1
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Ciolli Mattioli C, Avraham R. Protocol for comparing ribosomal levels in single bacterial cells at different growth stages using rRNA-FISH. STAR Protoc 2024; 5:103137. [PMID: 38878285 PMCID: PMC11234016 DOI: 10.1016/j.xpro.2024.103137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 07/13/2024] Open
Abstract
Ribosome quantification in single cells is typically achieved through fluorescence tagging of ribosomal proteins. Here, we present a protocol for comparing ribosomal levels in bacteria at different growth stages using fluorescence in situ hybridization of rRNA (rRNA-FISH), eliminating the need for genetic engineering of the strain of interest. We detail the steps for preparing bacterial samples, staining with fluorescent probes, and acquiring data using flow cytometry and microscopy. Furthermore, we provide guidelines on controlling for proper labeling through signal localization analysis. For complete details on the use and execution of this protocol, please refer to Ciolli Mattioli et al.1.
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Affiliation(s)
- Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Roi Avraham
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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2
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Ciolli Mattioli C, Avraham R. Single-Molecule Fluorescent In Situ Hybridization (smFISH) for RNA Detection in Bacteria. Methods Mol Biol 2024; 2784:3-23. [PMID: 38502475 DOI: 10.1007/978-1-0716-3766-1_1] [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: 03/21/2024]
Abstract
In this chapter, we describe in detail how to perform a successful smFISH experiment and how to quantify mRNA transcripts in bacterial cells. The flexibility of the method allows for straightforward adaptation to different bacterial species and experimental conditions. Thanks to the feasibility of the approach, the method can easily be adapted by other laboratories. Finally, we believe that this method has a great potential to generate insights into the complicated life of bacteria.
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Affiliation(s)
- Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Roi Avraham
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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3
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Grosboillot V, Keller I, Ernst C, Loessner MJ, Schuppler M. Ampicillin Treatment of Intracellular Listeria monocytogenes Triggers Formation of Persistent, Drug-Resistant L-Form Cells. Front Cell Infect Microbiol 2022; 12:869339. [PMID: 35646717 PMCID: PMC9133454 DOI: 10.3389/fcimb.2022.869339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/13/2022] [Indexed: 01/02/2023] Open
Abstract
Listeria monocytogenes is an opportunistic intracellular pathogen causing an infection termed listeriosis. Despite the low incidence of listeriosis, the high mortality rate in individuals at risk makes this bacterium one of the most dangerous foodborne pathogens. Reports about a relapse of infection after antibiotic treatment suggest that the bacteria may be able to evade antibiotic treatment and persist as a dormant, antibiotic-tolerant subpopulation. In this study, we observed intracellular generation of antibiotic-resistant L-forms of Listeria monocytogenes following Ampicillin treatment of Listeria monocytogenes infected cells. Detection and identification of intracellular Listeria L-forms was performed by a combination of fluorescence in-situ hybridization and confocal laser scanning microscopy. Using micromanipulation, it was possible to isolate single intracellular L-form cells that following transfer into fresh medium gave rise to pure cultures. In conclusion, the results obtained here provide strong evidence that antibiotic treatment of infected host cells can induce the formation of L-forms from intracellular Listeria monocytogenes. Furthermore, our results suggest that intracellular L-forms persist inside host cells and that they represent viable bacteria, which are still able to grow and proliferate.
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Affiliation(s)
| | | | | | | | - Markus Schuppler
- Institute for Food, Nutrition and Health, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
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4
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Zand E, Froehling A, Schoenher C, Zunabovic-Pichler M, Schlueter O, Jaeger H. Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review. Foods 2021; 10:3112. [PMID: 34945663 PMCID: PMC8701031 DOI: 10.3390/foods10123112] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022] Open
Abstract
As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.
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Affiliation(s)
- Elena Zand
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
| | - Antje Froehling
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Christoph Schoenher
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Marija Zunabovic-Pichler
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Oliver Schlueter
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Henry Jaeger
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
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5
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Irastortza-Olaziregi M, Amster-Choder O. RNA localization in prokaryotes: Where, when, how, and why. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1615. [PMID: 32851805 DOI: 10.1002/wrna.1615] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/27/2020] [Accepted: 06/02/2020] [Indexed: 12/27/2022]
Abstract
Only recently has it been recognized that the transcriptome of bacteria and archaea can be spatiotemporally regulated. All types of prokaryotic transcripts-rRNAs, tRNAs, mRNAs, and regulatory RNAs-may acquire specific localization and these patterns can be temporally regulated. In some cases bacterial RNAs reside in the vicinity of the transcription site, but in many others, transcripts show distinct localizations to the cytoplasm, the inner membrane, or the pole of rod-shaped species. This localization, which often overlaps with that of the encoded proteins, can be achieved either in a translation-dependent or translation-independent fashion. The latter implies that RNAs carry sequence-level features that determine their final localization with the aid of RNA-targeting factors. Localization of transcripts regulates their posttranscriptional fate by affecting their degradation and processing, translation efficiency, sRNA-mediated regulation, and/or propensity to undergo RNA modifications. By facilitating complex assembly and liquid-liquid phase separation, RNA localization is not only a consequence but also a driver of subcellular spatiotemporal complexity. We foresee that in the coming years the study of RNA localization in prokaryotes will produce important novel insights regarding the fundamental understanding of membrane-less subcellular organization and lead to practical outputs with biotechnological and therapeutic implications. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Mikel Irastortza-Olaziregi
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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6
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Aistleitner K, Sieper T, Stürz I, Jeske R, Tritscheller S, Mantel S, Tscherne A, Zange S, Stoecker K, Wölfel R. NOTIFy (non-toxic lyophilized field)-FISH for the identification of biological agents by Fluorescence in situ Hybridization. PLoS One 2020; 15:e0230057. [PMID: 32142548 PMCID: PMC7059943 DOI: 10.1371/journal.pone.0230057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/20/2020] [Indexed: 12/02/2022] Open
Abstract
The rapid and reliable diagnostics of highly pathogenic bacteria under restricted field conditions poses one of the major challenges to medical biodefense, especially since false positive or false negative reports might have far-reaching consequences. Fluorescence in situ hybridization (FISH) has the potential to represent a powerful microscopy-based addition to the existing molecular-based diagnostic toolbox. In this study, we developed a set of FISH-probes for the fast, matrix independent and simultaneous detection of thirteen highly pathogenic bacteria in different environmental and clinical sample matrices. Furthermore, we substituted formamide, a routinely used chemical that is toxic and volatile, by non-toxic urea. This will facilitate the application of FISH under resource limited field laboratory conditions. We demonstrate that hybridizations performed with urea show the same specificity and comparable signal intensities for the FISH-probes used in this study. To further simplify the use of FISH in the field, we lyophilized the reagents needed for FISH. The signal intensities obtained with these lyophilized reagents are comparable to freshly prepared reagents even after storage for a month at room temperature. Finally, we show that by the use of non-toxic lyophilized field (NOTIFy)-FISH, specific detection of microorganisms with simple and easily transportable equipment is possible in the field.
