1
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Tian S, Shi L, Ren Y, van der Mei HC, Busscher HJ. A normalized parameter for comparison of biofilm dispersants in vitro. Biofilm 2024; 7:100188. [PMID: 38495770 PMCID: PMC10943042 DOI: 10.1016/j.bioflm.2024.100188] [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: 12/01/2023] [Revised: 02/12/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Dispersal of infectious biofilms increases bacterial concentrations in blood. To prevent sepsis, the strength of a dispersant should be limited to allow the immune system to remove dispersed bacteria from blood, preferably without antibiotic administration. Biofilm bacteria are held together by extracellular polymeric substances that can be degraded by dispersants. Currently, comparison of the strength of dispersants is not possible by lack of a suitable comparison parameter. Here, a biofilm dispersal parameter is proposed that accounts for differences in initial biofilm properties, dispersant concentration and exposure time by using PBS as a control and normalizing outcomes with respect to concentration and time. The parameter yielded near-identical values based on dispersant-induced reductions in biomass or biofilm colony-forming-units and appeared strain-dependent across pathogens. The parameter as proposed is largely independent of experimental methods and conditions and suitable for comparing different dispersants with respect to different causative strains in particular types of infection.
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Affiliation(s)
- Shuang Tian
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AV, Groningen, the Netherlands
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, PR China
| | - Linqi Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, PR China
| | - Yijin Ren
- University of Groningen and University Medical Center Groningen, Department of Orthodontics, Hanzeplein 1, 9700, RB, Groningen, the Netherlands
| | - Henny C. van der Mei
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AV, Groningen, the Netherlands
| | - Henk J. Busscher
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AV, Groningen, the Netherlands
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2
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Slobodianyk-Kolomoiets M, Khlebas S, Mazur I, Rudnieva K, Potochilova V, Iungin O, Kamyshnyi O, Kamyshna I, Potters G, Spiers AJ, Moshynets O. Extracellular host DNA contributes to pathogenic biofilm formation during periodontitis. Front Cell Infect Microbiol 2024; 14:1374817. [PMID: 38779563 PMCID: PMC11109387 DOI: 10.3389/fcimb.2024.1374817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/09/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Periodontal diseases are known to be associated with polymicrobial biofilms and inflammasome activation. A deeper understanding of the subgingival cytological (micro) landscape, the role of extracellular DNA (eDNA) during periodontitis, and contribution of the host immune eDNA to inflammasome persistence, may improve our understanding of the mechanisms underlaying severe forms of periodontitis. Methods In this work, subgingival biolfilms developing on biologically neutral polyethylene terephthalate films placed in gingival cavities of patients with chronic periodontitis were investigated by confocal laser scanning microscopy (CLSM). This allowed examination of realistic cytological landscapes and visualization of extracellular polymeric substances (EPS) including amyloids, total proteins, carbohydrates and eDNA, as well as comparison with several single-strain in vitro model biofilms produced by oral pathogens such as Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus gordonii, S. sanguinis and S. mitis. Fluorescence in situ hybridization (FISH) analysis was also used to identify eDNA derived from eubacteria, streptococci and members of the Bacteroides-Porphyromonas-Prevotella (BPP) group associated with periodontitis. Results Analysis of subgingival biofilm EPS revealed low levels of amyloids and high levels of eDNA which appears to be the main matrix component. However, bacterial eDNA contributed less than a third of the total eDNA observed, suggesting that host-derived eDNA released in neutrophil extracellular traps may be of more importance in the development of biofilms causing periodontitis. Discussion eDNA derived from host immunocompetent cells activated at the onset of periodontitis may therefore be a major driver of bacterial persistence and pathogenesis.
