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Kameli N, Basode VK, Abdulhaq A, Alamoudi MUA, Zain KAM, Ghzwani AH. Prevalence of toxigenic Clostridium difficile in hospitalized patients in the southwestern province of Saudi Arabia: Confirmation using the GeneXpert analysis. Libyan J Med 2024; 19:2294571. [PMID: 38112195 DOI: 10.1080/19932820.2023.2294571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023] Open
Abstract
Clostridium difficile (Clostridioides difficile) is a leading cause of nosocomial infections in hospitalized patients worldwide. Stool samples were collected from 112 inpatients admitted to different hospitals and were screened for C. difficile GDH + toxin A + B by immunoassay, and all positive samples by immunoassay were processed for molecular detection of C. difficile using the GeneXpert assay. C. difficile strains were detected in 12 (10.71%) out of 112 stool samples using the GDH + toxin A + B immunoassay method and toxigenic C. difficile was confirmed in 5 stool samples using the GeneXpert molecular assay. C. difficile strains were also detected in 7 (8.97%) out of 78 stool samples from intensive care unit patients, 3 (25%) out of 12 stool samples from internal medicine ward patients, 1 (11.11%) out of 9 stool samples from surgery ward patients, and 1 (10%) out of 10 stool samples from isolation ward patients using the GDH + toxin A + B immunoassay method and the toxigenic C. difficile strain was confirmed in 1, 2, 1, and 1 stool samples, respectively, using the GeneXpert molecular assay. Toxigenic C. difficile was confirmed in patients at 4 (51.14%) out of 7 hospitals. In the present study, we also analyzed the clinical information of patients with C. difficile-positive stool samples who were receiving one or more antibiotics during hospitalization. The binary toxin gene (cdt), the tcdC gene, and the C. difficile strain polymerase chain reaction (PCR) ribotype 027 were not detected using the GeneXpert molecular assay among 12 C. difficile-positive samples by immunoassay. This study should aid in the prevention of unnecessary empiric therapy and increase the understanding of the toxigenic C. difficile burden on the healthcare system in the southwestern province of Saudi Arabia.
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Affiliation(s)
| | | | - Ahmed Abdulhaq
- Unit of Medical Microbiology, Department of Medical Lab Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan, Kingdom of Saudi Arabia
| | - Mohammed Uthman A Alamoudi
- Unit of Medical Microbiology, Department of Medical Lab Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan, Kingdom of Saudi Arabia
| | - Khalid Amaash Mohammed Zain
- Unit of Medical Microbiology, Department of Medical Lab Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan, Kingdom of Saudi Arabia
| | - Ahmad Hassn Ghzwani
- Unit of Medical Microbiology, Department of Medical Lab Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan, Kingdom of Saudi Arabia
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Becker HE, Kameli N, Rustichelli A, Heijnens BA, Stassen FR, Penders J, Jonkers DM. In vitro mucin degradation and paracellular permeability by fecal water from Crohn's disease patients. Future Microbiol 2024; 19:335-347. [PMID: 38470403 DOI: 10.2217/fmb-2022-0265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Aim: This study aimed to examine the impact of fecal water (FW) of active and remissive Crohn's disease (CD) patients on mucin degradation and epithelial barrier function. Methods: FW and bacterial membrane vesicles (MVs) were isolated from fresh fecal samples of six healthy controls (HCs) and 12 CD patients. Bacterial composition was determined by 16S rRNA gene amplicon sequencing. Results: In vitro FW-induced mucin degradation was higher in CD samples versus HC (p < 0.01), but not associated with specific bacterial genera. FW of three remissive samples decreased transepithelial electrical resistance in Caco-2 cells by 78-87% (p < 0.001). MVs did not induce barrier alterations. Conclusion: The higher mucin-degradation capacity of CD-derived FW might suggest contributions of microbial products to CD pathophysiology.
