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Dinçtürk E. Determination of Raman spectrum under different culture conditions: preliminary research on bacterial fish pathogens. Anim Biotechnol 2024; 35:2299733. [PMID: 38166494 DOI: 10.1080/10495398.2023.2299733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
The intensive labour and time required for conventional methods to identify bacterial fish pathogens have revealed the need to develop alternative methods. Raman spectroscopy has been used in the rapid optical identification of bacterial pathogens in recent years as an alternative method in microbiology. Strains of bacterial fish pathogens (Vibrio anguillarum, Lactococcus garvieae and Yersinia ruckeri) that often cause infectious diseases in fish were here identified and analyzed in terms of their biochemical structures in different media and at different incubation times, and the data were specified by using Raman spectroscopy. The results demonstrated that Raman spectroscopy presents species-specific Raman spectra of each disease-causing bacteria and that it would be more appropriate to choose general microbiological media over selective media for routine studies. Additionally, it was found that species-specific band regions did not differ in 24- and 48-hour cultures, but there could be a difference in peak intensity which may lead to difficult characterization of spectrum. The current study, conducted for the first time with bacterial fish pathogens under different incubation conditions, is believed to provide a basis for the routine use of Raman spectroscopy for quick pathogen identification and the precise determination of the methodology for further research.
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Affiliation(s)
- Ezgi Dinçtürk
- Fish Disease and Biotechnology Laboratory, Department of Aquaculture, Izmir Katip Celebi University, Izmir, Türkiye
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Cárdenas-Calle M, Patiño L, Pernia B, Erazo R, Muñoz C, Valencia-Avellan M, Lozada M, Regato-Arrata M, Barrera M, Aquino S, Fuentes S, Duque J, Velázquez-Araque L, Carpio B, Méndez-Roman C, Calle C, Cárdenas G, Guizado-Herrera D, Tello CL, Bravo-Basantes V, Francis J, Uyaguari M. Detection of thermotolerant coliforms and SARS-CoV-2 RNA in sewage and recreational waters in the Ecuadorian coast: A call for improving water quality regulation. PLoS One 2024; 19:e0302000. [PMID: 38709720 PMCID: PMC11073733 DOI: 10.1371/journal.pone.0302000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/26/2024] [Indexed: 05/08/2024] Open
Abstract
Wastewater surveillance represents an alternative approach to regulating contamination and the early detection of infectious agents and outbreaks of diseases of public health importance. This study evaluated domestic wastewater effects on recreational waters in estuarine and seawater bodies in Guayas and Santa Elena provinces in Ecuador, South America. Fecal indicator bacteria (thermotolerant coliforms) served as key indicators for evaluation. Physical, chemical, and microbiological quality markers following the Ecuadorian environmental quality standard and the discharge of effluents to the water resource were analyzed. Samples were collected from 44 coastal sites and 2 oxidation lagoons during the dry and rainy seasons of 2020 and 2021, respectively. SARS-CoV-2 RNA was detected in samples with higher E. coli concentrations using reverse transcription quantitative PCR to detect the genes N and ORF1ab. All samples analyzed for SARS-CoV-2 showed Ct ˂ 40 for at least one gene. Four samples showed at least 20 genome copies of gene N per reaction. These were at an artisanal fishing port, an estuarine area (Palmar), a recreational bay, and an oxidation lagoon. A moderate correlation was found between SARS-CoV-2 RNA, thermotolerant coliform and E. coli (p-value ≤ 0.0037), and a strong and positive correlation between thermotolerant coliform and E. coli. (p-value ≤ 0.00001), highlighting the utility of these established parameters as a proxy of the virus. Significant differences were found in the concentrations of thermotolerant coliforms between seasons (p-value = 0.016) and sites (p-value = 0.005). The highest levels of coliforms were found in the dry season (63000 MPN/100 mL) in Anconcito and during the rainy season (14000 MPN/100 mL) at Esterillo in Playas County. It is recommended that the decentralized autonomous governments of the surveyed provinces in Ecuador implement urgent corrective actions and establish medium-term mechanisms to minimize a potential contamination route. Additional parameters must be included in the monitoring, such as Enterococcus and intestinal parasites, due to their public health implications. In the oxidation lagoons, maintenance actions must be carried out, including the dissolution of sediments, an increase in water retention times, and in situ treatment of the sludge, to improve the system's performance.
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Affiliation(s)
- Maritza Cárdenas-Calle
- Interinstitutional Network for the Study of Aquatic Ecosystems of Ecuador, Guayaquil, Guayas, Ecuador
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
| | - Leandro Patiño
- Interinstitutional Network for the Study of Aquatic Ecosystems of Ecuador, Guayaquil, Guayas, Ecuador
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- National Institute for Public Health Research–INSPI- Dr. Leopoldo Izquieta Pérez, Technical Direction of Research, Development and Innovation, Guayaquil, Guayas, Ecuador
| | - Beatriz Pernia
- Interinstitutional Network for the Study of Aquatic Ecosystems of Ecuador, Guayaquil, Guayas, Ecuador
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- Faculty of Natural Sciences, Natural Resources Research Institute, University of Guayaquil, Guayaquil, Guayas, Ecuador
| | - Roberto Erazo
- Interinstitutional Network for the Study of Aquatic Ecosystems of Ecuador, Guayaquil, Guayas, Ecuador
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- Labcestta, Guayaquil, Guayas, Ecuador
| | - Carlos Muñoz
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
| | - Magaly Valencia-Avellan
- Interinstitutional Network for the Study of Aquatic Ecosystems of Ecuador, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- Facultad del Mar y Medio Ambiente, Universidad del Pacífico, Guayaquil, Guayas, Ecuador
| | - Mariana Lozada
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- Environmental Microbiology Laboratory, Institute of Biology of Marine Organisms, CONICET, Puerto Madryn, Chubut, Argentina
| | - Mary Regato-Arrata
- National Institute for Public Health Research–INSPI- Dr. Leopoldo Izquieta Pérez, National Reference Center for Exanthematous, Gastroenteric and Vector-borne Viruses, Guayaquil, Guayas, Ecuador
| | - Miguel Barrera
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
| | - Segundo Aquino
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
| | - Stefania Fuentes
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
| | - Javier Duque
- Interinstitutional Network for the Study of Aquatic Ecosystems of Ecuador, Guayaquil, Guayas, Ecuador
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
| | - Luis Velázquez-Araque
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
| | - Bertha Carpio
- Dirección del Medio Ambiente, Gobierno Provincial de Santa Elena, Santa Elena, Ecuador
| | - Carlos Méndez-Roman
- Área Nacional de Recreación Playas Villamil, Ministerio de Ambiente Agua y Transición Ecológica, Playas, Ecuador
| | - Carlos Calle
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
| | - Guillermo Cárdenas
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
| | - David Guizado-Herrera
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
- National Institute for Public Health Research–INSPI- Dr. Leopoldo Izquieta Pérez, Technical Direction of Research, Development and Innovation, Guayaquil, Guayas, Ecuador
| | - Clara Lucía Tello
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- National Institute for Public Health Research–INSPI- Dr. Leopoldo Izquieta Pérez, Technical Direction of Research, Development and Innovation, Guayaquil, Guayas, Ecuador
| | | | - Jhannelle Francis
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Miguel Uyaguari
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Frempong SB, Salbreiter M, Mostafapour S, Pistiki A, Bocklitz TW, Rösch P, Popp J. Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms. Molecules 2024; 29:1077. [PMID: 38474589 DOI: 10.3390/molecules29051077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
Raman spectroscopy is an emerging method for the identification of bacteria. Nevertheless, a lot of different parameters need to be considered to establish a reliable database capable of identifying real-world samples such as medical or environmental probes. In this review, the establishment of such reliable databases with the proper design in microbiological Raman studies is demonstrated, shining a light into all the parts that require attention. Aspects such as the strain selection, sample preparation and isolation requirements, the phenotypic influence, measurement strategies, as well as the statistical approaches for discrimination of bacteria, are presented. Furthermore, the influence of these aspects on spectra quality, result accuracy, and read-out are discussed. The aim of this review is to serve as a guide for the design of microbiological Raman studies that can support the establishment of this method in different fields.
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Affiliation(s)
- Sandra Baaba Frempong
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Markus Salbreiter
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Sara Mostafapour
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Aikaterini Pistiki
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Thomas W Bocklitz
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
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Abu Lila AS, Alharby TN, Alanazi J, Alanazi M, Abdallah MH, Rizvi SMD, Moin A, Khafagy ES, Tabrez S, Al Balushi AA, Hegazy WAH. Clinical Resistant Strains of Enterococci and Their Correlation to Reduced Susceptibility to Biocides: Phenotypic and Genotypic Analysis of Macrolides, Lincosamides, and Streptogramins. Antibiotics (Basel) 2023; 12:antibiotics12030461. [PMID: 36978327 PMCID: PMC10044631 DOI: 10.3390/antibiotics12030461] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Enterococci are troublesome nosocomial, opportunistic Gram-positive cocci bacteria showing enhanced resistance to many commonly used antibiotics. This study aims to investigate the prevalence and genetic basis of antibiotic resistance to macrolides, lincosamides, and streptogramins (MLS) in Enterococci, as well as the correlation between MLS resistance and biocide resistance. From 913 clinical isolates collected from King Khalid Hospital, Hail, Saudi Arabia, 131 isolates were identified as Enterococci spp. The susceptibility of the clinical enterococcal isolates to several MLS antibiotics was determined, and the resistance phenotype was detected by the triple disk method. The MLS-involved resistance genes were screened in the resistant isolates. The current results showed high resistance rates to MLS antibiotics, and the constitutive resistance to all MLS (cMLS) was the most prevalent phenotype, observed in 76.8% of resistant isolates. By screening the MLS resistance-encoding genes in the resistant isolates, the erythromycin ribosome methylase (erm) genes that are responsible for methylation of bacterial 23S rRNA were the most detected genes, in particular, ermB. The ereA esterase-encoding gene was the most detected MLS modifying-encoding genes, more than lnuA (adenylation) and mphC (phosphorylation). The minimum inhibitory concentrations (MICs) of commonly used biocides were detected in resistant isolates and correlated with the MICs of MLS antibiotics. The present findings showed a significant correlation between MLS resistance and reduced susceptibility to biocides. In compliance with the high incidence of the efflux-encoding genes, especially mefA and mefE genes in the tolerant isolates with higher MICs to both MLS antibiotics and biocides, the efflux of resistant isolates was quantified, and there was a significant increase in the efflux of resistant isolates with higher MICs as compared to those with lower MICs. This could explain the crucial role of efflux in developing cross-resistance to both MLS antibiotics and biocides.
