1
|
Kim S, Hyun H, Im JK, Lee MS, Koh H, Kang D, Nho SH, Kang JH, Kwon T, Kim H. Fast and accurate multi-bacterial identification using cleavable and FRET-based peptide nucleic acid probes. Biosens Bioelectron 2025; 271:116950. [PMID: 39631211 DOI: 10.1016/j.bios.2024.116950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 11/15/2024] [Accepted: 11/15/2024] [Indexed: 12/07/2024]
Abstract
Fast and accurate identification of pathogenic microbes in patient samples is crucial for the timely treatment of acute infectious diseases such as sepsis. The fluorescence in situ hybridization (FISH) technique allows the rapid detection and identification of microbes based on their variation in genomic sequence without time-consuming culturing or sequencing. However, the recent explosion of microbial genomic data has made it challenging to design an appropriate set of probes for microbial mixtures. We developed a novel set of peptide nucleic acid (PNA)-based FISH probes with optimal target specificity by analyzing the variations in 16S ribosomal RNA sequence across all bacterial species. Owing to their superior penetration into bacteria and higher mismatch sensitivity, the PNA probes distinguished seven bacterial species commonly observed in bacteremia with 96-99.9% accuracy using our optimized FISH procedure. Detection based on Förster resonance energy transfer (FRET) between pairs of adjacent binding PNA probes eliminated crosstalk between species. Rapid sequential species identification was implemented, using chemically cleavable fluorophores, without compromising detection accuracy. Owing to their outstanding accuracy and enhanced speed, this set of techniques shows great potential for clinical use.
Collapse
Affiliation(s)
- Sungho Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hwi Hyun
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jae-Kyeong Im
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Min Seok Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hwasoo Koh
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Donghoon Kang
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Si-Hyeong Nho
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Joo H Kang
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea; Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| | - Hajin Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea; Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| |
Collapse
|
2
|
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: 8] [Impact Index Per Article: 4.0] [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.
Collapse
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
| |
Collapse
|
3
|
Nácher-Vázquez M, Barbosa A, Armelim I, Azevedo AS, Almeida GN, Pizarro C, Azevedo NF, Almeida C, Cerqueira L. Development of a Novel Peptide Nucleic Acid Probe for the Detection of Legionella spp. in Water Samples. Microorganisms 2022; 10:1409. [PMID: 35889127 PMCID: PMC9318766 DOI: 10.3390/microorganisms10071409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023] Open
Abstract
Legionella are opportunistic intracellular pathogens that are found throughout the environment. The Legionella contamination of water systems represents a serious social problem that can lead to severe diseases, which can manifest as both Pontiac fever and Legionnaires' disease (LD) infections. Fluorescence in situ hybridization using nucleic acid mimic probes (NAM-FISH) is a powerful and versatile technique for bacterial detection. By optimizing a peptide nucleic acid (PNA) sequence based on fluorescently selective binding to specific bacterial rRNA sequences, we established a new PNA-FISH method that has been successfully designed for the specific detection of the genus Legionella. The LEG22 PNA probe has shown great theoretical performance, presenting 99.9% specificity and 96.9% sensitivity. We also demonstrated that the PNA-FISH approach presents a good signal-to-noise ratio when applied in artificially contaminated water samples directly on filtration membranes or after cells elution. For water samples with higher turbidity (from cooling tower water systems), there is still the need for further method optimization in order to detect cellular contents and to overcome interferents' autofluorescence, which hinders probe signal visualization. Nevertheless, this work shows that the PNA-FISH approach could be a promising alternative for the rapid (3-4 h) and accurate detection of Legionella.
Collapse
Affiliation(s)
- Montserrat Nácher-Vázquez
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- INIAV, IP—National Institute for Agrarian and Veterinary Research, Vairão, 4485-655 Vila Do Conde, Portugal;
| | - Ana Barbosa
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Inês Armelim
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
| | - Andreia Sofia Azevedo
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP—Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Gonçalo Nieto Almeida
- INIAV, IP—National Institute for Agrarian and Veterinary Research, Vairão, 4485-655 Vila Do Conde, Portugal;
| | - Cristina Pizarro
- INSA—National Institute of Health Doutor Ricardo Jorge, Rua Alexandre Herculano 321, 4000-055 Porto, Portugal;
| | - Nuno Filipe Azevedo
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Carina Almeida
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- INIAV, IP—National Institute for Agrarian and Veterinary Research, Vairão, 4485-655 Vila Do Conde, Portugal;
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Laura Cerqueira
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| |
Collapse
|
4
|
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: 8] [Impact Index Per Article: 2.7] [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.
Collapse
|
5
|
Kao YT, Calabrese S, Borst N, Lehnert M, Lai YK, Schlenker F, Juelg P, Zengerle R, Garstecki P, von Stetten F. Microfluidic One-Pot Digital Droplet FISH Using LNA/DNA Molecular Beacons for Bacteria Detection and Absolute Quantification. BIOSENSORS 2022; 12:bios12040237. [PMID: 35448297 PMCID: PMC9032532 DOI: 10.3390/bios12040237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/06/2022] [Accepted: 04/10/2022] [Indexed: 02/06/2023]
Abstract
We demonstrate detection and quantification of bacterial load with a novel microfluidic one-pot wash-free fluorescence in situ hybridization (FISH) assay in droplets. The method offers minimal manual workload by only requiring mixing of the sample with reagents and loading it into a microfluidic cartridge. By centrifugal microfluidic step emulsification, our method partitioned the sample into 210 pL (73 µm in diameter) droplets for bacterial encapsulation followed by in situ permeabilization, hybridization, and signal detection. Employing locked nucleic acid (LNA)/DNA molecular beacons (LNA/DNA MBs) and NaCl-urea based hybridization buffer, the assay was characterized with Escherichia coli, Klebsiella pneumonia, and Proteus mirabilis. The assay performed with single-cell sensitivity, a 4-log dynamic range from a lower limit of quantification (LLOQ) at ~3 × 103 bacteria/mL to an upper limit of quantification (ULOQ) at ~3 × 107 bacteria/mL, anda linearity R2 = 0.976. The total time-to-results for detection and quantification was around 1.5 hours.
Collapse
Affiliation(s)
- Yu-Ting Kao
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
| | - Silvia Calabrese
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Nadine Borst
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Michael Lehnert
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Yu-Kai Lai
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Franziska Schlenker
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
| | - Felix von Stetten
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
- Correspondence: ; Tel.: +49-761-203-73243
| |
Collapse
|
6
|
Sousa LGV, Castro J, França A, Almeida C, Muzny CA, Cerca N. A New PNA-FISH Probe Targeting Fannyhessea vaginae. Front Cell Infect Microbiol 2021; 11:779376. [PMID: 34869078 PMCID: PMC8637528 DOI: 10.3389/fcimb.2021.779376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/01/2021] [Indexed: 12/29/2022] Open
Abstract
Bacterial vaginosis (BV) is the most common vaginal infection in women of reproductive age and has been associated with serious health complications, mainly in pregnant women. It is characterized by a decrease in the number of Lactobacillus species in the healthy vaginal microbiota and an overgrowth of strict and facultative anaerobic bacteria that develop a polymicrobial biofilm. Despite over 60 years of research investigating BV, its etiology is not fully understood. Gardnerella spp. is a crucial microorganism that contributes to the formation of the biofilm and the development of BV, but the role of other BV-associated bacteria is not clear. Nevertheless, Fannyhessea vaginae (previously known as Atopobium vaginae) is a highly specific species for BV, and co-colonization with Gardnerella is thought to be a very specific diagnostic marker. The diagnosis of BV still presents some limitations, since currently used methods often fail to accurately detect BV. This work aims to develop a novel peptide nucleic acid (PNA) probe targeting F. vaginae. This probe was further validated in a multiplex assay, which included a Gardnerella-specific PNA probe, as a possible method for diagnosis of BV, and was compared with quantification by qPCR. The new PNA probe showed excellent sensitivity and specificity and could discriminate F. vaginae-Gardnerella biofilms, confirming the potential to be used for the detection of BV-associated pathogens.