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Affiliation(s)
- Heike Ef Becker
- Department of Gastroenterology/Hepatology, Division of Internal Medicine, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
- Department of Medical Microbiology, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Nader Kameli
- Department of Medical Microbiology, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
- Department of Medical Microbiology, Faculty of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | | | - Britt Am Heijnens
- Department of Gastroenterology/Hepatology, Division of Internal Medicine, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Frank Rm Stassen
- Department of Medical Microbiology, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - John Penders
- Department of Medical Microbiology, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
- Department of Medical Microbiology, Caphri School for Public Health & Primary Care, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Daisy Mae Jonkers
- Department of Gastroenterology/Hepatology, Division of Internal Medicine, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
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Algaissi A, Khan E, Tabassum H, Samreen S, Khamjan NA, Lohani M, Khan S, Kameli N, Madkhali F, Ahmad IZ. Campesterol and dithymoquinone as a potent inhibitors of SARS cov-2 main proteases-promising drug candidates for targeting its novel variants. J Biomol Struct Dyn 2024:1-15. [PMID: 38288958 DOI: 10.1080/07391102.2023.2301684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/13/2023] [Indexed: 02/16/2024]
Abstract
The sudden outbreak of the COVID-19 pandemic has currently taken approximately 2.4 million lives, with no specific medication and fast-tracked tested vaccines for prevention. These vaccines have their own adverse effects, which have severely affected the global healthcare system. The discovery of the main protease structure of coronavirus (Mpro/Clpro) has resulted in the identification of compounds having antiviral potential, especially from the herbal system. In this study, the computer-associated drug design tools were utilised to analyze the reported phytoconstituents of Nigella sativa for their antiviral activity against the main protease. Fifty-eight compounds were subjected to pharmacological parameter analysis to determine their lead likeness in comparison to the standard drugs (chloroquine and nirmatrelvir) used in the treatment of SARS-CoV-2. Nearly 31 compounds were docked against five different SARS-CoV-2 main proteases, and all compounds showed better binding affinity and inhibition constant against the proteases. However, dithymoquinone and campesterol displayed the best binding scores and hence were further subjected to dynamics and MMPBSA study for 100 ns. The stability analysis shows that dithymoquinone and campesterol show less variation in fluctuation in residues compared to standard complexes. Moreover, dithymoquinone exhibited higher binding affinity and favorable interaction followed by campesterol as compared to the standard drug. The in silico computational analysis provides a promising hit for regulating the main proteases activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdullah Algaissi
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Emerging and Epidemic Infectious Diseases Research Unit, Medical Research Center, Jazan University, Jazan, Saudi Arabia
| | - Elhan Khan
- Natural Products Laboratory, Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, India
| | - Heena Tabassum
- Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Sadiyah Samreen
- Natural Products Laboratory, Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, India
| | - Nizar A Khamjan
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohtashim Lohani
- Medical Research Centre, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Saif Khan
- Department of Basic Dental and Medical Sciences, College of Dentistry, Ha'il University, Ha'il, Saudi Arabia
| | - Nader Kameli
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Faisal Madkhali
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Iffat Zareen Ahmad
- Natural Products Laboratory, Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, India
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Dhayhi N, Kameli N, Salawi M, Shajri A, Basode VK, Algaissi A, Alamer E, Darraj M, Shrwani K, Alhazmi AH. Bacterial Contamination of Mobile Phones Used by Healthcare Workers in Critical Care Units: A Cross-Sectional Study from Saudi Arabia. Microorganisms 2023; 11:1986. [PMID: 37630546 PMCID: PMC10459851 DOI: 10.3390/microorganisms11081986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Healthcare-associated infections (HAIs) present a formidable challenge for healthcare institutions, resulting in heightened mortality, morbidity, and economic burden. Within healthcare settings, various equipment and materials, including mobile phones, can potentially act as sources of infection. This study sought to examine the occurrence of bacterial contamination on mobile phones utilized by healthcare workers (HCWs) in intensive care units (ICUs), pediatric intensive care units (PICUs), neonatal intensive care units (NICUs), and cardiac care units (CCUs) within a central hospital (CH) and two peripheral hospitals (PHs) situated in the southwestern province of Saudi Arabia. MATERIALS AND METHODS We collected a total of 157 samples from mobile phones utilized by HCWs across all ICUs in the CH and PHs. These samples underwent bacteriological analysis to evaluate the degree of bacterial contamination. RESULTS We found that 45 out of 55 samples from physicians (81.81%) and 58 out of 77 samples from nurses (75.32%) showed bacterial contamination. Contamination rates on HCWs' mobile phones in the ICU, PICU, and NICU departments of the CH were observed at 69.56%, 80.95%, and 70.27%, respectively. Furthermore, the overall contamination rates in the ICUs, NICUs, and CCUs of the PHs were 78.26%, 88.88%, and 66.66%, respectively. The overall contamination rates of mobile phones in the CH and PHs were 72.11% and 81.13%, respectively. CONCLUSION These findings underscore the necessity of routinely disinfecting the mobile phones of HCWs to mitigate the risk of cross-contamination. Implementing robust disinfection protocols can significantly contribute to curtailing the propagation of bacterial pathogens and reducing the incidence of HAIs in healthcare settings.