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Affiliation(s)
- Amr Selim Abu Lila
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha’il, Ha’il 81442, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
- Correspondence: (A.S.A.L.); (W.A.H.H.)
| | - Tareq Nafea Alharby
- Department of Clinical Pharmacy, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia
| | - Jowaher Alanazi
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia
| | - Muteb Alanazi
- Department of Clinical Pharmacy, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia
| | - Marwa H. Abdallah
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha’il, Ha’il 81442, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Syed Mohd Danish Rizvi
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha’il, Ha’il 81442, Saudi Arabia
| | - Afrasim Moin
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha’il, Ha’il 81442, Saudi Arabia
| | - El-Sayed Khafagy
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Shams Tabrez
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abdullah Ali Al Balushi
- Pharmacy Program, Department of Pharmaceutics, Oman College of Health Sciences, Muscat 113, Oman
| | - Wael A. H. Hegazy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
- Pharmacy Program, Department of Pharmaceutical Sciences, Oman College of Health Sciences, Muscat 113, Oman
- Correspondence: (A.S.A.L.); (W.A.H.H.)
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Kim SH, Chon JW, Jeong HW, Song KY, Kim DH, Bae D, Kim H, Seo KH. Identification and phylogenetic analysis of Enterococcus isolates using MALDI-TOF MS and VITEK 2. AMB Express 2023; 13:21. [PMID: 36813859 PMCID: PMC9947212 DOI: 10.1186/s13568-023-01525-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
The bacterial genus Enterococcus encompasses 38 species. Two of the most common species are E. faecalis and E. faecium. Recently, however, there has been an increase in clinical reports concerning less prevalent Enterococcus species, such as E. durans, E. hirae, and E. gallinarum. Rapid and accurate laboratory methods are needed to facilitate the identification of all these bacterial species. In the present study, we compared the relative accuracy of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS), VITEK 2, and 16S rRNA gene sequencing using 39 enterococci isolates from dairy samples, and compared the resultant phylogenetic trees. We found that MALDI-TOF MS correctly identified all isolates at the species level except for one, whereas the VITEK 2 system, which is an automated identification system using biochemical characteristics of species, misidentified ten isolates. However, phylogenetic trees constructed from both methods showed all isolates in similar positions. Our results clearly showed that MALDI-TOF MS is a reliable and rapid tool for identifying Enterococcus species with greater discriminatory power than the biochemical assay method of VITEK 2.
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Affiliation(s)
- Se-Hyung Kim
- grid.258676.80000 0004 0532 8339Center for One Health, Department of Veterinary Public Health, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029 Korea
| | - Jung-Whan Chon
- grid.258676.80000 0004 0532 8339Center for One Health, Department of Veterinary Public Health, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029 Korea
| | - Hyo-Won Jeong
- grid.484628.4 0000 0001 0943 2764Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyonggi-Do, 13818 Korea
| | - Kwang-Young Song
- grid.258676.80000 0004 0532 8339Center for One Health, Department of Veterinary Public Health, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029 Korea
| | - Dong-Hyeon Kim
- grid.258676.80000 0004 0532 8339Center for One Health, Department of Veterinary Public Health, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029 Korea
| | - Dongryeoul Bae
- grid.258676.80000 0004 0532 8339Center for One Health, Department of Veterinary Public Health, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029 Korea
| | - Hyunsook Kim
- grid.49606.3d0000 0001 1364 9317Department of Food and Nutrition, College of Human Ecology, Hanyang Univeristy, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763 Korea
| | - Kun-Ho Seo
- Center for One Health, Department of Veterinary Public Health, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Korea.
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Determination of Enterococcus faecalis and Enterococcus faecium Antimicrobial Resistance and Virulence Factors and Their Association with Clinical and Demographic Factors in Kenya. J Pathog 2022; 2022:3129439. [PMID: 36405031 PMCID: PMC9668473 DOI: 10.1155/2022/3129439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/12/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Background Enterococci are clinically significant because of their increasing antibiotic resistance and their ability to cause severe infections due to an arsenal of virulence genes. Few studies in the developing world have examined virulence factors that may significantly impact patient outcomes. This study describes the antimicrobial resistance profiles and prevalence of five key Enterococcal virulence genes gelE, asa, cylA, esp, and hyl in forty-four clinical Enterococcus faecalis and E. faecium isolates in Kenya and their association with patients' demographic and clinical characteristics. Results All E. faecium isolates were obtained from hospital-acquired skin and soft tissue infections. While E. faecalis was associated with community-acquired urinary tract infections. All isolates were resistant to erythromycin, whereas 11/44 (27.5%), 25/44 (56.8%), 28/44 (63.6%), 37/44 (84.1%), 40/44 (90.0%), and 43/44 (97.5%) were susceptible to tetracycline, levofloxacin, gentamicin, ampicillin, nitrofurantoin, and teicoplanin, respectively. All isolates were susceptible to tigecycline, vancomycin, and linezolid. There was little difference in the antibiotic resistance profiles between E. faecalis and E. faecium. The prevalence of the virulence genes among the 44 isolates were 27 (61.4%) for gelE, 26 (59.1%) for asa1, 16 (36.3%) for esp, 11 (25.0%) for cylA, and 1 (2.3%) for hyl. 72.9% of E. faecalis isolates had multiple virulence genes compared to 57% of E. faecium isolates with no virulence genes. The hyl gene was only detected in E. faecium, while cylA and asa1 were only detected in E. faecalis. A significant correlation was observed between the presence of asa1 and esp virulence genes and tetracycline resistance (P=0.0305 and 0.0363, respectively). A significant correlation was also observed between the presence of virulence genes gelE and asa1 and nitrofurantoin resistance (P=0.0175 and 0.0225, respectively) and ampicillin resistance (P=0.0005 and 0.0008, respectively). Conclusion The study highlights the high levels of erythromycin resistance in E. faecalis and E. faecium, the demographic factors influencing the species distribution among patients, and the accumulation of multiple virulence genes in E. faecalis. The significant association of gelE, asa1, and esp virulence genes with drug resistance could explain the pathogenic success of E. faecalis and provides a guide for future studies.
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An Overview of Healthcare Associated Infections and Their Detection Methods Caused by Pathogen Bacteria in Romania and Europe. J Clin Med 2022; 11:jcm11113204. [PMID: 35683591 PMCID: PMC9181229 DOI: 10.3390/jcm11113204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/25/2022] [Accepted: 06/01/2022] [Indexed: 11/16/2022] Open
Abstract
Healthcare-associated infections can occur in different care units and can affect both patients and healthcare professionals. Bacteria represent the most common cause of nosocomial infections and, due to the excessive and irrational use of antibiotics, resistant organisms have appeared. The most important healthcare-associated infections are central line-associated bloodstream infections, catheter-associated urinary tract infections, surgical site, soft tissue infections, ventilator-associated pneumonia, hospital acquired pneumonia, and Clostridioides difficile colitis. In Europe, some hospitalized patients develop nosocomial infections that lead to increased costs and prolonged hospitalizations. Healthcare-associated infection prevalence in developed countries is lower than in low-income and middle-income countries such as Romania, an Eastern European country, where several factors contribute to the occurrence of many nosocomial infections, but official data show a low reporting rate. For the rapid identification of bacteria that can cause these infections, fast, sensitive, and specific methods are needed, and they should be cost-effective. Therefore, this review focuses on the current situation regarding healthcare-associated infections in Europe and Romania, with discussions regarding the causes and possible solutions. As a possible weapon in the fight against the healthcare-associated infections, the diagnosis methods and tests used to determine the bacteria involved in healthcare-associated infections are evaluated.
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Ren ZQ, Hong HF, Li GF, Du XN, Zhang LG, Huang BC, Fan NS, Jin RC. A review on characterizing the metabolite property of anammox sludge by spectroscopy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:153065. [PMID: 35031359 DOI: 10.1016/j.scitotenv.2022.153065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/07/2022] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
As one of the most promising autotrophic biological nitrogen removal technology, anaerobic ammonia oxidation (anammox) has gained intense attention for the past decades and several full-scale facilities have been implemented worldwide. However, anammox bacteria are easily affected by disturbed external environmental factors, which commonly leads to the fluctuations in reactor performance. The response of anammox sludge to external stress results in changes in components and structural characteristics of intracellular and extracellular polymer substances. Real-time and convenient spectral analysis of anammox sludge metabolites can give early warning of performance deterioration under external stresses, which is of great significance to the stable operation of bioreactor. This review summarized the research progress on characterizing the intracellular and extracellular metabolites of anammox sludge through spectroscopic techniques. The correlation between anammox sludge activity and its key metabolites was analyzed. Also, the limitations and future prospects of applying spectral analytical techniques for anammox bioreactor monitoring were discussed and outlooked. This review may provide valuable information for both scientific study and engineering application of anammox based nitrogen removal technology.
