany
| | - Regina Konrad
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Veterinärstraße 2, 85764 Oberschleißheim, Germany
| | - Ingrid Huber
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Veterinärstraße 2, 85764 Oberschleißheim, Germany
| | - Ulrich Busch
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Veterinärstraße 2, 85764 Oberschleißheim, Germany
| | - Siegfried Scherer
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs-und Lebensmittelforschung (ZIEL), Technische Universität München, Weihenstephaner Berg 3, 85350 Freising, Germany; Lehrstuhl für Mikrobielle Ökologie, Department of Biosciences, Technische Universität München, D-85350 Freising, Germany
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27
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Corte L, Tiecco M, Roscini L, Germani R, Cardinali G. FTIR analysis of the metabolomic stress response induced by N-alkyltropinium bromide surfactants in the yeasts Saccharomyces cerevisiae and Candida albicans. Colloids Surf B Biointerfaces 2014; 116:761-71. [DOI: 10.1016/j.colsurfb.2014.01.054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 01/27/2014] [Accepted: 01/30/2014] [Indexed: 10/25/2022]
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28
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Candida identification: a journey from conventional to molecular methods in medical mycology. World J Microbiol Biotechnol 2014; 30:1437-51. [PMID: 24379160 DOI: 10.1007/s11274-013-1574-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 12/02/2013] [Indexed: 12/17/2022]
Abstract
The incidence of Candida infections have increased substantially in recent years due to aggressive use of immunosuppressants among patients. Use of broad-spectrum antibiotics and intravascular catheters in the intensive care unit have also attributed with high risks of candidiasis among immunocompromised patients. Among Candida species, C. albicans accounts for the majority of superficial and systemic infections, usually associated with high morbidity and mortality often caused due to increase in antimicrobial resistance and restricted number of antifungal drugs. Therefore, early detection of candidemia and correct identification of Candida species are indispensable pre-requisites for appropriate therapeutic intervention. Since blood culture based methods lack sensitivity, and species-specific identification by conventional method is time-consuming and often leads to misdiagnosis within closely related species, hence, molecular methods may provide alternative for accurate and rapid identification of Candida species. Although, several molecular approaches have been developed for accurate identification of Candida species but the internal transcribed spacer 1 and 2 (ITS1 and ITS2) regions of the rRNA gene are being used extensively in a variety of formats. Of note, ITS sequencing and PCR-RFLP analysis of ITS region seems to be promising as a rapid, easy, and cost-effective method for identification of Candida species. Here, we review a number of existing techniques ranging from conventional to molecular approaches currently in use for the identification of Candida species. Further, advantages and limitations of these methods are also discussed with respect to their discriminatory power, reproducibility, and ease of performance.
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Wenning M, Scherer S. Identification of microorganisms by FTIR spectroscopy: perspectives and limitations of the method. Appl Microbiol Biotechnol 2013; 97:7111-20. [PMID: 23860713 DOI: 10.1007/s00253-013-5087-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/26/2013] [Accepted: 06/27/2013] [Indexed: 11/29/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy was introduced in 1991 as a technique to identify and classify microbes. Since then, it has gained growing interest and has undergone a remarkable evolution. Highly sophisticated spectrometers have been developed, enabling a high sample throughput. Today, the generation of high-quality data in a short time and the application of the technique for rapid and reliable identification of microbes to the species level are well documented. What makes FTIR spectroscopy even more attractive is the fact that spectral information can also be exploited for strain typing purposes, which is particularly important for epidemiological analyses and some technological applications. Accordingly, in recent years, FTIR spectroscopy has been increasingly used for typing and classifying microorganisms below the species level. The intention of this review is to give an overview over current knowledge and strategies of using FTIR spectroscopy for species identification and to describe different approaches for strain typing.
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Affiliation(s)
- Mareike Wenning
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung-ZIEL, Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany.