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Affiliation(s)
| | - Tina Sieper
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Inga Stürz
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Rimma Jeske
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | - Sonja Mantel
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | - Sabine Zange
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Kilian Stoecker
- Bundeswehr Institute of Microbiology, Munich, Germany
- * E-mail:
| | - Roman Wölfel
- Bundeswehr Institute of Microbiology, Munich, Germany
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7
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Chen P, Wang JJ, Hong B, Tan L, Yan J, Zhang Z, Liu H, Pan Y, Zhao Y. Characterization of Mixed-Species Biofilm Formed by Vibrio parahaemolyticus and Listeria monocytogenes. Front Microbiol 2019; 10:2543. [PMID: 31787947 PMCID: PMC6856058 DOI: 10.3389/fmicb.2019.02543] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/21/2019] [Indexed: 12/15/2022] Open
Abstract
Mixed-species biofilms are the predominant form of biofilms found in nature. Research on biofilms have typically concentrated on single species biofilms and this study expands the horizon of biofilm research, where the characterization and dynamic changes of mono and mixed-species biofilms formed by the pathogens, Vibrio parahaemolyticus and Listeria monocytogenes were investigated. Compared to mono-species biofilm, the biomass, bio-volume, and thickness of mixed-species biofilms were significantly lower, which were confirmed using crystal violet staining, confocal laser scanning microscopy and scanning electron microscopy. Further experimental analysis showed these variations might result from the reduction of bacterial numbers, the down-regulation of biofilm-regulated genes and loss of metabolic activity in mixed-species biofilm. In addition, V. parahaemolyticus was located primarily on the surface layers of the mixed-species biofilms thus accruing competitive advantage. This competitive advantage was evidenced in a higher V. parahaemolyticus population density in the mixed-species biofilms. The adhesion to surfaces of the mixed-species biofilms were also reduced due to lower concentrations of extracellular polysaccharide and protein when the structure of the mixed-species was examined using Raman spectral analysis, phenol-sulfuric acid method and Lowry method. Furthermore, the minimum biofilm inhibitory concentration to antibiotics obviously decreased when V. parahaemolyticus co-exited with L. monocytogenes. This study firstly elucidated the interactive behavior in biofilm development of two foodborne pathogens, and future studies for biofilm control and antibiotic therapy should take into account interactions in mixed-species biofilms.
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Affiliation(s)
- Ping Chen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jing Jing Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquatic Product Processing and Preservation, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Bin Hong
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Ling Tan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jun Yan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquatic Product Processing and Preservation, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Zhaohuan Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Haiquan Liu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquatic Product Processing and Preservation, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China
- Engineering Research Center of Food Thermal-Processing Technology, Shanghai Ocean University, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquatic Product Processing and Preservation, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquatic Product Processing and Preservation, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China
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8
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Ma Z, Chu PM, Su Y, Yu Y, Wen H, Fu X, Huang S. Applications of single-cell technology on bacterial analysis. QUANTITATIVE BIOLOGY 2019. [DOI: 10.1007/s40484-019-0177-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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9
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Optimizing locked nucleic acid/2'-O-methyl-RNA fluorescence in situ hybridization (LNA/2'OMe-FISH) procedure for bacterial detection. PLoS One 2019; 14:e0217689. [PMID: 31150460 PMCID: PMC6544301 DOI: 10.1371/journal.pone.0217689] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 05/16/2019] [Indexed: 01/23/2023] Open
Abstract
Despite the successful application of LNA/2'OMe-FISH procedures for bacteria detection, there is a lack of knowledge on the properties that affect hybridization. Such information is crucial for the rational design of protocols. Hence, this work aimed to evaluate the effect of three essential factors on the LNA/2'OMe hybridization step-hybridization temperature, NaCl concentration and type and concentration of denaturant (formamide, ethylene carbonate and urea). This optimization was performed for 3 Gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa and Citrobacter freundii) and 2 Gram-positive bacteria (Enterococcus faecalis and Staphylococcus epidermidis), employing the response surface methodology and a Eubacteria probe. In general, it was observed that a high NaCl concentration is beneficial (from 2 M to 5 M), regardless of the denaturant used. Urea, formamide and ethylene carbonate are suitable denaturants for LNA/2'OMe-FISH applications; but urea provides higher fluorescence intensities among the different bacteria, especially for gram-positive bacteria and for P. aeruginosa. However, a unique optimal protocol was not found for all tested bacteria. Despite this, the results indicate that a hybridization solution with 2 M of urea and 4 M of NaCl would be a proper starting point. Furthermore, a hybridization temperature around 62°C, for 14 bp probes with LNA monomers at every third position of 2'OMe and 64% of GC content, should be use in initial optimization of new LNA/2'OMe-FISH protocols.
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10
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Prudent E, Raoult D. Fluorescence in situ hybridization, a complementary molecular tool for the clinical diagnosis of infectious diseases by intracellular and fastidious bacteria. FEMS Microbiol Rev 2018; 43:88-107. [DOI: 10.1093/femsre/fuy040] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 11/07/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Elsa Prudent
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
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11
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Kljujev I, Raicevic V, Jovicic-Petrovic J, Vujovic B, Mirkovic M, Rothballer M. Listeria monocytogenes – Danger for health safety vegetable production. Microb Pathog 2018; 120:23-31. [DOI: 10.1016/j.micpath.2018.04.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/12/2018] [Accepted: 04/19/2018] [Indexed: 10/17/2022]
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12
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Influence of the fixation/permeabilization step on peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria. PLoS One 2018; 13:e0196522. [PMID: 29851961 PMCID: PMC5979007 DOI: 10.1371/journal.pone.0196522] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/14/2018] [Indexed: 11/19/2022] Open
Abstract
Fluorescence in situ Hybridization (FISH) is a versatile, widespread and widely- used technique in microbiology. The first step of FISH—fixation/permeabilization—is crucial to the outcome of the method. This work aimed to systematically evaluate fixation/permeabilization protocols employing ethanol, triton X-100 and lysozyme in conjugation with paraformaldehyde for Peptide Nucleic Acid (PNA)-FISH. Response surface methodology was used to optimize these protocols for Gram-negative (Escherichia coli and Pseudomonas fluorescens) and Gram-positive species (Listeria innocua, Staphylococcus epidermidis and Bacillus cereus). In general, the optimal PNA-FISH fluorescent outcome in Gram-positive bacteria was obtained employing harsher permeabilization conditions when compared to Gram-negative optimal protocols. The observed differences arise from the intrinsic cell envelope properties of each species and the ability of the fixation/permeabilization compounds to effectively increase the permeability of these structures while maintaining structural integrity. Ultimately, the combination of paraformaldehyde and ethanol proved to have significantly superior performance for all tested bacteria, especially for Gram-positive species (p<0.05).