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Affiliation(s)
- Zhi-Qi Ren
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - He-Fang Hong
- Taizhou Municipal Ecology and Environment Bureau Linhai Branch, Taizhou 317000, China
| | - Gui-Feng Li
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xue-Ning Du
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Li-Ge Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Bao-Cheng Huang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Nian-Si Fan
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ren-Cun Jin
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
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Kashif M, Majeed MI, Nawaz H, Rashid N, Abubakar M, Ahmad S, Ali S, Hyat H, Bashir S, Batool F, Akbar S, Anwar MA. Surface-enhanced Raman spectroscopy for identification of food processing bacteria. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 261:119989. [PMID: 34087771 DOI: 10.1016/j.saa.2021.119989] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
Food processing bacteria play important role in providing flavors, ingredients and other beneficial characteristics to the food but at the same time some bacteria are responsible for food spoilage. Therefore, quick and reliable identification of these food processing bacteria is very necessary for the differentiation between different species which may help in the development of more useful food processing methodologies. In this study, analysis of different bacterial species (Lactobacillus fermentum, Fructobacillus fructosus, Pediococcus pentosaceus and Halalkalicoccus jeotgali) was performed with our in-house developed Ag NPs-based surface-enhanced Raman spectroscopy (SERS) method. The SERS spectral data was analyzed by multivariate data analysis techniques including principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA). Bacterial species were differentiated on the basis of SERS spectral features and potential of SERS was compared with the Raman spectroscopy (RS). SERS along with PCA and PLS-DA was found to be an efficient technique for identification and differentiation of food processing bacterial species. Differentiation with accuracy of 99.5% and sensitivity of 99.7% was depicted by PLS-DA model using leave one out cross validation.
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Affiliation(s)
- Muhammad Kashif
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | | | - Haq Nawaz
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan.
| | - Nosheen Rashid
- Department of Physics, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Abubakar
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Shamsheer Ahmad
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Saqib Ali
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Hamza Hyat
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Saba Bashir
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Fatima Batool
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Saba Akbar
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Munir Ahmad Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
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10
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Dat TTH, Steinert G, Cuc NTK, Smidt H, Sipkema D. Bacteria Cultivated From Sponges and Bacteria Not Yet Cultivated From Sponges-A Review. Front Microbiol 2021; 12:737925. [PMID: 34867854 PMCID: PMC8634882 DOI: 10.3389/fmicb.2021.737925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022] Open
Abstract
The application of high-throughput microbial community profiling as well as "omics" approaches unveiled high diversity and host-specificity of bacteria associated with marine sponges, which are renowned for their wide range of bioactive natural products. However, exploration and exploitation of bioactive compounds from sponge-associated bacteria have been limited because the majority of the bacteria remains recalcitrant to cultivation. In this review, we (i) discuss recent/novel cultivation techniques that have been used to isolate sponge-associated bacteria, (ii) provide an overview of bacteria isolated from sponges until 2017 and the associated culture conditions and identify the bacteria not yet cultured from sponges, and (iii) outline promising cultivation strategies for cultivating the uncultivated majority of bacteria from sponges in the future. Despite intensive cultivation attempts, the diversity of bacteria obtained through cultivation remains much lower than that seen through cultivation-independent methods, which is particularly noticeable for those taxa that were previously marked as "sponge-specific" and "sponge-enriched." This poses an urgent need for more efficient cultivation methods. Refining cultivation media and conditions based on information obtained from metagenomic datasets and cultivation under simulated natural conditions are the most promising strategies to isolate the most wanted sponge-associated bacteria.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Nguyen Thi Kim Cuc
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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11
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Locke A, Fitzgerald S, Mahadevan-Jansen A. Advances in Optical Detection of Human-Associated Pathogenic Bacteria. Molecules 2020; 25:E5256. [PMID: 33187331 PMCID: PMC7696695 DOI: 10.3390/molecules25225256] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial infection is a global burden that results in numerous hospital visits and deaths annually. The rise of multi-drug resistant bacteria has dramatically increased this burden. Therefore, there is a clinical need to detect and identify bacteria rapidly and accurately in their native state or a culture-free environment. Current diagnostic techniques lack speed and effectiveness in detecting bacteria that are culture-negative, as well as options for in vivo detection. The optical detection of bacteria offers the potential to overcome these obstacles by providing various platforms that can detect bacteria rapidly, with minimum sample preparation, and, in some cases, culture-free directly from patient fluids or even in vivo. These modalities include infrared, Raman, and fluorescence spectroscopy, along with optical coherence tomography, interference, polarization, and laser speckle. However, these techniques are not without their own set of limitations. This review summarizes the strengths and weaknesses of utilizing each of these optical tools for rapid bacteria detection and identification.
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Affiliation(s)
- Andrea Locke
- Vanderbilt Biophotonics Center, Nashville, TN 37232, USA; (A.L.); (S.F.)
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Sean Fitzgerald
- Vanderbilt Biophotonics Center, Nashville, TN 37232, USA; (A.L.); (S.F.)
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Anita Mahadevan-Jansen
- Vanderbilt Biophotonics Center, Nashville, TN 37232, USA; (A.L.); (S.F.)
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
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12
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Kepenek ES, Severcan M, Gozen AG, Severcan F. Discrimination of heavy metal acclimated environmental strains by chemometric analysis of FTIR spectra. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 202:110953. [PMID: 32800227 DOI: 10.1016/j.ecoenv.2020.110953] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Heavy metal acclimated bacteria are profoundly the preferred choice for bioremediation studies. Bacteria get acclimated to toxic concentrations of heavy metals by induction of specific enzymes and genetic selection favoring new metabolic abilities leading to activation of one or several of resistance mechanisms creating bacterial populations with differences in resistance profile and/or level. Therefore, to use in bioremediation processes, it is important to discriminate acclimated bacterial populations and choose a more resistant strain. In this study, we discriminated heavy metal acclimated bacteria by using Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy and multivariate analysis methods namely Hierarchical Cluster Analysis (HCA), Principal Component Analysis (PCA) and Soft Independent Modeling of Class Analogy (SIMCA). Two acclimation methods, acute and gradual, were used which cause differences in molecular changes resulting in bacterial populations with different molecular and resistance profiles. Brevundimonas sp., Gordonia sp., and Microbacterium oxydans were exposed to the toxic concentrations of Cd (30 μg/ml) or Pb (90 μg/ml) by using broth medium as a growth media. Our results revealed that PCA and HCA clearly discriminated the acute-acclimated, gradual-acclimated, and control bacteria from each other in protein, carbohydrate, and whole spectral regions. Furthermore, we classified acclimated (acute and gradual) and control bacteria more accurately by using SIMCA with 99.9% confidence. This study demonstrated that heavy metal acclimated and control group bacteria can be discriminated by using chemometric analysis of FTIR spectra in a powerful, cost-effective, and handy way. In addition to the determination of the most appropriate acclimation procedure, this approach can be used in the detection of the most resistant bacterial strains to be used in bioremediation studies.
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Affiliation(s)
- Eda Seyma Kepenek
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Mete Severcan
- Department of Electrical and Electronics Engineering, School of Engineering and Natural Sciences, Altinbas University, Istanbul, Turkey.
| | - Ayse Gul Gozen
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey; Department of Biophysics, Faculty of Medicine, Altinbas University, Istanbul, Turkey
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DeSalle R, Riley M. Should Networks Supplant Tree Building? Microorganisms 2020; 8:E1179. [PMID: 32756444 PMCID: PMC7466111 DOI: 10.3390/microorganisms8081179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/21/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022] Open
Abstract
Recent studies suggested that network methods should supplant tree building as the basis of genealogical analysis. This proposition is based upon two arguments. First is the observation that bacterial and archaeal lineages experience processes oppositional to bifurcation and hence the representation of the evolutionary process in a tree like structure is illogical. Second is the argument tree building approaches are circular-you ask for a tree and you get one, which pins a verificationist label on tree building that, if correct, should be the end of phylogenetic analysis as we currently know it. In this review, we examine these questions and suggest that rumors of the death of the bacterial tree of life are exaggerated at best.
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Affiliation(s)
- Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA;
| | - Margaret Riley
- Department of Biology, University of Massachusetts Amherst, 116 North Pleasant Street, Amherst, MA 01003, USA
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Biochemical characterization of pathogenic bacterial species using Raman spectroscopy and discrimination model based on selected spectral features. Lasers Med Sci 2020; 36:289-302. [PMID: 32500291 DOI: 10.1007/s10103-020-03028-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/22/2020] [Indexed: 01/09/2023]
Abstract
This study aimed to evaluate the differences in the Raman spectra of nine clinical species of bacteria isolated from infections (three Gram-positive and six Gram-negative species), correlating the spectra with the chemical composition of each species and to develop a classification model through discriminant analysis to categorize each bacterial strain using the peaks with the most significant differences. Bacteria were cultured in Mueller Hinton agar and a sample of biomass was harvested and placed in an aluminum sample holder. A total of 475 spectra from 115 different strains were obtained through a dispersive Raman spectrometer (830 nm) with exposure time of 50 s. The intensities of the peaks were evaluated by one-way analysis of variance (ANOVA) and the peaks with significant differences were related to the differences in the biochemical composition of the strains. Discriminant analysis based on quadratic distance applied to the peaks with the most significant differences and partial least squares applied to the whole spectrum showed 89.5% and 90.1% of global accuracy, respectively, for classification of the spectra in all the groups. Raman spectroscopy could be a promising technique to identify spectral differences related to the biochemical content of pathogenic microorganisms and to provide a faster diagnosis of infectious diseases.