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Fourier transform infrared spectral evaluation for the differentiation of clinically relevant Trichophyton species. J Microbiol Methods 2013; 93:218-23. [DOI: 10.1016/j.mimet.2013.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 11/18/2022]
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Bhat R. Potential Use of Fourier Transform Infrared Spectroscopy for Identification of Molds Capable of Producing Mycotoxins. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2013. [DOI: 10.1080/10942912.2011.609629] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Rajeev Bhat
- a Food Technology Division, School of Industrial Technology , Universiti Sains Malaysia , Penang , Malaysia
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Infectious Diseases, Vibrational Spectroscopic Approaches to Rapid Diagnostics. Infect Dis (Lond) 2013. [DOI: 10.1007/978-1-4614-5719-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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33
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Huff K, Aroonnual A, Littlejohn AEF, Rajwa B, Bae E, Banada PP, Patsekin V, Hirleman ED, Robinson JP, Richards GP, Bhunia AK. Light-scattering sensor for real-time identification of Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae colonies on solid agar plate. Microb Biotechnol 2012; 5:607-20. [PMID: 22613192 PMCID: PMC3815873 DOI: 10.1111/j.1751-7915.2012.00349.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 04/11/2012] [Indexed: 12/17/2022] Open
Abstract
The three most common pathogenic species of Vibrio, Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus, are of major concerns due to increased incidence of water‐ and seafood‐related outbreaks and illness worldwide. Current methods are lengthy and require biochemical and molecular confirmation. A novel label‐free forward light‐scattering sensor was developed to detect and identify colonies of these three pathogens in real time in the presence of other vibrios in food or water samples. Vibrio colonies grown on agar plates were illuminated by a 635 nm laser beam and scatter‐image signatures were acquired using a CCD (charge‐coupled device) camera in an automated BARDOT (BActerial Rapid Detection using Optical light‐scattering Technology) system. Although a limited number of Vibrio species was tested, each produced a unique light‐scattering signature that is consistent from colony to colony. Subsequently a pattern recognition system analysing the collected light‐scatter information provided classification in 1−2 min with an accuracy of 99%. The light‐scattering signatures were unaffected by subjecting the bacteria to physiological stressors: osmotic imbalance, acid, heat and recovery from a viable but non‐culturable state. Furthermore, employing a standard sample enrichment in alkaline peptone water for 6 h followed by plating on selective thiosulphate citrate bile salts sucrose agar at 30°C for ∼ 12 h, the light‐scattering sensor successfully detected V. cholerae, V. parahaemolyticus and V. vulnificus present in oyster or water samples in 18 h even in the presence of other vibrios or other bacteria, indicating the suitability of the sensor as a powerful screening tool for pathogens on agar plates.
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Affiliation(s)
- Karleigh Huff
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, USA
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Ciobanu CS, Iconaru SL, Gyorgy E, Radu M, Costache M, Dinischiotu A, Le Coustumer P, Lafdi K, Predoi D. Biomedical properties and preparation of iron oxide-dextran nanostructures by MAPLE technique. Chem Cent J 2012; 6:17. [PMID: 22410001 PMCID: PMC3353163 DOI: 10.1186/1752-153x-6-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 03/13/2012] [Indexed: 11/10/2022] Open
Abstract
Background In this work the chemical structure of dextran-iron oxide thin films was reported. The films were obtained by MAPLE technique from composite targets containing 10 wt. % dextran with 1 and 5 wt.% iron oxide nanoparticles (IONPs). The IONPs were synthesized by co-precipitation method. A KrF* excimer laser source (λ = 248 nm, τFWHM≅25 ns, ν = 10 Hz) was used for the growth of the hybrid, iron oxide NPs-dextran thin films. Results Dextran coated iron oxide nanoparticles thin films were indexed into the spinel cubic lattice with a lattice parameter of 8.36 Å. The particle sized calculated was estimated at around 7.7 nm. The XPS shows that the binding energy of the Fe 2p3/2 of two thin films of dextran coated iron oxide is consistent with Fe3+ oxides. The atomic percentage of the C, O and Fe are 66.71, 32.76 and 0.53 for the films deposited from composite targets containing 1 wt.% maghemite and 64.36, 33.92 and 1.72 respectively for the films deposited from composite targets containing 5 wt.% maghemite. In the case of cells cultivated on dextran coated 5% maghemite γ-Fe2O3, the number of cells and the level of F-actin were lower compared to the other two types of thin films and control. Conclusions The dextran-iron oxide continuous thin films obtained by MAPLE technique from composite targets containing 10 wt.% dextran as well as 1 and 5 wt.% iron oxide nanoparticles synthesized by co-precipitation method presented granular surface morphology. Our data proved a good viability of Hep G2 cells grown on dextran coated maghemite thin films. Also, no changes in cells morphology were noticed under phase contrast microscopy. The data strongly suggest the potential use of iron oxide-dextran nanocomposites as a potential marker for biomedical applications.
