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Jiang H, Li L, Bao Y, Cao X, Ma L. Microbiota in tumors: new factor influencing cancer development. Cancer Gene Ther 2024:10.1038/s41417-024-00833-0. [PMID: 39342031 DOI: 10.1038/s41417-024-00833-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/25/2024] [Accepted: 09/11/2024] [Indexed: 10/01/2024]
Abstract
Tumor microbiota research is a new field in oncology. With the advancement of high-throughput sequencing, there is growing evidence that a microbial community exists within tumor tissue. How these bacteria access tumor cells varies, including through the invasion of mucous membranes, the bloodstream, or the gut-organ axis. Previous literature has shown that microbes promote the development and progression of cancer through various mechanisms, such as affecting the host's immune system, promoting inflammation, regulating metabolism, and activating invasion and transfer. The study of the tumor microbiota offers a new perspective for the diagnosis and treatment of cancer, and it holds the potential for the development of new diagnostic tools and therapies. The role of the tumor microbiota in the pathogenesis of cancer is becoming increasingly evident, and future research will continue to uncover the specific mechanisms of action of these microbes, potentially shedding light on new strategies and methods for cancer prevention and therapy. This article reviews the latest advancements in this field, including how intratumor microbes migrate, their carcinogenic mechanisms, and the characteristics of different types of tumor microbes as well as the application of relevant methods in tumor microbiota research and the clinical values of targeting tumor microbes in cancer therapy.
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Affiliation(s)
- Haixia Jiang
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lan Li
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunxia Bao
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiongyue Cao
- Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Lifang Ma
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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2
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Liu J, Bao C, Zhang J, Han Z, Fang H, Lu H. Artificial intelligence with mass spectrometry-based multimodal molecular profiling methods for advancing therapeutic discovery of infectious diseases. Pharmacol Ther 2024; 263:108712. [PMID: 39241918 DOI: 10.1016/j.pharmthera.2024.108712] [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: 05/31/2024] [Revised: 07/22/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Infectious diseases, driven by a diverse array of pathogens, can swiftly undermine public health systems. Accurate diagnosis and treatment of infectious diseases-centered around the identification of biomarkers and the elucidation of disease mechanisms-are in dire need of more versatile and practical analytical approaches. Mass spectrometry (MS)-based molecular profiling methods can deliver a wealth of information on a range of functional molecules, including nucleic acids, proteins, and metabolites. While MS-driven omics analyses can yield vast datasets, the sheer complexity and multi-dimensionality of MS data can significantly hinder the identification and characterization of functional molecules within specific biological processes and events. Artificial intelligence (AI) emerges as a potent complementary tool that can substantially enhance the processing and interpretation of MS data. AI applications in this context lead to the reduction of spurious signals, the improvement of precision, the creation of standardized analytical frameworks, and the increase of data integration efficiency. This critical review emphasizes the pivotal roles of MS based omics strategies in the discovery of biomarkers and the clarification of infectious diseases. Additionally, the review underscores the transformative ability of AI techniques to enhance the utility of MS-based molecular profiling in the field of infectious diseases by refining the quality and practicality of data produced from omics analyses. In conclusion, we advocate for a forward-looking strategy that integrates AI with MS-based molecular profiling. This integration aims to transform the analytical landscape and the performance of biological molecule characterization, potentially down to the single-cell level. Such advancements are anticipated to propel the development of AI-driven predictive models, thus improving the monitoring of diagnostics and therapeutic discovery for the ongoing challenge related to infectious diseases.
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Affiliation(s)
- Jingjing Liu
- School of Chinese Medicine, Hong Kong Traditional Chinese Medicine Phenome Research Center, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Chaohui Bao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiaxin Zhang
- School of Chinese Medicine, Hong Kong Traditional Chinese Medicine Phenome Research Center, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Zeguang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Haitao Lu
- School of Chinese Medicine, Hong Kong Traditional Chinese Medicine Phenome Research Center, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China; Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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3
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Austin GI, Korem T. Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective. J Infect Dis 2024:jiae378. [PMID: 39189314 DOI: 10.1093/infdis/jiae378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Indexed: 08/28/2024] Open
Abstract
As investigations of low-biomass microbial communities have become more common, so too has the recognition of major challenges affecting these analyses. These challenges have been shown to compromise biological conclusions and have contributed to several controversies. Here, we review some of the most common and influential challenges in low-biomass microbiome research. We highlight key approaches to alleviate these potential pitfalls, combining experimental planning strategies and data analysis methods.
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Affiliation(s)
- George I Austin
- Department of Biomedical Informatics
- Program for Mathematical Genomics, Department of Systems Biology
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York
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4
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Massier L, Musat N, Stumvoll M, Tremaroli V, Chakaroun R, Kovacs P. Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges. Nat Metab 2024; 6:1209-1224. [PMID: 38898236 DOI: 10.1038/s42255-024-01065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024]
Abstract
Although the impact of the gut microbiome on health and disease is well established, there is controversy regarding the presence of microorganisms such as bacteria and their products in organs and tissues. However, recent contamination-aware findings of tissue-resident microbial signatures provide accumulating evidence in support of bacterial translocation in cardiometabolic disease. The latter provides a distinct paradigm for the link between microbial colonizers of mucosal surfaces and host metabolism. In this Perspective, we re-evaluate the concept of tissue-resident bacteria including their role in metabolic low-grade tissue and systemic inflammation. We examine the limitations and challenges associated with studying low bacterial biomass samples and propose experimental and analytical strategies to overcome these issues. Our Perspective aims to encourage further investigation of the mechanisms linking tissue-resident bacteria to host metabolism and their potentially actionable health implications for prevention and treatment.
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Affiliation(s)
- Lucas Massier
- Department of Medicine (H7), Karolinska Institutet, Stockholm, Sweden
| | - Niculina Musat
- Aarhus University, Department of Biology, Section for Microbiology, Århus, Denmark
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
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5
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Sahoo R, Jadhav S, Nema V. Journey of technological advancements in the detection of antimicrobial resistance. J Formos Med Assoc 2024; 123:430-441. [PMID: 37598038 DOI: 10.1016/j.jfma.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/19/2023] [Accepted: 08/07/2023] [Indexed: 08/21/2023] Open
Abstract
Increased uses rather an extensive misuse of antibiotics due to easy availability and easy access have resulted in antibiotic resistance as a global crisis. The speed of discovery of new antibiotics has slowed down recently. Therefore, there is a need to reduce the rate of increase in resistance against the presently available antibiotics, or else many infections may be left untreatable or difficult to be treated due to the high prevalence of resistance. The judicious use of broad-spectrum antibiotics can control the increase in resistance profile. Various techniques are presently being used for the detection of antibiotic resistance. Conventional phenotypic methods are preferred that are highly reliable but are much more time-consuming. The patients cannot spare more time as the infection keeps increasing. The results with genotypic methods are obtained within 24 h as compared to phenotypic methods. Hence, recent molecular methods like qPCR can be used for detection. In this review, we present an overview of various methods useful for the detection of antibiotic resistance, with emphasis on their advantages and limitations. The review also emphasizes qPCR to be the most preferred method out of all because of various advantageous factors.