Collapse
Affiliation(s)
- Lúcia G V Sousa
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), Campus de Gualtar, University of Minho, Braga, Portugal
| | - Joana Castro
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), Campus de Gualtar, University of Minho, Braga, Portugal
| | - Angela França
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), Campus de Gualtar, University of Minho, Braga, Portugal
| | - Carina Almeida
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), Campus de Gualtar, University of Minho, Braga, Portugal.,INIAV, IP- National Institute for Agrarian and Veterinary Research, Vila do Conde, Portugal
| | - Christina A Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Nuno Cerca
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), Campus de Gualtar, University of Minho, Braga, Portugal
| |
Collapse
|
7
|
Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost. mSystems 2021; 6:e0029421. [PMID: 34254828 PMCID: PMC8409480 DOI: 10.1128/msystems.00294-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
New approaches to characterizing microbiomes via high-throughput sequencing provide impressive gains in efficiency and cost reduction compared to approaches that were standard just a few years ago. However, the speed of method development has been such that staying abreast of the latest technological advances is challenging. Moreover, shifting laboratory protocols to include new methods can be expensive and time consuming. To facilitate adoption of new techniques, we provide a guide and review of recent advances that are relevant for single-locus sequence-based study of microbiomes—from extraction to library preparation—including a primer regarding the use of liquid-handling automation in small-scale academic settings. Additionally, we describe several amendments to published techniques to improve throughput, track contamination, and reduce cost. Notably, we suggest adding synthetic DNA molecules to each sample during nucleic acid extraction, thus providing a method of documenting incidences of cross-contamination. We also describe a dual-indexing scheme for Illumina sequencers that allows multiplexing of many thousands of samples with minimal PhiX input. Collectively, the techniques that we describe demonstrate that laboratory technology need not impose strict limitations on the scale of molecular microbial ecology studies. IMPORTANCE New methods to characterize microbiomes reduce technology-imposed limitations to study design, but many new approaches have not been widely adopted. Here, we present techniques to increase throughput and reduce contamination alongside a thorough review of current best practices.
Collapse
|
8
|
Shin H, Park SJ, Kim J, Lee JS, Min DH. A graphene oxide-based fluorescent nanosensor to identify antiviral agents via a drug repurposing screen. Biosens Bioelectron 2021; 183:113208. [PMID: 33839535 DOI: 10.1016/j.bios.2021.113208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/23/2021] [Accepted: 03/28/2021] [Indexed: 10/21/2022]
Abstract
Currently, there are no approved therapeutics for Dengue virus (DENV) infection, even though it can cause fatal complications. Understanding DENV infection and its propagation process in host cells is necessary to develop specific antiviral therapeutics. Here, we developed a graphene oxide-based fluorescent system (Graphene Oxide-based Viral RNA Analysis system, GOViRA) that enables sensitive and quantitative real-time monitoring of the intracellular viral RNA level in living cells. The GOViRA system consists of a fluorescent dye-labeled peptide nucleic acid (PNA) with a complementary sequence to the DENV genome and a dextran-coated reduced graphene oxide nanocolloid (DRGON). When the dye labeled PNA is adsorbed onto DRGON, the fluorescence of the dye is effectively quenched. The quenched fluorescence signal is recovered when the dye labeled PNA forms interaction with intracellular viral RNA in DENV infected host cells. We demonstrated the successful use of the GOViRA platform for high-throughput screening to discover novel antiviral compounds. Through a cell-based high-throughput screening of FDA-approved small-molecule drugs, we identified ulipristal, a selective progesterone receptor modulator (SPRM), as a potent inhibitor against DENV infection. The anti-DENV activity of ulipristal was confirmed both in vitro and in vivo. Moreover, we suggest that the mode of action of ulipristal is mediated by inhibiting viral entry into the host cells.
Collapse
Affiliation(s)
- Hojeong Shin
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Se-Jin Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jungho Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ji-Seon Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dal-Hee Min
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea; Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea; Institute of Biotherapeutics Convergence Technology, Lemonex Inc., Seoul, 08826, Republic of Korea.
| |
Collapse
|
9
|
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: 1.0] [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.
Collapse
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.
| |
Collapse
|
10
|
Kaushik AM, Hsieh K, Mach KE, Lewis S, Puleo CM, Carroll KC, Liao JC, Wang T. Droplet-Based Single-Cell Measurements of 16S rRNA Enable Integrated Bacteria Identification and Pheno-Molecular Antimicrobial Susceptibility Testing from Clinical Samples in 30 min. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003419. [PMID: 33747737 PMCID: PMC7967084 DOI: 10.1002/advs.202003419] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/13/2020] [Indexed: 05/06/2023]
Abstract
Empiric broad-spectrum antimicrobial treatments of urinary tract infections (UTIs) have contributed to widespread antimicrobial resistance. Clinical adoption of evidence-based treatments necessitates rapid diagnostic methods for pathogen identification (ID) and antimicrobial susceptibility testing (AST) with minimal sample preparation. In response, a microfluidic droplet-based platform is developed for achieving both ID and AST from urine samples within 30 min. In this platform, fluorogenic hybridization probes are utilized to detect 16S rRNA from single bacterial cells encapsulated in picoliter droplets, enabling molecular identification of uropathogenic bacteria directly from urine in as little as 16 min. Moreover, in-droplet single-bacterial measurements of 16S rRNA provide a surrogate for AST, shortening the exposure time to 10 min for gentamicin and ciprofloxacin. A fully integrated device and screening workflow were developed to test urine specimens for one of seven unique diagnostic outcomes including the presence/absence of Gram-negative bacteria, molecular ID of the bacteriaas Escherichia coli, an Enterobacterales, or other organism, and assessment of bacterial susceptibility to ciprofloxacin. In a 50-specimen clinical comparison study, the platform demonstrates excellent performance compared to clinical standard methods (areas-under-curves, AUCs >0.95), within a small fraction of the turnaround time, highlighting its clinical utility.
Collapse
Affiliation(s)
| | - Kuangwen Hsieh
- Department of Mechanical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
| | - Kathleen E. Mach
- Department of UrologyStanford University School of MedicineStanfordCA94305USA
| | - Shawna Lewis
- Division of Medical MicrobiologyDepartment of PathologyJohns Hopkins University School of MedicineBaltimoreMD21287USA
| | | | - Karen C. Carroll
- Division of Medical MicrobiologyDepartment of PathologyJohns Hopkins University School of MedicineBaltimoreMD21287USA
| | - Joseph C. Liao
- Department of UrologyStanford University School of MedicineStanfordCA94305USA
| | - Tza‐Huei Wang
- Department of Mechanical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMD21287USA
| |
Collapse
|
11
|
Perebikovsky A, Liu Y, Hwu A, Kido H, Shamloo E, Song D, Monti G, Shoval O, Gussin D, Madou M. Rapid sample preparation for detection of antibiotic resistance on a microfluidic disc platform. LAB ON A CHIP 2021; 21:534-545. [PMID: 33393956 DOI: 10.1039/d0lc00838a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Rapid, point-of-care (PoC) diagnostics for antibiotic susceptibility testing (AST) are critical in combating the antimicrobial resistance epidemic. While new, alternative technologies are capable of rapidly identifying antibiotic resistance, traditional AST methods, where a patient sample is incubated with different antibiotics, remain the most reliable and practical in determining antibiotic effectiveness. Here, we demonstrate a novel sample incubation technique on a microfluidic centrifugal disc (CD) as a proof of concept automated sample processing platform for AST. By using ribosomal RNA (rRNA) as a marker for cell growth, we demonstrated that incubation on the microfluidic CD was enhanced (>1.6 fold) for 11 out of 14 clinically relevant isolates of Escherichia coli compared to traditional shaker incubators. Finally, we utilize the system to identify antibiotic resistance of 11 E. coli isolates incubated with 5 different antibiotics in under 2 hours.
Collapse
Affiliation(s)
- Alexandra Perebikovsky
- Department of Physics and Astronomy, University of California, 4129 Frederick Reines Hall, Irvine, CA 92697, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Oliveira R, Almeida C, Azevedo NF. Detection of Microorganisms by Fluorescence In Situ Hybridization Using Peptide Nucleic Acid. Methods Mol Biol 2021; 2105:217-230. [PMID: 32088873 DOI: 10.1007/978-1-0716-0243-0_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Fluorescence in situ hybridization (FISH) is a 30-year-old technology that has evolved continuously and is now one of the most well-established molecular biology techniques. Traditionally, DNA probes are used for in situ hybridization. However, synthetic molecules are emerging as very promising alternatives, providing better hybridization performance and making FISH procedures easier and more efficient. In this chapter, we describe a universal FISH protocol, using nucleic acid probes, for the detection of bacteria. This protocol should be easily applied to different microorganisms as a way of identifying in situ relevant microorganisms (including pathogens) and their distribution patterns in different types of samples.