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Affiliation(s)
| | - Svitlana Khlebas
- Department of Dentistry, Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine
| | - Iryna Mazur
- Department of Dentistry, Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine
| | - Kateryna Rudnieva
- Central Clinical Diagnostic Laboratory, Kyiv Regional Clinical Hospital, Kyiv, Ukraine
- Department of Microbiology, Virology and Immunology, Bogomolets National Medical Academy, Kyiv, Ukraine
| | | | - Olga Iungin
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Biotechnology, Leather and Fur, Faculty of Chemical and Biopharmaceutical Technologies, Kyiv National University of Technologies and Design, Kyiv, Ukraine
| | - Olexandr Kamyshnyi
- Microbiology, Virology and Immunology Department, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Iryna Kamyshna
- Microbiology, Virology and Immunology Department, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Geert Potters
- Antwerp Maritime Academy, Antwerp, Belgium
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Andrew J. Spiers
- School of Applied Sciences, Abertay University, Dundee, United Kingdom
| | - Olena Moshynets
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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3
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Gnilitskyi I, Rymar S, Iungin O, Vyshnevskyy O, Parisse P, Potters G, Zayats AV, Moshynets O. Femtosecond laser modified metal surfaces alter biofilm architecture and reduce bacterial biofilm formation. NANOSCALE ADVANCES 2023; 5:6659-6669. [PMID: 38024323 PMCID: PMC10662203 DOI: 10.1039/d3na00599b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Biofilm formation, or microfouling, is a basic strategy of bacteria to colonise a surface and may happen on surfaces of any nature whenever bacteria are present. Biofilms are hard to eradicate due to the matrix in which the bacteria reside, consisting of strong, adhesive and adaptive self-produced polymers such as eDNA and functional amyloids. Targeting a biofilm matrix may be a promising strategy to prevent biofilm formation. Here, femtosecond laser irradiation was used to modify the stainless steel surface in order to introduce either conical spike or conical groove textures. The resulting topography consists of hierarchical nano-microstructures which substantially increase roughness. The biofilms of two model bacterial strains, P. aeruginosa PA01 and S. aureus ATCC29423, formed on such nanotextured metal surfaces, were considerably modified due to a substantial reduction in amyloid production and due to changes in eDNA surface adhesion, leading to significant reduction in biofilm biomass. Altering the topography of the metal surface, therefore, radically diminishes biofilm development solely by altering biofilm architecture. At the same time, growth and colonisation of the surface by eukaryotic adipose tissue-derived stem cells were apparently enhanced, leading to possible further advantages in controlling eukaryotic growth while suppressing prokaryotic contamination. The obtained results are important for developing anti-bacterial surfaces for numerous applications.
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Affiliation(s)
- Iaroslav Gnilitskyi
- Department of Physics and London Centre for Nanotechnology, King's College London Strand London WC2R 2LS UK
- NoviNano Lab LLC Lviv Ukraine
- Lviv Polytechnic National University Ukraine
| | - Svitlana Rymar
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine Kyiv Ukraine
| | - Olga Iungin
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine Kyiv Ukraine
- Kyiv National University of Technologies and Design Kyiv Ukraine
| | - Olexiy Vyshnevskyy
- M. P. Semenenko Institute of Geochemistry, Mineralogy and Ore Formation of National Academy of Sciences of Ukraine Kyiv Ukraine
| | - Pietro Parisse
- Istituto Officina dei Materiali (IOM)-CNR, Laboratorio TASC I-34149 Trieste Italy
| | - Geert Potters
- Antwerp Maritime Academy Antwerp Belgium
- Department of Bioscience Engineering, University of Antwerp Antwerp Belgium
| | - Anatoly V Zayats
- Department of Physics and London Centre for Nanotechnology, King's College London Strand London WC2R 2LS UK
| | - Olena Moshynets
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine Kyiv Ukraine
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4
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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5
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Zhao A, Sun J, Liu Y. Understanding bacterial biofilms: From definition to treatment strategies. Front Cell Infect Microbiol 2023; 13:1137947. [PMID: 37091673 PMCID: PMC10117668 DOI: 10.3389/fcimb.2023.1137947] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/09/2023] [Indexed: 04/08/2023] Open
Abstract
Bacterial biofilms are complex microbial communities encased in extracellular polymeric substances. Their formation is a multi-step process. Biofilms are a significant problem in treating bacterial infections and are one of the main reasons for the persistence of infections. They can exhibit increased resistance to classical antibiotics and cause disease through device-related and non-device (tissue) -associated infections, posing a severe threat to global health issues. Therefore, early detection and search for new and alternative treatments are essential for treating and suppressing biofilm-associated infections. In this paper, we systematically reviewed the formation of bacterial biofilms, associated infections, detection methods, and potential treatment strategies, aiming to provide researchers with the latest progress in the detection and treatment of bacterial biofilms.