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Affiliation(s)
- Rituparna Sahoo
- ICMR-National AIDS Research Institute, 73 G MIDC Bhosari, Pune, 411 026, India
| | - Sushama Jadhav
- ICMR-National AIDS Research Institute, 73 G MIDC Bhosari, Pune, 411 026, India
| | - Vijay Nema
- ICMR-National AIDS Research Institute, 73 G MIDC Bhosari, Pune, 411 026, India.
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Liu R, Xu R, Yan S, Li P, Jia C, Sun H, Sheng K, Wang Y, Zhang Q, Guo J, Xin X, Li X, Guo D. Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells. Front Genet 2024; 15:1377238. [PMID: 38586584 PMCID: PMC10995239 DOI: 10.3389/fgene.2024.1377238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/13/2024] [Indexed: 04/09/2024] Open
Abstract
The functional performance of immune cells relies on a complex transcriptional regulatory network. The three-dimensional structure of chromatin can affect chromatin status and gene expression patterns, and plays an important regulatory role in gene transcription. Currently available techniques for studying chromatin spatial structure include chromatin conformation capture techniques and their derivatives, chromatin accessibility sequencing techniques, and others. Additionally, the recently emerged deep learning technology can be utilized as a tool to enhance the analysis of data. In this review, we elucidate the definition and significance of the three-dimensional chromatin structure, summarize the technologies available for studying it, and describe the research progress on the chromatin spatial structure of dendritic cells, macrophages, T cells, B cells, and neutrophils.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Dianhao Guo
- School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
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7
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Rolph MJ, Bolfa P, Cavanaugh SM, Rolph KE. Fluorescent In Situ Hybridization for the Detection of Intracellular Bacteria in Companion Animals. Vet Sci 2024; 11:52. [PMID: 38275934 PMCID: PMC10821249 DOI: 10.3390/vetsci11010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
FISH techniques have been applied for the visualization and identification of intracellular bacteria in companion animal species. Most frequently, these techniques have focused on the identification of adhesive-invasive Escherichia coli in gastrointestinal disease, although various other organisms have been identified in inflammatory or neoplastic gastrointestinal disease. Previous studies have investigated a potential role of Helicobacter spp. in inflammatory gastrointestinal and hepatic conditions. Other studies evaluating the role of infectious organisms in hepatopathies have received some attention with mixed results. FISH techniques using both eubacterial and species-specific probes have been applied in inflammatory cardiovascular, urinary, and cutaneous diseases to screen for intracellular bacteria. This review summarizes the results of these studies.
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Affiliation(s)
| | | | | | - Kerry E. Rolph
- Center for Integrative Mammalian Research, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
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Muzny CA, Cerca N, Elnaggar JH, Taylor CM, Sobel JD, Van Der Pol B. State of the Art for Diagnosis of Bacterial Vaginosis. J Clin Microbiol 2023; 61:e0083722. [PMID: 37199636 PMCID: PMC10446871 DOI: 10.1128/jcm.00837-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
Bacterial vaginosis (BV) is the most common cause of vaginal discharge among reproductive-age women. It is associated with multiple adverse health outcomes, including increased risk of acquisition of HIV and other sexually transmitted infections (STIs), in addition to adverse birth outcomes. While it is known that BV is a vaginal dysbiosis characterized by a shift in the vaginal microbiota from protective Lactobacillus species to an increase in facultative and strict anaerobic bacteria, its exact etiology remains unknown. The purpose of this minireview is to provide an updated overview of the range of tests currently used for the diagnosis of BV in both clinical and research settings. This article is divided into two primary sections: traditional BV diagnostics and molecular diagnostics. Molecular diagnostic assays, particularly 16S rRNA gene sequencing, shotgun metagenomic sequencing, and fluorescence in situ hybridization (FISH), are specifically highlighted, in addition to multiplex nucleic acid amplification tests (NAATs), given their increasing use in clinical practice (NAATs) and research studies (16S rRNA gene sequencing, shotgun metagenomic sequencing, and FISH) regarding the vaginal microbiota and BV pathogenesis. We also provide a discussion of the strengths and weaknesses of current BV diagnostic tests and discuss future challenges in this field of research.
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Affiliation(s)
- Christina A. Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nuno Cerca
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| | - Jacob H. Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Christopher M. Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Jack D. Sobel
- Division of Infectious Diseases, Wayne State University, Detroit, Michigan, USA
| | - Barbara Van Der Pol
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
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9
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Yang TS, LaDouceur EEB, Baumgartner WA, Marr HS, Karounos M, Robertson J, Whitehurst N, Miller LS, Birkenheuer AJ. A practical protocol to prepare paraffin-embedded whole tick histology sections. Ticks Tick Borne Dis 2023; 14:102162. [PMID: 36965259 PMCID: PMC10652274 DOI: 10.1016/j.ttbdis.2023.102162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 02/05/2023] [Accepted: 02/26/2023] [Indexed: 03/27/2023]
Abstract
Ticks are important ectoparasites that are capable of transmitting multiple classes of pathogens and are currently linked with many emerging tick-borne diseases worldwide. With increasing occurrences of tick-borne diseases in both humans and veterinary species, there is a continuous need to further our understanding of ticks and the pathogens they transmit. Whole tick histology provides a full scope of the tick internal anatomy, allowing researchers to examine multiple organs of interest in a single section. This is in contrast to other techniques that are more commonly utilized in tick-borne disease research, such as electron microscopy and light microscopy of individual organs. There is a lack of literature describing a practical technique to process whole tick histologic sections. Therefore, the current study aims to provide researchers with a workable protocol to prepare high quality paraffin-embedded whole tick histology sections. Amblyomma americanum adults were used as an example species for this study. After a series of pilot experiments using a combination of various fixatives, softening agents and processing techniques, we elected to compare two common fixatives, 10% neutral-buffered formalin (NBF) and Bouin's solution for whole ticks. Equal numbers of A. americanum unfed adults (n = 10/fixative) were processed identically and their whole tick histology coronal sections were individually scored. Higher scores were assigned to whole tick sections that contained more internal organs that are crucial for tick-borne disease research (e.g. salivary glands and midgut), high integrity of tissues and exoskeleton on the section, and good fixation and staining quality of the tissues. The mean total scores for Bouin's-fixed ticks were significantly higher compared to NBF-fixed ticks (p = 0.001). To further assess our preferred technique, we also demonstrated the feasibility of producing high quality whole tick sections for three other common tick species of medical importance (Rhipicephalus sanguineus, Ixodes scapularis, and Dermacentor variabilis) using Bouin's solution. While this technique may require further optimization for other tick species, we described a feasible protocol that uses commonly available tools, reagents and standard histologic equipment. This should allow any investigator to easily make adjustments to this protocol as needed based on their experimental goals.
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Affiliation(s)
- Tzushan S Yang
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Elise E B LaDouceur
- Joint Pathology Center, Veterinary Pathology Services, Silver Spring, Maryland, USA
| | - Wes A Baumgartner
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | - Henry S Marr
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Michael Karounos
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - James Robertson
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA; Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Nathan Whitehurst
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Laura S Miller
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Adam J Birkenheuer
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA.
