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Sousa C, Ferreira R, Santos SB, Azevedo NF, Melo LDR. Advances on diagnosis of Helicobacter pylori infections. Crit Rev Microbiol 2023; 49:671-692. [PMID: 36264672 DOI: 10.1080/1040841x.2022.2125287] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022]
Abstract
The association of Helicobacter pylori to several gastric diseases, such as chronic gastritis, peptic ulcer disease, and gastric cancer, and its high prevalence worldwide, raised the necessity to use methods for a proper and fast diagnosis and monitoring the pathogen eradication. Available diagnostic methods can be classified as invasive or non-invasive, and the selection of the best relies on the clinical condition of the patient, as well as on the sensitivity, specificity, and accessibility of the diagnostic test. This review summarises all diagnostic methods currently available, including the invasive methods: endoscopy, histology, culture, and molecular methods, and the rapid urease test (RUT), as well as the non-invasive methods urea breath test (UBT), serological assays, biosensors, and microfluidic devices and the stool antigen test (SAT). Moreover, it lists the diagnostic advantages and limitations, as well as the main advances for each methodology. In the end, research on the development of new diagnostic methods, such as bacteriophage-based H. pylori diagnostic tools, is also discussed.
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Affiliation(s)
- Cláudia Sousa
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Rute Ferreira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Sílvio B Santos
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Luís D R Melo
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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2
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Barbosa A, Miranda S, Azevedo NF, Cerqueira L, Azevedo AS. Imaging biofilms using fluorescence in situ hybridization: seeing is believing. Front Cell Infect Microbiol 2023; 13:1195803. [PMID: 37284501 PMCID: PMC10239779 DOI: 10.3389/fcimb.2023.1195803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
Biofilms are complex structures with an intricate relationship between the resident microorganisms, the extracellular matrix, and the surrounding environment. Interest in biofilms is growing exponentially given its ubiquity in so diverse fields such as healthcare, environmental and industry. Molecular techniques (e.g., next-generation sequencing, RNA-seq) have been used to study biofilm properties. However, these techniques disrupt the spatial structure of biofilms; therefore, they do not allow to observe the location/position of biofilm components (e.g., cells, genes, metabolites), which is particularly relevant to explore and study the interactions and functions of microorganisms. Fluorescence in situ hybridization (FISH) has been arguably the most widely used method for an in situ analysis of spatial distribution of biofilms. In this review, an overview on different FISH variants already applied on biofilm studies (e.g., CLASI-FISH, BONCAT-FISH, HiPR-FISH, seq-FISH) will be explored. In combination with confocal laser scanning microscopy, these variants emerged as a powerful approach to visualize, quantify and locate microorganisms, genes, and metabolites inside biofilms. Finally, we discuss new possible research directions for the development of robust and accurate FISH-based approaches that will allow to dig deeper into the biofilm structure and function.
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Affiliation(s)
- Ana Barbosa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Sónia Miranda
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Laura Cerqueira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Andreia S. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
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Azevedo AS, Fernandes RM, Faria AR, Silvestre OF, Nieder JB, Lou C, Wengel J, Almeida C, Azevedo NF. Spectral imaging and nucleic acid mimics fluorescence in situ hybridization (SI-NAM-FISH) for multiplex detection of clinical pathogens. Front Microbiol 2022; 13:976639. [PMID: 36246234 PMCID: PMC9557775 DOI: 10.3389/fmicb.2022.976639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
The application of nucleic acid mimics (NAMs), such as locked nucleic acid (LNA) and 2′-O-methyl-RNA (2’OMe), has improved the performance of fluorescence in situ hybridization (FISH) methods for the detection/location of clinical pathogens since they provide design versatility and thermodynamic control. However, an important limitation of FISH techniques is the low number of distinguishable targets. The use of filters in fluorescence image acquisition limits the number of fluorochromes that can be simultaneously differentiated. Recent advances in fluorescence spectral image acquisition have allowed the unambiguous identification of several microorganisms in a single sample. In this work, we aimed to combine NAM-FISH and spectral image analysis to develop and validate a new FISH variant, the spectral imaging-NAM-FISH (SI-NAM-FISH), that allows a multiplexed, robust and rapid detection of clinical pathogens. In the first stage, to implement/validate the method, we have selected seven fluorochromes with distinct spectral properties and seven bacterial species (Pseudomonas aeruginosa, Citrobacter freundii, Staphylococcus aureus, Enterococcus faecalis, Klebsiella pneumoniae, Escherichia coli, and Acinetobacter calcoaceticus). As a strong variation in fluorescence intensities is found between species and between fluorochromes, seven versions of a EUB LNA/2’OMe probe, each conjugated to one of seven fluorochromes, were used to rank species/fluorochromes by FISH and then optimize species/fluorochrome pairing. Then, final validation tests were performed using mixed populations to evaluate the potential of the technique for separating/quantifying the different targets. Overall, validation tests with different proportions of bacteria labeled with the respective fluorochrome have shown the ability of the method to correctly distinguish the species.
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Affiliation(s)
- Andreia S. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
- *Correspondence: Andreia S. Azevedo,
| | - Ricardo M. Fernandes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Vila Do Conde, Portugal
| | - Ana R. Faria
- INL International Iberian Nanotechnology Laboratory, Av Mestre José Veiga s/n, Braga, Portugal
| | - Oscar F. Silvestre
- INL International Iberian Nanotechnology Laboratory, Av Mestre José Veiga s/n, Braga, Portugal
| | - Jana B. Nieder
- INL International Iberian Nanotechnology Laboratory, Av Mestre José Veiga s/n, Braga, Portugal
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Carina Almeida
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Vila Do Conde, Portugal
| | - Nuno F. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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4
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The role of Nucleic Acid Mimics (NAMs) on FISH-based techniques and applications for microbial detection. Microbiol Res 2022; 262:127086. [PMID: 35700584 DOI: 10.1016/j.micres.2022.127086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 01/07/2023]
Abstract
Fluorescent in situ hybridization (FISH) is a powerful tool that for more than 30 years has allowed to detect and quantify microorganisms as well as to study their spatial distribution in three-dimensional structured environments such as biofilms. Throughout these years, FISH has been improved in order to face some of its earlier limitations and to adapt to new research objectives. One of these improvements is related to the emergence of Nucleic Acid Mimics (NAMs), which are now employed as alternatives to the DNA and RNA probes that have been classically used in FISH. NAMs such as peptide and locked nucleic acids (PNA and LNA) have provided enhanced sensitivity and specificity to the FISH technique, as well as higher flexibility in terms of applications. In this review, we aim to cover the state-of-the-art of the different NAMs and explore their possible applications in FISH, providing a general overview of the technique advancement in the last decades.