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Affiliation(s)
- Nabil Dhayhi
- Infectious Diseases Unit, Department of Pediatric Medicine, King Fahad Central Hospital, Jazan 45142, Saudi Arabia
| | - Nader Kameli
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Medical Research Center, Jazan University, Jazan 45142, Saudi Arabia
| | - Mohammed Salawi
- Department of Pediatric Medicine, King Fahad Central Hospital, Jazan 45142, Saudi Arabia
| | - Amjad Shajri
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Vinod Kumar Basode
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Abdullah Algaissi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Medical Research Center, Jazan University, Jazan 45142, Saudi Arabia
| | - Edrous Alamer
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Medical Research Center, Jazan University, Jazan 45142, Saudi Arabia
| | - Majid Darraj
- Department of Medicine, Faculty of Medicine, Jazan University, Jazan 45142, Saudi Arabia
| | - Khalid Shrwani
- Saudi Public Health Authority, Vector-Borne Diseases Laboratory, Jazan 45142, Saudi Arabia
| | - Abdulaziz H. Alhazmi
- Medical Research Center, Jazan University, Jazan 45142, Saudi Arabia
- Department of Microbiology and Parasitology, Faculty of Medicine, Jazan University, Jazan 45142, Saudi Arabia
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Alzahrani FA, Khan MI, Kameli N, Alsahafi E, Riza YM. Plant-Derived Extracellular Vesicles and Their Exciting Potential as the Future of Next-Generation Drug Delivery. Biomolecules 2023; 13:biom13050839. [PMID: 37238708 DOI: 10.3390/biom13050839] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/08/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
Plant cells release tiny membranous vesicles called extracellular vesicles (EVs), which are rich in lipids, proteins, nucleic acids, and pharmacologically active compounds. These plant-derived EVs (PDEVs) are safe and easily extractable and have been shown to have therapeutic effects against inflammation, cancer, bacteria, and aging. They have shown promise in preventing or treating colitis, cancer, alcoholic liver disease, and even COVID-19. PDEVs can also be used as natural carriers for small-molecule drugs and nucleic acids through various administration routes such as oral, transdermal, or injection. The unique advantages of PDEVs make them highly competitive in clinical applications and preventive healthcare products in the future. This review covers the latest methods for isolating and characterizing PDEVs, their applications in disease prevention and treatment, and their potential as a new drug carrier, with special attention to their commercial viability and toxicological profile, as the future of nanomedicine therapeutics. This review champions the formation of a new task force specializing in PDEVs to address a global need for rigor and standardization in PDEV research.
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Affiliation(s)
- Faisal A Alzahrani
- Department of Biochemistry, Faculty of science, Embryonic Stem Cell Unit, King Fahad Center for Medical Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Centre of Artificial Intelligence for Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammad Imran Khan
- Centre of Artificial Intelligence for Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Nader Kameli
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan 82621, Saudi Arabia
- Medical Research Center, Jazan University, Jazan 45142, Saudi Arabia
| | - Elham Alsahafi
- Department of Basic and Clinical Sciences, Faculty of Dentistry, Umm AlQura University, P.O. Box 715, Mecca 21955, Saudi Arabia
| | - Yasir Mohamed Riza
- Department of Biochemistry, Faculty of science, Embryonic Stem Cell Unit, King Fahad Center for Medical Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Centre of Artificial Intelligence for Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Kameli N, Becker HEF, Welbers T, Jonkers DMAE, Penders J, Savelkoul P, Stassen FR. Metagenomic Profiling of Fecal-Derived Bacterial Membrane Vesicles in Crohn's Disease Patients. Cells 2021; 10:cells10102795. [PMID: 34685776 PMCID: PMC8535131 DOI: 10.3390/cells10102795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In the past, many studies suggested a crucial role for dysbiosis of the gut microbiota in the etiology of Crohn's disease (CD). However, despite being important players in host-bacteria interaction, the role of bacterial membrane vesicles (MV) has been largely overlooked in the pathogenesis of CD. In this study, we addressed the composition of the bacterial and MV composition in fecal samples of CD patients and compared this to the composition in healthy individuals. METHODS Fecal samples from six healthy subjects (HC) in addition to twelve CD patients (six active, six remission) were analyzed in this study. Fecal bacterial membrane vesicles (fMVs) were isolated by a combination of ultrafiltration and size exclusion chromatography. DNA was obtained from the fMV fraction, the pellet of dissolved feces as bacterial DNA (bDNA), or directly from feces as fecal DNA (fDNA). The fMVs were characterized by nanoparticle tracking analysis and cryo-electron microscopy. Amplicon sequencing of 16s rRNA V4 hypervariable gene regions was conducted to assess microbial composition of all fractions. RESULTS Beta-diversity analysis showed that the microbial community structure of the fMVs was significantly different from the microbial profiles of the fDNA and bDNA. However, no differences were observed in microbial composition between fDNA and bDNA. The microbial richness of fMVs was significantly decreased in CD patients compared to HC, and even lower in active patients. Profiling of fDNA and bDNA demonstrated that Firmicutes was the most dominant phylum in these fractions, while in fMVs Bacteroidetes was dominant. In fMV, several families and genera belonging to Firmicutes and Proteobacteria were significantly altered in CD patients when compared to HC. CONCLUSION The microbial alterations of MVs in CD patients particularly in Firmicutes and Proteobacteria suggest a possible role of MVs in host-microbe symbiosis and induction or progression of inflammation in CD pathogenesis. Yet, the exact role for these fMV in the pathogenesis of the disease needs to be elucidated in future studies.