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Sousa LGV, Almeida C, Muzny CA, Cerca N. Development of a Prevotella bivia PNA probe and a multiplex approach to detect three relevant species in bacterial vaginosis-associated biofilms. NPJ Biofilms Microbiomes 2023; 9:42. [PMID: 37353508 DOI: 10.1038/s41522-023-00411-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/13/2023] [Indexed: 06/25/2023] Open
Abstract
Bacterial vaginosis (BV) is the most common vaginal infection worldwide. We developed a peptide nucleic acid (PNA) probe targeting Prevotella bivia, a common BV-associated bacteria, and optimized a multiplex approach for detection of Gardnerella spp., P. bivia and Fannyhessea vaginae. Our P. bivia PNA probe specifically detected the target species, and the optimized multiplex approach was able to detect the presence of the three species in multi-species BV biofilms.
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Affiliation(s)
- Lúcia G V Sousa
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Carina Almeida
- INIAV, IP- National Institute for Agrarian and Veterinary Research, Vila do Conde, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Christina A Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nuno Cerca
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga, Portugal.
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11
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Li S, Wang Y, Wang S, Xie J, Fu T, Li S. In situ gelling hydrogel loaded with berberine liposome for the treatment of biofilm-infected wounds. Front Bioeng Biotechnol 2023; 11:1189010. [PMID: 37324421 PMCID: PMC10266532 DOI: 10.3389/fbioe.2023.1189010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Background: In recent years, the impact of bacterial biofilms on traumatic wounds and the means to combat them have become a major research topic in the field of medicine. The eradication of biofilms formed by bacterial infections in wounds has always been a huge challenge. Herein, we developed a hydrogel with the active ingredient berberine hydrochloride liposomes to disrupt the biofilm and thereby accelerate the healing of infected wounds in mice. Methods: We determined the ability of berberine hydrochloride liposomes to eradicate the biofilm by means of studies such as crystalline violet staining, measuring the inhibition circle, and dilution coating plate method. Encouraged by the in vitro efficacy, we chose to coat the berberine hydrochloride liposomes on the Poloxamer range of in-situ thermosensitive hydrogels to allow fuller contact with the wound surface and sustained efficacy. Eventually, relevant pathological and immunological analyses were carried out on wound tissue from mice treated for 14 days. Results: The final results show that the number of wound tissue biofilms decreases abruptly after treatment and that the various inflammatory factors in them are significantly reduced within a short period. In the meantime, the number of collagen fibers in the treated wound tissue, as well as the proteins involved in healing in the wound tissue, showed significant differences compared to the model group. Conclusion: From the results, we found that berberine liposome gel can accelerate wound healing in Staphylococcus aureus infections by inhibiting the inflammatory response and promoting re-epithelialization as well as vascular regeneration. Our work exemplifies the efficacy of liposomal isolation of toxins. This innovative antimicrobial strategy opens up new perspectives for tackling drug resistance and fighting wound infections.
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Affiliation(s)
- Sipan Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yongan Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Siting Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianjun Xie
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Tingming Fu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shaoguang Li
- Microsurgery Department of Senior Department of Orthopedics, The Fourth Medical Center of PLA General Hospital, Beijing, China
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Monné Rodríguez JM, Frisk AL, Kreutzer R, Lemarchand T, Lezmi S, Saravanan C, Stierstorfer B, Thuilliez C, Vezzali E, Wieczorek G, Yun SW, Schaudien D. European Society of Toxicologic Pathology (Pathology 2.0 Molecular Pathology Special Interest Group): Review of In Situ Hybridization Techniques for Drug Research and Development. Toxicol Pathol 2023; 51:92-111. [PMID: 37449403 PMCID: PMC10467011 DOI: 10.1177/01926233231178282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
In situ hybridization (ISH) is used for the localization of specific nucleic acid sequences in cells or tissues by complementary binding of a nucleotide probe to a specific target nucleic acid sequence. In the last years, the specificity and sensitivity of ISH assays were improved by innovative techniques like synthetic nucleic acids and tandem oligonucleotide probes combined with signal amplification methods like branched DNA, hybridization chain reaction and tyramide signal amplification. These improvements increased the application spectrum for ISH on formalin-fixed paraffin-embedded tissues. ISH is a powerful tool to investigate DNA, mRNA transcripts, regulatory noncoding RNA, and therapeutic oligonucleotides. ISH can be used to obtain spatial information of a cell type, subcellular localization, or expression levels of targets. Since immunohistochemistry and ISH share similar workflows, their combination can address simultaneous transcriptomics and proteomics questions. The goal of this review paper is to revisit the current state of the scientific approaches in ISH and its application in drug research and development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Seong-Wook Yun
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Dirk Schaudien
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
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13
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Jin R, Ning X, Liu X, Zhao Y, Ye G. Porphyromonas gingivalis-induced periodontitis could contribute to cognitive impairment in Sprague–Dawley rats via the P38 MAPK signaling pathway. Front Cell Neurosci 2023; 17:1141339. [PMID: 37056710 PMCID: PMC10086325 DOI: 10.3389/fncel.2023.1141339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
BackgroundPeriodontitis is one of the most common oral diseases and has been shown to be a risk factor for systemic diseases. Our aim was to investigate the relationship between periodontitis and cognitive impairment and to explore the role of the P38 MAPK signaling pathway in this process.MethodsWe established a periodontitis model by ligating the first molars of SD rats with silk thread and injecting Porphyromonas gingivalis (P. gingivalis) or P. gingivalis plus the P38 MAPK inhibitor SB203580 at the same time for ten weeks. We assessed alveolar bone resorption and spatial learning and memory using microcomputed tomography and the Morris water maze test, respectively. We used transcriptome sequencing to explore the genetic differences between the groups. The gingival tissue, peripheral blood and hippocampal tissue were assessed for the cytokines TNF-α, IL-1β, IL-6, IL-8 and C reactive protein (CRP) with enzyme-linked immunosorbent assay (ELISA) and reverse transcription polymerase chain reaction (RT–PCR). We observed the presence of P. gingivalis in the hippocampus of rats by paraffin-fluorescence in situ hybridization (FISH). We determined the activation of microglia by immunofluorescence. Finally, Western blot analysis was employed to determine the expression of amyloid precursor protein (APP), β-site APP-cleaving enzyme 1 (BACE1) and P38MAPK pathway activation.ResultsWe demonstrated that silk ligature-induced periodontitis plus injection of P. gingivalis into subgingival tissue could lead to memory and cognitive impairment. Transcriptome sequencing results suggested that there were neurodegenerative diseases in the P. gingivalis group, and the MWM test showed that periodontitis reduced the spatial learning and memory ability of mild cognitive impairment (MCI) model rats. We found high levels of inflammatory factors (TNF-α, IL-1β, IL-6, and IL-8) and CRP in the gingiva, peripheral blood and hippocampus, and the expression of APP and BACE1 was upregulated, as was the P38 MAPK pathway activation. Activated microglia and the presence of P. gingivalis were also found in the hippocampus. P38 MAPK inhibitors mitigated all of these changes.ConclusionOur findings strongly suggest that topical application of P. gingivalis increases the inflammatory burden in the peripheral and central nervous systems (CNS) and that neuroinflammation induced by activation of P38 MAPK leads to impaired learning and memory in SD rats. It can also modulate APP processing. Therefore, P38 MAPK may serve as a linking pathway between periodontitis and cognitive impairment.