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13
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Rohde A, Hammerl JA, Appel B, Dieckmann R, Al Dahouk S. FISHing for bacteria in food – A promising tool for the reliable detection of pathogenic bacteria? Food Microbiol 2015; 46:395-407. [DOI: 10.1016/j.fm.2014.09.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/15/2014] [Accepted: 09/05/2014] [Indexed: 12/28/2022]
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14
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Baysal AH. Comparison of conventional culture method and fluorescent in situ hybridization technique for detection of Listeria spp. in ground beef, turkey, and chicken breast fillets in İzmir, Turkey. J Food Prot 2014; 77:2021-30. [PMID: 25474046 DOI: 10.4315/0362-028x.jfp-14-034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The occurrence of Listeria species in refrigerated fresh chicken breast fillet, turkey breast fillet, and ground beef was evaluated, comparing the conventional culture method and fluorescent in situ hybridization (FISH). FISH uses hybridization of a nucleic acid sequence target of a microorganism with a specific DNA probe labeled with a fluorochrome and imaging by a fluorescence microscope. First, Listeria was inoculated in chicken breast fillet, turkey breast fillet, or ground beef, and the applicability of the FISH method was evaluated. Second, Listeria was detected in fresh chicken breast fillet, turkey breast fillet, and ground beef by culture and FISH methods. Listeria was isolated from 27 (37.4%) of 216 samples by the standard culture method, whereas FISH detected 25 (24.7%) preenriched samples. Of these isolates, 17 (63%) were L. innocua, 6 (22%) L. welshimeri, and 4 (14.8%) L. seeligeri. Overall, the prevalences of Listeria spp. found with the conventional culture method in chicken breast fillet, turkey breast fillet, and ground beef were 9.7, 6.9, and 20.8%, whereas with the FISH technique these values were 11.1, 6.9, and 16.7%, respectively. The molecular FISH technique appears to be a cheap, sensitive, and time-efficient procedure that could be used for routine detection of Listeria spp. in meat. This study showed that retail raw meats are potentially contaminated with Listeria spp. and are, thus, vehicles for transmitting diseases caused by foodborne pathogens, underlining the need for increased precautions, such as implementation of hazard analysis and critical control points and consumer food safety education.
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Affiliation(s)
- Ayse Handan Baysal
- Izmir Institute of Technology, Department of Food Engineering, 035430 a, Izmir, Turkey.
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15
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Smolina IV, Frank-Kamenetskii MD. PNA openers and their applications for bacterial DNA diagnostics. Methods Mol Biol 2014; 1050:121-30. [PMID: 24297355 DOI: 10.1007/978-1-62703-553-8_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The unique ability of triplex-forming PNAs to invade the double helix has made it possible to develop a highly specific and sensitive approach for bacterial detection. The method uses short, about 20-bp-long, signature sequences presented as a single copy in the bacterial genome. Bacterial cells are fixed on slides and the PD-loop structure is assembled on the signature site with the help of PNA openers, which includes the circular probe. The sensitivity of the method is achieved via Rolling Circle Amplification (RCA) of the circular probe. The obtained amplicon is detected using short ssDNA decorator probes carrying fluorophores and via standard fluorescent microscopy.
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Affiliation(s)
- Irina V Smolina
- Department of Biomedical Engineering, Boston University, Boston, USA
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16
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Smolina I. Application of PNA openers for fluorescence-based detection of bacterial DNA. Methods Mol Biol 2014; 1039:223-31. [PMID: 24026699 DOI: 10.1007/978-1-62703-535-4_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptide nucleic acid (PNA) openers have the unique ability to invade double-stranded DNA with high efficiency and sequence specificity, making it possible to detect short (about 20 bp), single-copy bacterial DNA sequences. PNA openers bind to a target signature site on one strand of bacterial DNA, leaving the other strand open for hybridization with a circularizable oligonucleotide probe. The assembled complex serves as a template for rolling circle amplification. The obtained amplicon is decorated with short, single-stranded DNA probes carrying fluorophores and detected via fluorescence microscopy.
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Affiliation(s)
- Irina Smolina
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
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17
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Yamazaki K. Development of a Rapid Enumeration Method Based on Fluorescence in situ Hybridization and the Control of Food-borne Pathogens. J JPN SOC FOOD SCI 2014. [DOI: 10.3136/nskkk.61.259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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18
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Li H, Guo J, Lian J, Zhao L, Xi Z, Du H, Yang J. Effective and characteristics of anthraquinone-2,6-disulfonate (AQDS) on denitrification by Paracoccus versutus sp.GW1. ENVIRONMENTAL TECHNOLOGY 2013; 34:2563-2570. [PMID: 24527617 DOI: 10.1080/09593330.2013.781198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The effects of anthraquinone-2,6-disulfonate (AQDS) on microbial populations and the biocatalysing characteristics of AQDS on denitrifying strain GW1 are discussed. The results showed that microbial population abundances were 30, 6, 12 and 18% during the different periods (1st, 5th, 10th and 20th days). Strain GW1 utilized AQDS as an electron acceptor in the respiration chain and reduced AQDS to hydroquinone (QH2). The nitrate removal efficiency of strain GW1 was increased 1.14-1.63 fold with 0.04-0.32 mmol/L AQDS. A linear correlation was found between the nitrate removal reaction constant k[gNO3(-)- N/(gVSS x d)] (where VSS is volatile suspended solids) and AQDS concentration (CAQDS), which was k = 19.332 C(AQDS) + 11.115 (R2 = 0.9749). The stabilized oxidation-reduction potential (ORP) values with AQDS were lower 22-92 mv than the control during the denitrification process. The concentration of nitrite sequentially accumulated up to around 250 mg/L when nitrate have removed completely. The results suggested that AQDS as redox mediator was capable of biocatalysing the nitrate and nitrite removal rate.
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Affiliation(s)
- Haibo Li
- School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, PR China
| | - Jianbo Guo
- School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, PR China
| | - Jing Lian
- School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, PR China
| | - Lijun Zhao
- School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, PR China
| | - Zhenhua Xi
- School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, PR China
| | - Haifeng Du
- School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, PR China
| | - Jingliang Yang
- School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, PR China
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19
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Fluorescence in situ hybridization (FISH) detection of nitrite reductase transcripts (nirS mRNA) in Pseudomonas stutzeri biofilms relative to a microscale oxygen gradient. Syst Appl Microbiol 2012; 35:513-7. [DOI: 10.1016/j.syapm.2011.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/17/2011] [Accepted: 12/19/2011] [Indexed: 11/19/2022]
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20
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Kubota K. CARD-FISH for environmental microorganisms: technical advancement and future applications. Microbes Environ 2012; 28:3-12. [PMID: 23124765 PMCID: PMC4070690 DOI: 10.1264/jsme2.me12107] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) has become a standard technique in environmental microbiology. More than 20 years have passed since this technique was first described, and it is currently used for the detection of ribosomal RNA, messenger RNA, and functional genes encoded on chromosomes. This review focuses on the advancement and applications of FISH combined with catalyzed reporter deposition (CARD, also known as tyramide signal amplification or TSA), in the detection of environmental microorganisms. Significant methodological improvements have been made in CARD-FISH technology, including its combination with other techniques and instruments.
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Affiliation(s)
- Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Miyagi, Japan.
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21
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Detection and enumeration of viable Listeria monocytogenes cells from ready-to-eat and processed vegetable foods by culture and DVC-FISH. Food Control 2012. [DOI: 10.1016/j.foodcont.2012.04.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Smith JP, Uhernik AL, Li L, Liu Z, Drewes LR. Regulation of Mct1 by cAMP-dependent internalization in rat brain endothelial cells. Brain Res 2012; 1480:1-11. [PMID: 22925948 DOI: 10.1016/j.brainres.2012.08.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/08/2012] [Accepted: 08/15/2012] [Indexed: 10/28/2022]
Abstract
In the cerebrovascular endothelium, monocarboxylic acid transporter 1 (Mct1) controls blood-brain transport of short chain monocarboxylic and keto acids, including pyruvate and lactate, to support brain energy metabolism. Mct1 function is acutely decreased in rat brain cerebrovascular endothelial cells by β-adrenergic signaling through cyclic adenosine monophosphate (cAMP); however, the mechanism for this acute reduction in transport capacity is unknown. In this report, we demonstrate that cAMP induces the dephosphorylation and internalization of Mct1 from the plasma membrane into caveolae and early endosomes in the RBE4 rat brain cerebrovascular endothelial cell line. Additionally, we provide evidence that Mct1 constitutively cycles through clathrin vesicles and recycling endosomes in a pathway that is not dependent upon cAMP signaling in these cells. Our results are important because they show for the first time the regulated and unregulated vesicular trafficking of Mct1 in cerebrovascular endothelial cells; processes which have significance for better understanding normal brain energy metabolism, and the etiology and potential therapeutic approaches to treating brain diseases, such as stroke, in which lactic acidosis is a key component.