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Deb R, Pal P, Chaudhary P, Bhadsavle S, Behera M, Parmanand, Gautam D, Roshan M, Vats A, Ludri A, Gupta VK, De S. Development of gold nanoparticle-based visual assay for rapid detection of Escherichia coli specific DNA in milk of cows affected with mastitis. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Rombouts S, Nollmann M. RNA imaging in bacteria. FEMS Microbiol Rev 2021; 45:5917984. [PMID: 33016325 DOI: 10.1093/femsre/fuaa051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/01/2020] [Indexed: 12/25/2022] Open
Abstract
The spatiotemporal regulation of gene expression plays an essential role in many biological processes. Recently, several imaging-based RNA labeling and detection methods, both in fixed and live cells, were developed and now enable the study of transcript abundance, localization and dynamics. Here, we review the main single-cell techniques for RNA visualization with fluorescence microscopy and describe their applications in bacteria.
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Affiliation(s)
- Sara Rombouts
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 Rue de Navacelles, 34090, Montpellier, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 Rue de Navacelles, 34090, Montpellier, France
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Pereira S, Yao R, Gomes M, Jørgensen PT, Wengel J, Azevedo NF, Sobral Santos R. Can Vitamin B12 Assist the Internalization of Antisense LNA Oligonucleotides into Bacteria? Antibiotics (Basel) 2021; 10:antibiotics10040379. [PMID: 33916701 PMCID: PMC8065541 DOI: 10.3390/antibiotics10040379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/18/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022] Open
Abstract
The emergence of bacterial resistance to traditional small-molecule antibiotics is fueling the search for innovative strategies to treat infections. Inhibiting the expression of essential bacterial genes using antisense oligonucleotides (ASOs), particularly composed of nucleic acid mimics (NAMs), has emerged as a promising strategy. However, their efficiency depends on their association with vectors that can translocate the bacterial envelope. Vitamin B12 is among the largest molecules known to be taken up by bacteria and has very recently started to gain interest as a trojan-horse vector. Gapmers and steric blockers were evaluated as ASOs against Escherichia coli (E. coli). Both ASOs were successfully conjugated to B12 by copper-free azide-alkyne click-chemistry. The biological effect of the two conjugates was evaluated together with their intracellular localization in E. coli. Although not only B12 but also both B12-ASO conjugates interacted strongly with E. coli, they were mostly colocalized with the outer membrane. Only 6–9% were detected in the cytosol, which showed to be insufficient for bacterial growth inhibition. These results suggest that the internalization of B12-ASO conjugates is strongly affected by the low uptake rate of the B12 in E. coli and that further studies are needed before considering this strategy against biofilms in vivo.
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Affiliation(s)
- Sara Pereira
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, R. Dr. Roberto Frias, 4200-465 Porto, Portugal; (S.P.); (M.G.); (N.F.A.)
| | - Ruwei Yao
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (R.Y.); (P.T.J.); (J.W.)
| | - Mariana Gomes
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, R. Dr. Roberto Frias, 4200-465 Porto, Portugal; (S.P.); (M.G.); (N.F.A.)
| | - Per Trolle Jørgensen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (R.Y.); (P.T.J.); (J.W.)
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (R.Y.); (P.T.J.); (J.W.)
| | - Nuno Filipe Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, R. Dr. Roberto Frias, 4200-465 Porto, Portugal; (S.P.); (M.G.); (N.F.A.)
| | - Rita Sobral Santos
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, R. Dr. Roberto Frias, 4200-465 Porto, Portugal; (S.P.); (M.G.); (N.F.A.)
- Correspondence:
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8
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Oliveira R, Azevedo AS, Mendes L. Application of Nucleic Acid Mimics in Fluorescence In Situ Hybridization. Methods Mol Biol 2021; 2246:69-86. [PMID: 33576983 DOI: 10.1007/978-1-0716-1115-9_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Traditionally, RNA and DNA probes are used in fluorescence in situ hybridization (FISH) methods for microbial detection and characterization of communities' structure and diversity. However, the recent introduction of nucleic acid mimics (NAMs) has improved the robustness of the FISH methods in terms of sensitivity and specificity. Several NAMs have been used, of which the most relevant are peptide nucleic acid (PNA), locked nucleic acids (LNA), 2'-O-methyl RNA (2'OMe), and phosphorothioates (PS). In this chapter, we describe a protocol using PNA and LNA/2'OMe probes for microbial detection by FISH, pointing out the differences between them. These protocols are easily adapted to different microorganisms and different probe sequences.
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Affiliation(s)
- Ricardo Oliveira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Andreia S Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal.,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Luzia Mendes
- FMDUP - Faculty of Dental Medicine, University of Porto, Porto, Portugal.
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Abstract
FISH has gained an irreplaceable place in microbiology because of its ability to detect and locate a microorganism, or a group of organisms, within complex samples. However, FISH role has evolved drastically in the last few decades and its value has been boosted by several advances in signal intensity, imaging acquisitions, automation, method robustness, and, thus, versatility. This has resulted in a range of FISH variants that gave researchers the ability to access a variety of other valuable information such as complex population composition, metabolic activity, gene detection/quantification, or subcellular location of genetic elements. In this chapter, we will review the more relevant FISH variants, their intended use, and how they address particular challenges of classical FISH.
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Affiliation(s)
- Nuno M Guimarães
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.
| | - Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
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Teixeira H, Sousa AL, Azevedo AS. Bioinformatic Tools and Guidelines for the Design of Fluorescence In Situ Hybridization Probes. Methods Mol Biol 2021; 2246:35-50. [PMID: 33576981 DOI: 10.1007/978-1-0716-1115-9_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Fluorescence in situ hybridization (FISH) is a well-established technique that allows the detection of microorganisms in diverse types of samples (e.g., clinical, food, environmental samples, and biofilm communities). The FISH probe design is an essential step in this technique. For this, two strategies can be used, the manual form based on multiple sequence alignment to identify conserved regions and programs/software specifically developed for the selection of the sequence of the probe. Additionally, databases/software for the theoretical evaluation of the probes in terms of specificity, sensitivity, and thermodynamic parameters (melting temperature and Gibbs free energy change) are used. The purpose of this chapter is to describe the essential steps and guidelines for the design of FISH probes (e.g., DNA and Nucleic Acid Mimic (NAM) probes), and its theoretical evaluation through the application of diverse bioinformatic tools.