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Affiliation(s)
- Ru Jin
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences and Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Stomatological Hospital, Chongqing Medical University, Chongqing, China
| | - Xiaoqiao Ning
- The First People’s Hospital of Wanzhou, Chongqing, China
| | - Xiang Liu
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences and Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Stomatological Hospital, Chongqing Medical University, Chongqing, China
| | - Yueyang Zhao
- Department of Anatomy, Chongqing Medical University, Chongqing, China
| | - Guo Ye
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences and Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Stomatological Hospital, Chongqing Medical University, Chongqing, China
- *Correspondence: Guo Ye,
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Cao Z, Zuo W, Wang L, Chen J, Qu Z, Jin F, Dai L. Spatial profiling of microbial communities by sequential FISH with error-robust encoding. Nat Commun 2023; 14:1477. [PMID: 36932092 PMCID: PMC10023729 DOI: 10.1038/s41467-023-37188-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Spatial analysis of microbiomes at single cell resolution with high multiplexity and accuracy has remained challenging. Here we present spatial profiling of a microbiome using sequential error-robust fluorescence in situ hybridization (SEER-FISH), a highly multiplexed and accurate imaging method that allows mapping of microbial communities at micron-scale. We show that multiplexity of RNA profiling in microbiomes can be increased significantly by sequential rounds of probe hybridization and dissociation. Combined with error-correction strategies, we demonstrate that SEER-FISH enables accurate taxonomic identification in complex microbial communities. Using microbial communities composed of diverse bacterial taxa isolated from plant rhizospheres, we apply SEER-FISH to quantify the abundance of each taxon and map microbial biogeography on roots. At micron-scale, we identify clustering of microbial cells from multiple species on the rhizoplane. Under treatment of plant metabolites, we find spatial re-organization of microbial colonization along the root and alterations in spatial association among microbial taxa. Taken together, SEER-FISH provides a useful method for profiling the spatial ecology of complex microbial communities in situ.
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Affiliation(s)
- Zhaohui Cao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenlong Zuo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lanxiang Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Junyu Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zepeng Qu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Fan Jin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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15
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Diedrich CM, Verhorstert KWJ, Riool M, Schuster H, de Boer L, Kikhney J, Moter A, Zaat SAJ, Roovers JPWR. Transvaginal Mesh-related Complications and the Potential Role of Bacterial Colonization: An Exploratory Observational Study. J Minim Invasive Gynecol 2023; 30:205-215. [PMID: 36442754 DOI: 10.1016/j.jmig.2022.11.011] [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: 06/28/2022] [Revised: 10/12/2022] [Accepted: 11/19/2022] [Indexed: 11/27/2022]
Abstract
STUDY OBJECTIVE This study aimed to investigate the potential role of transvaginal mesh bacterial colonization in the development of mesh-related complications (MRCs). DESIGN An observational and exploratory study. SETTING Tertiary referral center (Amsterdam UMC, location AMC, Amsterdam, The Netherlands). PATIëNTS: 49 patients indicated for mesh removal and 20 women of whom vaginal tissue was retrieved during prolapse surgery as a reference cohort. INTERVENTIONS collection of mesh-tissue complex (patient cohort) or vaginal tissue (reference cohort) MEASUREMENTS AND MAIN RESULTS: Homogenized samples were used for quantitative microbiological culture. Inflammation and fibrosis were semiquantitatively histologically scored; Gram staining and fluorescence in situ hybridization were used to detect bacteria and bacterial biofilms. Of the 49 patients, 44 samples (90%) were culture positive, with a higher diversity of species and more Gram-negative bacteria and polymicrobial cultures in the MRC cohort than the reference cohort, with mostly staphylococci, streptococci, Actinomyces spp., Cutibacterium acnes, and Escherichia coli. Patients with clinical signs of infection or exposure had the highest bacterial counts. Histology demonstrated moderate to severe inflammation in most samples. Gram staining showed bacteria in 57% of culture-positive samples, and in selected samples, fluorescence in situ hybridization illustrated a polymicrobial biofilm. CONCLUSION In this study, we observed distinct differences in bacterial numbers and species between patients with MRCs and a reference cohort. Bacteria were observed at the mesh-tissue interface in a biofilm. These results strongly support the potential role of bacterial mesh colonization in the development of MRCs.
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Affiliation(s)
- Chantal M Diedrich
- Department of Obstetrics and Gynecology, Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Schuster, and Roovers), Amsterdam, The Netherlands; Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Riool, Zaa, and Schuster, Ms. de Boer), Amsterdam, The Netherlands.
| | - Kim W J Verhorstert
- Department of Obstetrics and Gynecology, Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Schuster, and Roovers), Amsterdam, The Netherlands; Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Riool, Zaa, and Schuster, Ms. de Boer), Amsterdam, The Netherlands
| | - Martijn Riool
- Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Riool, Zaa, and Schuster, Ms. de Boer), Amsterdam, The Netherlands
| | - Heleen Schuster
- Department of Obstetrics and Gynecology, Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Schuster, and Roovers), Amsterdam, The Netherlands; Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Riool, Zaa, and Schuster, Ms. de Boer), Amsterdam, The Netherlands
| | - Leonie de Boer
- Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Riool, Zaa, and Schuster, Ms. de Boer), Amsterdam, The Netherlands
| | - Judith Kikhney
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Microbiology, Infectious Diseases, and Immunology, Biofilmcenter, Hindenburgdamm 30 (Drs. Kikhney and Moter), 12203 Berlin, Germany; MoKi Analytics GmbH, Hindenburgdamm 30 (Drs. Kikhney and Moter) 12203 Berlin, Germany
| | - Annette Moter
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Microbiology, Infectious Diseases, and Immunology, Biofilmcenter, Hindenburgdamm 30 (Drs. Kikhney and Moter), 12203 Berlin, Germany; MoKi Analytics GmbH, Hindenburgdamm 30 (Drs. Kikhney and Moter) 12203 Berlin, Germany; Practice Moter Diagnostics (practice), Marienplatz 9 (Dr. Moter), 12207 Berlin, Germany
| | - Sebastian A J Zaat
- Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Riool, Zaa, and Schuster, Ms. de Boer), Amsterdam, The Netherlands
| | - Jan-Paul W R Roovers
- Department of Obstetrics and Gynecology, Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, Meibergdreef 9 (Drs. Diedrich, Verhorstert, Schuster, and Roovers), Amsterdam, The Netherlands
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16
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Tammina SK, Khan A, Rhim JW. Advances and prospects of carbon dots for microplastic analysis. CHEMOSPHERE 2023; 313:137433. [PMID: 36460157 DOI: 10.1016/j.chemosphere.2022.137433] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/16/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Microplastics have become the world's most emerging pollutants today due to the ubiquitous use of plastics in everyday life and their ability to migrate from micro to nanoscale to every corner of the natural world, leading to ecological imbalances and global catastrophes. However, a standardized method for separating and analyzing microplastics from actual food or environmental samples has not been established. Therefore, it is necessary to develop a simple, fast, cost-effective, and accurate method that can accurately measure the degree of contamination of microplastics. As one of these methods, fluorometry has been proposed as a cost-effective method to detect, quantify and differentiate individual plastic particles. Therefore, this review discussed the technique for analyzing microplastics using fluorescent carbon dots (CDs). This review provided an overview of the impact of microplastics and the feasibility of using CDs to detect and analyze microplastics. In particular, this review will discuss novel microplastic analysis methods using CD and future application studies. The method using CDs will overcome the limitations of current microplastic analysis technology and may become a new method for detecting and analyzing microplastics.