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Affiliation(s)
- Jeffrey P Smith
- Colorado State University-Pueblo, Department of Biology, 2200 Bonforte Blvd., Pueblo, CO 81001, USA.
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23
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Hall-Stoodley L, Stoodley P, Kathju S, Høiby N, Moser C, Costerton JW, Moter A, Bjarnsholt T. Towards diagnostic guidelines for biofilm-associated infections. ACTA ACUST UNITED AC 2012; 65:127-45. [PMID: 22469292 DOI: 10.1111/j.1574-695x.2012.00968.x] [Citation(s) in RCA: 240] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/21/2012] [Accepted: 03/25/2012] [Indexed: 12/17/2022]
Abstract
Biofilms associated with the human body, particularly in typically sterile locations, are difficult to diagnose and treat effectively because of their recalcitrance to conventional antibiotic therapy and host immune responses. The study of biofilms in medicine today requires a translational approach, with examination of clinically relevant biofilms in the context of specific anatomic sites, host tissues, and diseases, focusing on what can be done to mitigate their pathologic consequences. This review, which grew out of a discussion session on clinical biofilms at the 5th ASM Biofilm Conference in Cancun, Mexico, is designed to give an overview of biofilm-associated infections (BAI) and to propose a platform for further discussion that includes clinicians, medical microbiologists, and biofilm researchers who are stakeholders in advancing the scientific pursuit of better diagnosis and treatment of BAI to mitigate their human and healthcare costs. It also highlights the need for better diagnostic markers, which exploit the difference between planktonic and biofilm cells.
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Affiliation(s)
- Luanne Hall-Stoodley
- Wellcome Trust Clinical Research Facility, University Hospital Southampton Foundation Trust, Southampton, UK.
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24
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Musat N, Foster R, Vagner T, Adam B, Kuypers MMM. Detecting metabolic activities in single cells, with emphasis on nanoSIMS. FEMS Microbiol Rev 2012; 36:486-511. [DOI: 10.1111/j.1574-6976.2011.00303.x] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 08/22/2011] [Indexed: 11/30/2022] Open
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25
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Wagner M, Haider S. New trends in fluorescence in situ hybridization for identification and functional analyses of microbes. Curr Opin Biotechnol 2011; 23:96-102. [PMID: 22079351 DOI: 10.1016/j.copbio.2011.10.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 10/22/2011] [Indexed: 11/16/2022]
Abstract
Fluorescence in situ hybridization (FISH) has become an indispensable tool for rapid and direct single-cell identification of microbes by detecting signature regions in their rRNA molecules. Recent advances in this field include new web-based tools for assisting probe design and optimization of experimental conditions, easy-to-implement signal amplification strategies, innovative multiplexing approaches, and the combination of FISH with transmission electron microscopy or extracellular staining techniques. Further emerging developments focus on sorting FISH-identified cells for subsequent single-cell genomics and on the direct detection of specific genes within single microbial cells by advanced FISH techniques employing various strategies for massive signal amplification.
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Affiliation(s)
- Michael Wagner
- Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
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26
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Locked nucleic acid and flow cytometry-fluorescence in situ hybridization for the detection of bacterial small noncoding RNAs. Appl Environ Microbiol 2011; 78:14-20. [PMID: 22057868 DOI: 10.1128/aem.06399-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe the development and testing of a high-throughput method that enables the detection of small noncoding RNAs (ncRNAs) from single bacterial cells using locked nucleic acid probes (LNA) and flow cytometry-fluorescence in situ hybridization (flow-FISH). The LNA flow-FISH method and quantitative reverse transcription-PCR (qRT-PCR) were used to monitor the expression of three ncRNAs (6S, CsrB, and TPP-2) in Vibrio campbellii ATCC BAA-1116 cultures during lag phase, mid-log phase, and stationary phase. Both LNA flow-FISH and qRT-PCR revealed that CsrB and TPP-2 were highly expressed during lag phase but markedly reduced in mid-log phase and stationary phase, whereas 6S demonstrated no to little expression during lag phase but increased thereafter. Importantly, while LNA flow-FISH and qRT-PCR demonstrated similar overall expression trends, only LNA flow-FISH, which enabled the detection of ncRNAs in individual cells as opposed to the lysate-based ensemble measurements generated by qRT-PCR, was able to capture the cell-to-cell heterogeneity in ncRNA expression. As such, this study demonstrates a new method that simultaneously enables the in situ detection of ncRNAs and the determination of gene expression heterogeneity within an isogenic bacterial population.
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27
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Moreno Y, Ballesteros L, García-Hernández J, Santiago P, González A, Ferrús MA. Specific detection of viable Listeria monocytogenes in Spanish wastewater treatment plants by Fluorescent In Situ Hybridization and PCR. WATER RESEARCH 2011; 45:4634-4640. [PMID: 21762946 DOI: 10.1016/j.watres.2011.06.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 06/15/2011] [Accepted: 06/15/2011] [Indexed: 05/31/2023]
Abstract
Listeria monocytogenes detection in wastewater can be difficult because of the large amount of background microbiota and the presence of viable but non-culturable forms in this environment. The aim of this study was to evaluate a Fluorescent In Situ Hybridization (FISH) assay combined with Direct Viable Count (DVC) method for detecting viable L. monocytogenes in wastewater samples, as an alternative to conventional culture methods. 16S rRNA sequence data were used to design a specific oligonucleotide probe. In order to assess the suitability of the method, the assays were performed on naturally (n=87) and artificially (n=14) contaminated samples and results were compared to those obtained with the isolation of cells on selective media and with a PCR method. The detection limit of FISH and PCR assays was 10(4) cells/mL without enrichment and 10 cells/mL after enrichment. A total of 47 samples, including 3 samples from effluent sites, yielded FISH positive results for L. monocytogenes. Using DVC-FISH technique, the presence of viable L. monocytogenes cells was detected in 23 out of these 47 FISH positive wastewater samples. PCR and culture methods yielded 27 and 23 positive results, respectively. According to these results, FISH technique has the potential to be used as a sensitive method for the detection and enumeration of L. monocytogenes in environmental wastewater samples.