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Affiliation(s)
- Nader Kameli
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands; (H.E.F.B.); (T.W.); (J.P.); (P.S.)
- Department of Medical Microbiology, Faculty of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Correspondence: (N.K.); (F.R.S.)
| | - Heike E. F. Becker
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands; (H.E.F.B.); (T.W.); (J.P.); (P.S.)
- Department of Internal Medicine, Division of Gastroenterology/Hepatology, NUTRIM school of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, 6200 MD Maastricht, The Netherlands;
| | - Tessa Welbers
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands; (H.E.F.B.); (T.W.); (J.P.); (P.S.)
| | - Daisy M. A. E. Jonkers
- Department of Internal Medicine, Division of Gastroenterology/Hepatology, NUTRIM school of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, 6200 MD Maastricht, The Netherlands;
| | - John Penders
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands; (H.E.F.B.); (T.W.); (J.P.); (P.S.)
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Centre+, 6229 ER Maastricht, The Netherlands
| | - Paul Savelkoul
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands; (H.E.F.B.); (T.W.); (J.P.); (P.S.)
- Department of Medical Microbiology and Infection Control, VU University Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Frank R. Stassen
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands; (H.E.F.B.); (T.W.); (J.P.); (P.S.)
- Correspondence: (N.K.); (F.R.S.)
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Kameli N, Dragojlovic-Kerkache A, Savelkoul P, Stassen FR. Plant-Derived Extracellular Vesicles: Current Findings, Challenges, and Future Applications. Membranes (Basel) 2021; 11:membranes11060411. [PMID: 34072600 PMCID: PMC8226527 DOI: 10.3390/membranes11060411] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022]
Abstract
In recent years, plant-derived extracellular vesicles (PDEVs) have gained the interest of many experts in fields such as microbiology and immunology, and research in this field has exponentially increased. These nano-sized particles have provided researchers with a number of interesting findings, making their application in human health and disease very promising. Both in vitro and in vivo experiments have shown that PDEVs can exhibit a multitude of effects, suggesting that these vesicles may have many potential future applications, including therapeutics and nano-delivery of compounds. While the preliminary results are promising, there are still some challenges to face, such as a lack of protocol standardization, as well as knowledge gaps that need to be filled. This review aims to discuss various aspects of PDEV knowledge, including their preliminary findings, challenges, and future uses, giving insight into the complexity of conducting research in this field.
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Affiliation(s)
- Nader Kameli
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center, 6200MD Maastricht, The Netherlands; (N.K.); (A.D.-K.); (P.S.)
- Department of Medical Microbiology, Faculty of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Anya Dragojlovic-Kerkache
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center, 6200MD Maastricht, The Netherlands; (N.K.); (A.D.-K.); (P.S.)
| | - Paul Savelkoul
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center, 6200MD Maastricht, The Netherlands; (N.K.); (A.D.-K.); (P.S.)
- Department of Medical Microbiology and Infection Control, VU University Medical Center, 1007MB Amsterdam, The Netherlands
| | - Frank R. Stassen
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center, 6200MD Maastricht, The Netherlands; (N.K.); (A.D.-K.); (P.S.)