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15
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Evaluation of the impact of buffered peptone water composition on the discrimination between Salmonella enterica and Escherichia coli by Raman spectroscopy. Anal Bioanal Chem 2020; 412:3595-3604. [PMID: 32248395 DOI: 10.1007/s00216-020-02596-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/19/2020] [Accepted: 03/11/2020] [Indexed: 10/24/2022]
Abstract
The detection of Salmonella spp. in food samples is regulated by the ISO 6579:2002 standard, which requires that precise procedures are followed to ensure the reliability of the detection process. This standard requires buffered peptone water as a rich medium for the enrichment of bacteria. However, the effects of different brands of buffered peptone water on the identification of microorganisms by Raman spectroscopy are unknown. In this regard, our study evaluated the discrimination between two bacterial species, Salmonella enterica and Escherichia coli, inoculated and analyzed with six of the most commonly used buffered peptone water brands. The results showed that bacterial cells behaved differently according to the brand used in terms of biomass production and the spectral fingerprint. The identification accuracy of the analyzed strains was between 85% and 100% depending on the given brand. Several batches of two brands were studied to evaluate the classification rates between the analyzed bacterial species. The chemical analysis performed on these brands showed that the nutrient content was slightly different and probably explained the observed effects. On the basis of these results, Raman spectroscopy operators are encouraged to select an adequate culture medium and continue its use throughout the identification process to guarantee optimal recognition of the microorganism of interest.
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16
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Tanniche I, Collakova E, Denbow C, Senger RS. Characterizing metabolic stress-induced phenotypes of Synechocystis PCC6803 with Raman spectroscopy. PeerJ 2020; 8:e8535. [PMID: 32266110 PMCID: PMC7115747 DOI: 10.7717/peerj.8535] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 01/08/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND During their long evolution, Synechocystis sp. PCC6803 developed a remarkable capacity to acclimate to diverse environmental conditions. In this study, Raman spectroscopy and Raman chemometrics tools (RametrixTM) were employed to investigate the phenotypic changes in response to external stressors and correlate specific Raman bands with their corresponding biomolecules determined with widely used analytical methods. METHODS Synechocystis cells were grown in the presence of (i) acetate (7.5-30 mM), (ii) NaCl (50-150 mM) and (iii) limiting levels of MgSO4 (0-62.5 mM) in BG-11 media. Principal component analysis (PCA) and discriminant analysis of PCs (DAPC) were performed with the RametrixTM LITE Toolbox for MATLABⓇ. Next, validation of these models was realized via RametrixTM PRO Toolbox where prediction of accuracy, sensitivity, and specificity for an unknown Raman spectrum was calculated. These analyses were coupled with statistical tests (ANOVA and pairwise comparison) to determine statistically significant changes in the phenotypic responses. Finally, amino acid and fatty acid levels were measured with well-established analytical methods. The obtained data were correlated with previously established Raman bands assigned to these biomolecules. RESULTS Distinguishable clusters representative of phenotypic responses were observed based on the external stimuli (i.e., acetate, NaCl, MgSO4, and controls grown on BG-11 medium) or its concentration when analyzing separately. For all these cases, RametrixTM PRO was able to predict efficiently the corresponding concentration in the culture media for an unknown Raman spectra with accuracy, sensitivity and specificity exceeding random chance. Finally, correlations (R > 0.7) were observed for all amino acids and fatty acids between well-established analytical methods and Raman bands.
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Affiliation(s)
- Imen Tanniche
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Eva Collakova
- School of Plant & Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Cynthia Denbow
- School of Plant & Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Ryan S. Senger
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
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17
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18
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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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Abstract
Abstract
A potential role of optical technologies in medicine including micro-Raman spectroscopy is diagnosis of bacteria, cells and tissues which is covered in this chapter. The main advantage of Raman-based methods to complement and augment diagnostic tools is that unsurpassed molecular specificity is achieved without labels and in a nondestructive way. Principles and applications of micro-Raman spectroscopy in the context of medicine will be described. First, Raman spectra of biomolecules representing proteins, nucleic acids, lipids and carbohydrates are introduced. Second, microbial applications are summarized with the focus on typing on species and strain level, detection of infections, antibiotic resistance and biofilms. Third, cytological applications are presented to classify single cells and study cell metabolism and drug–cell interaction. Fourth, applications to tissue characterization start with discussion of lateral resolution for Raman imaging followed by Raman-based detection of pathologies and combination with other modalities. Finally, an outlook is given to translate micro-Raman spectroscopy as a clinical tool to solve unmet needs in point-of-care applications and personalized treatment of diseases.
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20
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Sanderson H, Ortega-Polo R, McDermott K, Zaheer R, Brown RS, Majury A, McAllister T, Liss SN. Comparison of biochemical and genotypic speciation methods for vancomycin-resistant enterococci isolated from urban wastewater treatment plants. J Microbiol Methods 2019; 161:102-110. [PMID: 31071353 DOI: 10.1016/j.mimet.2019.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 11/24/2022]
Abstract
Enterococci species in wastewater including Enterococcus faecalis, Enterococcus faecium, Enterococcus casseliflavus and Enterococcus gallinarum isolates (n = 308) with low or high level vancomycin resistance were determined and compared using a phenotypic method (RapID™ STR system), 16S rRNA sequencing, and multi-locus (atpA, groESL, and pheS) sequence analysis (MLSA). Error rates for the RapID™ STR system were E. faecalis (15.9%), E. faecium (21.5%), and E. casseliflavus/E. gallinarum (56.9%) when referenced to the consensus of all methods tested. Comparison of single nucleotide polymorphism (SNP) distances and phylogenetic trees suggested that the groESL locus delineated species more effectively than other loci. The groESL locus was the most reliable loci for the correct identification of Enterococcus spp., including E. casseliflavus and E. gallinarum, with high congruence compared to the consensus (Adjusted Rand Index = 0.954; Adjusted Wallace Co-efficient = 0.941). All of the methods were compared to whole genome sequencing, which acted as a gold standard, for the isolates from this study and those downloaded from NCBI.
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Affiliation(s)
- Haley Sanderson
- School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada; Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta T1J 4P4, Canada
| | - Rodrigo Ortega-Polo
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta T1J 4P4, Canada; Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 6T5, Canada
| | | | - Rahat Zaheer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta T1J 4P4, Canada
| | - R Stephen Brown
- School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada; Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Anna Majury
- School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada; Public Health Ontario, Kingston, Ontario K7L 3K3, Canada
| | - Tim McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta T1J 4P4, Canada.
| | - Steven N Liss
- School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada; Department of Biology, Ryerson University, Toronto, Ontario M5B 2K3, Canada.
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21
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Comparison of Standard and Impedance Methods for the Detection of Enterococci Contamination in Medicinal Herbs in Iran. Jundishapur J Nat Pharm Prod 2018. [DOI: 10.5812/jjnpp.64341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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22
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Leal L, Nogueira M, Canevari R, Carvalho L. Vibration spectroscopy and body biofluids: Literature review for clinical applications. Photodiagnosis Photodyn Ther 2018; 24:237-244. [DOI: 10.1016/j.pdpdt.2018.09.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 09/03/2018] [Accepted: 09/17/2018] [Indexed: 12/19/2022]
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Han Y, Jian L, Yao Y, Wang X, Han L, Liu X. Insight into Rapid DNA-Specific Identification of Animal Origin Based on FTIR Analysis: A Case Study. Molecules 2018; 23:molecules23112842. [PMID: 30388819 PMCID: PMC6278494 DOI: 10.3390/molecules23112842] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 11/29/2022] Open
Abstract
In this study, a methodology has been proposed to identify the origin of animal DNA, employing high throughput extension accessory Fourier transform infrared (HT-FTIR) spectroscopy coupled with chemometrics. Important discriminatory characteristics were identified in the FTIR spectral peaks of 51 standard DNA samples (25 from bovine and 26 from fish origins), including 1710, 1659, 1608, 1531, 1404, 1375, 1248, 1091, 1060, and 966 cm−1. In particular, the bands at 1708 and 1668 cm−1 were higher in fish DNA than in bovine DNA, while the reverse was true for the band at 1530 cm−1 was shown the opposite result. It was also found that the PO2− Vas/Vs ratio (1238/1094 cm−1) was significantly higher (p < 0.05) in bovine DNA than in fish DNA. These discriminatory characteristics were further revealed to be closely related to the base content and base sequences of different samples. Multivariate analyses, such as principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) were conducted, and both the sensitivity and specificity values of PLS-DA model were one. This methodology has been further validated by 20 meat tissue samples (4 from bovine, 5 from ovine, 5 from porcine, and 6 from fish origins), and these were successfully differentiated. This case study demonstrated that FTIR spectroscopy coupled with PLS-DA discriminant model could provide a rapid, sensitive, and reliable approach for the identification of DNA of animal origin. This methodology could be widely applied in food, feed, forensic science, and archaeology studies.
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Affiliation(s)
- Yahong Han
- College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Lin Jian
- College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Yumei Yao
- College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Xinlei Wang
- College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Lujia Han
- College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Xian Liu
- College of Engineering, China Agricultural University, Beijing 100083, China.
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Muhamadali H, Subaihi A, Mohammadtaheri M, Xu Y, Ellis DI, Ramanathan R, Bansal V, Goodacre R. Rapid, accurate, and comparative differentiation of clinically and industrially relevant microorganisms via multiple vibrational spectroscopic fingerprinting. Analyst 2018; 141:5127-36. [PMID: 27414261 DOI: 10.1039/c6an00883f] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Despite the fact that various microorganisms (e.g., bacteria, fungi, viruses, etc.) have been linked with infectious diseases, their crucial role towards sustaining life on Earth is undeniable. The huge biodiversity, combined with the wide range of biochemical capabilities of these organisms, have always been the driving force behind their large number of current, and, as of yet, undiscovered future applications. The presence of such diversity could be said to expedite the need for the development of rapid, accurate and sensitive techniques which allow for the detection, differentiation, identification and classification of such organisms. In this study, we employed Fourier transform infrared (FT-IR), Raman, and surface enhanced Raman scattering (SERS) spectroscopies, as molecular whole-organism fingerprinting techniques, combined with multivariate statistical analysis approaches for the classification of a range of industrial, environmental or clinically relevant bacteria (P. aeruginosa, P. putida, E. coli, E. faecium, S. lividans, B. subtilis, B. cereus) and yeast (S. cerevisiae). Principal components-discriminant function analysis (PC-DFA) scores plots of the spectral data collected from all three techniques allowed for the clear differentiation of all the samples down to sub-species level. The partial least squares-discriminant analysis (PLS-DA) models generated using the SERS spectral data displayed lower accuracy (74.9%) when compared to those obtained from conventional Raman (97.8%) and FT-IR (96.2%) analyses. In addition, whilst background fluorescence was detected in Raman spectra for S. cerevisiae, this fluorescence was quenched when applying SERS to the same species, and conversely SERS appeared to introduce strong fluorescence when analysing P. putida. It is also worth noting that FT-IR analysis provided spectral data of high quality and reproducibility for the whole sample set, suggesting its applicability to a wider range of samples, and perhaps the most suitable for the analysis of mixed cultures in future studies. Furthermore, our results suggest that while each of these spectroscopic approaches may favour different organisms (sample types), when combined, they would provide complementary and more in-depth knowledge (structural and/or metabolic state) of biological systems. To the best of our knowledge, this is the first time that such a comparative and combined spectroscopic study (using FT-IR, Raman and SERS) has been carried out on microbial samples.