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Affiliation(s)
- Sai Kumar Tammina
- Department of Food and Nutrition, BioNanocomposite Research Center, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Ajahar Khan
- Department of Food and Nutrition, BioNanocomposite Research Center, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Jong-Whan Rhim
- Department of Food and Nutrition, BioNanocomposite Research Center, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea.
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17
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Zheng Q, Chang PV. Shedding Light on Bacterial Physiology with Click Chemistry. Isr J Chem 2023; 63:e202200064. [PMID: 37841997 PMCID: PMC10569449 DOI: 10.1002/ijch.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Indexed: 11/11/2022]
Abstract
Bacteria constitute a major lifeform on this planet and play numerous roles in ecology, physiology, and human disease. However, conventional methods to probe their activities are limited in their ability to visualize and identify their functions in these diverse settings. In the last two decades, the application of click chemistry to label these microbes has deepened our understanding of bacterial physiology. With the development of a plethora of chemical tools that target many biological molecules, it is possible to track these microorganisms in real-time and at unprecedented resolution. Here, we review click chemistry, including bioorthogonal reactions, and their applications in imaging bacterial glycans, lipids, proteins, and nucleic acids using chemical reporters. We also highlight significant advances that have enabled biological discoveries that have heretofore remained elusive.
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Affiliation(s)
- Qiuyu Zheng
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Pamela V Chang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853
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18
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Application of Fluorescence In Situ Hybridization (FISH) in Oral Microbial Detection. Pathogens 2022; 11:pathogens11121450. [PMID: 36558784 PMCID: PMC9788346 DOI: 10.3390/pathogens11121450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022] Open
Abstract
Varieties of microorganisms reside in the oral cavity contributing to the occurrence and development of microbes associated with oral diseases; however, the distribution and in situ abundance in the biofilm are still unclear. In order to promote the understanding of the ecosystem of oral microbiota and the diagnosis of oral diseases, it is necessary to monitor and compare the oral microorganisms from different niches of the oral cavity in situ. The fluorescence in situ hybridization (FISH) has proven to be a powerful tool for representing the status of oral microorganisms in the oral cavity. FISH is one of the most routinely used cytochemical techniques for genetic detection, identification, and localization by a fluorescently labeled nucleic acid probe, which can hybridize with targeted nucleic acid sequences. It has the advantages of rapidity, safety, high sensitivity, and specificity. FISH allows the identification and quantification of different oral microorganisms simultaneously. It can also visualize microorganisms by combining with other molecular biology technologies to represent the distribution of each microbial community in the oral biofilm. In this review, we summarized and discussed the development of FISH technology and the application of FISH in oral disease diagnosis and oral ecosystem research, highlighted its advantages in oral microbiology, listed the existing problems, and provided suggestions for future development..
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19
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Ishii PE, Suchodolski JS, Duarte R, Pereira ARC, Lidbury JA, Steiner JM, Giaretta PR. Detection of invasive Escherichia coli in dogs with granulomatous colitis using immunohistochemistry. J Vet Diagn Invest 2022; 34:990-994. [PMID: 35993285 PMCID: PMC9597337 DOI: 10.1177/10406387221119712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Granulomatous colitis in dogs can be associated with infection of the colonic mucosa by invasive strains of Escherichia coli. To date, fluorescence in situ hybridization (FISH) is the gold-standard method to assess intramucosal and intracellular bacterial invasion. However, FISH requires expensive fluorescence microscopy equipment and is therefore not widely available. We investigated the use of immunohistochemistry (IHC) as an alternative method to detect invasive E. coli in dogs with granulomatous colitis. Archived paraffin-embedded blocks were selected from 26 dogs with colitis, in which FISH had been performed by an outside laboratory. Using a polyclonal antibody, IHC for E. coli was performed on sections cut from the same blocks, and the presence of invasive E. coli was recorded. All 11 specimens in which FISH had detected E. coli were also positive on IHC, with strong immunolabeling in the cytoplasm of macrophages and extracellularly in the lamina propria; all 15 specimens that were negative for invasive bacteria on FISH were also negative on IHC. We found that IHC is a sensitive technique for the detection of invasive E. coli in dogs with granulomatous colitis.
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Affiliation(s)
- Patricia Eri Ishii
- Gastrointestinal Laboratory, Department of Small Animal
Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M
University, College Station, TX, USA
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal
Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M
University, College Station, TX, USA
| | | | - Ana R. C. Pereira
- School of Veterinary Medicine and Animal Science of
University of Sao Paulo, Sao Paulo, Brazil
| | - Jonathan A. Lidbury
- Gastrointestinal Laboratory, Department of Small Animal
Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M
University, College Station, TX, USA
| | - Joerg M. Steiner
- Gastrointestinal Laboratory, Department of Small Animal
Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M
University, College Station, TX, USA
| | - Paula R. Giaretta
- Gastrointestinal Laboratory, Department of Small Animal
Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M
University, College Station, TX, USA
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20
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Horowitz RI, Freeman PR. Efficacy of Short-Term High Dose Pulsed Dapsone Combination Therapy in the Treatment of Chronic Lyme Disease/Post-Treatment Lyme Disease Syndrome (PTLDS) and Associated Co-Infections: A Report of Three Cases and Literature Review. Antibiotics (Basel) 2022; 11:912. [PMID: 35884166 PMCID: PMC9311795 DOI: 10.3390/antibiotics11070912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/26/2022] [Accepted: 07/04/2022] [Indexed: 02/06/2023] Open
Abstract
Lyme disease and associated co-infections are increasing worldwide and approximately 20% of individuals develop chronic Lyme disease (CLD)/Post-Treatment Lyme Disease Syndrome (PTLDS) despite early antibiotics. A seven- to eight-week protocol of double dose dapsone combination therapy (DDDCT) for CLD/PTLDS results in symptom remission in approximately 50% of patients for one year or longer, with published culture studies indicating higher doses of dapsone demonstrate efficacy against resistant biofilm forms of Borrelia burgdorferi. The purpose of this study was, therefore, to evaluate higher doses of dapsone in the treatment of resistant CLD/PTLDS and associated co-infections. A total of 25 patients with a history of Lyme and associated co-infections, most of whom had ongoing symptoms despite several courses of DDDCT, took one or more courses of high dose pulsed dapsone combination therapy (200 mg dapsone × 3-4 days and/or 200 mg BID × 4 days), depending on persistent symptoms. The majority of patients noticed sustained improvement in eight major Lyme symptoms, including fatigue, pain, headaches, neuropathy, insomnia, cognition, and sweating, where dapsone dosage, not just the treatment length, positively affected outcomes. High dose pulsed dapsone combination therapy may represent a novel therapeutic approach for the treatment of resistant CLD/PTLDS, and should be confirmed in randomized, controlled clinical trials.