Collapse
Affiliation(s)
- Ricardo Oliveira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Vairao, Portugal
| | - Carina Almeida
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Vairao, Portugal.,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal.
| |
Collapse
|
13
|
Allkja J, Azevedo AS. Characterization of Social Interactions and Spatial Arrangement of Individual Bacteria in MultiStrain or Multispecies Biofilm Systems Using Nucleic Acid Mimics-Fluorescence In Situ Hybridization. Methods Mol Biol 2021; 2246:97-109. [PMID: 33576985 DOI: 10.1007/978-1-0716-1115-9_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biofilms are often composed of different bacterial and fungal species/strains, which form complex structures based on social interactions with each other. Fluorescence in situ hybridization (FISH) can help us identify the different species/strains present within a biofilm , and when coupled with confocal scanning laser microscopy (CSLM), it enables the visualization of the three-dimensional (3D) structure of the biofilm and the spatial arrangement of each individual species/strain within it. In this chapter, we describe the protocol for characterizing multistrain or multispecies biofilm formation using NAM-FISH and CSLM.
Collapse
Affiliation(s)
- Jontana Allkja
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, 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.
| |
Collapse
|
14
|
Alhede M, Alhede M, Qvortrup K, Kragh KN, Jensen PØ, Stewart PS, Bjarnsholt T. The origin of extracellular DNA in bacterial biofilm infections in vivo. Pathog Dis 2020; 78:5810662. [PMID: 32196074 PMCID: PMC7150582 DOI: 10.1093/femspd/ftaa018] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/19/2020] [Indexed: 02/03/2023] Open
Abstract
Extracellular DNA (eDNA) plays an important role in both the aggregation of bacteria and in the interaction of the resulting biofilms with polymorphonuclear leukocytes (PMNs) during an inflammatory response. Here, transmission electron and confocal scanning laser microscopy were used to examine the interaction between biofilms of Pseudomonas aeruginosa and PMNs in a murine implant model and in lung tissue from chronically infected cystic fibrosis patients. PNA FISH, DNA staining, labeling of PMN DNA with a thymidine analogue and immunohistochemistry were applied to localize bacteria, eDNA, PMN-derived eDNA, PMN-derived histone H3 (H3), neutrophil elastase (NE) and citrullinated H3 (citH3). Host-derived eDNA was observed surrounding bacterial biofilms but not within the biofilms. H3 localized to the lining of biofilms while NE was found throughout biofilms. CitH3, a marker for neutrophil extracellular traps (NETs) was detected only sporadically indicating that most host-derived eDNA in vivo was not a result of NETosis. Together these observations show that, in these in vivo biofilm infections with P. aeruginosa, the majority of eDNA is found external to the biofilm and derives from the host.
Collapse
Affiliation(s)
- Maria Alhede
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N., Denmark
| | - Morten Alhede
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N., Denmark
| | - Klaus Qvortrup
- CFIM/Department of Biomedical Sciences, University of Copenhagen, Blegdmasvej 3, DK-2200 Copenhagen N., Denmark
| | - Kasper Nørskov Kragh
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N., Denmark
| | - Peter Østrup Jensen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N., Denmark.,Department of Clinical Microbiology, H:S Rigshospitalet, Juliane Maries Vej 22, DK-2100 Copenhagen Ø., Denmark
| | - Philip Shook Stewart
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, P.O. Box 173980, Bozeman, MT 59717-3980, USA
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N., Denmark.,Department of Clinical Microbiology, H:S Rigshospitalet, Juliane Maries Vej 22, DK-2100 Copenhagen Ø., Denmark
| |
Collapse
|
15
|
He H, Xia X, Yang H, Peng Q, Zheng J. A pilot study: a possible implication of Candida as an etiologically endogenous pathogen for oral lichen planus. BMC Oral Health 2020; 20:72. [PMID: 32171292 PMCID: PMC7071738 DOI: 10.1186/s12903-020-1042-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/10/2020] [Indexed: 02/03/2023] Open
Abstract
Background The aim of this study was to investigate the prevalence and genotypic profiles of Candida albicans in patients with oral lichen planus (OLP). Materials and methods Positive rates and genotypic profiles of Candida albicans strains from OLP patients and healthy controls were analyzed. Random amplified polymorphic DNA and internal transcribed spacer of ribosome DNA polymerase chain reactions were used to sequence the DNA of these strains, and then their genetic similarity was measured using BLAST, UIV Band, and Vector NTI Suite Sequence Analyses Software. Results The prevalence of C. albicans strains detected from erosive-OLP, non-erosive OLP, and normal individuals was 18.87, 18.75, and 7.92%, respectively. Four different genotypes were revealed by the two methods. To be specific, type I was found only in the healthy subjects; type II a and II b were found in non-erosive OLP, and type III was identified in erosive OLP. Intragroup similarity coefficients, i.e. SAB were 100%, and inter-groups similarity coefficients, i.e. SAB were less than 30%. Conclusions The genotypic results of C. albicans in OLP revealed an endogenous rather than exogenous infection of C. albicans. In addition, a possible pathogenic role of C. albicans in OLP, with the etiologic sense contributing to a more proper recognition on the pathogenesis, development, and progression of OLP, as well as some strategies for its diagnosis and treatment were identified.
Collapse
Affiliation(s)
- Hong He
- The Affiliated Stomatology Hospital, Zhejiang University School of Medicine, Yan'an Road, Hangzhou, 310006, China. .,Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, China.
| | - Xinyu Xia
- The Affiliated Stomatology Hospital, Zhejiang University School of Medicine, Yan'an Road, Hangzhou, 310006, China
| | - Haiping Yang
- The Affiliated Stomatology Hospital, Zhejiang University School of Medicine, Yan'an Road, Hangzhou, 310006, China.,Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, China
| | - Qiao Peng
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiaoer Zheng
- The Affiliated Stomatology Hospital, Zhejiang University School of Medicine, Yan'an Road, Hangzhou, 310006, China. .,Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, China.
| |
Collapse
|
16
|
Canady TD, Berlyoung AS, Martinez JA, Emanuelson C, Telmer CA, Bruchez MP, Armitage BA. Enhanced Hybridization Selectivity Using Structured GammaPNA Probes. Molecules 2020; 25:molecules25040970. [PMID: 32098111 PMCID: PMC7070858 DOI: 10.3390/molecules25040970] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 11/30/2022] Open
Abstract
High affinity nucleic acid analogues such as gammaPNA (γPNA) are capable of invading stable secondary and tertiary structures in DNA and RNA targets but are susceptible to off-target binding to mismatch-containing sequences. We introduced a hairpin secondary structure into a γPNA oligomer to enhance hybridization selectivity compared with a hairpin-free analogue. The hairpin structure features a five base PNA mask that covers the proximal five bases of the γPNA probe, leaving an additional five γPNA bases available as a toehold for target hybridization. Surface plasmon resonance experiments demonstrated that the hairpin probe exhibited slower on-rates and faster off-rates (i.e., lower affinity) compared with the linear probe but improved single mismatch discrimination by up to a factor of five, due primarily to slower on-rates for mismatch vs. perfect match targets. The ability to discriminate against single mismatches was also determined in a cell-free mRNA translation assay using a luciferase reporter gene, where the hairpin probe was two-fold more selective than the linear probe. These results validate the hairpin design and present a generalizable approach to improving hybridization selectivity.
Collapse
Affiliation(s)
- Taylor D. Canady
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA; (T.D.C.); (A.S.B.); (J.A.M.); (C.E.); (M.P.B.)
| | - April S. Berlyoung
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA; (T.D.C.); (A.S.B.); (J.A.M.); (C.E.); (M.P.B.)
| | - Joe A. Martinez
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA; (T.D.C.); (A.S.B.); (J.A.M.); (C.E.); (M.P.B.)
| | - Cole Emanuelson
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA; (T.D.C.); (A.S.B.); (J.A.M.); (C.E.); (M.P.B.)
| | - Cheryl A. Telmer
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA;
| | - Marcel P. Bruchez
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA; (T.D.C.); (A.S.B.); (J.A.M.); (C.E.); (M.P.B.)
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA;
| | - Bruce A. Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA; (T.D.C.); (A.S.B.); (J.A.M.); (C.E.); (M.P.B.)
- Correspondence:
| |
Collapse
|
17
|
Zhang Y, Hu A, Andini N, Yang S. A 'culture' shift: Application of molecular techniques for diagnosing polymicrobial infections. Biotechnol Adv 2019; 37:476-490. [PMID: 30797092 PMCID: PMC6447436 DOI: 10.1016/j.biotechadv.2019.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/04/2019] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
With the advancement of microbiological discovery, it is evident that many infections, particularly bloodstream infections, are polymicrobial in nature. Consequently, new challenges have emerged in identifying the numerous etiologic organisms in an accurate and timely manner using the current diagnostic standard. Various molecular diagnostic methods have been utilized as an effort to provide a fast and reliable identification in lieu or parallel to the conventional culture-based methods. These technologies are mostly based on nucleic acid, proteins, or physical properties of the pathogens with differing advantages and limitations. This review evaluates the different molecular methods and technologies currently available to diagnose polymicrobial infections, which will help determine the most appropriate option for future diagnosis.