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Affiliation(s)
- Helena Teixeira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Ana L Sousa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Andreia S Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal. .,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal. .,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
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Lahiri H, Mishra S, Mukhopadhyay R. Nanoscale Nucleic Acid Recognition at the Solid-Liquid Interface Using Xeno Nucleic Acid Probes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8875-8888. [PMID: 30398876 DOI: 10.1021/acs.langmuir.8b02770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Challenges in reliable nucleic acid detection are manifold. The major ones are related to false positive or negative signals due to a lack of target specificity in detection and to low sensitivity, especially when a plethora of background sequences are present that can mask the specific recognition signal. Utilizing designed synthetic nucleic acids that are commonly called xeno nucleic acids could offer potential routes to meeting such challenges. In this article, we present the general framework of nucleic acid detection, especially for nanoscale applications, and discuss how and why the xeno nucleic acids could be truly an alternative to the DNA probes. Two specific cases, locked nucleic acid (LNA) and peptide nucleic acid (PNA), which are nuclease-resistant and can form thermally stable duplexes with DNA, are addressed. It is shown that the relative ease of the conformationally rigid LNA probe to be oriented upright on the substrate surface and of the nonionic PNA probe to result into high probe density assists in their use in nanoscale nucleic acid recognition. It is anticipated that success with these probes may lead to important developments such as PCR-independent approaches where the major aim is to detect a small number of target sequences present in the analyte medium.
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Affiliation(s)
- Hiya Lahiri
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Sourav Mishra
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Rupa Mukhopadhyay
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
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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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Andersen VL, Vinther M, Kumar R, Ries A, Wengel J, Nielsen JS, Kjems J. A self-assembled, modular nucleic acid-based nanoscaffold for multivalent theranostic medicine. Am J Cancer Res 2019; 9:2662-2677. [PMID: 31131060 PMCID: PMC6525989 DOI: 10.7150/thno.32060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
Rationale: Within the field of personalized medicine there is an increasing focus on designing flexible, multifunctional drug delivery systems that combine high efficacy with minimal side effects, by tailoring treatment to the individual. Methods: We synthesized a chemically stabilized ~4 nm nucleic acid nanoscaffold, and characterized its assembly, stability and functional properties in vitro and in vivo. We tested its flexibility towards multifunctionalization by conjugating various biomolecules to the four modules of the system. The pharmacokinetics, targeting capability and bioimaging properties of the structure were investigated in mice. The role of avidity in targeted liver cell internalization was investigated by flow cytometry, confocal microscopy and in vivo by fluorescent scanning of the blood and organs of the animals. Results: We have developed a nanoscaffold that rapidly and with high efficiency can self-assemble four chemically conjugated functionalities into a stable, in vivo-applicable system with complete control of stoichiometry and site specificity. The circulation time of the nanoscaffold could be tuned by functionalization with various numbers of polyethylene glycol polymers or with albumin-binding fatty acids. Highly effective hepatocyte-specific internalization was achieved with increasing valencies of tri-antennary galactosamine (triGalNAc) in vitro and in vivo. Conclusion: With its facile functionalization, stoichiometric control, small size and high serum- and thermostability, the nanoscaffold presented here constitutes a novel and flexible platform technology for theranostics.
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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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15
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Mishra S, Lee Y, Park JW. Direct Quantification of Trace Amounts of a Chronic Myeloid Leukemia Biomarker Using Locked Nucleic Acid Capture Probes. Anal Chem 2018; 90:12824-12831. [PMID: 30272952 DOI: 10.1021/acs.analchem.8b03350] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular monitoring is indispensable for the clinical management of chronic myeloid leukemia (CML) patients. Real-time quantitative polymerase chain reaction (RT-qPCR) is the gold standard for the quantitative assessment of BCR-ABL transcript levels, which are critical in clinical decision-making. However, the frequent recurrence of the disease after drug discontinuation for 60% of patients has necessitated more sensitive and specific techniques to detect residual BCR-ABL transcripts. Here, we describe a quantification method for the detection of BCR-ABL targets at very low concentrations (<10 copies/sample) in the presence of a million copies of normal BCR and ABL genes. In this method, a fully modified locked nucleic acid (LNA) and a LNA/DNA chimera were used as capture probes, and the quantitative imaging mode of atomic force microscopy (AFM) was employed. Targets with one of the major breakpoints (found in more than 95% of CML patients), b3a2 and b2a2, were quantified. The BCR-ABL target captured on a miniaturized LNA-probe spot was scanned at nanometric resolution, and the samples containing one to ten copies of the BCR-ABL genes were examined. It was observed that the highest sensitivity, i.e., the detection of a single copy of the target gene, could be achieved through multiple runs, and the observed cluster number was well correlative (adjusted R2 = 0.999) to the target copy number in the sample solution. This observation clearly demonstrates that the LNA-based platform is effective in quantifying BCR-ABL targets with extremely low copy numbers, highlighting the potential applicability of AFM for use in the direct quantification of such targets without amplification or labeling.
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Affiliation(s)
- Sourav Mishra
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Yoonhee Lee
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Joon Won Park
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
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16
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Lima JF, Carvalho J, Pinto-Ribeiro I, Almeida C, Wengel J, Cerqueira L, Figueiredo C, Oliveira C, Azevedo NF. Targeting miR-9 in gastric cancer cells using locked nucleic acid oligonucleotides. BMC Mol Biol 2018; 19:6. [PMID: 29879907 PMCID: PMC5992815 DOI: 10.1186/s12867-018-0107-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 05/28/2018] [Indexed: 12/21/2022] Open
Abstract
Background Gastric cancer is the third leading cause of cancer-related mortality worldwide. Recently, it has been demonstrated that gastric cancer cells display a specific miRNA expression profile, with increasing evidence of the role of miRNA-9 in this disease. miRNA-9 upregulation has been shown to influence the expression of E-cadherin-encoding gene, triggering cell motility and invasiveness. Results In this study, we designed LNA anti-miRNA oligonucleotides with a complementary sequence to miRNA-9 and tested their properties to both detect and silence the target miRNA. We could identify and visualize the in vitro uptake of low-dosing LNA-based anti-miRNA oligonucleotides without any carrier or transfection agent, as early as 2 h after the addition of the oligonucleotide sequence to the culture medium. Furthermore, we were able to assess the silencing potential of miRNA-9, using different LNA anti-miRNA oligonucleotide designs, and to observe its subsequent effect on E-cadherin expression. Conclusions The administration of anti-miRNA sequences even at low-doses, rapidly repressed the target miRNA, and influenced the expression of E-cadherin by significantly increasing its levels.