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Affiliation(s)
- Ailing Zhao
- Department of Gastroenterology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, China
| | - Jiazheng Sun
- Department of Vasculocardiology, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Yipin Liu
- Department of Gastroenterology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, China
- *Correspondence: Yipin Liu,
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6
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Moshynets OV, Baranovskyi TP, Iungin OS, Krikunov AA, Potochilova VV, Rudnieva KL, Potters G, Pokholenko I. Therapeutic Potential of an Azithromycin-Colistin Combination against XDR K. pneumoniae in a 3D Collagen-Based In Vitro Wound Model of a Biofilm Infection. Antibiotics (Basel) 2023; 12:antibiotics12020293. [PMID: 36830203 PMCID: PMC9952533 DOI: 10.3390/antibiotics12020293] [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: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
A therapeutic combination of azithromycin (AZM) and colistin methanesulfonate (CMS) was shown to be effective against both non-PDR and PDR Klebsiella pneumoniae biofilms in vitro. These anti-biofilm effects, however, may not correlate with effects observed in standard plate assays, nor will they representative of in vivo therapeutic action. After all, biofilm-associated infection processes are also impacted by the presence of wound bed components, such as host cells or wound fluids, which can all affect the antibiotic effectiveness. Therefore, an in vitro wound model of biofilm infection which partially mimics the complex microenvironment of infected wounds was developed to investigate the therapeutic potential of an AZM-CMS combination against XDR K. pneumoniae isolates. The model consists of a 3D collagen sponge-like scaffold seeded with HEK293 cells submerged in a fluid milieu mimicking the wound bed exudate. Media that were tested were all based on different strengths of Dulbecco's modified Eagles/high glucose medium supplemented with fetal bovine serum, and/or Bacto Proteose peptone. Use of this model confirmed AZM to be a highly effective antibiofilm component, when applied alone or in combination with CMS, whereas CMS alone had little antibacterial effectiveness or even stimulated biofilm development. The wound model proposed here proves therefore, to be an effective aid in the study of drug combinations under realistic conditions.
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Affiliation(s)
- Olena V. Moshynets
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Zabolotnoho Str. 150, 03680 Kyiv, Ukraine
- Correspondence: (O.V.M.); (G.P.)
| | - Taras P. Baranovskyi
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, A-1090 Vienna, Austria
| | - Olga S. Iungin
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Zabolotnoho Str. 150, 03680 Kyiv, Ukraine
- Department of Biotechnology, Leather and Fur, Faculty of Chemical and Biopharmaceutical Technologies, Kyiv National University of Technologies and Design, Nemyrovycha-Danchenka Street 2, 01011 Kyiv, Ukraine
| | - Alexey A. Krikunov
- National Amosov Institute of Cardio-Vascular Surgery Affiliated to National Academy of Medical Sciences of Ukraine, Amosov Str. 6, 02000 Kyiv, Ukraine
| | | | - Kateryna L. Rudnieva
- Kyiv Regional Clinical Hospital, Baggovutovskaya Str. 1, 04107 Kyiv, Ukraine
- Department of Microbiology, Virology and Immunology, Bogomolets National Medical University, Shevchenka Blvd. 13, 01601 Kyiv, Ukraine
| | - Geert Potters
- Antwerp Maritime Academy, Noordkasteel Oost 6, 2030 Antwerp, Belgium
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Correspondence: (O.V.M.); (G.P.)