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Affiliation(s)
- Yolanda Moreno
- Departamento de Biotecnología, Universidad Politécnica de Valencia, Camino de Vera 14, 46022 Valencia, Spain
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28
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Applications of Fluorescence In Situ Hybridization in Diagnostic Microbiology. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Moraru C, Lam P, Fuchs BM, Kuypers MMM, Amann R. GeneFISH--an in situ technique for linking gene presence and cell identity in environmental microorganisms. Environ Microbiol 2011; 12:3057-73. [PMID: 20629705 DOI: 10.1111/j.1462-2920.2010.02281.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Our knowledge concerning the metabolic potentials of as yet to be cultured microorganisms has increased tremendously with the advance of sequencing technologies and the consequent discoveries of novel genes. On the other hand, it is often difficult to reliably assign a particular gene to a phylogenetic clade, because these sequences are usually found on genomic fragments that carry no direct marker of cell identity, such as rRNA genes. Therefore, the aim of the present study was to develop geneFISH - a protocol for linking gene presence with cell identity in environmental samples, the signals of which can be visualized at a single cell level. This protocol combines rRNA-targeted catalysed reporter deposition - fluorescence in situ hybridization and in situ gene detection. To test the protocol, it was applied to seawater samples from the Benguela upwelling system. For gene detection, a polynucleotide probe mix was used, which was designed based on crenarchaeotal amoA clone libraries prepared from each seawater sample. Each probe in the mix was selected to bind to targets with up to 5% mismatches. To determine the hybridization parameters, the T(m) of probes, targets and hybrids was estimated based on theoretical calculations and in vitro measurements. It was shown that at least 30%, but potentially the majority of the Crenarchaeota present in these samples harboured the amoA gene and were therefore likely to be catalysing the oxidation of ammonia.
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Affiliation(s)
- Cristina Moraru
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
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30
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Kumar S, Dagar SS, Mohanty AK, Sirohi SK, Puniya M, Kuhad RC, Sangu KPS, Griffith GW, Puniya AK. Enumeration of methanogens with a focus on fluorescence in situ hybridization. Naturwissenschaften 2011; 98:457-72. [PMID: 21475941 DOI: 10.1007/s00114-011-0791-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 03/19/2011] [Accepted: 03/20/2011] [Indexed: 10/18/2022]
Abstract
Methanogens, the members of domain Archaea are potent contributors in global warming. Being confined to the strict anaerobic environment, their direct cultivation as pure culture is quite difficult. Therefore, a range of culture-independent methods have been developed to investigate their numbers, substrate uptake patterns, and identification in complex microbial communities. Unlike other approaches, fluorescence in situ hybridization (FISH) is not only used for faster quantification and accurate identification but also to reveal the physiological properties and spatiotemporal dynamics of methanogens in their natural environment. Aside from the methodological aspects and application of FISH, this review also focuses on culture-dependent and -independent techniques employed in enumerating methanogens along with associated problems. In addition, the combination of FISH with micro-autoradiography that could also be an important tool in investigating the activities of methanogens is also discussed.
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Affiliation(s)
- Sanjay Kumar
- Dairy Microbiology Division, National Dairy Research Institute, Karnal 132001, India
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31
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Moraru C, Moraru G, Fuchs BM, Amann R. Concepts and software for a rational design of polynucleotide probes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:69-78. [PMID: 23761233 DOI: 10.1111/j.1758-2229.2010.00189.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Fluorescence in situ hybridization (FISH) of genes and mRNA is most often based on polynucleotide probes. However, so far there was no published framework for the rational design of polynucleotide probes. The well-established concepts for oligonucleotide probe design cannot be transferred to polynucleotides. Due to the high allele diversity of genes, a single probe is not sufficient to detect all alleles of a gene. Therefore, the main objective of this study was to develop a concept and software (PolyPro) for rational design of polynucleotide probe mixes to target particular genes. PolyPro consists of three modules: a GenBank Taxonomy Extractor (GTE), a Polynucleotide Probe Designer (PPD) and a Hybridization Parameters Calculator (HPC). The new concept proposes the construction of defined polynucleotide mixes to target the habitat specific sequence diversity of a particular gene. The concept and the software are intended as a first step towards a more frequent application of polynucleotides for in situ identification of mRNA and genes in environmental microbiology.
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Affiliation(s)
- Cristina Moraru
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany HeracleSoftware, Im krummen Arm 2, 28865 Lilienthal, Germany
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32
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Linking Microbial and Ecosystem Ecology Using Ecological Stoichiometry: A Synthesis of Conceptual and Empirical Approaches. Ecosystems 2010. [DOI: 10.1007/s10021-010-9408-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility. Appl Environ Microbiol 2009; 76:922-6. [PMID: 19966029 DOI: 10.1128/aem.02456-09] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) with singly labeled rRNA-targeted oligonucleotide probes is widely applied for direct identification of microbes in the environment or in clinical specimens. Here we show that a replacement of singly labeled oligonucleotide probes with 5'-, 3'-doubly labeled probes at least doubles FISH signal intensity without causing specificity problems. Furthermore, Cy3-doubly labeled probes strongly increase in situ accessibility of rRNA target sites and thus provide more flexibility for probe design.
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34
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Fluorescent in situ hybridization in combination with filter cultivation (FISHFC) method for specific detection and enumeration of viable Clostridium perfringens. Food Microbiol 2009; 26:425-31. [DOI: 10.1016/j.fm.2009.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 02/09/2009] [Accepted: 02/15/2009] [Indexed: 11/18/2022]
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35
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Pilhofer M, Pavlekovic M, Lee NM, Ludwig W, Schleifer KH. Fluorescence in situ hybridization for intracellular localization of nifH mRNA. Syst Appl Microbiol 2009; 32:186-92. [PMID: 19217232 DOI: 10.1016/j.syapm.2008.12.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 12/01/2008] [Accepted: 12/09/2008] [Indexed: 11/18/2022]
Abstract
Few reports on in situ mRNA detection in bacteria have been published, even though a major aim in environmental microbiology is to link function/activity to the identity of the organisms. This study reports a reliable approach for the in situ detection of nifH mRNA using fluorescence hybridization based on a previously described protocol for pmoA. nifH codes for a dinitrogenase reductase, a key enzyme in dinitrogen fixation. nifH mRNA was hybridized with a digoxigenin-labelled polynucleotide probe. The hybrid was detected with an anti-DIG-antibody labelled with horseradish peroxidase. Subsequently, the signal was amplified by catalyzed reporter deposition (CARD) with fluorochrome-labelled tyramides. Furthermore, the imaged organisms were identified using standard fluorescence in situ hybridization of rRNA. Thus, the approach enabled us specifically to link in situ the information from the dinitrogen fixation activity of an organism to its identity. Unexpectedly, the signals derived from nifH mRNA hybridization showed a distinct uneven pattern within the cells. This indicated that the method used could even give insights about the localization of the detected mRNA within the cell, which is a potential use of mRNA fluorescence in situ hybridization (FISH) that has not been reported up to now for bacterial cells.
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Affiliation(s)
- Martin Pilhofer
- Technische Universität München, Lehrstuhl für Mikrobiologie, Am Hochanger 4, 85350 Freising, Germany.