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Affiliation(s)
- Joana Filipa Lima
- Department of Chemical Engineering, LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal. .,Biomode, 2 S.A., Braga, Portugal. .,i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.
| | - Joana Carvalho
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Inês Pinto-Ribeiro
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,FMUP, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agricultural and Veterinary Research (INIAV), Vairão, Vila do Conde, Portugal
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, Odense, Denmark
| | - Laura Cerqueira
- Department of Chemical Engineering, LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.,Biomode, 2 S.A., Braga, Portugal
| | - Céu Figueiredo
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,FMUP, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Carla Oliveira
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,FMUP, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Nuno Filipe Azevedo
- Department of Chemical Engineering, LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
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17
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Müller V, Sousa JM, Ceylan Koydemir H, Veli M, Tseng D, Cerqueira L, Ozcan A, Azevedo NF, Westerlund F. Identification of pathogenic bacteria in complex samples using a smartphone based fluorescence microscope. RSC Adv 2018; 8:36493-36502. [PMID: 35558922 PMCID: PMC9088845 DOI: 10.1039/c8ra06473c] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/21/2018] [Indexed: 11/21/2022] Open
Abstract
Diagnostics based on fluorescence imaging of biomolecules is typically performed in well-equipped laboratories and is in general not suitable for remote and resource limited settings. Here we demonstrate the development of a compact, lightweight and cost-effective smartphone-based fluorescence microscope, capable of detecting signals from fluorescently labeled bacteria. By optimizing a peptide nucleic acid (PNA) based fluorescence in situ hybridization (FISH) assay, we demonstrate the use of the smartphone-based microscope for rapid identification of pathogenic bacteria. We evaluated the use of both a general nucleic acid stain as well as species-specific PNA probes and demonstrated that the mobile platform can detect bacteria with a sensitivity comparable to that of a conventional fluorescence microscope. The PNA-based FISH assay, in combination with the smartphone-based fluorescence microscope, allowed us to qualitatively analyze pathogenic bacteria in contaminated powdered infant formula (PIF) at initial concentrations prior to cultivation as low as 10 CFU per 30 g of PIF. Importantly, the detection can be done directly on the smartphone screen, without the need for additional image analysis. The assay should be straightforward to adapt for bacterial identification also in clinical samples. The cost-effectiveness, field-portability and simplicity of this platform will create various opportunities for its use in resource limited settings and point-of-care offices, opening up a myriad of additional applications based on other fluorescence-based diagnostic assays. A smartphone-based fluorescence microscope for detection of bacteria in complex samples using a species-specific peptide nucleic acid probe.![]()
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
| | | | - Hatice Ceylan Koydemir
- Electrical and Computer Engineering Department
- University of California
- Los Angeles
- USA
- Bioengineering Department
| | - Muhammed Veli
- Electrical and Computer Engineering Department
- University of California
- Los Angeles
- USA
- Bioengineering Department
| | - Derek Tseng
- Electrical and Computer Engineering Department
- University of California
- Los Angeles
- USA
- Bioengineering Department
| | | | - Aydogan Ozcan
- Electrical and Computer Engineering Department
- University of California
- Los Angeles
- USA
- Bioengineering Department
| | - Nuno F. Azevedo
- LEPABE
- Department of Chemical Engineering
- Faculty of Engineering of the University of Porto
- 4200-465 Porto
- Portugal
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
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18
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Sinigaglia C, Thiel D, Hejnol A, Houliston E, Leclère L. A safer, urea-based in situ hybridization method improves detection of gene expression in diverse animal species. Dev Biol 2017; 434:15-23. [PMID: 29197505 DOI: 10.1016/j.ydbio.2017.11.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/20/2017] [Accepted: 11/27/2017] [Indexed: 01/27/2023]
Abstract
In situ hybridization is a widely employed technique allowing spatial visualization of gene expression in fixed specimens. It has greatly advanced our understanding of biological processes, including developmental regulation. In situ protocols are today routinely followed in numerous laboratories, and although details might change, they all include a hybridization step, where specific antisense RNA or DNA probes anneal to the target nucleic acid sequence. This step is generally carried out at high temperatures and in a denaturing solution, called hybridization buffer, commonly containing 50% (v/v) formamide - a hazardous chemical. When applied to the soft-bodied hydrozoan medusa Clytia hemisphaerica, we found that this traditional hybridization approach was not fully satisfactory, causing extensive deterioration of morphology and tissue texture which compromised our observation and interpretation of results. We thus tested alternative solutions for in situ detection of gene expression and, inspired by optimized protocols for Northern and Southern blot analysis, we substituted the 50% formamide with an equal volume of 8M urea solution in the hybridization buffer. Our new protocol not only yielded better morphologies and tissue consistency, but also notably improved the resolution of the signal, allowing more precise localization of gene expression and reducing aspecific staining associated with problematic areas. Given the improved results and reduced manipulation risks, we tested the urea protocol on other metazoans, two brachiopod species (Novocrania anomala and Terebratalia transversa) and the priapulid worm Priapulus caudatus, obtaining a similar reduction of aspecific probe binding. Overall, substitution of formamide by urea during in situ hybridization offers a safer alternative, potentially of widespread use in research, medical and teaching contexts. We encourage other workers to test this approach on their study organisms, and hope that they will also obtain better sample preservation, more precise expression patterns and fewer problems due to aspecific staining, as we report here for Clytia medusae and Novocrania and Terebratalia developing larvae.
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Affiliation(s)
- Chiara Sinigaglia
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Villefranche-sur-mer, France.
| | - Daniel Thiel
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
| | - Evelyn Houliston
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Villefranche-sur-mer, France
| | - Lucas Leclère
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Villefranche-sur-mer, France
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19
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Costa AM, Mergulhão FJ, Briandet R, Azevedo NF. It is all about location: how to pinpoint microorganisms and their functions in multispecies biofilms. Future Microbiol 2017; 12:987-999. [PMID: 28745517 DOI: 10.2217/fmb-2017-0053] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Multispecies biofilms represent the dominant mode of life for the vast majority of microorganisms. Bacterial spatial localization in such biostructures governs ecological interactions between different populations and triggers the overall community functions. Here, we discuss the pros and cons of fluorescence-based techniques used to decipher bacterial species patterns in biofilms at single cell level, including fluorescence in situ hybridization and the use of genetically modified bacteria that express fluorescent proteins, reporting the significant improvements of those techniques. The development of tools for spatial and temporal study of multispecies biofilms will allow live imaging and spatial localization of cells in naturally occurring biofilms coupled with metabolic information, increasing insight of microbial community and the relation between its structure and functions.