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Affiliation(s)
- Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Abdu Subaihi
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Mahsa Mohammadtaheri
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, Australia
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - David I Ellis
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Rajesh Ramanathan
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, Australia
| | - Vipul Bansal
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, Australia
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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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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Pudlas M, Koch S, Bolwien C, Walles H. Raman Spectroscopy as a Tool for Quality and Sterility Analysis for Tissue Engineering Applications like Cartilage Transplants. Int J Artif Organs 2018. [DOI: 10.1177/039139881003300407] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
At present, the production of tissue engineered cartilage requires the concurrent production of two identical transplants. One transplant is used for destructive quality control and the second one is implanted into the patient. A non-invasive characterization of such tissue engineering samples would be a promising tool to achieve a production process of just one transplant that is both implanted and tested. Raman spectroscopy is a method that satisfies this requirement by analyzing cells without lysis, fixation or the use of any chemicals. This pure optical technique is based on inelastic scattering of laser photons by molecular vibrations of biopolymers. Characteristic peaks in Raman spectra of cells could be assigned to typical biochemical molecules present in biological samples. For the analysis of chondrocytes present in cartilage transplants, the determination of the cell vitality as well as the discrimination of another cell type have been studied by Raman spectroscopy. Another bottleneck in such biological processes under GMP conditions is sterility control, as most of the commonly used methods require long cultivation times. Raman spectroscopy provides a good alternative to conventional methods in terms of time saving. In this study, the potential of Raman spectroscopy as a quality and sterility control tool for tissue engineering applications was studied by analyzing and comparing the spectra of cell and bacteria cultures.
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Affiliation(s)
- Marieke Pudlas
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart - Germany
- University of Stuttgart, Medical Interfacial Engineering, Stuttgart - Germany
| | - Steffen Koch
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart - Germany
- University of Stuttgart, Medical Interfacial Engineering, Stuttgart - Germany
| | - Carsten Bolwien
- Fraunhofer Institute for Physical Measurement Techniques, Freiburg - Germany
| | - Heike Walles
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart - Germany
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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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Understanding the antimicrobial activity of selected disinfectants against methicillin-resistant Staphylococcus aureus (MRSA). PLoS One 2017; 12:e0186375. [PMID: 29036196 PMCID: PMC5643108 DOI: 10.1371/journal.pone.0186375] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/30/2017] [Indexed: 01/09/2023] Open
Abstract
Disinfectants and biocidal products have been widely used to combat Methicillin-resistant Staphylococcus aureus (MRSA) infections in homes and healthcare environments. Although disruption of cytoplasmic membrane integrity has been documented as the main bactericidal effect of biocides, little is known about the biochemical alterations induced by these chemical agents. In this study, we used Fourier transform infrared (FT-IR) spectroscopy and chemometric tools as an alternative non-destructive technique to determine the bactericidal effects of commonly used disinfectants against MRSA USA-300. FTIR spectroscopy permits a detailed characterization of bacterial reactivity, allowing an understanding of the fundamental mechanism of action involved in the interaction between bacteria and disinfectants. The disinfectants studied were ethanol 70% (N = 5), isopropanol (N = 5), sodium hypochlorite (N = 5), triclosan (N = 5) and triclocarban (N = 5). Results showed less than 5% colony forming units growth of MRSA treated with triclocarban and no growth in the other groups. Nearly 70,000 mid-infrared spectra from the five treatments and the two control (untreated; N = 4) groups of MRSA (bacteria grown in TSB and incubated at 37°C (Control I) / at ambient temperature (Control II), for 24h) were pre-processed and analyzed using principal component analysis followed by linear discriminant analysis (PCA-LDA). Clustering of strains of MRSA belonging to five treatments and the discrimination between each treatment and two control groups in MRSA (untreated) were investigated. PCA-LDA discriminatory frequencies suggested that ethanol-treated spectra are the most similar to isopropanol-treated spectra biochemically. Also reported here are the biochemical alterations in the structure of proteins, lipid membranes, and phosphate groups of MRSA produced by sodium hypochlorite, triclosan, and triclocarban treatments. These findings provide mechanistic information involved in the interaction between MRSA strains and hygiene products; thereby demonstrating the potential of spectroscopic analysis as an objective, robust, and label-free tool for evaluating the macromolecular changes involved in disinfectant-treated MRSA.
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Jaureguiberry M, Madoz LV, Giuliodori MJ, Wagener K, Prunner I, Grunert T, Ehling-Schulz M, Drillich M, de la Sota RL. Identification of Escherichia coli and Trueperella pyogenes isolated from the uterus of dairy cows using routine bacteriological testing and Fourier transform infrared spectroscopy. Acta Vet Scand 2016; 58:81. [PMID: 27894322 PMCID: PMC5126838 DOI: 10.1186/s13028-016-0262-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 11/09/2016] [Indexed: 11/11/2022] Open
Abstract
Background Uterine disorders are common postpartum diseases in dairy cows. In practice, uterine treatment is often based on systemic or locally applied antimicrobials with no previous identification of pathogens. Accurate on-farm diagnostics are not available, and routine testing is time-consuming and cost intensive. An accurate method that could simplify the identification of uterine pathogenic bacteria and improve pathogen-specific treatments could be an important advance to practitioners. The objective of the present study was to evaluate whether a database built with uterine bacteria from European dairy cows could be used to identify bacteria from Argentinean cows by Fourier transformed infrared (FTIR) spectroscopy. Uterine samples from 64 multiparous dairy cows with different types of vaginal discharge (VD) were collected between 5 and 60 days postpartum, analyzed by routine bacteriological testing methods and then re-evaluated by FTIR spectroscopy (n = 27). Results FTIR spectroscopy identified Escherichia coli in 12 out of 14 samples and Trueperella pyogenes in 8 out of 10 samples. The agreement between the two methods was good with a Kappa coefficient of 0.73. In addition, the likelihood for bacterial growth of common uterine pathogens such as E. coli and T. pyogenes tended to increase with VD score. The odds for a positive result to E. coli or T. pyogenes was 1.88 times higher in cows with fetid VD than in herdmates with clear normal VD. Conclusions We conclude that the presence of E. coli and T. pyogenes in uterine samples from Argentinean dairy cows can be detected with FTIR with the use of a database built with uterine bacteria from European dairy cows. Future studies are needed to determine if FTIR can be used as an alternative to routine bacteriological testing methods.
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Vibrational spectroscopies to investigate concretions and ectopic calcifications for medical diagnosis. CR CHIM 2016. [DOI: 10.1016/j.crci.2016.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Komiyama EY, Lepesqueur LSS, Yassuda CG, Samaranayake LP, Parahitiyawa NB, Balducci I, Koga-Ito CY. Enterococcus Species in the Oral Cavity: Prevalence, Virulence Factors and Antimicrobial Susceptibility. PLoS One 2016; 11:e0163001. [PMID: 27631785 PMCID: PMC5025163 DOI: 10.1371/journal.pone.0163001] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/01/2016] [Indexed: 11/18/2022] Open
Abstract
Enterococci are considered as transient constituent components of the oral microbiome that may cause a variety of oral and systemic infections. As there is sparse data on the oral enterococcal prevalence, we evaluated the Enterococcus spp. and their virulence attributes including antimicrobial resistance in a healthy Brazilian cohort. A total of 240 individuals in different age groups were studied (children 4–11 yrs, adolescents 12–17 yrs, young adults 18–29 yrs, adults 30–59 yrs, elderly over 60 yrs). Oral rinses were collected and isolates were identified by API 20 Strep and confirmed by 16S rDNA sequencing. E. faecalis isolates, in particular, were evaluated for virulence attributes such as their biofilm formation potential, and susceptibility to antimicrobials and an antiseptic, chlorhexidine gluconate. A total of 40 individuals (16.6%) and 10% children, 4% adolescents, 14% young adults, 30% adults, and 25% elderly carried oral enterococci. The oral enterococcal burden in adolescents was significantly lower than in the adults (p = 0.000) and elderly (p = 0.004). The proportion of carriers was higher among females (p = 0.001). E. faecalis was the most frequent isolate in all the age groups (p = 0.000), followed by E. durans and E. faecium. Whilst all the clinical isolates were able to form biofilms, only a proportion of them were able to produce lipase (92%), hemolysin (38%), and gelatinase (39%). Of all the isolates 53.8% were resistant to tetracycline, 12.3% to amoxicillin, 16.0% to ampicillin, 20.8% to chloramphenicol and 43.4% to erythromycin. None of the isolates were resistant to vancomycin. Our data suggest that in this Brazilian cohort the oral cavity may act as a significant reservoir of rather virulent and antibiotic resistant enterococci, with an increasing degree of carriage in the adults and elderly. Hence clinicians should be cognizant of this silent reservoir of virulent enterococci that may pose a particular threat of nosocomial infection.