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21
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Erba PA, Bartoli F, Sollini M, Raffaella B, Zanca R, Enrica E, Lazzeri E. Alternative Nuclear Imaging Tools for Infection Imaging. Curr Cardiol Rep 2022; 24:879-891. [PMID: 35696046 PMCID: PMC9288362 DOI: 10.1007/s11886-022-01708-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 11/30/2022]
Abstract
Purpose of Review Cardiovascular infections are serious disease associated with high morbidity and mortality. Their diagnosis is challenging, requiring a proper management for a prompt recognition of the clinical manifestations, and a multidisciplinary approach involving cardiologists, cardiothoracic surgeons, infectious diseases specialist, imagers, and microbiologists. Imaging plays a central role in the diagnostic workout, including molecular imaging techniques. In this setting, two different strategies might be used to image infections: the first is based on the use of agents targeting the microorganism responsible for the infection. Alternatively, we can target the components of the pathophysiological changes of the inflammatory process and/or the host response to the infectious pathogen can be considered. Understanding the strength and limitations of each strategy is crucial to select the most appropriate imaging tool. Recent Findings Currently, multislice computed tomography (MSCT) and nuclear imaging (18F-fluorodeoxyglucose positron emission tomography/computed tomography, and leucocyte scintigraphy) are part of the diagnostic strategies. The main role of nuclear medicine imaging (PET/CT and SPECT/CT) is the confirmation of valve/CIED involvement and/or associated perivalvular infection and the detection of distant septic embolism. Proper patients’ preparation, imaging acquisition, and reconstruction as well as imaging reading are crucial to maximize the diagnostic information. Summary In this manuscript, we described the use of molecular imaging techniques, in particular WBC imaging, in patients with infective endocarditis, cardiovascular implantable electronic device infections, and infections of composite aortic graft, underlying the strength and limitations of such approached as compared to the other imaging modalities.
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Affiliation(s)
- Paola Anna Erba
- Regional Center of Nuclear Medicine, Department of Translational Research and Advanced Technologies in Medicine and Surgery, University of Pisa, Via Roma 57, 56126, Pisa, Italy.
- Medical Imaging Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Francesco Bartoli
- Regional Center of Nuclear Medicine, Department of Translational Research and Advanced Technologies in Medicine and Surgery, University of Pisa, Via Roma 57, 56126, Pisa, Italy
| | - Martina Sollini
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Berchiolli Raffaella
- Vascular Surgery Unit, Department of Translational Research and Advanced Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Roberta Zanca
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Esposito Enrica
- Regional Center of Nuclear Medicine, Department of Translational Research and Advanced Technologies in Medicine and Surgery, University of Pisa, Via Roma 57, 56126, Pisa, Italy
| | - Elena Lazzeri
- Regional Center of Nuclear Medicine, Department of Translational Research and Advanced Technologies in Medicine and Surgery, University of Pisa, Via Roma 57, 56126, Pisa, Italy
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22
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The role of Nucleic Acid Mimics (NAMs) on FISH-based techniques and applications for microbial detection. Microbiol Res 2022; 262:127086. [PMID: 35700584 DOI: 10.1016/j.micres.2022.127086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 01/07/2023]
Abstract
Fluorescent in situ hybridization (FISH) is a powerful tool that for more than 30 years has allowed to detect and quantify microorganisms as well as to study their spatial distribution in three-dimensional structured environments such as biofilms. Throughout these years, FISH has been improved in order to face some of its earlier limitations and to adapt to new research objectives. One of these improvements is related to the emergence of Nucleic Acid Mimics (NAMs), which are now employed as alternatives to the DNA and RNA probes that have been classically used in FISH. NAMs such as peptide and locked nucleic acids (PNA and LNA) have provided enhanced sensitivity and specificity to the FISH technique, as well as higher flexibility in terms of applications. In this review, we aim to cover the state-of-the-art of the different NAMs and explore their possible applications in FISH, providing a general overview of the technique advancement in the last decades.
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23
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A panoptic review of techniques for finfish disease diagnosis: The status quo and future perspectives. J Microbiol Methods 2022; 196:106477. [DOI: 10.1016/j.mimet.2022.106477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
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Renaud C, Kollef MH. Classical and Molecular Techniques to Diagnose HAP/VAP. Semin Respir Crit Care Med 2022; 43:219-228. [PMID: 35042263 DOI: 10.1055/s-0041-1739359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nosocomial pneumonia, including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), are the most common nosocomial infections occurring in critically ill patients requiring intensive care. However, challenges exist in making a timely and accurate diagnosis of HAP and VAP. Under diagnosis of HAP and VAP can result in greater mortality risk, especially if accompanied by delays in the administration of appropriate antimicrobial treatment. Over diagnosis of HAP and VAP results in the unnecessary administration of broad spectrum antibiotics that can lead to further escalation of antibiotic resistance. Optimal diagnosis and management of HAP and VAP require a systematic approach that combines clinical and radiographic assessments along with proper microbiologic techniques. The use of more invasive sampling methods (bronchoalveolar lavage and protected specimen brush) may enhance specimen collection resulting in more specific diagnoses to limit unnecessary antibiotic exposure. Molecular techniques, currently in use and investigational technique, may improve the diagnosis of HAP and VAP by allowing more rapid identification of offending pathogens, if present, thus increasing both appropriate antibiotic treatment and avoiding unnecessary drug exposure.
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Affiliation(s)
- Cherie Renaud
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Marin H Kollef
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri
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25
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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.
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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
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Liu G, Zhang T. Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation. Int J Mol Sci 2021; 22:ijms22137124. [PMID: 34281175 PMCID: PMC8268824 DOI: 10.3390/ijms22137124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
Oligonucleotides fluorescence in situ hybridization (Oligo-FISH) is an emerging technology and is an important tool in research areas such as detection of chromosome variation, identification of allopolyploid, and deciphering of three-dimensional (3D) genome structures. Based on the demand for highly efficient oligo probes for oligo-FISH experiments, increasing numbers of tools have been developed for probe design in recent years. Obsolete oligonucleotide design tools have been adapted for oligo-FISH probe design because of their similar considerations. With the development of DNA sequencing and large-scale synthesis, novel tools have been designed to increase the specificity of designed oligo probes and enable genome-scale oligo probe design, which has greatly improved the application of single copy oligo-FISH. Despite this, few studies have introduced the development of the oligo-FISH probe design tools and their application in FISH experiments systematically. Besides, a comprehensive comparison and evaluation is lacking for the available tools. In this review, we provide an overview of the oligo-FISH probe design process, summarize the development and application of the available tools, evaluate several state-of-art tools, and eventually provide guidance for single copy oligo-FISH probe design.
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Affiliation(s)
- Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
- Institutes of Agricultural Science and Technology Development, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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Veselinyová D, Mašlanková J, Kalinová K, Mičková H, Mareková M, Rabajdová M. Selected In Situ Hybridization Methods: Principles and Application. Molecules 2021; 26:molecules26133874. [PMID: 34202914 PMCID: PMC8270300 DOI: 10.3390/molecules26133874] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
We are experiencing rapid progress in all types of imaging techniques used in the detection of various numbers and types of mutation. In situ hybridization (ISH) is the primary technique for the discovery of mutation agents, which are presented in a variety of cells. The ability of DNA to complementary bind is one of the main principles in every method used in ISH. From the first use of in situ techniques, scientists paid attention to the improvement of the probe design and detection, to enhance the fluorescent signal intensity and inhibition of cross-hybrid presence. This article discusses the individual types and modifications, and is focused on explaining the principles and limitations of ISH division on different types of probes. The article describes a design of probes for individual types of in situ hybridization (ISH), as well as the gradual combination of several laboratory procedures to achieve the highest possible sensitivity and to prevent undesirable events accompanying hybridization. The article also informs about applications of the methodology, in practice and in research, to detect cell to cell communication and principles of gene silencing, process of oncogenesis, and many other unknown processes taking place in organisms at the DNA/RNA level.