- Correspondence:
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Kameli N, Borman R, Lpez-Iglesias C, Savelkoul P, Stassen FRM. Characterization of Feces-Derived Bacterial Membrane Vesicles and the Impact of Their Origin on the Inflammatory Response. Front Cell Infect Microbiol 2021; 11:667987. [PMID: 34026664 PMCID: PMC8139245 DOI: 10.3389/fcimb.2021.667987] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/06/2021] [Indexed: 12/21/2022] Open
Abstract
The human gastrointestinal tract harbors a diverse and complex microbiome, which interacts in a variety of ways with the host. There is compelling evidence that gut microbial dysbiosis, defined as an alteration of diversity and abundance in intestinal microbes, is an etiological factor in inflammatory bowel disease (IBD). Membrane vesicles (MVs), which are nano-sized particles released by bacteria, have been found to interact with the host and modulate the development and function of the immune system. As a result MVs have been suggested to play a critical role in both health and disease. In this study we developed a method to isolate, characterize and assess the immunoreactivity of heterogeneous populations of MVs from fecal samples (fMVs) of healthy volunteers. We successfully isolated 2*109-2*1010 particles/ml from 0.5 gram of feces by using a combination of ultrafiltration and size exclusion chromatography (SEC) from 10 fecal samples. Bead-based flowcytometry in combination with tunable resistive pulse sensing (TRPS) provided a reliable method for (semi-)quantitative determination of fMVs originating from both Gram-positive and Gram-negative bacteria, while transmission electron microscopy confirmed the presence of fMVs. Real time 16s PCR on bacterial cell fractions or isolated fMVs DNA of the most common phyla (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria) revealed differences in the relative abundance between bacteria and the fMVs. Moreover, fMVs evoke the release of TNF- by THP-1 cells in a dose-dependent matter. Also, a significant positive correlation was found between Actinobacteria/-Proteobacteria derived vesicles and the release of TNF-. It has become increasingly clear that fMVs could provide an additional layer to the definition of homeostasis or dysbiosis of the microbiota. The current study supports their potential involvement in the intestinal homeostasis or inflammatory disorders and provides putative interesting incentives for future research.
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Affiliation(s)
- Nader Kameli
- School of Nutrition and Translational Research in Metabolism (NUTRIM), Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, Netherlands.,Department of Medical Microbiology, Faculty of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Reitske Borman
- School of Nutrition and Translational Research in Metabolism (NUTRIM), Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Carmen Lpez-Iglesias
- Microscopy CORE Lab, The Maastricht Multimodal Molecular Imaging Institute M4I, Faculty of Health, Medicine, and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Paul Savelkoul
- School of Nutrition and Translational Research in Metabolism (NUTRIM), Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, Netherlands.,Dept of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, location VUmc, Amsterdam, Netherlands
| | - Frank R M Stassen
- School of Nutrition and Translational Research in Metabolism (NUTRIM), Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, Netherlands
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Akaberi D, Bergfors A, Kjellin M, Kameli N, Lidemalm L, Kolli B, Shafer RW, Palanisamy N, Lennerstrand J. Baseline dasabuvir resistance in Hepatitis C virus from the genotypes 1, 2 and 3 and modeling of the NS5B-dasabuvir complex by the in silico approach. Infect Ecol Epidemiol 2018; 8:1528117. [PMID: 30319736 PMCID: PMC6179053 DOI: 10.1080/20008686.2018.1528117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/13/2018] [Indexed: 02/08/2023] Open
Abstract
Background: Current combination treatments with direct-acting antiviral agents (DAAs) can cure more than 95% of hepatitis C virus (HCV) infections. However, resistance-associated substitutions (RASs) may emerge and can also be present in treatment-naïve patients. Methods, results and discussion: In this study, a semi-pan-genotypic population sequencing method was developed and used to assess all NS5B amino acid variants between residue positions 310 and 564. Our method successfully sequenced more than 90% of genotype (GT) 1a, 1b, 2b and 3a samples. By using the population sequencing method with a cut-off of 20%, we found the dasabuvir RASs A553V and C445F to be a baseline polymorphism of GT 2b (8 out of 8) and GT 3a (18 out of 18) sequences, respectively. In GT 1a and 1b treatment-naïve subjects (n=25), no high-fold resistance polymorphism/RASs were identified. We further predicted dasabuvir’s binding pose with the NS5B polymerase using the in silico methods to elucidate the reasons associated with the resistance of clinically relevant RASs. Dasabuvir was docked at the palm-I site and was found to form hydrogen bonds with the residues S288, I447, Y448, N291 and D318. The RAS positions 316, 414, 448, 553 and 556 were found to constitute the dasabuvir binding pocket.
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Affiliation(s)
- Dario Akaberi
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Assar Bergfors
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Midori Kjellin
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Nader Kameli
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Medical Microbiology, NUTRIM school of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Louise Lidemalm
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Bhavya Kolli
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Robert W Shafer
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Navaneethan Palanisamy
- HBIGS, University of Heidelberg, Heidelberg, Germany.,Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Johan Lennerstrand
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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