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Affiliation(s)
- Edson Yukio Komiyama
- Department of Oral Biosciences and Diagnosis, Oral Biopathology Graduate Program, Institute of Science and Technology, Universidade Estadual Paulista/UNESP, São José dos Campos, São Paulo, Brazil
| | - Laura Soares Souto Lepesqueur
- Department of Oral Biosciences and Diagnosis, Oral Biopathology Graduate Program, Institute of Science and Technology, Universidade Estadual Paulista/UNESP, São José dos Campos, São Paulo, Brazil
| | - Cinthia Gomes Yassuda
- Department of Oral Biosciences and Diagnosis, Oral Biopathology Graduate Program, Institute of Science and Technology, Universidade Estadual Paulista/UNESP, São José dos Campos, São Paulo, Brazil
| | - Lakshman P. Samaranayake
- UQ Oral Health Centre, School of Dentistry, The University of Queensland, Brisbane, Queensland, Australia
| | - Nipuna B. Parahitiyawa
- Department of Oral Bio-Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, SAR, China
| | - Ivan Balducci
- Department of Social Dentistry, Institute of Science and Technology, Universidade Estadual Paulista/UNESP, São José dos Campos, São Paulo, Brazil
| | - Cristiane Yumi Koga-Ito
- Department of Oral Biosciences and Diagnosis, Oral Biopathology Graduate Program, Institute of Science and Technology, Universidade Estadual Paulista/UNESP, São José dos Campos, São Paulo, Brazil
- Department of Environmental Engineering, Institute of Science and Technology, Universidade Estadual Paulista/UNESP, São José dos Campos, São Paulo, Brazil
- * E-mail:
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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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Le Corvec M, Charpentier F, Kachenoura A, Bensaid S, Henno S, Bardou-Jacquet E, Turlin B, Monbet V, Senhadji L, Loréal O, Sire O, Betagne J, Tariel H, Lainé F. Fast and Non-Invasive Medical Diagnostic Using Mid Infrared Sensor. Ing Rech Biomed 2016. [DOI: 10.1016/j.irbm.2016.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Ferguson DM, Weisberg SB, Hagedorn C, De Leon K, Mofidi V, Wolfe J, Zimmerman M, Jay JA. Enterococcus growth on eelgrass (Zostera marina); implications for water quality. FEMS Microbiol Ecol 2016; 92:fiw047. [PMID: 26976844 DOI: 10.1093/femsec/fiw047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2016] [Indexed: 11/13/2022] Open
Abstract
Enterococci are fecal indicator bacteria used to monitor fecal pollution of recreational waters. When enterococci levels exceed health standards, fecal pollution is assumed as the cause. Enterococci growing on plants limit their usefulness as fecal indicator bacteria. Here we examined enterococcal growth on eelgrass in Mission Bay, CA where enterococci levels have exceeded water quality thresholds. A total of 69 eelgrass samples were collected from six sites, shaken to remove enterococci attached to plant surfaces and the eluant filtered onto culture media. Isolates were then identified to species using biochemical methods, and DNA typing by pulsed-field gel electrophoresis was done to assess clonality of strains. Enterococci concentrations among eelgrass ranged from 8 to 14 000 CFU g(-1) dry weight. The most predominant enterococcal species found were Enterococcus casseliflavus and E. hirae followed by E. faecalis. Cluster analysis indicated a high level of clonality among isolates across all species, with clonal isolates consistently associated with individual eelgrass samples. Finding high densities of E. casseliflavus, E. hirae and E. faecalis on eelgrass that included clonal strains indicates the capability of enterococcal growth on eelgrass. Amplification of enterococci on eelgrass presents challenges for regulatory agencies that interpret elevated levels of these bacteria as an indication of fecal pollution.
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Affiliation(s)
- Donna M Ferguson
- Environmental Health Sciences Department, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Stephen B Weisberg
- Southern California Coastal Water Research Project, Suite 110, 3535 Harbor Blvd., Costa Mesa, CA 92626, USA
| | - Charles Hagedorn
- Department of Crop and Soil Environmental Sciences, Virginia Tech, RB 1880, Suite 1129, Blacksburg, VA 24061, USA
| | - Kristine De Leon
- Department of Biology, California State University Long Beach, 1250 Bellflower Blvd., Long Beach, CA 90840, USA
| | - Vida Mofidi
- Orange County Public Health Laboratory, 1729 W. 17th St., Santa Ana, CA 92706, USA
| | - Julia Wolfe
- Orange County Public Health Laboratory, 1729 W. 17th St., Santa Ana, CA 92706, USA
| | - May Zimmerman
- Department of Biology, California State University Long Beach, 1250 Bellflower Blvd., Long Beach, CA 90840, USA
| | - Jennifer A Jay
- Department of Civil and Environmental Engineering, University of California Los Angeles, Los Angeles, CA 90095, USA
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Characterizing the Phenotypic Responses of Escherichia coli to Multiple 4-Carbon Alcohols with Raman Spectroscopy. FERMENTATION-BASEL 2016. [DOI: 10.3390/fermentation2010003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Albert JD, Monbet V, Jolivet-Gougeon A, Fatih N, Le Corvec M, Seck M, Charpentier F, Coiffier G, Boussard-Pledel C, Bureau B, Guggenbuhl P, Loréal O. A novel method for a fast diagnosis of septic arthritis using mid infrared and deported spectroscopy. Joint Bone Spine 2015; 83:318-23. [PMID: 26677999 DOI: 10.1016/j.jbspin.2015.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/28/2015] [Indexed: 10/22/2022]
Abstract
OBJECTIVE To assess the ability of mid infrared deported spectroscopy to discriminate synovial fluids samples of septic arthritis patients from other causes of joint effusion. METHODS Synovial fluids obtained from patients with clinically suspected arthritis were collected, analysed and classified according to standard diagnostic procedures as septic or non-septic. A spectroscopic analysis on synovial fluid samples was then performed using a coiled optical fiber made with chalcogenide glass. After a factorial analysis of the normalized spectra and the computation of a Fisher test used to select the most relevant components, a logistic regression model was fitted, allowing to attribute a score between 0 - non-septic -, and 1 - septic. RESULTS In a first phase, we analysed the synovial fluids from 122 different synovial fluids including 6 septic arthritis among arthritis of various origins. Septic synovial fluids were identified with a sensitivity of 95.8% and a specificity of 93.9% and an AUROC of 0.977. The analysis of an independent set of samples (n=42, including two septic arthritis) gave similar values. CONCLUSIONS Our data strongly supports the interest of mid infrared deported spectroscopy, which could be used potentially at point of care, for a rapid and easy diagnosis of septic arthritis. Now, the precision of the diagnosis must be evaluated through a multicentric study on a larger panel of patients.
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Affiliation(s)
- Jean-David Albert
- Department of Rheumatology, CHU of Rennes, 2, rue Henri-le-Guilloux, 35000 Rennes, France; INSERM UMR 991, 35033 Rennes, France.
| | - Valérie Monbet
- University of Rennes 1, 35043 Rennes, France; UMR-CNRS 6625, IRMAR Mathematics Research Institute of Rennes, 35033 Rennes, France; INRIA/ASPI, 35033 Rennes, France
| | - Anne Jolivet-Gougeon
- Pole of Biology, EA 1254 Microbiologie, CHU of Rennes, University of Rennes 1, 35033 Rennes, France
| | - Nadia Fatih
- Diafir™, avenue Chardonnet, Parc Lorans, 26J, 35700 Rennes, France
| | - Maëna Le Corvec
- Diafir™, avenue Chardonnet, Parc Lorans, 26J, 35700 Rennes, France; Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), University of Bretagne-Sud, CER Yves-Coppens, BP 573, 56017 Vannes cedex, France
| | - Malik Seck
- University of Rennes 1, 35043 Rennes, France
| | | | - Guillaume Coiffier
- Department of Rheumatology, CHU of Rennes, 2, rue Henri-le-Guilloux, 35000 Rennes, France; INSERM UMR 991, 35033 Rennes, France
| | | | - Bruno Bureau
- ISCR UMR-CNRS 6226, Verres et Céramiques, Université de Rennes 1, 35042 Rennes, France
| | - Pascal Guggenbuhl
- Department of Rheumatology, CHU of Rennes, 2, rue Henri-le-Guilloux, 35000 Rennes, France; INSERM UMR 991, 35033 Rennes, France; University of Rennes 1, 35043 Rennes, France
| | - Olivier Loréal
- INSERM UMR 991, 35033 Rennes, France; University of Rennes 1, 35043 Rennes, France
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Lai HC, Ng TH, Ando M, Lee CT, Chen IT, Chuang JC, Mavichak R, Chang SH, Yeh MD, Chiang YA, Takeyama H, Hamaguchi HO, Lo CF, Aoki T, Wang HC. Pathogenesis of acute hepatopancreatic necrosis disease (AHPND) in shrimp. FISH & SHELLFISH IMMUNOLOGY 2015; 47:1006-14. [PMID: 26549178 DOI: 10.1016/j.fsi.2015.11.008] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/26/2015] [Accepted: 11/02/2015] [Indexed: 05/21/2023]
Abstract
Acute hepatopancreatic necrosis disease (AHPND), also called early mortality syndrome (EMS), is a recently emergent shrimp bacterial disease that has resulted in substantial economic losses since 2009. AHPND is known to be caused by strains of Vibrio parahaemolyticus that contain a unique virulence plasmid, but the pathology of the disease is still unclear. In this study, we show that AHPND-causing strains of V. parahaemolyticus secrete the plasmid-encoded binary toxin PirAB(vp) into the culture medium. We further determined that, after shrimp were challenged with AHPND-causing bacteria, the bacteria initially colonized the stomach, where they started to produce PirAB(vp) toxin. At the same early time point (6 hpi), PirB(vp) toxin, but not PirA(vp) toxin, was detected in the hepatopancreas, and the characteristic histopathological signs of AHPND, including sloughing of the epithelial cells of the hepatopancreatic tubules, were also seen. Although some previous studies have found that both components of the binary PirAB(vp) toxin are necessary to induce a toxic effect, our present results are consistent with other studies which have suggested that PirB(vp) alone may be sufficient to cause cellular damage. At later time points, the bacteria and PirA(vp) and PirB(vp) toxins were all detected in the hepatopancreas. We also show that Raman spectroscopy "Whole organism fingerprints" were unable to distinguish between AHPND-causing and non-AHPND causing strains. Lastly, by using minimum inhibitory concentrations, we found that both virulent and non-virulent V. parahaemolyticus strains were resistant to several antibiotics, suggesting that the use of antibiotics in shrimp culture should be more strictly regulated.