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Driskell JD, Tripp RA. Infectious Diseases, Vibrational Spectroscopic Approaches to Rapid Diagnostics. Infect Dis (Lond) 2012. [DOI: 10.1007/978-1-0716-2463-0_532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
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Adt I, Kohler A, Gognies S, Budin J, Sandt C, Belarbi A, Manfait M, Sockalingum GD. FTIR spectroscopic discrimination of Saccharomyces cerevisiae and Saccharomyces bayanus strains. Can J Microbiol 2010; 56:793-801. [PMID: 20921989 DOI: 10.1139/w10-062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, we tested the potential of Fourier-transform infrared absorption spectroscopy to screen, on the one hand, Saccharomyces cerevisiae and non-S. cerevisiae strains and, on the other hand, to discriminate between S. cerevisiae and Saccharomyces bayanus strains. Principal components analysis (PCA), used to compare 20 S. cerevisiae and 21 non-Saccharomyces strains, showed only 2 misclassifications. The PCA model was then used to classify spectra from 14 Samos strains. All 14 Samos strains clustered together with the S. cerevisiae group. This result was confirmed by a routinely used electrophoretic pattern obtained by pulsed-field gel electrophoresis. The method was then tested to compare S. cerevisiae and S. bayanus strains. Our results indicate that identification at the strain level is possible. This first result shows that yeast classification and S. bayanus identification can be feasible in a single measurement.
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Affiliation(s)
- Isabelle Adt
- MéDIAN, Université de Reims Champagne-Ardenne, MEDyC CNRS UMR 6237, UFR Pharmacie, IFR53, 51 rue Cognacq-jay, 51096 REIMS CEDEX, France.
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Putignani L, Del Chierico F, Onori M, Mancinelli L, Argentieri M, Bernaschi P, Coltella L, Lucignano B, Pansani L, Ranno S, Russo C, Urbani A, Federici G, Menichella D. MALDI-TOF mass spectrometry proteomic phenotyping of clinically relevant fungi. MOLECULAR BIOSYSTEMS 2010; 7:620-9. [PMID: 20967323 DOI: 10.1039/c0mb00138d] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteomics is particularly suitable for characterising human pathogens with high life cycle complexity, such as fungi. Protein content and expression levels may be affected by growth states and life cycle morphs and correlate to species and strain variation. Identification and typing of fungi by conventional methods are often difficult, time-consuming and frequently, for unusual species, inconclusive. Proteomic phenotypes from MALDI-TOF MS were employed as analytical and typing expression profiling of yeast, yeast-like species and strain variants in order to achieve a microbial proteomics population study. Spectra from 303 clinical isolates were generated and processed by standard pattern matching with a MALDI-TOF Biotyper (MT). Identifications (IDs) were compared to a reference biochemical-based system (Vitek-2) and, when discordant, MT IDs were verified with genotyping IDs, obtained by sequencing the 25-28S rRNA hypervariable D2 region. Spectra were converted into virtual gel-like formats, and hierarchical clustering analysis was performed for 274 Candida profiles to investigate species and strain typing correlation. MT provided 257/303 IDs consistent with Vitek-2 ones. However, amongst 26/303 discordant MT IDs, only 5 appeared "true". No MT identification was achieved for 20/303 isolates for incompleteness of database species variants. Candida spectra clustering agreed with identified species and topology of Candida albicans and Candida parapsilosis specific dendrograms. MT IDs show a high analytical performance and profiling heterogeneity which seems to complement or even outclass existing typing tools. This variability reflects the high biological complexity of yeasts and may be properly exploited to provide epidemiological tracing and infection dispersion patterns.