Collapse
Affiliation(s)
- Yi Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore.
| | - Anne Hu
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Nadya Andini
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Samuel Yang
- Emergency Medicine, Stanford University, Stanford, California 94305, USA.
| |
Collapse
|
18
|
Mach KE, Kaushik AM, Hsieh K, Wong PK, Wang TH, Liao JC. Optimizing peptide nucleic acid probes for hybridization-based detection and identification of bacterial pathogens. Analyst 2019; 144:1565-1574. [PMID: 30656297 PMCID: PMC7039532 DOI: 10.1039/c8an02194e] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Point-of-care (POC) diagnostics for infectious diseases have the potential to improve patient care and antibiotic stewardship. Nucleic acid hybridization is at the core of many amplification-free molecular diagnostics and detection probe configuration is key to diagnostic performance. Modified nucleic acids such as peptide nucleic acid (PNA) offer advantages compared to conventional DNA probes allowing for faster hybridization, better stability and minimal sample preparation for direct detection of pathogens. Probes with tethered fluorophore and quencher allow for solution-based assays and eliminate the need for washing steps thereby facilitating integration into microfluidic devices. Here, we compared the sensitivity and specificity of double stranded PNA probes (dsPNA) and PNA molecular beacons targeting E. coli and P. aeruginosa for direct detection of bacterial pathogens. In bulk fluid assays, the dsPNAs had an overall higher fluorescent signal and better sensitivity and specificity than the PNA beacons for pathogen detection. We further designed and tested an expanded panel of dsPNA probes for detection of a wide variety of pathogenic bacteria including probes for universal detection of eubacteria, Enterobacteriaceae family, and P. mirablis. To confirm that the advantage translated to other assay types we compared the PNA beacon and dsPNA in a prototype droplet microfluidic device. Beyond the bulk fluid assay and droplet devices, use of dsPNA probes may be advantageous in a wide variety of assays that employ homogenous nucleic acid hybridization.
Collapse
Affiliation(s)
- Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA.
| | | | | | | | | | | |
Collapse
|
19
|
Lippmann T, Braubach P, Ettinger M, Kuehnel M, Laenger F, Jonigk D. Fluorescence in Situ Hybridization (FISH) for the Diagnosis of Periprosthetic Joint Infection in Formalin-Fixed Paraffin-Embedded Surgical Tissues. J Bone Joint Surg Am 2019; 101:e5. [PMID: 30653049 DOI: 10.2106/jbjs.18.00243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND As the number of arthroplasties performed increases, periprosthetic joint infection (PJI) represents a common and challenging problem. The Musculoskeletal Infection Society (MSIS) recommends diagnosing PJI according to its guidelines. The aim of the current study was to assess whether fluorescence in situ hybridization (FISH) analysis of formalin-fixed paraffin-embedded periprosthetic membranes can successfully improve the diagnosis of infection in patients with orthopaedic implants. METHODS We retrospectively analyzed 88 periprosthetic membranes of joint prostheses using FISH analysis according to a standard protocol, with a probe targeting a sequence found in most bacteria. We compared the results with routine clinical classification according to the guidelines of the MSIS, microbiological culture, and histopathological classification according to Morawietz and Krenn. We additionally performed FISH analysis using 2 species-specific probes for several culture-positive cases. RESULTS FISH successfully detected bacteria in 38 (95%) of 40 periprosthetic membranes that were rated positive by clinical classification. FISH results compared with clinical classification demonstrated a sensitivity of 95% (95% confidence interval [CI], 83.08% to 99.39%), a specificity of 85.42% (95% CI, 72.24% to 93.93%), a positive predictive value of 84.44% (95% CI, 70.55% to 93.50%), and a negative predictive value of 95.35% (95% CI, 84.19% to 99.43%). FISH results compared with histopathological classification demonstrated a sensitivity of 95.12% (95% CI, 83.47% to 99.40%), a specificity of 87.23% (95% CI, 74.26% to 95.17%), a positive predictive value of 86.67% (95% CI, 73.21% to 94.95%), and a negative predictive value of 95.35% (95% CI, 84.19% to 99.43%). We successfully detected Pseudomonas aeruginosa and Staphylococcus aureus with species-specific FISH probes in all cases that were positive for these respective bacteria by microbiological culture. CONCLUSIONS FISH-based diagnosis of PJI is feasible and can be used as an additional diagnostic criterion. FISH not only can detect bacteria in periprosthetic membranes but can also differentiate pathogens at the species level. FISH represents a fast and reliable tool for detecting PJI in periprosthetic membranes, especially in combination with clinical and histopathological classification. LEVEL OF EVIDENCE Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Collapse
Affiliation(s)
- Torsten Lippmann
- Institute of Pathology (T.L., P.B., M.K., F.L., and D.J.) and Department of Orthopaedic Surgery (M.E.), Hannover Medical School (MHH), Hannover, Germany
| | - Peter Braubach
- Institute of Pathology (T.L., P.B., M.K., F.L., and D.J.) and Department of Orthopaedic Surgery (M.E.), Hannover Medical School (MHH), Hannover, Germany
| | - Max Ettinger
- Institute of Pathology (T.L., P.B., M.K., F.L., and D.J.) and Department of Orthopaedic Surgery (M.E.), Hannover Medical School (MHH), Hannover, Germany
| | - Mark Kuehnel
- Institute of Pathology (T.L., P.B., M.K., F.L., and D.J.) and Department of Orthopaedic Surgery (M.E.), Hannover Medical School (MHH), Hannover, Germany
| | - Florian Laenger
- Institute of Pathology (T.L., P.B., M.K., F.L., and D.J.) and Department of Orthopaedic Surgery (M.E.), Hannover Medical School (MHH), Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (Deutsches Zentrum für Lungenforschung [DZL]), Hannover, Germany
| | - Danny Jonigk
- Institute of Pathology (T.L., P.B., M.K., F.L., and D.J.) and Department of Orthopaedic Surgery (M.E.), Hannover Medical School (MHH), Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (Deutsches Zentrum für Lungenforschung [DZL]), Hannover, Germany
| |
Collapse
|
20
|
Tubia I, Prasad K, Pérez-Lorenzo E, Abadín C, Zumárraga M, Oyanguren I, Barbero F, Paredes J, Arana S. Beverage spoilage yeast detection methods and control technologies: A review of Brettanomyces. Int J Food Microbiol 2018; 283:65-76. [DOI: 10.1016/j.ijfoodmicro.2018.06.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/21/2018] [Accepted: 06/25/2018] [Indexed: 12/28/2022]
|
21
|
Alhede M, Stavnsbjerg C, Bjarnsholt T. The use of fluorescent staining techniques for microscopic investigation of polymorphonuclear leukocytes and bacteria. APMIS 2018; 126:779-794. [DOI: 10.1111/apm.12888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/14/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Maria Alhede
- Costerton Biofilm Center; Department of International Health, Immunology and Microbiology; University of Copenhagen; Copenhagen Denmark
| | - Camilla Stavnsbjerg
- Costerton Biofilm Center; Department of International Health, Immunology and Microbiology; University of Copenhagen; Copenhagen Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center; Department of International Health, Immunology and Microbiology; University of Copenhagen; Copenhagen Denmark
- Department of Immunology and Microbiology; Rigshospitalet; Copenhagen Denmark
| |
Collapse
|
22
|
Prudent E, Lepidi H, Angelakis E, Raoult D. Fluorescence In Situ Hybridization (FISH) and Peptide Nucleic Acid Probe-Based FISH for Diagnosis of Q Fever Endocarditis and Vascular Infections. J Clin Microbiol 2018; 56:e00542-18. [PMID: 29899006 PMCID: PMC6113452 DOI: 10.1128/jcm.00542-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 06/11/2018] [Indexed: 01/07/2023] Open
Abstract
Endocarditis and vascular infections are common manifestations of persistent localized infection due to Coxiella burnetii, and recently, fluorescence in situ hybridization (FISH) was proposed as an alternative tool for their diagnosis. In this study, we evaluated the efficiency of FISH in a series of valve and vascular samples infected by C. burnetii We tested 23 C. burnetii-positive valves and thrombus samples obtained from patients with Q fever endocarditis. Seven aneurysms and thrombus specimens were retrieved from patients with Q fever vascular infections. Samples were analyzed by culture, immunochemistry, and FISH with oligonucleotide and PNA probes targeting C. burnetii-specific 16S rRNA sequences. The immunohistochemical analysis was positive for five (17%) samples with significantly more copies of C. burnetii DNA than the negative ones (P = 0.02). FISH was positive for 13 (43%) samples and presented 43% and 40% sensitivity compared to that for quantitative PCR (qPCR) and culture, respectively. PNA FISH detected C. burnetii in 18 (60%) samples and presented 60% and 55% sensitivity compared to that for qPCR and culture, respectively. Immunohistochemistry had 38% and 28% sensitivity compared to that for FISH and PNA FISH, respectively. Samples found positive by both immunohistochemistry and PNA FISH contained significantly more copies of C. burnetii DNA than the negative ones (P = 0.03). Finally, PNA FISH was more sensitive than FISH (60% versus 43%, respectively) for the detection of C. burnetii We provide evidence that PNA FISH and FISH are important assays for the diagnosis of C. burnetii endocarditis and vascular infections.