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Affiliation(s)
- Hung-Chiao Lai
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC
| | - Tze Hann Ng
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC
| | - Masahiro Ando
- Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Tokyo 162-0041, Japan
| | - Chung-Te Lee
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - I-Tung Chen
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | | | - Rapeepat Mavichak
- Aquatic Animal Health Research Center, Charoen Pokphand Foods, Bangkok, Thailand
| | - Sheng-Hsiung Chang
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC
| | - Mi-De Yeh
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC
| | - Yi-An Chiang
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
| | - Hiro-o Hamaguchi
- College of Science, National Ciao Tung University, 300, Taiwan, ROC
| | - Chu-Fang Lo
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - Takashi Aoki
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC.
| | - Han-Ching Wang
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC.
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Muhamadali H, Weaver D, Subaihi A, AlMasoud N, Trivedi DK, Ellis DI, Linton D, Goodacre R. Chicken, beams, and Campylobacter: rapid differentiation of foodborne bacteria via vibrational spectroscopy and MALDI-mass spectrometry. Analyst 2015; 141:111-22. [PMID: 26523729 DOI: 10.1039/c5an01945a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Campylobacter species are one of the main causes of food poisoning worldwide. Despite the availability of established culturing and molecular techniques, due to the fastidious nature of these microorganisms, simultaneous detection and species differentiation still remains challenging. This study focused on the differentiation of eleven Campylobacter strains from six species, using Fourier transform infrared (FT-IR) and Raman spectroscopies, together with matrix-assisted laser desorption ionisation-time of flight-mass spectrometry (MALDI-TOF-MS), as physicochemical approaches for generating biochemical fingerprints. Cluster analysis of data from each of the three analytical approaches provided clear differentiation of each Campylobacter species, which was generally in agreement with a phylogenetic tree based on 16S rRNA gene sequences. Notably, although C. fetus subspecies fetus and venerealis are phylogenetically very closely related, using FT-IR and MALDI-TOF-MS data these subspecies were readily differentiated based on differences in the lipid (2920 and 2851 cm(-1)) and fingerprint regions (1500-500 cm(-1)) of the FT-IR spectra, and the 500-2000 m/z region of the MALDI-TOF-MS data. A finding that was further investigated with targeted lipidomics using liquid chromatography-mass spectrometry (LC-MS). Our results demonstrate that such metabolomics approaches combined with molecular biology techniques may provide critical information and knowledge related to the risk factors, virulence, and understanding of the distribution and transmission routes associated with different strains of foodborne Campylobacter spp.
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Affiliation(s)
- Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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Gurbanov R, Simsek Ozek N, Gozen AG, Severcan F. Quick Discrimination of Heavy Metal Resistant Bacterial Populations Using Infrared Spectroscopy Coupled with Chemometrics. Anal Chem 2015; 87:9653-61. [DOI: 10.1021/acs.analchem.5b01659] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rafig Gurbanov
- Department of Biochemistry and ‡Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Nihal Simsek Ozek
- Department of Biochemistry and ‡Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ayse Gul Gozen
- Department of Biochemistry and ‡Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Feride Severcan
- Department of Biochemistry and ‡Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
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FTIR spectral signature of anticancer drugs. Can drug mode of action be identified? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:85-101. [PMID: 26327318 DOI: 10.1016/j.bbapap.2015.08.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 08/18/2015] [Accepted: 08/25/2015] [Indexed: 12/26/2022]
Abstract
Infrared spectroscopy has brought invaluable information about proteins and about the mechanism of action of enzymes. These achievements are difficult to transpose to living organisms as all biological molecules absorb in the mid infrared, with usually a high degree of overlap. Deciphering the contribution of each enzyme is therefore almost impossible. On the other hand, small changes in the infrared spectra of cells induced by environmental conditions or drugs may provide an accurate signature of the metabolic shift experienced by the cell as a response to a change in the growth medium. The present paper aims at reviewing the contribution of infrared spectroscopy to the description of small chemical changes that occur in cells when they are exposed to a drug. In particular, this review will focus on cancer cells and anti-cancer drugs. Results accumulated so far tend to demonstrate that infrared spectroscopy could be a very accurate descriptor of the mode of action of anticancer drugs. If confirmed, such a segmentation of potential drugs according to their "mode of action" will be invaluable for the discovery of new therapeutic molecules. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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Assmann C, Kirchhoff J, Beleites C, Hey J, Kostudis S, Pfister W, Schlattmann P, Popp J, Neugebauer U. Identification of vancomycin interaction with Enterococcus faecalis within 30 min of interaction time using Raman spectroscopy. Anal Bioanal Chem 2015; 407:8343-52. [DOI: 10.1007/s00216-015-8912-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/30/2015] [Accepted: 07/09/2015] [Indexed: 12/22/2022]
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Rapid detection of Listeria monocytogenes in milk using confocal micro-Raman spectroscopy and chemometric analysis. Int J Food Microbiol 2015; 204:66-74. [DOI: 10.1016/j.ijfoodmicro.2015.03.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/16/2015] [Accepted: 03/22/2015] [Indexed: 12/14/2022]
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Schröder UC, Bokeloh F, O'Sullivan M, Glaser U, Wolf K, Pfister W, Popp J, Ducrée J, Neugebauer U. Rapid, culture-independent, optical diagnostics of centrifugally captured bacteria from urine samples. BIOMICROFLUIDICS 2015; 9:044118. [PMID: 26339318 PMCID: PMC4537478 DOI: 10.1063/1.4928070] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/24/2015] [Indexed: 05/25/2023]
Abstract
This work presents a polymeric centrifugal microfluidic platform for the rapid and sensitive identification of bacteria directly from urine, thus eliminating time-consuming cultivation steps. This "Lab-on-a-Disc" platform utilizes the rotationally induced centrifugal field to efficiently capture bacteria directly from suspension within a glass-polymer hybrid chip. Once trapped in an array of small V-shaped structures, the bacteria are readily available for spectroscopic characterization, such as Raman spectroscopic fingerprinting, providing valuable information on the characteristics of the captured bacteria. Utilising fluorescence microscopy, quantification of the bacterial load has been achieved for concentrations above 2 × 10(-7) cells ml(-1) within a 4 μl sample. As a pilot application, we characterize urine samples from patients with urinary tract infections. Following minimal sample preparation, Raman spectra of the bacteria are recorded following centrifugal capture in stopped-flow sedimentation mode. Utilizing advanced analysis algorithms, including extended multiplicative scattering correction, high-quality Raman spectra of different pathogens, such as Escherichia coli or Enterococcus faecalis, are obtained from the analyzed patient samples. The whole procedure, including sample preparation, requires about 1 h to obtain a valuable result, marking a significant reduction in diagnosis time when compared to the 24 h and more typically required for standard microbiological methods. As this cost-efficient centrifugal cartridge can be operated using low-complexity, widely automated instrumentation, while providing valuable bacterial identification in urine samples in a greatly reduced time-period, our opto-microfluidic Lab-on-a-Disc device demonstrates great potential for next-generation patient diagnostics at the of point-of-care.
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Affiliation(s)
| | | | - Mary O'Sullivan
- Biomedical Diagnostics Institute, National Centre of Sensor Research, School of Physical Sciences, Dublin City University , Glasnevin, Dublin 9, Ireland
| | | | - Katharina Wolf
- Institute of Medical Microbiology, Jena University Hospital , 07747 Jena, Germany
| | - Wolfgang Pfister
- Institute of Medical Microbiology, Jena University Hospital , 07747 Jena, Germany
| | | | - Jens Ducrée
- Biomedical Diagnostics Institute, National Centre of Sensor Research, School of Physical Sciences, Dublin City University , Glasnevin, Dublin 9, Ireland
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Tanniou A, Vandanjon L, Gonçalves O, Kervarec N, Stiger-Pouvreau V. Rapid geographical differentiation of the European spread brown macroalga Sargassum muticum using HRMAS NMR and Fourier-Transform Infrared spectroscopy. Talanta 2015; 132:451-6. [PMID: 25476330 DOI: 10.1016/j.talanta.2014.09.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 08/21/2014] [Accepted: 09/02/2014] [Indexed: 12/13/2022]
Abstract
Two recent techniques based on chemical footprinting analysis, HRMAS NMR and FTIR spectroscopy, were tested on a brown macroalgal model. These powerful and easily-to-use techniques allowed us to discriminate Sargassum muticum specimens collected in five different countries along Atlantic coasts, from Portugal to Norway. HRMAS NMR and FTIR permitted the obtaining of an overview of metabolites produced by the alga. Based on spectra analysis, results allowed us to successfully group the samples according to their geographical origin. HRMAS NMR and FTIR spectroscopy respectively point out the relation between the geographical localization and the chemical composition and demonstrated macromolecules variations regarding to environmental stress. Then, our results are discussed in regard of the powerful of these techniques together with the variability of the main molecules produced by Sargassum muticum along the Atlantic coasts.