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Affiliation(s)
- Lorenza Putignani
- Microbiology Unit, Children's Hospital and Research Institute Bambino Gesù, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
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Büchl N, Hutzler M, Mietke-Hofmann H, Wenning M, Scherer S. Differentiation of probiotic and environmental Saccharomyces cerevisiae strains in animal feed. J Appl Microbiol 2010; 109:783-91. [DOI: 10.1111/j.1365-2672.2010.04705.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Wenning M, Büchl NR, Scherer S. Species and strain identification of lactic acid bacteria using FTIR spectroscopy and artificial neural networks. JOURNAL OF BIOPHOTONICS 2010; 3:493-505. [PMID: 20422658 DOI: 10.1002/jbio.201000015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Lactic acid bacteria (LAB) are a heterogeneous group of micro-organisms with high relevance for fermented food and beverages as well as human and animal health. Identification of LAB is complicated by species richness, a high degree of heterogeneity between species and the presence of very closely related species at the same time. In the present study we developed identification systems based on FTIR spectra and artificial neural networks (ANNs) for species identification of 92 LAB species out of nine genera and strain identification of probiotic and environmental Enterococcus faecium strains used as additives for animal feed. The reference databases established in this work permit reliable identification of LAB with accuracies of 93.2% at species and 97.1% at strain level for Ec. faecium, demonstrating the excellent suitability of FTIR spectroscopy as a technique applicable for simultaneous species and strain identification.
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Affiliation(s)
- Mareike Wenning
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung ZIEL, Technische Universität München, Freising, Germany.
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Roscini L, Corte L, Antonielli L, Rellini P, Fatichenti F, Cardinali G. Influence of cell geometry and number of replicas in the reproducibility of whole cell FTIR analysis. Analyst 2010; 135:2099-105. [PMID: 20523945 DOI: 10.1039/c0an00127a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fourier Transform InfraRed (FTIR) spectroscopy is an increasingly used technique in biology, especially for whole cell metabolomic fingerprint. The reproducibility of this technique is influenced by a large number of factors such as the physiological state of cells, sample manipulation and growth conditions. Evidence exists suggesting that the cell shape and dimension can be further elements to consider in whole cell FTIR analysis. In this study we aimed to address the effect of cell geometry on the FTIR spectra and to define the extent of variability occurring between machine and biological replicas with a standardized protocol. The yeast species Saccharomyces cerevisiae (large oval-shaped cells) and Debaryomyces hansenii (small round shaped cells) were employed for their different morphology. Thirty machine replicas of each were analyzed separately and after averaging in groups of three, showing a three to four-fold reduction of the variability. Similarly, a two-fold reduction of variability was observed when thirty biological replicas of the two yeast species were analyzed. The optimal number of replicas to average was then estimated with a bootstrap-like procedure in which biological and machine replicas were randomly resampled 2000 times and averaged in groups spanning from 2 to 12 replicas. This simulation has shown that little if any advantage can be obtained by increasing the number of replicas over five and that the variability exhibited by the small regular cells of D. hansenii was always roughly half of that displayed by the large S. cerevisiae cells, confirming the results obtained with standard non-bootstrapped averages.
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Affiliation(s)
- Luca Roscini
- Department Applied Biology-Microbiology, University of Perugia, Borgo 20 Giugno, 74, I-06121 Perugia, Italy
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FT-IR Spectroscopy for Rapid Differentiation of Aspergillus flavus, Aspergillus fumigatus, Aspergillus parasiticus and Characterization of Aflatoxigenic Isolates Collected from Agricultural Environments. Mycopathologia 2010; 170:131-42. [DOI: 10.1007/s11046-010-9304-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 03/11/2010] [Indexed: 10/19/2022]
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Fourier transform infrared as a powerful technique for the identification and characterization of filamentous fungi and yeasts. Res Microbiol 2010; 161:168-75. [DOI: 10.1016/j.resmic.2009.12.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 10/27/2009] [Accepted: 12/21/2009] [Indexed: 11/17/2022]
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Characterization of a neutral polysaccharide with antioxidant capacity from red wine. Carbohydr Res 2009; 344:1095-101. [DOI: 10.1016/j.carres.2009.03.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 03/16/2009] [Accepted: 03/19/2009] [Indexed: 11/21/2022]