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36
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Park JJ, Byun IG, Park SR, Park TJ. Nitrifying bacterial communities and its activities in aerobic biofilm reactors under different temperature conditions. KOREAN J CHEM ENG 2008. [DOI: 10.1007/s11814-008-0238-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Cerqueira L, Azevedo NF, Almeida C, Jardim T, Keevil CW, Vieira MJ. DNA mimics for the rapid identification of microorganisms by fluorescence in situ hybridization (FISH). Int J Mol Sci 2008; 9:1944-60. [PMID: 19325728 PMCID: PMC2635612 DOI: 10.3390/ijms9101944] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 09/24/2008] [Accepted: 10/06/2008] [Indexed: 12/23/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a well-established technique that is used for a variety of purposes, ranging from pathogen detection in clinical diagnostics to the determination of chromosomal stability in stem cell research. The key step of FISH involves the detection of a nucleic acid region and as such, DNA molecules have typically been used to probe for the sequences of interest. However, since the turn of the century, an increasing number of laboratories have started to move on to the more robust DNA mimics methods, most notably peptide and locked nucleic acids (PNA and LNA). In this review, we will cover the state-of-the-art of the different DNA mimics in regard to their application as efficient markers for the presence of individual microbial cells, and consider their potential advantages and pitfalls. Available PNA probes are then reassessed in terms of sensitivity and specificity using rRNA databases. In addition, we also attempt to predict the applicability of DNA mimics in well-known techniques attempting to detect in situ low number of copies of specific nucleic acid sequences such as catalyzed reporter deposition (CARD) and recognition of individual genes (RING) FISH.
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Affiliation(s)
- Laura Cerqueira
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal. E-Mails:
(L. C.);
(C. A.);
(T. J.);
(M. V.)
| | - Nuno F. Azevedo
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal. E-Mails:
(L. C.);
(C. A.);
(T. J.);
(M. V.)
- Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK. E-Mail:
(N. A.)
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +351-253605413; Fax: +351-253678986
| | - Carina Almeida
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal. E-Mails:
(L. C.);
(C. A.);
(T. J.);
(M. V.)
- Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK. E-Mail:
(N. A.)
| | - Tatiana Jardim
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal. E-Mails:
(L. C.);
(C. A.);
(T. J.);
(M. V.)
| | - Charles William Keevil
- Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK. E-Mail:
(N. A.)
| | - Maria J. Vieira
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal. E-Mails:
(L. C.);
(C. A.);
(T. J.);
(M. V.)
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Fuchizawa I, Shimizu S, Kawai Y, Yamazaki K. Specific detection and quantitative enumeration ofListeriaspp. using fluorescentin situhybridization in combination with filter cultivation (FISHFC). J Appl Microbiol 2008; 105:502-9. [DOI: 10.1111/j.1365-2672.2008.03767.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Quantification of target molecules needed to detect microorganisms by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH. Appl Environ Microbiol 2008; 74:5068-77. [PMID: 18552182 DOI: 10.1128/aem.00208-08] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is a method that is widely used to detect and quantify microorganisms in environmental samples and medical specimens by fluorescence microscopy. Difficulties with FISH arise if the rRNA content of the probe target organisms is low, causing dim fluorescence signals that are not detectable against the background fluorescence. This limitation is ameliorated by technical modifications such as catalyzed reporter deposition (CARD)-FISH, but the minimal numbers of rRNA copies needed to obtain a visible signal of a microbial cell after FISH or CARD-FISH have not been determined previously. In this study, a novel competitive FISH approach was developed and used to determine, based on a thermodynamic model of probe competition, the numbers of 16S rRNA copies per cell required to detect bacteria by FISH and CARD-FISH with oligonucleotide probes in mixed pure cultures and in activated sludge. The detection limits of conventional FISH with Cy3-labeled probe EUB338-I were found to be 370 +/- 45 16S rRNA molecules per cell for Escherichia coli hybridized on glass microscope slides and 1,400 +/- 170 16S rRNA copies per E. coli cell in activated sludge. For CARD-FISH the values ranged from 8.9 +/- 1.5 to 14 +/- 2 and from 36 +/- 6 to 54 +/- 7 16S rRNA molecules per cell, respectively, indicating that the sensitivity of CARD-FISH was 26- to 41-fold higher than that of conventional FISH. These results suggest that optimized FISH protocols using oligonucleotide probes could be suitable for more recent applications of FISH (for example, to detect mRNA in situ in microbial cells).
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Wilhartitz I, Mach RL, Teira E, Reinthaler T, Herndl GJ, Farnleitner AH. Prokaryotic community analysis with CARD-FISH in comparison with FISH in ultra-oligotrophic ground- and drinking water. J Appl Microbiol 2008; 103:871-81. [PMID: 17897189 PMCID: PMC3160464 DOI: 10.1111/j.1365-2672.2007.03319.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS We compared the applicability of catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and FISH to enumerate prokaryotic populations in ultra-oligotrophic alpine groundwaters and bottled mineral water METHODS AND RESULTS Fluorescent oligonucleotide probes EUB338 and EUB338mix (EUB338/EUB338-II/EUB338-III) were used to enumerate bacteria and probes EURY806 and CREN537 for Euryarchaea and Crenarchaea, respectively. Improved detection of Planctomycetales by probe EUB338-II was tested using a different permeabilization step (proteinase K instead of lysozyme). Total detection efficiency of cells in spring water of four different alpine karst aquifers was on average 83% for CARD-FISH and only 15% for FISH. Applying CARD-FISH on bottled natural mineral waters resulted in an average total hybridization efficiency of 89%, with 78% (range 77-96%) bacteria and 11% (range 3-22%) identified as Archaea. CONCLUSIONS CARD-FISH resulted in substantially higher recovery efficiency than FISH. Hence, CARD-FISH appears very suitable for the enumeration of specific prokaryotic groups in ground- and drinking water. SIGNIFICANCE AND IMPACT OF THE STUDY This study represents the first evaluation of CARD-FISH on ultra-oligotrophic ground- and drinking water. Results are relevant for basic research and drinking water distributors. Archaea can comprise a significant fraction of the prokaryotic community in bottled mineral water.
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Affiliation(s)
- Inés Wilhartitz
- Institute of Chemical Engineering, Department for Applied Biochemistry and Gene Technology, Vienna University of Technology, Getreidemarkt 166-9, A-1060 Vienna
| | - Robert L. Mach
- Institute of Chemical Engineering, Department for Applied Biochemistry and Gene Technology, Vienna University of Technology, Getreidemarkt 166-9, A-1060 Vienna
| | - Eva Teira
- Departamento Ecoloxía e Bioloxía Animal, Universidade de Vigo, Campus Lagoas-Marcosende, 36200-Vigo, Spain
| | - Thomas Reinthaler
- Netherlands Institute for Sea Research, Department of Biological Oceanography, 1790 AB Den Burg, Texel
| | - Gerhard J. Herndl
- Netherlands Institute for Sea Research, Department of Biological Oceanography, 1790 AB Den Burg, Texel
| | - Andreas H. Farnleitner
- Institute of Chemical Engineering, Department for Applied Biochemistry and Gene Technology, Vienna University of Technology, Getreidemarkt 166-9, A-1060 Vienna
- For correspondence. ; +43-1-58801-17252, Institute of Chemical Engineering, Department for Applied Biochemistry and Gene Technology, Vienna University of Technology, Getreidemarkt 166-9, A-1060 Vienna
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mRNA-targeted fluorescent in situ hybridization (FISH) of Gram-negative bacteria without template amplification or tyramide signal amplification. J Microbiol Methods 2007; 71:246-55. [DOI: 10.1016/j.mimet.2007.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 08/15/2007] [Accepted: 09/03/2007] [Indexed: 11/21/2022]
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Smolina I, Lee C, Frank-Kamenetskii M. Detection of low-copy-number genomic DNA sequences in individual bacterial cells by using peptide nucleic acid-assisted rolling-circle amplification and fluorescence in situ hybridization. Appl Environ Microbiol 2007; 73:2324-8. [PMID: 17293504 PMCID: PMC1855634 DOI: 10.1128/aem.02038-06] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An approach is proposed for in situ detection of short signature DNA sequences present in single copies per bacterial genome. The site is locally opened by peptide nucleic acids, and a circular oligonucleotide is assembled. The amplicon generated by rolling circle amplification is detected by hybridization with fluorescently labeled decorator probes.