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Affiliation(s)
- Anaëlle Tanniou
- LEMAR UMR CNRS UBO IRD IFREMER 6539, Université de Bretagne Occidentale (UBO), Institut Universitaire Européen de la Mer (IUEM), Technopôle Brest-Iroise, Rue Dumont d׳Urville, Plouzané 29280, France
| | - Laurent Vandanjon
- GEPEA UMR CNRS 6144, Université de Nantes, Laboratoire GEPEA, CRTT, 44602 Saint-Nazaire, France; LBCM EA 3884, Université de Bretagne Sud (UBS), IUEM, Campus de Tohannic, 56000 Vannes, France
| | - Olivier Gonçalves
- GEPEA UMR CNRS 6144, Université de Nantes, Laboratoire GEPEA, CRTT, 44602 Saint-Nazaire, France
| | - Nelly Kervarec
- Service RMN-RPE, UFR Sciences et Techniques, Université de Bretagne Occidentale (UBO), Avenue Le Gorgeu, 29200 Brest, France
| | - Valérie Stiger-Pouvreau
- LEMAR UMR CNRS UBO IRD IFREMER 6539, Université de Bretagne Occidentale (UBO), Institut Universitaire Européen de la Mer (IUEM), Technopôle Brest-Iroise, Rue Dumont d׳Urville, Plouzané 29280, France.
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Mathey R, Dupoy M, Espagnon I, Leroux D, Mallard F, Novelli-Rousseau A. Viability of 3h grown bacterial micro-colonies after direct Raman identification. J Microbiol Methods 2014; 109:67-73. [PMID: 25500131 DOI: 10.1016/j.mimet.2014.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 10/24/2022]
Abstract
Clinical diagnostics in routine microbiology still mostly relies on bacterial growth, a time-consuming process that prevents test results to be used directly as key decision-making elements for therapeutic decisions. There is some evidence that Raman micro-spectroscopy provides clinically relevant information from a limited amount of bacterial cells, thus holding the promise of reduced growth times and accelerated result delivery. Indeed, bacterial identification at the species level directly from micro-colonies at an early time of growth (6h) directly on their growth medium has been demonstrated. However, such analysis is suspected to be partly destructive and could prevent the further growth of the colony needed for other tests, e.g. antibiotic susceptibility testing (AST). In the present study, we evaluated the effect of the powerful laser excitation used for Raman identification on micro-colonies probed after very short growth times. We show here, using envelope integrity markers (Syto 9 and Propidium Iodide) directly on ultra-small micro-colonies of a few tens of Escherichia coli and Staphylococcus epidermidis cells (3h growth time), that only the cells that are directly impacted by the laser lose their membrane integrity. Growth kinetics experiments show that the non-probed surrounding cells are sometimes also affected but that the micro-colonies keep their ability to grow, resulting in normal aspect and size of colonies after 15h of growth. Thus, Raman spectroscopy could be used for very early (<3h) identification of grown micro-organisms without impairing further antibiotics susceptibility characterization steps.
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Affiliation(s)
- R Mathey
- bioMérieux, Technology Research Department, 5 rue des Berges, 38000 Grenoble, France
| | - M Dupoy
- CEA, LETI, MINATEC, 17 rue des Martyrs, 38054 Grenoble Cedex, 9, France
| | - I Espagnon
- CEA, LIST, Département Métrologie, Instrumentation et Information, 91191 Gif-sur-Yvette, France
| | - D Leroux
- bioMérieux, Technology Research Department, Chemin de l'Orme, 69280 Marcy l'Etoile, France
| | - F Mallard
- bioMérieux, Technology Research Department, 5 rue des Berges, 38000 Grenoble, France
| | - A Novelli-Rousseau
- bioMérieux, Technology Research Department, 5 rue des Berges, 38000 Grenoble, France.
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Picciolini S, Mehn D, Morasso C, Vanna R, Bedoni M, Pellacani P, Marchesini G, Valsesia A, Prosperi D, Tresoldi C, Ciceri F, Gramatica F. Polymer nanopillar-gold arrays as surface-enhanced Raman spectroscopy substrate for the simultaneous detection of multiple genes. ACS NANO 2014; 8:10496-10506. [PMID: 25280123 DOI: 10.1021/nn503873d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In our study, 2D nanopillar arrays with plasmonic crystal properties are optimized for surface-enhanced Raman spectroscopy (SERS) application and tested in a biochemical assay for the simultaneous detection of multiple genetic leukemia biomarkers. The special fabrication process combining soft lithography and plasma deposition techniques allows tailoring of the structural and chemical parameters of the crystal surfaces. In this way, it has been possible to tune the plasmonic resonance spectral position close to the excitation wavelength of the monochromatic laser light source in order to maximize the enhancing properties of the substrate. Samples are characterized by scanning electron microscopy and reflectance measurements and tested for SERS activity using malachite green. Besides, as the developed substrate had been prepared on a simple glass slide, SERS detection from the support side is also demonstrated. The optimized substrate is functionalized with thiol-modified capture oligonucleotides, and concentration-dependent signal of the target nucleotide is detected in a sandwich assay with labeled gold nanoparticles. Gold nanoparticles functionalized with different DNA and various Raman reporters are applied in a microarray-based assay recognizing a disease biomarker (Wilms tumor gene) and housekeeping gene expressions in the same time on spatially separated microspots. The multiplexing performance of the SERS-based bioassay is illustrated by distinguishing Raman dyes based on their complex spectral fingerprints.
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Affiliation(s)
- Silvia Picciolini
- Fondazione Don Carlo Gnocchi ONLUS , Piazzale Morandi 6, 20121 Milan, Italy
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Benard A, Desmedt C, Smolina M, Szternfeld P, Verdonck M, Rouas G, Kheddoumi N, Rothé F, Larsimont D, Sotiriou C, Goormaghtigh E. Infrared imaging in breast cancer: automated tissue component recognition and spectral characterization of breast cancer cells as well as the tumor microenvironment. Analyst 2014; 139:1044-56. [PMID: 24418921 DOI: 10.1039/c3an01454a] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Current evaluation of histological sections of breast cancer samples remains unsatisfactory. The search for new predictive and prognostic factors is ongoing. Infrared spectroscopy and its potential to probe tissues and cells at the molecular level without requirement for contrast agents could be an attractive tool for clinical and diagnostic analysis of breast cancer. In this study, we report the successful application of FTIR (Fourier transform infrared) imaging for breast tissue component characterization. We show that specific FTIR spectral signatures can be assigned to the major tissue components of breast tumor samples. We demonstrate that a tissue component classifier can be built based on a spectral database of well-annotated tissues and successfully validated on independent breast samples. We also demonstrate that spectral features can reveal subtle differences within a tissue component, capturing for instance lymphocytic and stromal activation. By investigating in parallel lymph nodes, tonsils and wound healing tissues, we prove the uniqueness of the signature of both lymphocytic infiltrate and tumor microenvironment in the breast disease context. Finally, we demonstrate that the biochemical information reflected in the epithelial spectra might be clinically relevant for the grading purpose, suggesting potential to improve breast cancer management in the future.
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Affiliation(s)
- Audrey Benard
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Bld du Triomphe 2, CP206/2, B1050 Brussels, Belgium.
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Lv X, Ge W, Li Q, Wu Y, Jiang H, Wang X. Rapid and ultrasensitive electrochemical detection of multidrug-resistant bacteria based on nanostructured gold coated ITO electrode. ACS APPLIED MATERIALS & INTERFACES 2014; 6:11025-31. [PMID: 24950258 DOI: 10.1021/am5016099] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Rapid and ultrasensitive detection of pathogenic bacteria and their relevant multidrug resistance is particularly important in clinical diagnosis, disease control, and environmental monitoring. In this contribution, we have explored the possibility to rapidly detect some important disease related bacteria based on a nanostructured Au modified indium tin oxide electrode through the antibiotic agents such as doxorubicin. The rapid and real-time electrochemical detection of multidrug resistant bacteria like Escherichia coli and Staphylococcus aureus could be readily realized through the nanostructured Au based biosensor with high sensitivity. The observations of surface-enhanced Raman spectroscopy and laser confocal fluorescence microscopy also demonstrate the effectiveness of the relevant new strategy for the rapid and ultrasensitive electrochemical detection of some disease related bacteria.
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Affiliation(s)
- Xiayi Lv
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Laboratory), Department of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
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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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Assaf A, Cordella CBY, Thouand G. Raman spectroscopy applied to the horizontal methods ISO 6579:2002 to identify Salmonella spp. in the food industry. Anal Bioanal Chem 2014; 406:4899-910. [PMID: 24908409 DOI: 10.1007/s00216-014-7909-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/09/2014] [Accepted: 05/17/2014] [Indexed: 10/25/2022]
Abstract
Food safety is a major concern for suppliers in the food chain to ensure the safety of their products. The identification procedure requested by norms is tedious, and it often requires systematic controls and qualified staff to perform the necessary analyses. Raman spectroscopy offers new opportunities to rapidly and efficiently ascertain the presence of pathogens in samples. Nevertheless, this technique requires a standardized procedure to be applied in the industrial context. Our study shows that the variability between spectral fingerprints is related to the physiological state of the microbial species and the growth phase of the bacteria plays a crucial role in its identification by Raman spectroscopy. To improve the discrimination between closely related bacterial species, a procedure based on the selection of bacterial spectra in the exponential growth phase was proposed. Different ways to introduce Raman spectroscopy in the ISO 6579:2002 standards are also proposed from the entire process to a shorter protocol. In the latter case, the identification of bacterial colonies after the selective enrichment step was proposed with the advantages of this path in terms of simplicity and rapidity (analysis time is reduced up to 50 h from the 100 h required by the standard). The protocol validated using six food categories from industrial partners have presented a good correlation by confirmation with other laboratory classical methods. In the future, this procedure could be introduced to the control system of the food production chain with a reliable database for various microorganisms encountered in this field.
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Affiliation(s)
- A Assaf
- University of Nantes, UMR CNRS GEPEA 6144, CBAC, 18 Boulevard Gaston Defferre, CS50020, 85035, Nantes, La Roche sur Yon, France
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