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Affiliation(s)
- Dominika Veselinyová
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia; (D.V.); (K.K.); (M.M.); (M.R.)
| | - Jana Mašlanková
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia; (D.V.); (K.K.); (M.M.); (M.R.)
- Correspondence:
| | - Katarina Kalinová
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia; (D.V.); (K.K.); (M.M.); (M.R.)
| | - Helena Mičková
- Department of Medical Biology, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia;
| | - Mária Mareková
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia; (D.V.); (K.K.); (M.M.); (M.R.)
| | - Miroslava Rabajdová
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia; (D.V.); (K.K.); (M.M.); (M.R.)
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28
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Mariano S, Tacconi S, Fidaleo M, Rossi M, Dini L. Micro and Nanoplastics Identification: Classic Methods and Innovative Detection Techniques. FRONTIERS IN TOXICOLOGY 2021; 3:636640. [PMID: 35295124 PMCID: PMC8915801 DOI: 10.3389/ftox.2021.636640] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/22/2021] [Indexed: 12/13/2022] Open
Abstract
Micro and nanoplastics are fragments with dimensions less than a millimeter invading all terrestrial and marine environments. They have become a major global environmental issue in recent decades and, indeed, recent scientific studies have highlighted the presence of these fragments all over the world even in environments that were thought to be unspoiled. Analysis of micro/nanoplastics in isolated samples from abiotic and biotic environmental matrices has become increasingly common. Hence, the need to find valid techniques to identify these micro and nano-sized particles. In this review, we discuss the current and potential identification methods used in microplastic analyses along with their advantages and limitations. We discuss the most suitable techniques currently available, from physical to chemical ones, as well as the challenges to enhance the existing methods and develop new ones. Microscopical techniques (i.e., dissect, polarized, fluorescence, scanning electron, and atomic force microscopy) are one of the most used identification methods for micro/nanoplastics, but they have the limitation to produce incomplete results in analyses of small particles. At present, the combination with chemical analysis (i.e., spectroscopy) overcome this limit together with recently introduced alternative approaches. For example, holographic imaging in microscope configuration images microplastics directly in unfiltered water, thus discriminating microplastics from diatoms and differentiates different sizes, shapes, and plastic types. The development of new analytical instruments coupled with each other or with conventional and innovative microscopy could solve the current problems in the identification of micro/nanoplastics.
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Affiliation(s)
- Stefania Mariano
- Department of Biological and Environmental Science and Technology, University of Salento, Lecce, Italy
| | - Stefano Tacconi
- Department of Biological and Environmental Science and Technology, University of Salento, Lecce, Italy
| | - Marco Fidaleo
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Marco Rossi
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Rome, Italy
- Research Center for Nanotechnologies Applied to Engineering, CNIS Sapienza University of Rome, Rome, Italy
- National Research Council Nanotec, Lecce, Italy
| | - Luciana Dini
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
- Research Center for Nanotechnologies Applied to Engineering, CNIS Sapienza University of Rome, Rome, Italy
- National Research Council Nanotec, Lecce, Italy
- *Correspondence: Luciana Dini
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Kikhney J, Moter A. Quality Control in Diagnostic Fluorescence In Situ Hybridization (FISH) in Microbiology. Methods Mol Biol 2021; 2246:301-316. [PMID: 33576998 DOI: 10.1007/978-1-0716-1115-9_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This overview addresses fluorescence in situ hybridization (FISH) in a diagnostic microbiology setting with its associated problems and pitfalls and how to control them, but also the advantages and opportunities the method offers. This article focuses mainly on diagnostic FISH assays on tissue sections and on techniques and experiences in our laboratory. FISH in a routine diagnostic setting in microbiology requires strict quality control measures to ensure consistent high-quality and reliable assay results. Here, for the first time, we define quality control requirements for microbiological diagnostic FISH applications and discuss their impact and possible future developments of the FISH technique for infection diagnostics. We focus on diagnosis of biofilm-associated infections including infective endocarditis, oral biofilms, and device-associated infections as well as infections due to fastidious or yet uncultured microorganisms like Treponema spp., Tropheryma whipplei, Bartonella, Coxiella burnetii, or Brachyspira.
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Affiliation(s)
- Judith Kikhney
- Biofilmcenter, Institute for Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- MoKi Analytics GmbH, Berlin, Germany
| | - Annette Moter
- Biofilmcenter, Institute for Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Teixeira H, Sousa AL, Azevedo AS. Bioinformatic Tools and Guidelines for the Design of Fluorescence In Situ Hybridization Probes. Methods Mol Biol 2021; 2246:35-50. [PMID: 33576981 DOI: 10.1007/978-1-0716-1115-9_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Fluorescence in situ hybridization (FISH) is a well-established technique that allows the detection of microorganisms in diverse types of samples (e.g., clinical, food, environmental samples, and biofilm communities). The FISH probe design is an essential step in this technique. For this, two strategies can be used, the manual form based on multiple sequence alignment to identify conserved regions and programs/software specifically developed for the selection of the sequence of the probe. Additionally, databases/software for the theoretical evaluation of the probes in terms of specificity, sensitivity, and thermodynamic parameters (melting temperature and Gibbs free energy change) are used. The purpose of this chapter is to describe the essential steps and guidelines for the design of FISH probes (e.g., DNA and Nucleic Acid Mimic (NAM) probes), and its theoretical evaluation through the application of diverse bioinformatic tools.
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Affiliation(s)
- Helena Teixeira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Ana L Sousa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Andreia S Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal. .,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal. .,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
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31
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Qu D, Qiao DF, Klintschar M, Qu Z, Yue X. High-throughput 16S rDNA sequencing assisting in the detection of bacterial pathogen candidates: a fatal case of necrotizing fasciitis in a child. Int J Legal Med 2020; 135:399-407. [PMID: 32895762 DOI: 10.1007/s00414-020-02421-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/02/2020] [Indexed: 12/19/2022]
Abstract
Postmortem detection of pathogens in infectious deaths is quite important for diagnosing the cause of death and public health. However, it is difficult to detect possible bacterial pathogens in forensic practice using conventional methods like bacterial culture, especially in cases with putrefaction and antibiotic treatment. We report a fatal case caused by necrotizing fasciitis due to bacterial infection. An 8-year-old girl was found dead during sleep 4 days after a minor trauma to her left knee. The gross autopsy suggested that bacterial soft tissue infection might be the cause of death, and the microscopic examination confirmed the diagnosis. The slight putrefaction found at gross autopsy might interfere through postmortem bacterial translocation and reproduction with bacterial culture. High-throughput 16S rDNA sequencing was employed to identify possible pathogens. Bacterial DNA sequencing results suggested Streptococcus pyogenes and Staphylococcus, typical pathogens of necrotizing fasciitis in the tissue. 16S rDNA sequencing might thus be a useful tool for accurate detection of pathogens in forensic practice.