Collapse
Affiliation(s)
- Elsa Prudent
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Hubert Lepidi
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Emmanouil Angelakis
- Aix Marseille Université, IRD, AP-HM, VITROME, IHU-Méditerranée Infection, Marseille, France
- French Reference Center for the Diagnosis and Study of Rickettsioses, Q fever and Bartonelloses, IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| |
Collapse
|
23
|
Fitzpatrick CR, Lu-Irving P, Copeland J, Guttman DS, Wang PW, Baltrus DA, Dlugosch KM, Johnson MTJ. Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies. MICROBIOME 2018; 6:144. [PMID: 30121081 PMCID: PMC6098832 DOI: 10.1186/s40168-018-0534-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/14/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND The ability to efficiently characterize microbial communities from host individuals can be limited by co-amplification of host organellar sequences (mitochondrial and/or plastid), which share a common ancestor and thus sequence similarity with extant bacterial lineages. One promising approach is the use of sequence-specific peptide nucleic acid (PNA) clamps, which bind to, and block amplification of, host-derived DNA. Universal PNA clamps have been proposed to block host plant-derived mitochondrial (mPNA) and plastid (pPNA) sequences at the V4 16S rRNA locus, but their efficacy across a wide range of host plant species has not been experimentally tested. RESULTS Using the universal PNA clamps, we amplified and sequenced root microbial communities from replicate individuals of 32 plant species with a most recent common ancestor inferred at 140 MYA. We found the average rate of host plastid contamination across plant species was 23%, however, particular lineages exhibited much higher rates (62-94%), with the highest levels of contamination occurring in the Asteraceae. We investigated chloroplast sequence variation at the V4 locus across 500 land plant species (Embryophyta) and found six lineages with mismatches between plastid and the universal pPNA sequence, including all species within the Asteraceae. Using a modified pPNA for the Asteraceae sequence, we found (1) host contamination in Asteraceae species was reduced from 65 to 23%; and (2) host contamination in non-Asteraceae species was increased from 12 to 69%. These results demonstrate that even single nucleotide mismatches can lead to drastic reductions in pPNA efficacy in blocking host amplification. Importantly, we found that pPNA type (universal or modified) had no effect on the detection of individual bacterial taxa, or estimates of within and between sample bacterial diversity, suggesting that our modification did not introduce bias against particular bacterial lineages. CONCLUSIONS When high similarity exists between host organellar DNA and PCR target sequences, PNA clamps are an important molecular tool to reduce host contamination during amplification. Here, we provide a validated framework to modify universal PNA clamps to accommodate host variation in organellar sequences.
Collapse
Affiliation(s)
- Connor R Fitzpatrick
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada.
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.
| | - Patricia Lu-Irving
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Julia Copeland
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Pauline W Wang
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Katrina M Dlugosch
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Marc T J Johnson
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| |
Collapse
|
24
|
Influence of the fixation/permeabilization step on peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria. PLoS One 2018; 13:e0196522. [PMID: 29851961 PMCID: PMC5979007 DOI: 10.1371/journal.pone.0196522] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/14/2018] [Indexed: 11/19/2022] Open
Abstract
Fluorescence in situ Hybridization (FISH) is a versatile, widespread and widely- used technique in microbiology. The first step of FISH—fixation/permeabilization—is crucial to the outcome of the method. This work aimed to systematically evaluate fixation/permeabilization protocols employing ethanol, triton X-100 and lysozyme in conjugation with paraformaldehyde for Peptide Nucleic Acid (PNA)-FISH. Response surface methodology was used to optimize these protocols for Gram-negative (Escherichia coli and Pseudomonas fluorescens) and Gram-positive species (Listeria innocua, Staphylococcus epidermidis and Bacillus cereus). In general, the optimal PNA-FISH fluorescent outcome in Gram-positive bacteria was obtained employing harsher permeabilization conditions when compared to Gram-negative optimal protocols. The observed differences arise from the intrinsic cell envelope properties of each species and the ability of the fixation/permeabilization compounds to effectively increase the permeability of these structures while maintaining structural integrity. Ultimately, the combination of paraformaldehyde and ethanol proved to have significantly superior performance for all tested bacteria, especially for Gram-positive species (p<0.05).
Collapse
|
25
|
|
26
|
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: 36] [Impact Index Per Article: 5.1] [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.![]()
Collapse
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
| |
Collapse
|
27
|
Ferreira AM, Cruz-Moreira D, Cerqueira L, Miranda JM, Azevedo NF. Yeasts identification in microfluidic devices using peptide nucleic acid fluorescence in situ hybridization (PNA-FISH). Biomed Microdevices 2017; 19:11. [PMID: 28144839 DOI: 10.1007/s10544-017-0150-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) is a highly specific molecular method widely used for microbial identification. Nonetheless, and due to the detection limit of this technique, a time-consuming pre-enrichment step is typically required before identification. In here we have developed a lab-on-a-chip device to concentrate cell suspensions and speed up the identification process in yeasts. The PNA-FISH protocol was optimized to target Saccharomyces cerevisiae, a common yeast that is very relevant for several types of food industries. Then, several coin-sized microfluidic devices with different geometries were developed. Using Computational fluid dynamics (CFD), we modeled the hydrodynamics inside the microchannels and selected the most promising options. SU-8 structures were fabricated based on the selected designs and used to produce polydimethylsiloxane-based microchips by soft lithography. As a result, an integrated approach combining microfluidics and PNA-FISH for the rapid identification of S. cerevisiae was achieved. To improve fluid flow inside microchannels and the PNA-FISH labeling, oxygen plasma treatment was applied to the microfluidic devices and a new methodology to introduce the cell suspension and solutions into the microchannels was devised. A strong PNA-FISH signal was observed in cells trapped inside the microchannels, proving that the proposed methodology works as intended. The microfluidic designs and PNA-FISH procedure described in here should be easily adaptable for detection of other microorganisms of similar size.
Collapse
Affiliation(s)
- André M Ferreira
- LEPABE- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, s, /n 4200-465, Porto, Portugal.,CEFT-Transport Phenomena Research Center, Department of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, s, /n 4200-465, Porto, Portugal
| | - Daniela Cruz-Moreira
- LEPABE- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, s, /n 4200-465, Porto, Portugal.,CEFT-Transport Phenomena Research Center, Department of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, s, /n 4200-465, Porto, Portugal
| | - Laura Cerqueira
- LEPABE- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, s, /n 4200-465, Porto, Portugal.,Biomode 2, S.A.-Edifício GNRation, Praça Conde de Agrolongo, n°, 123 4700-312, Braga, Portugal
| | - João M Miranda
- CEFT-Transport Phenomena Research Center, Department of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, s, /n 4200-465, Porto, Portugal
| | - Nuno F Azevedo
- LEPABE- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, s, /n 4200-465, Porto, Portugal.
| |
Collapse
|
28
|
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: 11] [Impact Index Per Article: 1.4] [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.
Collapse
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
| |
Collapse
|
29
|
Braubach P, Lippmann T, Raoult D, Lagier JC, Anagnostopoulos I, Zender S, Länger FP, Kreipe HH, Kühnel MP, Jonigk D. Fluorescence In Situ Hybridization for Diagnosis of Whipple's Disease in Formalin-Fixed Paraffin-Embedded Tissue. Front Med (Lausanne) 2017; 4:87. [PMID: 28691008 PMCID: PMC5479881 DOI: 10.3389/fmed.2017.00087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 06/07/2017] [Indexed: 12/12/2022] Open
Abstract
Whipple’s disease (WD) is a rare chronic systemic infection with a wide range of clinical symptoms, routinely diagnosed in biopsies from the small intestine and other tissues by periodic acid–Schiff (PAS) diastase staining and immunohistological analysis with specific antibodies. The aim of our study was to improve the pathological diagnosis of WD. Therefore, we analyzed the potential of fluorescence in situ hybridization (FISH) for diagnosing WD, using a Tropheryma (T.) whipplei-specific probe. 19 formalin-fixed paraffin-embedded (FFPE) duodenal biopsy specimens of 12 patients with treated (6/12) and untreated (6/12) WD were retrospectively examined using PAS diastase staining, immunohistochemistry, and FISH. 20 biopsy specimens with normal intestinal mucosa, Helicobacter pylori, or mycobacterial infection, respectively, served as controls. We successfully detected T. whipplei in tissue biopsies with a sensitivity of 83% in untreated (5/6) and 40% in treated (4/10) cases of WD. In our study, we show that FISH-based diagnosis of individual vital T. whipplei in FFPE specimens is feasible and can be considered as ancillary diagnostic tool for the diagnosis of WD in FFPE material. We show that FISH not only detect active WD but also be helpful as an indicator for the efficiency of antibiotic treatment and for detection of recurrence of disease when the signal of PAS diastase and immunohistochemistry lags behind the recurrence of disease, especially if the clinical course of the patient and antimicrobial treatment is considered.