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Affiliation(s)
- Irina Smolina
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington St., Boston, MA 02215, USA
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43
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Tubbs RR, Das K, Cook JR, Pettay JD, Roche PC, Grogan T. Genotyping of phenotypically defined cells in neoplasia: enhanced immunoFISH via tyramide signal amplification (TSA) segregates immunophenotypically-defined cell populations for gated genotyping. J Mol Histol 2007; 38:129-34. [PMID: 17205377 DOI: 10.1007/s10735-006-9074-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Accepted: 12/11/2006] [Indexed: 12/31/2022]
Abstract
Molecular morphologic tools exist for simultaneously visualizing immunophenotype and genotype of tumors, but are frequently hampered by a delicate balance between removing sufficient amount of the protein blocking full access of the probe to hybridize to target nucleic acids while still preserving sufficient target antigen for immunophenotyping. The result is often suboptimal, with either insufficiently visualized gene deletions and amplifications due to masking protein, or overdigestion of the protein target. Our purpose was to design and validate a gated genotyping assay that enables optimal and concomitant detection of both gene and protein. Using the proliferating endothelial cell compartment within gliomas organized in a tissue microarray (TMA), we tested the hypothesis that tyramide signal amplification (TSA) with deposition of a fluorochrome could be used during immunophenotyping, permitting sufficient protein digestion while insuring probe accessibility to nucleic acid target. The method was successfully validated using a TMA containing 38 glioma cases previously genotyped for EGFR amplification. CD31 positive endothelial cells were segregated via TSA-based Alexa-Fluor 647 immunofluorescence for analysis of EGFR amplification of the gliomas organized in the TMA. Enhanced immunoFISH (TSA) successfully segregates immunophenotypically-defined cell populations for gated genotyping.
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Affiliation(s)
- Raymond R Tubbs
- Department of Clinical Pathology - L11, Cleveland Clinic Foundation and the Cleveland Clinic Lerner College of Medicine, Cleveland, OH 44195, USA.
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Moroni O, Kheadr E, Boutin Y, Lacroix C, Fliss I. Inactivation of adhesion and invasion of food-borne Listeria monocytogenes by bacteriocin-producing Bifidobacterium strains of human origin. Appl Environ Microbiol 2006; 72:6894-901. [PMID: 16936051 PMCID: PMC1636179 DOI: 10.1128/aem.00928-06] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Accepted: 08/14/2006] [Indexed: 01/16/2023] Open
Abstract
Three bacteriocin-producing bifidobacterial isolates from newborns were identified as Bifidobacterium thermacidophilum (two strains) and B. thermophilum (one strain). This study was undertaken to evaluate the ability of these strains to compete with food-borne Listeria monocytogenes for adhesion and invasion sites on Caco-2 and HT-29 cells. The bifidobacteria adhered at levels ranging from 4% to 10% of the CFU added, but none of the bifidobacteria were able to invade cells. The abilities of Listeria to adhere to and to invade cells varied widely depending on the strain tested. Three groups of Listeria were identified based on invasiveness: weakly invasive, moderately invasive, and highly invasive strains. One strain from each group was tested in competition with bifidobacteria. B. thermacidophilum RBL70 was the most effective in blocking invasion of Listeria, and the decreases in invasion ranged from 38% to 90%. For all three bifidobacterial strains, contact between the cell monolayer and the bifidobacteria for 1 h before exposure to Listeria increased the degree of inhibition. Finally, visualization of competition for adhesion sites on cells by fluorescent in situ hybridization suggested that the two bacteria tended to adhere in close proximity.
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Affiliation(s)
- Olivier Moroni
- STELA Dairy Research Center, Nutraceuticals and Functional Foods Institute (INAF), Pavillon Paul Comtois, Université Laval, Québec, Québec, Canada
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Bottari B, Ercolini D, Gatti M, Neviani E. Application of FISH technology for microbiological analysis: current state and prospects. Appl Microbiol Biotechnol 2006; 73:485-94. [PMID: 17051413 DOI: 10.1007/s00253-006-0615-z] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 07/13/2006] [Accepted: 08/08/2006] [Indexed: 02/07/2023]
Abstract
In order to identify and quantify the microorganisms present in a certain ecosystem, it has become necessary to develop molecular methods avoiding cultivation, which allows to characterize only the countable part of the microorganisms in the sample, therefore losing the information related to the microbial component which presents a vitality condition, although it cannot duplicate in culture medium. In this context, one of the most used techniques is fluorescence in situ hybridization (FISH) with ribosomal RNA targeted oligonucleotide probes. Owing to its speed and sensitivity, this technique is considered a powerful tool for phylogenetic, ecological, diagnostic and environmental studies in microbiology. Through the use of species-specific probes, it is possible to identify different microorganisms in complex microbial communities, thus providing a solid support to the understanding of inter-species interaction. The knowledge of the composition and distribution of microorganisms in natural habitats can be interesting for ecological reasons in microbial ecology, and for safety and technological aspects in food microbiology. Methodological aspects, use of different probes and applications of FISH to microbial ecosystems are presented in this review.
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Affiliation(s)
- Benedetta Bottari
- Department of Genetic, Biology of Microorganisms, Anthropology, Evolution, University of Parma, via Usberti 11/A, 43100 Parma, Italy.
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46
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Kubota K, Ohashi A, Imachi H, Harada H. Visualization of mcr mRNA in a methanogen by fluorescence in situ hybridization with an oligonucleotide probe and two-pass tyramide signal amplification (two-pass TSA–FISH). J Microbiol Methods 2006; 66:521-8. [PMID: 16545875 DOI: 10.1016/j.mimet.2006.02.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Revised: 02/03/2006] [Accepted: 02/07/2006] [Indexed: 10/24/2022]
Abstract
Two-pass tyramide signal amplification-fluorescence in situ hybridization (two-pass TSA-FISH) with a horseradish peroxidase (HRP)-labeled oligonucleotide probe was applied to detect prokaryotic mRNA. In this study, mRNA of a key enzyme for methanogenesis, methyl coenzyme M reductase (mcr), in Methanococcus vannielii was targeted. Applicability of mRNA-targeted probes to in situ hybridization was verified by Clone-FISH. It was observed that sensitivity of two-pass TSA-FISH was significantly higher than that of TSA-FISH, which was further increased by the addition of dextran sulphate in TSA working solution. Signals from two-pass TSA-FISH were more reliable compared to the weak, spotty signals yielded by TSA-FISH.