| | - Ianina Pokholenko
- Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Str., 03680 Kyiv, Ukraine
- The Polymer Chemistry & Biomaterials Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4-Bis, 9000 Ghent, Belgium
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7
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Moshynets OV, Pokholenko I, Iungin O, Potters G, Spiers AJ. eDNA, Amyloid Fibers and Membrane Vesicles Identified in Pseudomonas fluorescens SBW25 Biofilms. Int J Mol Sci 2022; 23:ijms232315096. [PMID: 36499433 PMCID: PMC9738004 DOI: 10.3390/ijms232315096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
Pseudomonas fluorescens SBW25 is a model soil- and plant-associated bacterium capable of forming a variety of air-liquid interface biofilms in experimental microcosms and on plant surfaces. Previous investigations have shown that cellulose is the primary structural matrix component in the robust and well-attached Wrinkly Spreader biofilm, as well as in the fragile Viscous Mass biofilm. Here, we demonstrate that both biofilms include extracellular DNA (eDNA) which can be visualized using confocal laser scanning microscopy (CLSM), quantified by absorbance measurements, and degraded by DNase I treatment. This eDNA plays an important role in cell attachment and biofilm development. However, exogenous high-molecular-weight DNA appears to decrease the strength and attachment levels of mature Wrinkly Spreader biofilms, whereas low-molecular-weight DNA appears to have little effect. Further investigation with CLSM using an amyloid-specific fluorophore suggests that the Wrinkly Spreader biofilm might also include Fap fibers, which might be involved in attachment and contribute to biofilm strength. The robust nature of the Wrinkly Spreader biofilm also allowed us, using MALDI-TOF mass spectrometry, to identify matrix-associated proteins unable to diffuse out of the structure, as well as membrane vesicles which had a different protein profile compared to the matrix-associated proteins. CLSM and DNase I treatment suggest that some vesicles were also associated with eDNA. These findings add to our understanding of the matrix components in this model pseudomonad, and, as found in other biofilms, biofilm-specific products and material from lysed cells contribute to these structures through a range of complex interactions.
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Affiliation(s)
- Olena V. Moshynets
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Ianina Pokholenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Olga Iungin
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
- Department of Biotechnology, Leather and Fur, Kyiv National University of Technologies and Design, 01011 Kyiv, Ukraine
| | - Geert Potters
- Antwerp Maritime Academy, 2030 Antwerp, Belgium
- Department of Bioscience Engineering, University of Antwerp, 2000 Antwerp, Belgium
- Correspondence:
| | - Andrew J. Spiers
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
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8
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Moshynets OV, Baranovskyi TP, Cameron S, Iungin OS, Pokholenko I, Jerdan R, Kamyshnyi A, Krikunov AA, Potochilova VV, Rudnieva KL, Spiers AJ. Azithromycin possesses biofilm–inhibitory activity and potentiates non-bactericidal colistin methanesulfonate (CMS) and polymyxin B against Klebsiella pneumonia. PLoS One 2022; 17:e0270983. [PMID: 35776759 PMCID: PMC9249213 DOI: 10.1371/journal.pone.0270983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/21/2022] [Indexed: 11/30/2022] Open
Abstract
Novel antibiotic combinations may act synergistically to inhibit the growth of multidrug-resistant bacterial pathogens but predicting which combination will be successful is difficult, and standard antimicrobial susceptibility testing may not identify important physiological differences between planktonic free-swimming and biofilm-protected surface-attached sessile cells. Using a nominally macrolide-resistant model Klebsiella pneumoniae strain (ATCC 10031) we demonstrate the effectiveness of several macrolides in inhibiting biofilm growth in multi-well plates, and the ability of azithromycin (AZM) to improve the effectiveness of the antibacterial last-agent-of-choice for K. pneumoniae infections, colistin methanesulfonate (CMS), against biofilms. This synergistic action was also seen in biofilm tests of several K. pneumoniae hospital isolates and could also be identified in polymyxin B disc-diffusion assays on azithromycin plates. Our work highlights the complexity of antimicrobial-resistance in bacterial pathogens and the need to test antibiotics with biofilm models where potential synergies might provide new therapeutic opportunities not seen in liquid culture or colony-based assays.