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Affiliation(s)
- Angela M Costa
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal.,INEB - Institute of Biomedical Engineering, University of Porto, Porto, Portugal
| | - Filipe J Mergulhão
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Nuno F Azevedo
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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20
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Santos RS, Dakwar GR, Zagato E, Brans T, Figueiredo C, Raemdonck K, Azevedo NF, De Smedt SC, Braeckmans K. Intracellular delivery of oligonucleotides in Helicobacter pylori by fusogenic liposomes in the presence of gastric mucus. Biomaterials 2017; 138:1-12. [PMID: 28550752 DOI: 10.1016/j.biomaterials.2017.05.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/17/2017] [Accepted: 05/18/2017] [Indexed: 12/13/2022]
Abstract
The rising antimicrobial resistance contributes to 25000 annual deaths in Europe. This threat to the public health can only be tackled if novel antimicrobials are developed, combined with a more precise use of the currently available antibiotics through the implementation of fast, specific, diagnostic methods. Nucleic acid mimics (NAMs) that are able to hybridize intracellular bacterial RNA have the potential to become such a new class of antimicrobials and additionally could serve as specific detection probes. However, an essential requirement is that these NAMs should be delivered into the bacterial cytoplasm, which is a particular challenge given the fact that they are charged macromolecules. We consider these delivery challenges in relation to the gastric pathogen Helicobacter pylori, the most frequent chronic infection worldwide. In particular, we evaluate if cationic fusogenic liposomes are suitable carriers to deliver NAMs across the gastric mucus barrier and the bacterial envelope. Our study shows that DOTAP-DOPE liposomes post-PEGylated with DSPE-PEG (DSPE Lpx) can indeed successfully deliver NAMs into Helicobacter pylori, while offering protection to the NAMs from binding and inactivation in gastric mucus isolated from pigs. DSPE Lpx thus offer exciting new possibilities for in vivo diagnosis and treatment of Helicobacter pylori infections.
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MESH Headings
- Animals
- Anti-Infective Agents/administration & dosage
- Anti-Infective Agents/chemical synthesis
- Anti-Infective Agents/metabolism
- Cytoplasm/metabolism
- Drug Delivery Systems
- Drug Resistance, Microbial
- Fatty Acids, Monounsaturated/chemistry
- Fluorescent Dyes/chemistry
- Helicobacter Infections/diagnosis
- Helicobacter Infections/drug therapy
- Helicobacter Infections/microbiology
- Helicobacter pylori/genetics
- Helicobacter pylori/metabolism
- In Situ Hybridization, Fluorescence
- Liposomes
- Molecular Mimicry
- Mucus/chemistry
- Mucus/microbiology
- Oligonucleotides/administration & dosage
- Oligonucleotides/chemical synthesis
- Oligonucleotides/genetics
- Oligonucleotides/metabolism
- Oligonucleotides, Antisense/administration & dosage
- Oligonucleotides, Antisense/chemical synthesis
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/metabolism
- Phosphatidylethanolamines/chemistry
- Polyethylene Glycols/chemistry
- Quaternary Ammonium Compounds/chemistry
- RNA, Bacterial/antagonists & inhibitors
- RNA, Bacterial/genetics
- RNA, Ribosomal/antagonists & inhibitors
- RNA, Ribosomal/genetics
- Stomach/microbiology
- Swine
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Affiliation(s)
- Rita S Santos
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium; LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Porto, Portugal; i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - George R Dakwar
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium
| | - Elisa Zagato
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium; Center for Nano- and Biophotonics, Ghent University, Ghent, Belgium
| | - Toon Brans
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium; Center for Nano- and Biophotonics, Ghent University, Ghent, Belgium
| | - Céu Figueiredo
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal; Department of Pathology and Oncology, Faculty of Medicine of the University of Porto, Portugal
| | - Koen Raemdonck
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium
| | - Nuno F Azevedo
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Porto, Portugal
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium.
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium; Center for Nano- and Biophotonics, Ghent University, Ghent, Belgium
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21
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Frickmann H, Zautner AE, Moter A, Kikhney J, Hagen RM, Stender H, Poppert S. Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review. Crit Rev Microbiol 2017; 43:263-293. [PMID: 28129707 DOI: 10.3109/1040841x.2016.1169990] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.
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Affiliation(s)
- Hagen Frickmann
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | - Andreas Erich Zautner
- b Department of Medical Microbiology, University Medical Center Göttingen , Göttingen , Germany
| | - Annette Moter
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Judith Kikhney
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Ralf Matthias Hagen
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | | | - Sven Poppert
- e Institute for Medical Microbiology, Justus-Liebig-University Giessen , Giessen , Germany
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22
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Detection of Helicobacter pylori in the Gastric Mucosa by Fluorescence In Vivo Hybridization. Methods Mol Biol 2017; 1616:137-146. [PMID: 28600766 DOI: 10.1007/978-1-4939-7037-7_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this chapter, we describe a fluorescence in vivo hybridization (FIVH) protocol, using nucleic acid probes, for the detection of the bacterium Helicobacter pylori in the gastric mucosa of an infected C57BL/6 mouse model. This protocol should be easily extended to other microorganisms not only as a way to identify in vivo important microorganisms and their patterns of distribution within specific or at different anatomic sites, but also to better understand interaction mechanisms involving the microbiome and the human body.
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23
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Vizzini P, Iacumin L, Comi G, Manzano M. Development and application of DNA molecular probes. AIMS BIOENGINEERING 2017. [DOI: 10.3934/bioeng.2017.1.113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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24
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Fontenete S, Carvalho D, Lourenço A, Guimarães N, Madureira P, Figueiredo C, Azevedo NF. FISHji: New ImageJ macros for the quantification of fluorescence in epifluorescence images. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Abstract
Labeling RNA is of utmost interest, particularly in living cells, and thus RNA imaging is an emerging field. There are numerous methods relying on different concepts ranging from hybridization-based probes, over RNA-binding proteins to chemo-enzymatic modification of RNA. These methods have different benefits and limitations. This review aims to outline the current state-of-the-art techniques and point out their benefits and limitations.