Collapse
Affiliation(s)
- Peter Braubach
- Institute of Pathology, Hannover Medical School (MHH), Hanover, Germany
| | - Torsten Lippmann
- Institute of Pathology, Hannover Medical School (MHH), Hanover, Germany
| | - Didier Raoult
- Aix Marseille University, CNRS, IRD, INSERM, AP-HM, URMITE, IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille University, CNRS, IRD, INSERM, AP-HM, URMITE, IHU Méditerranée Infection, Marseille, France
| | | | - Steffen Zender
- Department of Gastroenterology, Hepatology, and Endocrinology, Centre for Internal Medicine, Hannover Medical School (MHH), Hanover, Germany
| | | | | | | | - Danny Jonigk
- Institute of Pathology, Hannover Medical School (MHH), Hanover, Germany
| |
Collapse
|
30
|
|
31
|
Yadav R, Shukla P. An overview of advanced technologies for selection of probiotics and their expediency: A review. Crit Rev Food Sci Nutr 2017; 57:3233-3242. [DOI: 10.1080/10408398.2015.1108957] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ruby Yadav
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| |
Collapse
|
32
|
Davenport M, Mach KE, Shortliffe LMD, Banaei N, Wang TH, Liao JC. New and developing diagnostic technologies for urinary tract infections. Nat Rev Urol 2017; 14:296-310. [PMID: 28248946 PMCID: PMC5473291 DOI: 10.1038/nrurol.2017.20] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Timely and accurate identification and determination of the antimicrobial susceptibility of uropathogens is central to the management of UTIs. Urine dipsticks are fast and amenable to point-of-care testing, but do not have adequate diagnostic accuracy or provide microbiological diagnosis. Urine culture with antimicrobial susceptibility testing takes 2-3 days and requires a clinical laboratory. The common use of empirical antibiotics has contributed to the rise of multidrug-resistant organisms, reducing treatment options and increasing costs. In addition to improved antimicrobial stewardship and the development of new antimicrobials, novel diagnostics are needed for timely microbial identification and determination of antimicrobial susceptibilities. New diagnostic platforms, including nucleic acid tests and mass spectrometry, have been approved for clinical use and have improved the speed and accuracy of pathogen identification from primary cultures. Optimization for direct urine testing would reduce the time to diagnosis, yet these technologies do not provide comprehensive information on antimicrobial susceptibility. Emerging technologies including biosensors, microfluidics, and other integrated platforms could improve UTI diagnosis via direct pathogen detection from urine samples, rapid antimicrobial susceptibility testing, and point-of-care testing. Successful development and implementation of these technologies has the potential to usher in an era of precision medicine to improve patient care and public health.
Collapse
Affiliation(s)
- Michael Davenport
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Linda M Dairiki Shortliffe
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, California 94304 USA
| | - Tza-Huei Wang
- Departments of Mechanical and Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA
| | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, California 94304 USA
| |
Collapse
|
33
|
Riedel S, Carroll KC. Early Identification and Treatment of Pathogens in Sepsis: Molecular Diagnostics and Antibiotic Choice. Clin Chest Med 2017; 37:191-207. [PMID: 27229637 DOI: 10.1016/j.ccm.2016.01.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Sepsis and septic shock are serious conditions associated with high morbidity and mortality. Rapid molecular methods for detection of microorganisms and antimicrobial resistance genes from positive blood cultures or whole blood have evolved over the past 10 years. Such diagnostic methods coupled with therapeutic interventional programs are desirable to improve the overall clinical outcome and mortality. This article discusses the usefulness of current molecular test methods for the diagnosis of sepsis and their potential to enhance the success of antimicrobial stewardship programs. Clinicians and laboratories alike must appreciate key factors influencing the appropriate use and potential impact of these methods.
Collapse
Affiliation(s)
- Stefan Riedel
- Department of Pathology, Harvard Medical School, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins Hospital, The Johns Hopkins University School of Medicine, 600 North Wolfe Street, Meyer B1-193, Baltimore, MD 21287, USA
| |
Collapse
|
34
|
Machado A, Cerca N. Multiplex Peptide Nucleic Acid Fluorescence In Situ Hybridization (PNA-FISH) for Diagnosis of Bacterial Vaginosis. Methods Mol Biol 2017; 1616:209-219. [PMID: 28600771 DOI: 10.1007/978-1-4939-7037-7_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fluorescence in situ hybridization (FISH) is a molecular method used to identify and quantify microorganisms in a wide range of samples. This technique combines the simplicity of microscopic observation and the specificity of DNA/rRNA hybridization, allowing detection of selected bacterial species and morphologic visualization. Here, we describe a quantitative molecular diagnosis of bacterial vaginosis, based on the classical Nugent score. Our probes are able to differentiate Lactobacillus spp. and Gardnerella vaginalis from the other undefined bacterial species considered in the Nugent score.
Collapse
Affiliation(s)
- Antonio Machado
- Microbiology Institute, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Cumbayá, Quito, 170157, Ecuador
| | - Nuno Cerca
- CEB-Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| |
Collapse
|
35
|
Hnedzko D, McGee DW, Rozners E. Synthesis and properties of peptide nucleic acid labeled at the N-terminus with HiLyte Fluor 488 fluorescent dye. Bioorg Med Chem 2016; 24:4199-4205. [PMID: 27430566 DOI: 10.1016/j.bmc.2016.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/02/2016] [Accepted: 07/05/2016] [Indexed: 11/16/2022]
Abstract
Fluorescently labeled peptide nucleic acids (PNAs) are important tools in fundamental research and biomedical applications. However, synthesis of labeled PNAs, especially using modern and expensive dyes, is less explored than similar preparations of oligonucleotide dye conjugates. Herein, we present a simple procedure for labeling of the PNA N-terminus with HiLyte Fluor 488 as the last step of solid phase PNA synthesis. A minimum excess of 1.25equiv of activated carboxylic acid achieved labeling yields close to 90% providing a good compromise between the price of dye and the yield of product and significant improvement over previous literature procedures. The HiLyte Fluor 488-labeled PNAs retained the RNA binding ability and in live cell fluorescence microscopy experiments were brighter and significantly more photostable than PNA labeled with carboxyfluorescein. In contrast to fluorescein-labeled PNA, the fluorescence of PNAs labeled with HiLyte Fluor 488 was independent of pH in the biologically relevant range of 5-8. The potential of HiLyte Fluor 488-labeling for studies of PNA cellular uptake and distribution was demonstrated in several cell lines.
Collapse
Affiliation(s)
- Dziyana Hnedzko
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, United States
| | - Dennis W McGee
- Department of Biological Sciences, Binghamton University, The State University of New York, Binghamton, NY 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, United States.
| |
Collapse
|
36
|
Rocha R, Santos RS, Madureira P, Almeida C, Azevedo NF. Optimization of peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria: The effect of pH, dextran sulfate and probe concentration. J Biotechnol 2016; 226:1-7. [PMID: 27021959 DOI: 10.1016/j.jbiotec.2016.03.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 01/17/2023]
Abstract
Fluorescence in situ hybridization (FISH) is a molecular technique widely used for the detection and characterization of microbial populations. FISH is affected by a wide variety of abiotic and biotic variables and the way they interact with each other. This is translated into a wide variability of FISH procedures found in the literature. The aim of this work is to systematically study the effects of pH, dextran sulfate and probe concentration in the FISH protocol, using a general peptide nucleic acid (PNA) probe for the Eubacteria domain. For this, response surface methodology was used to optimize these 3 PNA-FISH parameters for Gram-negative (Escherichia coli and Pseudomonas fluorescens) and Gram-positive species (Listeria innocua, Staphylococcus epidermidis and Bacillus cereus). The obtained results show that a probe concentration higher than 300nM is favorable for both groups. Interestingly, a clear distinction between the two groups regarding the optimal pH and dextran sulfate concentration was found: a high pH (approx. 10), combined with lower dextran sulfate concentration (approx. 2% [w/v]) for Gram-negative species and near-neutral pH (approx. 8), together with higher dextran sulfate concentrations (approx. 10% [w/v]) for Gram-positive species. This behavior seems to result from an interplay between pH and dextran sulfate and their ability to influence probe concentration and diffusion towards the rRNA target. This study shows that, for an optimum hybridization protocol, dextran sulfate and pH should be adjusted according to the target bacteria.