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Affiliation(s)
- Olena V. Moshynets
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kyiv, Ukraine
- * E-mail: (OVM); (AJS)
| | - Taras P. Baranovskyi
- Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine
- Kyiv Regional Clinical Hospital, Kyiv, Ukraine
| | - Scott Cameron
- School of Applied Sciences, Abertay University, Dundee, United Kingdom
| | - Olga S. Iungin
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Kyiv National University of Technologies and Design, Kyiv, Ukraine
| | - Ianina Pokholenko
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Robyn Jerdan
- School of Applied Sciences, Abertay University, Dundee, United Kingdom
| | | | | | | | | | - Andrew J. Spiers
- School of Applied Sciences, Abertay University, Dundee, United Kingdom
- * E-mail: (OVM); (AJS)
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9
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Volynets GP, Barthels F, Hammerschmidt SJ, Moshynets OV, Lukashov SS, Starosyla SA, Vyshniakova HV, Iungin OS, Bdzhola VG, Prykhod'ko AO, Syniugin AR, Sapelkin VM, Yarmoluk SM, Schirmeister T. Identification of novel small-molecular inhibitors of Staphylococcus aureus sortase A using hybrid virtual screening. J Antibiot (Tokyo) 2022; 75:321-332. [PMID: 35440771 PMCID: PMC9016125 DOI: 10.1038/s41429-022-00524-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 01/18/2023]
Abstract
Staphylococcus aureus is one of the most dangerous pathogens commonly associated with high levels of morbidity and mortality. Sortase A is considered as a promising molecular target for the development of antistaphylococcal agents. Using hybrid virtual screening approach and FRET analysis, we have identified five compounds able to decrease the activity of sortase A by more than 50% at the concentration of 200 µM. The most promising compound was 2-(2-amino-3-chloro-benzoylamino)-benzoic acid which was able to inhibit S. aureus sortase A at the IC50 value of 59.7 µM. This compound was selective toward sortase A compared to other four cysteine proteases - cathepsin L, cathepsin B, rhodesain, and the SARS-CoV2 main protease. Microscale thermophoresis experiments confirmed that this compound bound sortase A with KD value of 189 µM. Antibacterial and antibiofilm assays also confirmed high specificity of the hit compound against two standard and three wild-type, S. aureus hospital infection isolates. The effect of the compound on biofilms produced by two S. aureus ATCC strains was also observed suggesting that the compound reduced biofilm formation by changing the biofilm structure and thickness.
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Affiliation(s)
- Galyna P Volynets
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine.
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Stefan J Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Olena V Moshynets
- Biofilm study group, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Sergiy S Lukashov
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Sergiy A Starosyla
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine.,RECEPTOR.AI, Boston, MA, USA
| | - Hanna V Vyshniakova
- L.V. Gromashevsky Institute of Epidemiology and Infectious Diseases NAMS of Ukraine, 5 Amosova St, 03038, Kyiv, Ukraine
| | - Olga S Iungin
- Department of Functional Genomics, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Volodymyr G Bdzhola
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Andrii O Prykhod'ko
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine.,Research and Development Department, Scientific Services Company Otava Ltd, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Anatolii R Syniugin
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Vladislav M Sapelkin
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Sergiy M Yarmoluk
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz, Staudinger Weg 5, 55128, Mainz, Germany
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10
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Moshynets OV, Baranovskyi TP, Iungin OS, Kysil NP, Metelytsia LO, Pokholenko I, Potochilova VV, Potters G, Rudnieva KL, Rymar SY, Semenyuta IV, Spiers AJ, Tarasyuk OP, Rogalsky SP. eDNA Inactivation and Biofilm Inhibition by the PolymericBiocide Polyhexamethylene Guanidine Hydrochloride (PHMG-Cl). Int J Mol Sci 2022; 23:ijms23020731. [PMID: 35054915 PMCID: PMC8775615 DOI: 10.3390/ijms23020731] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/03/2022] [Accepted: 01/03/2022] [Indexed: 01/05/2023] Open
Abstract
The choice of effective biocides used for routine hospital practice should consider the role of disinfectants in the maintenance and development of local resistome and how they might affect antibiotic resistance gene transfer within the hospital microbial population. Currently, there is little understanding of how different biocides contribute to eDNA release that may contribute to gene transfer and subsequent environmental retention. Here, we investigated how different biocides affect the release of eDNA from mature biofilms of two opportunistic model strains Pseudomonas aeruginosa ATCC 27853 (PA) and Staphylococcus aureus ATCC 25923 (SA) and contribute to the hospital resistome in the form of surface and water contaminants and dust particles. The effect of four groups of biocides, alcohols, hydrogen peroxide, quaternary ammonium compounds, and the polymeric biocide polyhexamethylene guanidine hydrochloride (PHMG-Cl), was evaluated using PA and SA biofilms. Most biocides, except for PHMG-Cl and 70% ethanol, caused substantial eDNA release, and PHMG-Cl was found to block biofilm development when used at concentrations of 0.5% and 0.1%. This might be associated with the formation of DNA–PHMG-Cl complexes as PHMG-Cl is predicted to bind to AT base pairs by molecular docking assays. PHMG-Cl was found to bind high-molecular DNA and plasmid DNA and continued to inactivate DNA on surfaces even after 4 weeks. PHMG-Cl also effectively inactivated biofilm-associated antibiotic resistance gene eDNA released by a pan-drug-resistant Klebsiella strain, which demonstrates the potential of a polymeric biocide as a new surface-active agent to combat the spread of antibiotic resistance in hospital settings.