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Variabilidad molecular de aislamientos de Candida spp. por la técnica de polimorfismos de ADN amplificados aleatoriamente (Random Amplified Polymorphic DNA, RAPD) en mujeres de Armenia, Colombia. INFECTIO 2009. [DOI: 10.1016/s0123-9392(09)70140-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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45
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Babrah J, McCarthy K, Lush RJ, Rye AD, Bessant C, Stone N. Fourier transform infrared spectroscopic studies of T-cell lymphoma, B-cell lymphoid and myeloid leukaemia cell lines. Analyst 2009; 134:763-8. [DOI: 10.1039/b807967f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Büchl NR, Wenning M, Seiler H, Mietke-Hofmann H, Scherer S. Reliable identification of closely relatedIssatchenkiaandPichiaspecies using artificial neural network analysis of Fourier-transform infrared spectra. Yeast 2008; 25:787-98. [DOI: 10.1002/yea.1633] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Al-Qadiri HM, Al-Alami NI, Al-Holy MA, Rasco BA. Using Fourier transform infrared (FT-IR) absorbance spectroscopy and multivariate analysis to study the effect of chlorine-induced bacterial injury in water. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:8992-8997. [PMID: 18778073 DOI: 10.1021/jf801604p] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The effect of chlorine-induced bacterial injury on spectral features using Fourier transform infrared (FT-IR) absorbance spectroscopy was studied using a mixed bacterial culture of (1:1) ca. 500 CFU/mL each Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 15442 in 0.9% saline. Bacterial cells were treated with 0, 0.3, or 1.0 ppm of initial free chlorine (21 degrees C, 1 h of contact time). Chlorine-injured and dead bacterial cells retained the ATR spectral properties of uninjured or live cells in the region of C-O-C stretching vibrations of polysaccharides, indicative of the cell wall peptidoglycan layer and lipopolysaccharide outer leaflet. This confirms the observations of others that extensive bacterial membrane damage is not a key factor in the inactivation of bacteria by chlorine. The bactericidal effect of chlorine caused changes in the spectral features of bacterial ester functional groups of lipids, structural proteins, and nucleic acids, with apparent denaturation reflected between 1800 and 1300 cm (-1) for injured bacterial cells. Three-dimensional principal component analysis (PCA) showed distinct segregation and clustering of chlorine-treated and untreated cells. Cells exposed to chlorine at 0.3 or 1.0 ppm could be distinguished from the untreated control 73 and 80% of the time, respectively, using soft independent modeling of class analogy (SIMCA) analysis. This study suggests that FT-IR spectroscopy may be applicable for detecting the presence of injured and viable but not culturable (VBNC) waterborne pathogens that are underestimated or not discernible using conventional microbial techniques.
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Affiliation(s)
- Hamzah M Al-Qadiri
- Department of Nutrition and Food Technology, Faculty of Agriculture, The University of Jordan, Amman 11942 Jordan.
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Pradhan N, Pradhan SK, Nayak BB, Mukherjee PS, Sukla LB, Mishra BK. Micro-Raman analysis and AFM imaging of Acidithiobacillus ferrooxidans biofilm grown on uranium ore. Res Microbiol 2008; 159:557-61. [PMID: 18640267 DOI: 10.1016/j.resmic.2008.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 06/05/2008] [Accepted: 06/13/2008] [Indexed: 11/29/2022]
Abstract
Acidithiobacillus ferrooxidans biofilm grown on uranium ore substrate was analyzed by a micro-Raman spectrometer and an atomic force microscope (AFM). The bacterium employed for this study, A. ferrooxidans BM1, was isolated from a uranium mine (Jaduguda, India). Micro-Raman analysis revealed the different constituents of molecular fragments present in microbial cells and in secreted extracellular polymeric substances (EPSs). AFM images clearly revealed bacterial cells surrounded by EPS. From Raman spectral data, the composition of EPS from A. ferrooxidans BM1 appeared to be similar to that of EPS secreted in a different Pseudomonas bacterium.
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Affiliation(s)
- Nilotpala Pradhan
- Institute of Minerals and Materials Technology, Bhubaneswar 751013, Orissa, India.
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AL-QADIRI HAMZAHM, AL-ALAMI NIVINI, LIN MENGSHI, AL-HOLY MURAD, CAVINATO ANNAG, RASCO BARBARAA. STUDYING OF THE BACTERIAL GROWTH PHASES USING FOURIER TRANSFORM INFRARED SPECTROSCOPY AND MULTIVARIATE ANALYSIS. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1745-4581.2008.00117.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Al-Qadiri H, Lin M, Al-Holy M, Cavinato A, Rasco B. Detection of Sublethal Thermal Injury in Salmonella enterica Serotype Typhimurium and Listeria monocytogenes Using Fourier Transform Infrared (FT-IR) Spectroscopy (4000 to 600 cm−1). J Food Sci 2008; 73:M54-61. [DOI: 10.1111/j.1750-3841.2007.00640.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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