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Affiliation(s)
- Lilith V.J.C. Mannack
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
- Cells in Motion, Cluster of Excellence, Münster, Germany
| | - Sebastian Eising
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
- Cells in Motion, Cluster of Excellence, Münster, Germany
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26
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Fontenete S, Leite M, Cappoen D, Santos R, Ginneken CV, Figueiredo C, Wengel J, Cos P, Azevedo NF. Fluorescence In Vivo Hybridization (FIVH) for Detection of Helicobacter pylori Infection in a C57BL/6 Mouse Model. PLoS One 2016; 11:e0148353. [PMID: 26848853 PMCID: PMC4743915 DOI: 10.1371/journal.pone.0148353] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/18/2016] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION In this study, we applied fluorescence in vivo hybridization (FIVH) using locked nucleic acid (LNA) probes targeting the bacterial rRNA gene for in vivo detection of H. pylori infecting the C57BL/6 mouse model. A previously designed Cy3_HP_LNA/2OMe_PS probe, complementary to a sequence of the H. pylori 16S rRNA gene, was used. First, the potential cytotoxicity and genotoxicity of the probe was assessed by commercial assays. Further, the performance of the probe for detecting H. pylori at different pH conditions was tested in vitro, using fluorescence in situ hybridization (FISH). Finally, the efficiency of FIVH to detect H. pylori SS1 strain in C57BL/6 infected mice was evaluated ex vivo in mucus samples, in cryosections and paraffin-embedded sections by epifluorescence and confocal microscopy. RESULTS H. pylori SS1 strain infecting C57BL/6 mice was successfully detected by the Cy3_HP_LNA/2OMe_PS probe in the mucus, attached to gastric epithelial cells and colonizing the gastric pits. The specificity of the probe for H. pylori was confirmed by microscopy. CONCLUSIONS In the future this methodology can be used in combination with a confocal laser endomicroscope for in vivo diagnosis of H. pylori infection using fluorescent LNA probes, which would be helpful to obtain an immediate diagnosis. Our results proved for the first time that FIVH method is applicable inside the body of a higher-order animal.
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Affiliation(s)
- Sílvia Fontenete
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
- ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Marina Leite
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Davie Cappoen
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Rita Santos
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Gent, Belgium
| | - Chris Van Ginneken
- Laboratory of Applied Veterinary Morphology, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Céu Figueiredo
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FMUP, Faculty of Medicine of the University of Porto, University, Porto, Portugal
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Nuno Filipe Azevedo
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
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27
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Vilas Boas D, Almeida C, Sillankorva S, Nicolau A, Azeredo J, Azevedo NF. Discrimination of bacteriophage infected cells using locked nucleic acid fluorescent in situ hybridization (LNA-FISH). BIOFOULING 2016; 32:179-190. [PMID: 26813295 DOI: 10.1080/08927014.2015.1131821] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/04/2015] [Indexed: 06/05/2023]
Abstract
Bacteriophage-host interaction studies in biofilm structures are still challenging due to the technical limitations of traditional methods. The aim of this study was to provide a direct fluorescence in situ hybridization (FISH) method based on locked nucleic acid (LNA) probes, which targets the phage replication phase, allowing the study of population dynamics during infection. Bacteriophages specific for two biofilm-forming bacteria, Pseudomonas aeruginosa and Acinetobacter, were selected. Four LNA probes were designed and optimized for phage-specific detection and for bacterial counterstaining. To validate the method, LNA-FISH counts were compared with the traditional plaque forming unit (PFU) technique. To visualize the progression of phage infection within a biofilm, colony-biofilms were formed and infected with bacteriophages. A good correlation (r = 0.707) was observed between LNA-FISH and PFU techniques. In biofilm structures, LNA-FISH provided a good discrimination of the infected cells and also allowed the assessment of the spatial distribution of infected and non-infected populations.
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Affiliation(s)
- Diana Vilas Boas
- b Laboratory for Process, Environment, Biotechnology and Energy Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Carina Almeida
- a LIBRO -Laboratório de Investigação em Biofilmes Rosário Oliveira , Centre of Biological Engineering, University of Minho , Braga , Portugal
- b Laboratory for Process, Environment, Biotechnology and Energy Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Sanna Sillankorva
- a LIBRO -Laboratório de Investigação em Biofilmes Rosário Oliveira , Centre of Biological Engineering, University of Minho , Braga , Portugal
| | - Ana Nicolau
- b Laboratory for Process, Environment, Biotechnology and Energy Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Joana Azeredo
- b Laboratory for Process, Environment, Biotechnology and Energy Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Nuno F Azevedo
- b Laboratory for Process, Environment, Biotechnology and Energy Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
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Santos RS, Dakwar GR, Xiong R, Forier K, Remaut K, Stremersch S, Guimarães N, Fontenete S, Wengel J, Leite M, Figueiredo C, De Smedt SC, Braeckmans K, Azevedo NF. Effect of Native Gastric Mucus on in vivo Hybridization Therapies Directed at Helicobacter pylori. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e269. [PMID: 26645765 PMCID: PMC5014538 DOI: 10.1038/mtna.2015.46] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 10/28/2015] [Indexed: 12/17/2022]
Abstract
Helicobacter pylori infects more than 50% of the worldwide population. It is mostly found deep in the gastric mucus lining of the stomach, being a major cause of peptic ulcers and gastric adenocarcinoma. To face the increasing resistance of H. pylori to antibiotics, antimicrobial nucleic acid mimics are a promising alternative. In particular, locked nucleic acids (LNA)/2'-OMethyl RNA (2'OMe) have shown to specifically target H. pylori, as evidenced by in situ hybridization. The success of in vivo hybridization depends on the ability of these nucleic acids to penetrate the major physical barriers-the highly viscoelastic gastric mucus and the bacterial cell envelope. We found that LNA/2'OMe is capable of diffusing rapidly through native, undiluted, gastric mucus isolated from porcine stomachs, without degradation. Moreover, although LNA/2'OMe hybridization was still successful without permeabilization and fixation of the bacteria, which is normally part of in vitro studies, the ability of LNA/2'OMe to efficiently hybridize with H. pylori was hampered by the presence of mucus. Future research should focus on developing nanocarriers that shield LNA/2'OMe from components in the gastric mucus, while remaining capable of diffusing through the mucus and delivering these nucleic acid mimics directly into the bacteria.