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Affiliation(s)
- Dong Qu
- Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.,Institute of Legal Medicine, Hannover Medical School, 30625, Hannover, Germany
| | - Dong-Fang Qiao
- Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Michael Klintschar
- Institute of Legal Medicine, Hannover Medical School, 30625, Hannover, Germany
| | - Zhi Qu
- Institute for Epidemiology, Social Medicine and Health Systems Research, Hannover Medical School, 30625, Hannover, Germany
| | - Xia Yue
- Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
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32
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Evolving Technologies in Gastrointestinal Microbiome Era and Their Potential Clinical Applications. J Clin Med 2020; 9:jcm9082565. [PMID: 32784731 PMCID: PMC7464388 DOI: 10.3390/jcm9082565] [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] [Received: 06/18/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 12/12/2022] Open
Abstract
The human gastrointestinal microbiota (GIM) is a complex and diverse ecosystem that consists of community of fungi, viruses, protists and majorly bacteria. The association of several human illnesses, such as inflammatory bowel disease, allergy, metabolic syndrome and cancers, have been linked directly or indirectly to compromise in the integrity of the GIM, for which some medical interventions have been proposed or attempted. This review highlights and gives update on various technologies, including microfluidics, high-through-put sequencing, metabolomics, metatranscriptomics and culture in GIM research and their applications in gastrointestinal microbiota therapy, with a view to raise interest in the evaluation, validation and eventual use of these technologies in diagnosis and the incorporation of therapies in routine clinical practice.
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33
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Edouard S, Luciani L, Lagier JC, Raoult D. Current knowledge for the microbiological diagnosis of Tropheryma whipplei infection. Expert Opin Orphan Drugs 2020. [DOI: 10.1080/21678707.2020.1791700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sophie Edouard
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - Léa Luciani
- IHU-Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
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The Role of Single-Cell Technology in the Study and Control of Infectious Diseases. Cells 2020; 9:cells9061440. [PMID: 32531928 PMCID: PMC7348906 DOI: 10.3390/cells9061440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
The advent of single-cell research in the recent decade has allowed biological studies at an unprecedented resolution and scale. In particular, single-cell analysis techniques such as Next-Generation Sequencing (NGS) and Fluorescence-Activated Cell Sorting (FACS) have helped show substantial links between cellular heterogeneity and infectious disease progression. The extensive characterization of genomic and phenotypic biomarkers, in addition to host-pathogen interactions at the single-cell level, has resulted in the discovery of previously unknown infection mechanisms as well as potential treatment options. In this article, we review the various single-cell technologies and their applications in the ongoing fight against infectious diseases, as well as discuss the potential opportunities for future development.
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35
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Rodriguez-Mateos P, Azevedo NF, Almeida C, Pamme N. FISH and chips: a review of microfluidic platforms for FISH analysis. Med Microbiol Immunol 2020; 209:373-391. [PMID: 31965296 PMCID: PMC7248050 DOI: 10.1007/s00430-019-00654-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/19/2019] [Indexed: 12/12/2022]
Abstract
Fluorescence in situ hybridization (FISH) allows visualization of specific nucleic acid sequences within an intact cell or a tissue section. It is based on molecular recognition between a fluorescently labeled probe that penetrates the cell membrane of a fixed but intact sample and hybridizes to a nucleic acid sequence of interest within the cell, rendering a measurable signal. FISH has been applied to, for example, gene mapping, diagnosis of chromosomal aberrations and identification of pathogens in complex samples as well as detailed studies of cellular structure and function. However, FISH protocols are complex, they comprise of many fixation, incubation and washing steps involving a range of solvents and temperatures and are, thus, generally time consuming and labor intensive. The complexity of the process, the relatively high-priced fluorescent probes and the fairly high-end microscopy needed for readout render the whole process costly and have limited wider uptake of this powerful technique. In recent years, there have been attempts to transfer FISH assay protocols onto microfluidic lab-on-a-chip platforms, which reduces the required amount of sample and reagents, shortens incubation times and, thus, time to complete the protocol, and finally has the potential for automating the process. Here, we review the wide variety of approaches for lab-on-chip-based FISH that have been demonstrated at proof-of-concept stage, ranging from FISH analysis of immobilized cell layers, and cells trapped in arrays, to FISH on tissue slices. Some researchers have aimed to develop simple devices that interface with existing equipment and workflows, whilst others have aimed to integrate the entire FISH protocol into a fully autonomous FISH on-chip system. Whilst the technical possibilities for FISH on-chip are clearly demonstrated, only a small number of approaches have so far been converted into off-the-shelf products for wider use beyond the research laboratory.
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Affiliation(s)
- Pablo Rodriguez-Mateos
- Department of Chemistry and Biochemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK
| | - Nuno Filipe 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
- Biomode SA, Av. Mestre José Veiga, 4715-330, Braga, Portugal
| | - Carina Almeida
- Biomode SA, Av. Mestre José Veiga, 4715-330, Braga, Portugal
- INIAV, I.P.-National Institute for Agricultural and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, 4485-655, Vila Do Conde, Portugal
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Nicole Pamme
- Department of Chemistry and Biochemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK.
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Wang X, Zhao Z, Tang N, Zhao Y, Xu J, Li L, Qian L, Zhang J, Fan Y. Microbial Community Analysis of Saliva and Biopsies in Patients With Oral Lichen Planus. Front Microbiol 2020; 11:629. [PMID: 32435231 PMCID: PMC7219021 DOI: 10.3389/fmicb.2020.00629] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 03/20/2020] [Indexed: 12/25/2022] Open
Abstract
The specific etiology and pathogenesis of oral lichen planus (OLP) remain elusive, and microbial dysbiosis may play an important role in OLP. We evaluated the saliva and tissue bacterial community of patients with OLP and identified the colonization of bacteria in OLP tissues. The saliva (n = 60) and tissue (n = 24) samples from OLP patients and the healthy controls were characterized by 16S rDNA gene sequencing and the bacterial signals in OLP tissues were detected by fluorescence in situ hybridization (FISH) targeting the bacterial 16S rDNA gene. Results indicate that the OLP tissue microbiome was different from the microbiota of OLP saliva. Compared with the healthy controls, Capnocytophaga and Gemella were higher in OLP saliva, while Escherichia–Shigella and Megasphaera were higher in OLP tissues, whereas seven taxa, including Carnobacteriaceae, Flavobacteriaceae, and Megasphaera, were enriched in both saliva and tissues of OLP patients. Furthermore, FISH found that the average optical density (AOD) of bacteria in the lamina propria of OLP tissues was higher than that of the healthy controls, and the AOD of bacteria in OLP epithelium and lamina propria was positively correlated. These data provide a different perspective for future investigation on the OLP microbiome.
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Affiliation(s)
- Xuewei Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral Medicine, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Zhibai Zhao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral Medicine, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Nan Tang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral Medicine, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yuping Zhao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral Medicine, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Juanyong Xu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral Medicine, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Liuyang Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral Medicine, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Ling Qian
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral Medicine, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Junfeng Zhang
- Medical School, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuan Fan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral Medicine, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
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