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MESH Headings
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- Fluorescent Dyes/chemistry
- Horseradish Peroxidase/chemistry
- In Situ Hybridization, Fluorescence/methods
- Methanococcus/enzymology
- Methanococcus/genetics
- Microscopy, Fluorescence
- Oligonucleotide Probes
- Oxidoreductases/genetics
- Oxidoreductases/isolation & purification
- Polymerase Chain Reaction
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- Sensitivity and Specificity
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Affiliation(s)
- Kengo Kubota
- Department of Environmental Systems Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
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Kutter S, Hartmann A, Schmid M. Colonization of barley (Hordeum vulgare) with Salmonella enterica and Listeria spp. FEMS Microbiol Ecol 2006; 56:262-71. [PMID: 16629755 DOI: 10.1111/j.1574-6941.2005.00053.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Colonization of barley plants by the food-borne pathogens Salmonella enterica serovar typhimurium and three Listeria spp. (L. monocytogenes, L. ivanovii, L. innocua) was investigated in a monoxenic system. Herbaspirillum sp. N3 was used as a positive control and Escherichia coli HB101 as a negative control for endophytic root colonization. Colonization of the plants was tested 1-4 weeks after inoculation by determination of CFU, specific PCR assays and fluorescence in situ hybridization (FISH) with fluorescently labelled oligonucleotide probes in combination with confocal laser scanning microscopy (CLSM). Both S. enterica strains were found as endophytic colonizers of barley roots and reached up to 2.3 x 10(6) CFU per g root fresh weight after surface sterilization. The three Listeria strains had 10-fold fewer cell numbers after surface sterilization on the roots and therefore were similar to the results of nonendophytic colonizers, such as E. coli HB101. The FISH/CSLM approach demonstrated not only high-density colonization of the root hairs and the root surface by S. enterica but also a spreading to subjacent rhizodermis layers and the inner root cortex. By contrast, the inoculated Listeria spp. colonized the root hair zone but did not colonize other parts of the root surface. Endophytic colonization of Listeria spp. was not observed. Finally, a systemic spreading of S. enterica to the plant shoot (stems and leaves) was demonstrated using a specific PCR analysis and plate count technique.
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Affiliation(s)
- Stefan Kutter
- GSF-National Research Center for Environment and Health, Department of Rhizosphere Biology, Institute of Soil Ecology, Neuherberg, Germany
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Maruyama F, Kenzaka T, Yamaguchi N, Tani K, Nasu M. Visualization and enumeration of bacteria carrying a specific gene sequence by in situ rolling circle amplification. Appl Environ Microbiol 2006; 71:7933-40. [PMID: 16332770 PMCID: PMC1317385 DOI: 10.1128/aem.71.12.7933-7940.2005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Rolling circle amplification (RCA) generates large single-stranded and tandem repeats of target DNA as amplicons. This technique was applied to in situ nucleic acid amplification (in situ RCA) to visualize and count single Escherichia coli cells carrying a specific gene sequence. The method features (i) one short target sequence (35 to 39 bp) that allows specific detection; (ii) maintaining constant fluorescent intensity of positive cells permeabilized extensively after amplicon detection by fluorescence in situ hybridization, which facilitates the detection of target bacteria in various physiological states; and (iii) reliable enumeration of target bacteria by concentration on a gelatin-coated membrane filter. To test our approach, the presence of the following genes were visualized by in situ RCA: green fluorescent protein gene, the ampicillin resistance gene and the replication origin region on multicopy pUC19 plasmid, as well as the single-copy Shiga-like toxin gene on chromosomes inside E. coli cells. Fluorescent antibody staining after in situ RCA also simultaneously identified cells harboring target genes and determined the specificity of in situ RCA. E. coli cells in a nonculturable state from a prolonged incubation were periodically sampled and used for plasmid uptake study. The numbers of cells taking up plasmids determined by in situ RCA was up to 10(6)-fold higher than that measured by selective plating. In addition, in situ RCA allowed the detection of cells taking up plasmids even when colony-forming cells were not detected during the incubation period. By optimizing the cell permeabilization condition for in situ RCA, this method can become a valuable tool for studying free DNA uptake, especially in nonculturable bacteria.
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Affiliation(s)
- Fumito Maruyama
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka 565-0871, Japan
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Churchill RLT, Lee H, Hall JC. Detection of Listeria monocytogenes and the toxin listeriolysin O in food. J Microbiol Methods 2005; 64:141-70. [PMID: 16310269 DOI: 10.1016/j.mimet.2005.10.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2005] [Revised: 10/14/2005] [Accepted: 10/14/2005] [Indexed: 10/25/2022]
Abstract
Listeria monocytogenes is an emerging bacterial foodborne pathogen responsible for listeriosis, an illness characterized by meningitis, encephalitis, and septicaemia. Less commonly, infection can result in cutaneous lesions and flu-like symptoms. In pregnant women, the pathogen can cause bacteraemia, and stillbirth or premature birth of the fetus. The mortality rate for those contracting listeriosis is approximately 20%. Currently, the United States has a zero tolerance policy regarding the presence of L. monocytogenes in food, while Canada allows only 100 cfu/g of food. As such, it is essential to be able to detect the pathogen in low numbers in food samples. One of the best ways to detect and confirm the pathogen is through the detection of one of the virulence factors, listeriolysin O (LLO) produced by the microorganism. The LLO-encoding gene (hlyA) is present only in virulent strains of the species and is required for virulence. LLO is a secreted protein toxin that can be detected easily with the use of blood agar or haemolysis assays and it is well characterized and understood. This paper focuses on some of the common methods used to detect the pathogen and the LLO toxin in food products and comments on some of the potential uses and drawbacks for the food industry.
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Affiliation(s)
- Robin L T Churchill
- Department of Environmental Biology, University of Guelph, Guelph, ON, Canada
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50
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Brehm-Stecher BF, Hyldig-Nielsen JJ, Johnson EA. Design and evaluation of 16S rRNA-targeted peptide nucleic acid probes for whole-cell detection of members of the genus Listeria. Appl Environ Microbiol 2005; 71:5451-7. [PMID: 16151137 PMCID: PMC1214657 DOI: 10.1128/aem.71.9.5451-5457.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Six fluorescein-labeled peptide nucleic acid oligomers targeting Listeria-specific sequences on the 16S ribosomal subunit were evaluated for their abilities to hybridize to whole cells by fluorescence in situ hybridization (FISH). Four of these probes yielded weak or no fluorescent signals after hybridization and were not investigated further. The remaining two FISH-compatible probes, LisUn-3 and LisUn-11, were evaluated for their reactivities against 22 Listeria strains and 17 other bacterial strains belonging to 10 closely related genera. Hybridization with BacUni-1, a domain-specific eubacterial probe, was used as a positive control for target accessibility in both Listeria spp. and nontarget cells. RNase T1 treatment of select cell types was used to confirm that positive fluorescence responses were rRNA dependent and to examine the extent of nonspecific staining of nontarget cells. Both LisUn-3 and LisUn-11 yielded rapid, bright, and genus-specific hybridizations at probe concentrations of approximately 100 pmol ml(-1). LisUn-11 was the brightest probe and stained all six Listeria species. LisUn-3 hybridized with all Listeria spp. except for L. grayi, for which it had two mismatched bases. A simple ethanolic fixation yielded superior results with Listeria spp. compared to fixation in 10% buffered formalin and was applicable to all cell types studied. This study highlights the advantages of peptide nucleic acid probes for FISH-based detection of gram-positive bacteria and provides new tools for the rapid detection of Listeria spp. These probes may be useful for the routine monitoring of food production environments in support of efforts to control L. monocytogenes.
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Affiliation(s)
- Byron F Brehm-Stecher
- Department of Food Science and Human Nutrition, 2312 Food Sciences Building, Iowa State University, Ames, IA 50011, USA.
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