Collapse
Affiliation(s)
- Rui Rocha
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Biomode, Ed. GNRATION, Praça Conde Agrolongo no 123, 4700-312 Braga, Portugal.
| | - Rita S Santos
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Gent, 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
| | - Pedro Madureira
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre n.° 823, 4150-180 Porto, Portugal; ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira n.° 228, 4050-313 Porto, Portugal; i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Carina Almeida
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Biomode, Ed. GNRATION, Praça Conde Agrolongo no 123, 4700-312 Braga, Portugal
| | - Nuno F Azevedo
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| |
Collapse
|
37
|
Thung I, Aramin H, Vavinskaya V, Gupta S, Park JY, Crowe SE, Valasek MA. Review article: the global emergence of Helicobacter pylori antibiotic resistance. Aliment Pharmacol Ther 2016; 43:514-33. [PMID: 26694080 PMCID: PMC5064663 DOI: 10.1111/apt.13497] [Citation(s) in RCA: 548] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/04/2015] [Accepted: 11/19/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Helicobacter pylori is one of the most prevalent global pathogens and can lead to gastrointestinal disease including peptic ulcers, gastric marginal zone lymphoma and gastric carcinoma. AIM To review recent trends in H. pylori antibiotic resistance rates, and to discuss diagnostics and treatment paradigms. METHODS A PubMed literature search using the following keywords: Helicobacter pylori, antibiotic resistance, clarithromycin, levofloxacin, metronidazole, prevalence, susceptibility testing. RESULTS The prevalence of bacterial antibiotic resistance is regionally variable and appears to be markedly increasing with time in many countries. Concordantly, the antimicrobial eradication rate of H. pylori has been declining globally. In particular, clarithromycin resistance has been rapidly increasing in many countries over the past decade, with rates as high as approximately 30% in Japan and Italy, 50% in China and 40% in Turkey; whereas resistance rates are much lower in Sweden and Taiwan, at approximately 15%; there are limited data in the USA. Other antibiotics show similar trends, although less pronounced. CONCLUSIONS Since the choice of empiric therapies should be predicated on accurate information regarding antibiotic resistance rates, there is a critical need for determination of current rates at a local scale, and perhaps in individual patients. Such information would not only guide selection of appropriate empiric antibiotic therapy but also inform the development of better methods to identify H. pylori antibiotic resistance at diagnosis. Patient-specific tailoring of effective antibiotic treatment strategies may lead to reduced treatment failures and less antibiotic resistance.
Collapse
Affiliation(s)
- I. Thung
- Division of Anatomic PathologyDepartment of PathologyUniversity of California San Diego Medical CenterSan DiegoCAUSA
| | - H. Aramin
- Division of Anatomic PathologyDepartment of PathologyUniversity of California San Diego Medical CenterSan DiegoCAUSA
| | - V. Vavinskaya
- Division of Anatomic PathologyDepartment of PathologyUniversity of California San Diego Medical CenterSan DiegoCAUSA
| | - S. Gupta
- Division of GastroenterologyDepartment of MedicineUniversity of California San Diego Medical CenterLa JollaCAUSA
| | - J. Y. Park
- Department of Pathology and the Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical Center and Children's Medical CenterDallasTXUSA
| | - S. E. Crowe
- Division of GastroenterologyDepartment of MedicineUniversity of California San Diego Medical CenterLa JollaCAUSA
| | - M. A. Valasek
- Division of Anatomic PathologyDepartment of PathologyUniversity of California San Diego Medical CenterSan DiegoCAUSA
| |
Collapse
|
38
|
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: 2.6] [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.
Collapse
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
| |
Collapse
|
39
|
Sanchez-Vizuete P, Orgaz B, Aymerich S, Le Coq D, Briandet R. Pathogens protection against the action of disinfectants in multispecies biofilms. Front Microbiol 2015; 6:705. [PMID: 26236291 PMCID: PMC4500986 DOI: 10.3389/fmicb.2015.00705] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/26/2015] [Indexed: 01/09/2023] Open
Abstract
Biofilms constitute the prevalent way of life for microorganisms in both natural and man-made environments. Biofilm-dwelling cells display greater tolerance to antimicrobial agents than those that are free-living, and the mechanisms by which this occurs have been investigated extensively using single-strain axenic models. However, there is growing evidence that interspecies interactions may profoundly alter the response of the community to such toxic exposure. In this paper, we propose an overview of the studies dealing with multispecies biofilms resistance to biocides, with particular reference to the protection of pathogenic species by resident surface flora when subjected to disinfectants treatments. The mechanisms involved in such protection include interspecies signaling, interference between biocides molecules and public goods in the matrix, or the physiology and genetic plasticity associated with a structural spatial arrangement. After describing these different mechanisms, we will discuss the experimental methods available for their analysis in the context of complex multispecies biofilms.
Collapse
Affiliation(s)
- Pilar Sanchez-Vizuete
- INRA, UMR1319 MICALIS, Jouy-en-JosasFrance
- AgroParisTech, UMR MICALIS, Jouy-en-JosasFrance
| | - Belen Orgaz
- Department of Nutrition, Food Science and Technology, Faculty of Veterinary, Complutense University de MadridMadrid, Spain
| | - Stéphane Aymerich
- INRA, UMR1319 MICALIS, Jouy-en-JosasFrance
- AgroParisTech, UMR MICALIS, Jouy-en-JosasFrance
| | - Dominique Le Coq
- INRA, UMR1319 MICALIS, Jouy-en-JosasFrance
- AgroParisTech, UMR MICALIS, Jouy-en-JosasFrance
- CNRS, Jouy-en-JosasFrance
| | - Romain Briandet
- INRA, UMR1319 MICALIS, Jouy-en-JosasFrance
- AgroParisTech, UMR MICALIS, Jouy-en-JosasFrance
| |
Collapse
|
40
|
Machado A, Castro J, Cereija T, Almeida C, Cerca N. Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method. PeerJ 2015; 3:e780. [PMID: 25737820 PMCID: PMC4338769 DOI: 10.7717/peerj.780] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/30/2015] [Indexed: 11/20/2022] Open
Abstract
Bacterial vaginosis (BV) is one of most common vaginal infections. However, its diagnosis by classical methods reveals low specificity. Our goal was to evaluate the accuracy diagnosis of 150 vaginal samples with research gold standard methods and our Peptide Nucleic Acid (PNA) probes by Fluorescence in situ Hybridization (FISH) methodology. Also, we described the first PNA-FISH methodology for BV diagnosis, which provides results in approximately 3 h. The results showed a sensitivity of 84.6% (95% confidence interval (CI), from 64.3 to 95.0%) and a specificity of 97.6% (95% CI [92.6-99.4%]), demonstrating the higher specificity of the PNA-FISH method and showing false positive results in BV diagnosis commonly obtained by the classical methods. This methodology combines the specificity of PNA probes for Lactobacillus species and G. vaginalis visualization and the calculation of the microscopic field by Nugent score, allowing a trustful evaluation of the bacteria present in vaginal microflora and avoiding the occurrence of misleading diagnostics. Therefore, the PNA-FISH methodology represents a valuable alternative for BV diagnosis.
Collapse
Affiliation(s)
- António Machado
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| | - Joana Castro
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| | - Tatiana Cereija
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| | - Carina Almeida
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| | - Nuno Cerca
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| |
Collapse
|
41
|
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: 1.3] [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]
|
42
|
Artificial Nucleic Acid Probes and Their Applications in Clinical Microbiology. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
43
|
Design and evaluation of peptide nucleic acid probes for specific identification of Candida albicans. J Clin Microbiol 2014; 53:511-21. [PMID: 25428160 DOI: 10.1128/jcm.02417-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Candida albicans is an important cause of systemic fungal infections, and rapid diagnostics for identifying and differentiating C. albicans from other Candida species are critical for the timely application of appropriate antimicrobial therapy, improved patient outcomes, and pharmaceutical cost savings. In this work, two 28S rRNA-directed peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) probes, P-Ca726 (targeting a novel region of the ribosome) and P-CalB2208 (targeting a previously reported region), were evaluated. Hybridization conditions were optimized by using both fluorescence microscopy (FM) and flow cytometry (FCM), and probes were screened for specificity and discriminative ability against a panel of C. albicans and various nontarget Candida spp. The performance of these PNA probes was compared quantitatively against that of DNA probes or DNA probe/helper combinations directed against the same target regions. Ratiometric analyses of FCM results indicated that both the hybridization quality and yield of the PNA probes were higher than those of the DNA probes. In FCM-based comparisons of the PNA probes, P-Ca726 was found to be highly specific, showing 2.5- to 5.5-fold-higher discriminatory power for C. albicans than P-CalB2208. The use of formamide further improved the performance of the new probe. Our results reinforce the significant practical and diagnostic advantages of PNA probes over their DNA counterparts for FISH and indicate that P-Ca726 may be used advantageously for the rapid and specific identification of C. albicans in clinical and related applications, especially when combined with FCM.