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Affiliation(s)
- Rita S Santos
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Porto, Portugal
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - George R Dakwar
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Ranhua Xiong
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- Center for Nano- and Biophotonics, Ghent University, Ghent, Belgium
| | - Katrien Forier
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- Center for Nano- and Biophotonics, Ghent University, Ghent, Belgium
| | - Katrien Remaut
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Stephan Stremersch
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Nuno Guimarães
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Porto, Portugal
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Sílvia Fontenete
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Porto, Portugal
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Marina Leite
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Céu Figueiredo
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Department of Pathology and Oncology, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Kevin Braeckmans
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- Center for Nano- and Biophotonics, Ghent University, Ghent, Belgium
| | - Nuno F Azevedo
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Porto, Portugal
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Azevedo AS, Almeida C, Pereira B, Madureira P, Wengel J, Azevedo NF. Detection and discrimination of biofilm populations using locked nucleic acid/2′-O-methyl-RNA fluorescence in situ hybridization (LNA/2′OMe-FISH). Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.04.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Mégraud F, Bénéjat L, Ontsira Ngoyi EN, Lehours P. Molecular Approaches to Identify Helicobacter pylori Antimicrobial Resistance. Gastroenterol Clin North Am 2015; 44:577-96. [PMID: 26314669 DOI: 10.1016/j.gtc.2015.05.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Antimicrobial susceptibility testing is needed to adapt Helicobacter pylori treatment to obtain the best results. Beside the standard phenotypic methods, molecular methods are increasingly used. The value of these molecular tests is that they are quick, independent of the transport conditions, easy to standardize, and commercial kits are available. In this article, these methods are reviewed, focusing on the determination of H pylori resistance to macrolides and fluoroquinolones, and mentioning also the methods used for tetracycline and rifampin.
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Affiliation(s)
- Francis Mégraud
- Bacteriology Laboratory, INSERM U853, University of Bordeaux, Bordeaux F-33000, France.
| | - Lucie Bénéjat
- Bacteriology Laboratory, INSERM U853, University of Bordeaux, Bordeaux F-33000, France
| | | | - Philippe Lehours
- Bacteriology Laboratory, INSERM U853, University of Bordeaux, Bordeaux F-33000, France
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Fontenete S, Leite M, Guimarães N, Madureira P, Ferreira RM, Figueiredo C, Wengel J, Azevedo NF. Towards Fluorescence In Vivo Hybridization (FIVH) Detection of H. pylori in Gastric Mucosa Using Advanced LNA Probes. PLoS One 2015; 10:e0125494. [PMID: 25915865 PMCID: PMC4410960 DOI: 10.1371/journal.pone.0125494] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/12/2015] [Indexed: 12/13/2022] Open
Abstract
In recent years, there have been several attempts to improve the diagnosis of infection caused by Helicobacter pylori. Fluorescence in situ hybridization (FISH) is a commonly used technique to detect H. pylori infection but it requires biopsies from the stomach. Thus, the development of an in vivo FISH-based method (FIVH) that directly detects and allows the visualization of the bacterium within the human body would significantly reduce the time of analysis, allowing the diagnosis to be performed during endoscopy. In a previous study we designed and synthesized a phosphorothioate locked nucleic acid (LNA)/ 2’ O-methyl RNA (2’OMe) probe using standard phosphoramidite chemistry and FISH hybridization was then successfully performed both on adhered and suspended bacteria at 37°C. In this work we simplified, shortened and adapted FISH to work at gastric pH values, meaning that the hybridization step now takes only 30 minutes and, in addition to the buffer, uses only urea and probe at non-toxic concentrations. Importantly, the sensitivity and specificity of the FISH method was maintained in the range of conditions tested, even at low stringency conditions (e.g., low pH). In conclusion, this methodology is a promising approach that might be used in vivo in the future in combination with a confocal laser endomicroscope for H. pylori visualization.
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Affiliation(s)
- Sílvia Fontenete
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
- ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
- * E-mail:
| | - Marina Leite
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Nuno Guimarães
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Pedro Madureira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
- IBMC, Institute for Molecular Biology and Cell Biology, Porto, Portugal
| | - Rui Manuel Ferreira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Céu Figueiredo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FMUP, Faculty of Medicine of Porto University, Porto, Portugal
| | - Jesper Wengel
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Nuno Filipe Azevedo
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
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Silvia F, Joana B, Pedro M, Céu F, Jesper W, Filipe AN. Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids. Appl Microbiol Biotechnol 2015; 99:3961-9. [DOI: 10.1007/s00253-015-6389-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/07/2014] [Accepted: 11/08/2014] [Indexed: 10/24/2022]
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Fontenete S, Guimarães N, Wengel J, Azevedo NF. Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models. Crit Rev Biotechnol 2015; 36:566-77. [PMID: 25586037 DOI: 10.3109/07388551.2014.993589] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The thermodynamics and kinetics of DNA hybridization, i.e. the process of self-assembly of one, two or more complementary nucleic acid strands, has been studied for many years. The appearance of the nearest-neighbor model led to several theoretical and experimental papers on DNA thermodynamics that provide reasonably accurate thermodynamic information on nucleic acid duplexes and allow estimation of the melting temperature. Because there are no thermodynamic models specifically developed to predict the hybridization temperature of a probe used in a fluorescence in situ hybridization (FISH) procedure, the melting temperature is used as a reference, together with corrections for certain compounds that are used during FISH. However, the quantitative relation between melting and experimental FISH temperatures is poorly described. In this review, various models used to predict the melting temperature for rRNA targets, for DNA oligonucleotides and for nucleic acid mimics (chemically modified oligonucleotides), will be addressed in detail, together with a critical assessment of how this information should be used in FISH.
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Affiliation(s)
- Sílvia Fontenete
- a Department of Chemical Engineering, Faculty of Engineering, LEPABE , University of Porto , Porto , Portugal .,b Institute of Molecular Pathology and Immunology of the University of Porto , Porto , Portugal .,c Department of Physics, Chemistry and Pharmacy , Nucleic Acid Center, University of Southern Denmark , Odense M , Denmark , and.,d ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto , Porto , Portugal
| | - Nuno Guimarães
- a Department of Chemical Engineering, Faculty of Engineering, LEPABE , University of Porto , Porto , Portugal .,b Institute of Molecular Pathology and Immunology of the University of Porto , Porto , Portugal .,c Department of Physics, Chemistry and Pharmacy , Nucleic Acid Center, University of Southern Denmark , Odense M , Denmark , and
| | - Jesper Wengel
- c Department of Physics, Chemistry and Pharmacy , Nucleic Acid Center, University of Southern Denmark , Odense M , Denmark , and
| | - Nuno Filipe Azevedo
- a Department of Chemical Engineering, Faculty of Engineering, LEPABE , University of Porto , Porto , Portugal
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Navarro E, Serrano-Heras G, Castaño MJ, Solera J. Real-time PCR detection chemistry. Clin Chim Acta 2014; 439:231-50. [PMID: 25451956 DOI: 10.1016/j.cca.2014.10.017] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 10/09/2014] [Accepted: 10/11/2014] [Indexed: 12/28/2022]
Abstract
Real-time PCR is the method of choice in many laboratories for diagnostic and food applications. This technology merges the polymerase chain reaction chemistry with the use of fluorescent reporter molecules in order to monitor the production of amplification products during each cycle of the PCR reaction. Thus, the combination of excellent sensitivity and specificity, reproducible data, low contamination risk and reduced hand-on time, which make it a post-PCR analysis unnecessary, has made real-time PCR technology an appealing alternative to conventional PCR. The present paper attempts to provide a rigorous overview of fluorescent-based methods for nucleic acid analysis in real-time PCR described in the literature so far. Herein, different real-time PCR chemistries have been classified into two main groups; the first group comprises double-stranded DNA intercalating molecules, such as SYBR Green I and EvaGreen, whereas the second includes fluorophore-labeled oligonucleotides. The latter, in turn, has been divided into three subgroups according to the type of fluorescent molecules used in the PCR reaction: (i) primer-probes (Scorpions, Amplifluor, LUX, Cyclicons, Angler); (ii) probes; hydrolysis (TaqMan, MGB-TaqMan, Snake assay) and hybridization (Hybprobe or FRET, Molecular Beacons, HyBeacon, MGB-Pleiades, MGB-Eclipse, ResonSense, Yin-Yang or displacing); and (iii) analogues of nucleic acids (PNA, LNA, ZNA, non-natural bases: Plexor primer, Tiny-Molecular Beacon). In addition, structures, mechanisms of action, advantages and applications of such real-time PCR probes and analogues are depicted in this review.