Collapse
|
44
|
Pham HH, Murphy CT, Sureshkumar G, Ly DH, Opresko PL, Armitage BA. Cooperative hybridization of γPNA miniprobes to a repeating sequence motif and application to telomere analysis. Org Biomol Chem 2014; 12:7345-7354. [PMID: 25115693 PMCID: PMC4162129 DOI: 10.1039/c4ob00953c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
GammaPNA oligomers having one or two repeats of the sequence AATCCC were designed to hybridize to DNA having one or more repeats of the complementary TTAGGG sequence found in the human telomere. UV melting curves and surface plasmon resonance experiments demonstrate high affinity and cooperativity for hybridization of these miniprobes to DNA having multiple complementary repeats. Fluorescence spectroscopy for Cy3-labeled miniprobes demonstrate increases in fluorescence intensity for assembling multiple short probes on a DNA target compared with fewer longer probes. The fluorescent γPNA miniprobes were then used to stain telomeres in metaphase chromosomes derived from U2OS cells possessing heterogeneous long telomeres and Jurkat cells harboring homogenous short telomeres. The miniprobes yielded comparable fluorescence intensity to a commercially available PNA 18mer probe in U2OS cells, but significantly brighter fluorescence was observed for telomeres in Jurkat cells. These results suggest that γPNA miniprobes can be effective telomere-staining reagents with applications toward analysis of critically short telomeres, which have been implicated in a range of human diseases.
Collapse
Affiliation(s)
- Ha H. Pham
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Connor T. Murphy
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Department of Environmental and Occupational Health, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA 15219
| | - Gopalsamy Sureshkumar
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Danith H. Ly
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Patricia L. Opresko
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Department of Environmental and Occupational Health, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA 15219
| | - Bruce A. Armitage
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| |
Collapse
|
45
|
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: 2.7] [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.
Collapse
|
46
|
Parcell BJ, Orange GV. PNA-FISH assays for early targeted bacteraemia treatment. J Microbiol Methods 2013; 95:253-5. [PMID: 24055387 DOI: 10.1016/j.mimet.2013.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/01/2013] [Accepted: 09/07/2013] [Indexed: 02/04/2023]
Abstract
PNA-FISH S. aureus/CNS and GNR Traffic Light assays were compared with standard culture methods for identifying bacteraemia in 156 blood cultures from 131 patients. Results correlated with final culture results in 153 cultures. Retrospective case note review revealed that earlier targeted treatment would have occurred in 10.7% of cases.
Collapse
Affiliation(s)
- B J Parcell
- Department of Medical Microbiology, Ninewells Hospital and Medical School, NHS Tayside, Dundee, United Kingdom.
| | | |
Collapse
|
47
|
Pence MA, McElvania TeKippe E, Burnham CAD. Diagnostic Assays for Identification of Microorganisms and Antimicrobial Resistance Determinants Directly from Positive Blood Culture Broth. Clin Lab Med 2013; 33:651-84. [DOI: 10.1016/j.cll.2013.03.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
48
|
Bjarnsholt T, Alhede M, Alhede M, Eickhardt-Sørensen SR, Moser C, Kühl M, Jensen PØ, Høiby N. The in vivo biofilm. Trends Microbiol 2013; 21:466-74. [PMID: 23827084 DOI: 10.1016/j.tim.2013.06.002] [Citation(s) in RCA: 532] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/26/2013] [Accepted: 06/05/2013] [Indexed: 11/15/2022]
Abstract
Bacteria can grow and proliferate either as single, independent cells or organized in aggregates commonly referred to as biofilms. When bacteria succeed in forming a biofilm within the human host, the infection often becomes very resistant to treatment and can develop into a chronic state. Biofilms have been studied for decades using various in vitro models, but it remains debatable whether such in vitro biofilms actually resemble in vivo biofilms in chronic infections. In vivo biofilms share several structural characteristics that differ from most in vitro biofilms. Additionally, the in vivo experimental time span and presence of host defenses differ from chronic infections and the chemical microenvironment of both in vivo and in vitro biofilms is seldom taken into account. In this review, we discuss why the current in vitro models of biofilms might be limited for describing infectious biofilms, and we suggest new strategies for improving this discrepancy.
Collapse
Affiliation(s)
- Thomas Bjarnsholt
- Department of International Health, Immunology, and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Microbiology 9301, Juliane Mariesvej 22, Copenhagen University Hospital, Copenhagen, Denmark.
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Machado A, Almeida C, Salgueiro D, Henriques A, Vaneechoutte M, Haesebrouck F, Vieira MJ, Rodrigues L, Azevedo NF, Cerca N. Fluorescence in situ Hybridization method using Peptide Nucleic Acid probes for rapid detection of Lactobacillus and Gardnerella spp. BMC Microbiol 2013; 13:82. [PMID: 23586331 PMCID: PMC3637831 DOI: 10.1186/1471-2180-13-82] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/27/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial vaginosis (BV) is a common vaginal infection occurring in women of reproductive age. It is widely accepted that the microbial switch from normal microflora to BV is characterized by a decrease in vaginal colonization by Lactobacillus species together with an increase of Gardnerella vaginalis and other anaerobes. Our goal was to develop and optimize a novel Peptide Nucleic Acid (PNA) Fluorescence in situ Hybridization assay (PNA FISH) for the detection of Lactobacillus spp. and G. vaginalis in mixed samples. RESULTS Therefore, we evaluated and validated two specific PNA probes by using 36 representative Lactobacillus strains, 22 representative G. vaginalis strains and 27 other taxonomically related or pathogenic bacterial strains commonly found in vaginal samples. The probes were also tested at different concentrations of G. vaginalis and Lactobacillus species in vitro, in the presence of a HeLa cell line. Specificity and sensitivity of the PNA probes were found to be 98.0% (95% confidence interval (CI), from 87.8 to 99.9%) and 100% (95% CI, from 88.0 to 100.0%), for Lactobacillus spp.; and 100% (95% CI, from 92.8 to 100%) and 100% (95% CI, from 81.5 to 100.0%) for G. vaginalis. Moreover, the probes were evaluated in mixed samples mimicking women with BV or normal vaginal microflora, demonstrating efficiency and applicability of our PNA FISH. CONCLUSIONS This quick method accurately detects Lactobacillus spp. and G. vaginalis species in mixed samples, thus enabling efficient evaluation of the two bacterial groups, most frequently encountered in the vagina.
Collapse
Affiliation(s)
- António Machado
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Machado A, Almeida C, Carvalho A, Boyen F, Haesebrouck F, Rodrigues L, Cerca N, Azevedo NF. Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of Lactobacillus spp. in milk samples. Int J Food Microbiol 2013; 162:64-70. [PMID: 23357093 DOI: 10.1016/j.ijfoodmicro.2012.09.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 09/11/2012] [Accepted: 09/30/2012] [Indexed: 10/27/2022]
Abstract
Lactobacillus species constitute one of the dominant and beneficial bacteria in our body and are used in developed countries as a microbial adjuvant. Identification of these probiotic bacteria is traditionally performed by culture-based techniques. However, such methods are very time-consuming and can give inaccurate results, especially when Lactobacillus is present in mixed bacterial complex communities. Our study aimed to accurately identify Lactobacillus spp. using a novel Peptide Nucleic Acid (PNA) Fluorescence In Situ Hybridization (FISH) probe. The probe (Lac663) was tested on 36 strains belonging to different Lactobacillus species and on 20 strains of other bacterial species. The sensitivity and specificity of the method were 100% (95% confidence interval (CI), 88.0 to 100.0%) and 95.0% (95% CI, 73.1 to 99.7%), respectively. Additionally, we tested the applicability of the method on milk samples added with Lactobacillus strains at probiotic range concentrations and other taxonomically related bacteria, as well as pathogenic bacteria. The Lac663 probe bound exclusively to Lactobacillus strains and the described PNA-FISH method was capable of directly quantifying Lactobacillus spp. in concentrations at which these potential probiotic bacteria are considered to have an effective benefit on human health.
Collapse
Affiliation(s)
- Antonio Machado
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | | | | | | | | | | | | | | |
Collapse
|