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Affiliation(s)
- E Navarro
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - G Serrano-Heras
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - M J Castaño
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - J Solera
- Internal Medicine Department, General University Hospital, Hermanos Falcó 37, 02006 Albacete, Spain.
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Patel SK, Pratap CB, Jain AK, Gulati AK, Nath G. Diagnosis of Helicobacter pylori: What should be the gold standard? World J Gastroenterol 2014; 20:12847-12859. [PMID: 25278682 PMCID: PMC4177467 DOI: 10.3748/wjg.v20.i36.12847] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 02/10/2014] [Accepted: 06/26/2014] [Indexed: 02/06/2023] Open
Abstract
Since the discovery of Helicobacter pylori (H. pylori) in 1983, numerous detection methods for the presence of the bacterium have been developed. Each one of them has been associated with advantages and disadvantages. Noninvasive tests such as serology, 13C urea breath test (UBT) and stool antigen tests are usually preferred by the clinicians. Serology has its own limitation especially in endemic areas while 13C UBT is technically very demanding. The stool antigen detection method, although specific, is usually associated with poor sensitivity. The 13C UBT is believed to be specific, but with present revelation of the fact that stomach is colonized by many other urease producing bacteria makes it questionable. Histology, culture, rapid urease test and polymerase chain reaction (PCR) are the tests which are carried out on antral biopsies collected by invasive means. Histology has been proposed to be very sensitive and specific but the question is how by simply looking the morphology of the bacteria in the microscope, one can claim that the curved bacterium is exclusively H. pylori. Rapid urease test (RUT), the doctor’s test, is also challenged because the presence of other urease producing bacteria in the stomach cannot be denied. Moreover, RUT has been reported with poor sensitivity specially, when density of the bacterium is low. Isolation of H. pylori is essential to investigate its growth requirements, antibiotic susceptibility testing, studying virulence factor to develop vaccine and many more explorations. It has also got several disadvantages i.e., special condition for transporting, media, incubation and few days waiting for the colonies to appear, apart from the speed essentially needed to process the specimens. Till date, majority of the microbiological laboratories in the world are not equipped and trained to isolate such fastidious bacterium. The option left is PCR methods to detect H. pylori’s DNA in gastric mucosa, gastric juice, saliva, dental plaques and environmental specimens. There are speculations for false positivity due to detection of non-pylori Helicobacters due to genetic sharing; and false negativity due to low bacterial counts and presence of PCR inhibitors. However, specimen collection, transportation and processing do not require speed and special conditions. PCR based diagnosis may be considered as gold standard by designing primers extremely specific to H. pylori and targeting at least more than one conserved genes. Similarly specificity of PCR may be improved by use of internal Primers. Further, nested PCR will take care of false negatives by countering the effect of PCR inhibitors and low bacterial counts. Therefore, nested PCR based methods if performed properly, may be proposed as gold standard test.
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Percival SL, Suleman L. Biofilms and Helicobacter pylori: Dissemination and persistence within the environment and host. World J Gastrointest Pathophysiol 2014; 5:122-132. [PMID: 25133015 PMCID: PMC4133512 DOI: 10.4291/wjgp.v5.i3.122] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/23/2014] [Accepted: 05/19/2014] [Indexed: 02/06/2023] Open
Abstract
The presence of viable Helicobacter pylori (H. pylori) in the environment is considered to contribute to the levels of H. pylori found in the human population, which also aids to increase its genetic variability and its environmental adaptability and persistence. H. pylori form biofilms both within the in vitro and in vivo environment. This represents an important attribute that assists the survival of this bacterium within environments that are both hostile and adverse to proliferation. It is the aim of this paper to review the ability of H. pylori to form biofilms in vivo and in vitro and to address the inherent mechanisms considered to significantly enhance its persistence within the host and in external environments. Furthermore, the dissemination of H. pylori in the external environment and within the human body and its impact upon infection control will be discussed.
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Optimization of a peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) method for the detection of bacteria and disclosure of a formamide effect. J Biotechnol 2014; 187:16-24. [PMID: 25034435 DOI: 10.1016/j.jbiotec.2014.06.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/13/2014] [Accepted: 06/25/2014] [Indexed: 11/23/2022]
Abstract
Despite the fact that fluorescence in situ hybridization (FISH) is a well-established technique to identify microorganisms, there is a lack of understanding concerning the interaction of the different factors affecting the obtained fluorescence. In here, we used flow cytometry to study the influence of three essential factors in hybridization - temperature, time and formamide concentration - in an effort to optimize the performance of a Peptide Nucleic Acid (PNA) probe targeting bacteria (EUB338). The PNA-FISH optimization was performed with bacteria representing different families employing response surface methodology. Surprisingly, the optimum concentration of formamide varied according to the bacterium tested. While hybridization on the bacteria possessing the thickest peptidoglycan was more successful at nearly 50% (v/v) formamide, hybridization on all other microorganisms appeared to improve with much lower formamide concentrations. Gram staining and transmission electron microscopy allowed us to confirm that the overall effect of formamide concentration on the fluorescence intensity is a balance between a harmful effect on the bacterial cell envelope, affecting cellular integrity, and the beneficial denaturant effect in the hybridization process. We also conclude that microorganisms belonging to different families will require different hybridization parameters for the same FISH probe, meaning that an optimum universal PNA-FISH procedure is non-existent for these situations.
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