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Affiliation(s)
- Olena V. Moshynets
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Str., 03680 Kiev, Ukraine; (O.S.I.); (I.P.); (S.Y.R.)
- Correspondence: (O.V.M.); (S.P.R.)
| | - Taras P. Baranovskyi
- Department of Dermatovenerology, Allergology, Clinical and Laboratory Immunology, Shupyk National Healthcare University of Ukraine, 9 Dorohozhytska Str., 03680 Kiev, Ukraine;
- Kyiv Regional Clinical Hospital, 1 Baggovutivska Street, 04107 Kiev, Ukraine; (V.V.P.); (K.L.R.)
| | - Olga S. Iungin
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Str., 03680 Kiev, Ukraine; (O.S.I.); (I.P.); (S.Y.R.)
- Department of Biotechnology, Leather and Fur, Faculty of Chemical and Biopharmaceutical Technologies, Kyiv National University of Technologies and Design, Nemyrovycha-Danchenka Street, 2, 01011 Kiev, Ukraine
| | - Nadiia P. Kysil
- National Children’s Specialized Hospital “Okhmatdyt”, 28/1 Chornovola Str., 01135 Kiev, Ukraine;
| | - Larysa O. Metelytsia
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 50 Kharkivske Schose, 01135 Kiev, Ukraine; (L.O.M.); (I.V.S.); (O.P.T.)
| | - Ianina Pokholenko
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Str., 03680 Kiev, Ukraine; (O.S.I.); (I.P.); (S.Y.R.)
| | - Viktoria V. Potochilova
- Kyiv Regional Clinical Hospital, 1 Baggovutivska Street, 04107 Kiev, Ukraine; (V.V.P.); (K.L.R.)
| | - Geert Potters
- Antwerp Maritime Academy, Noordkasteel Oost 6, 2030 Antwerp, Belgium;
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Kateryna L. Rudnieva
- Kyiv Regional Clinical Hospital, 1 Baggovutivska Street, 04107 Kiev, Ukraine; (V.V.P.); (K.L.R.)
| | - Svitlana Y. Rymar
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Str., 03680 Kiev, Ukraine; (O.S.I.); (I.P.); (S.Y.R.)
| | - Ivan V. Semenyuta
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 50 Kharkivske Schose, 01135 Kiev, Ukraine; (L.O.M.); (I.V.S.); (O.P.T.)
| | - Andrew J. Spiers
- School of Applied Sciences, Abertay University, Bell Street, Dundee DD1 1HG, UK;
| | - Oksana P. Tarasyuk
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 50 Kharkivske Schose, 01135 Kiev, Ukraine; (L.O.M.); (I.V.S.); (O.P.T.)
| | - Sergiy P. Rogalsky
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 50 Kharkivske Schose, 01135 Kiev, Ukraine; (L.O.M.); (I.V.S.); (O.P.T.)
- Correspondence: (O.V.M.); (S.P.R.)
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Chernii S, Gerasymchuk Y, Losytskyy M, Szymański D, Tretyakova I, Łukowiak A, Pekhnyo V, Yarmoluk S, Chernii V, Kovalska V. Modification of insulin amyloid aggregation by Zr phthalocyanines functionalized with dehydroacetic acid derivatives. PLoS One 2021; 16:e0243904. [PMID: 33411832 PMCID: PMC7790233 DOI: 10.1371/journal.pone.0243904] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
Amyloid fibrils are widely studied both as target in conformational disorders and as basis for the development of protein-based functional materials. The three Zr phthalocyanines bearing dehydroacetic acid residue (PcZr(L1)2) and its condensed derivatives (PcZr(L2)2 and PcZr(L3)2) as out-of-plane ligands were synthesized and their influence on insulin fibril formation was studied by amyloid-sensitive fluorescent dye based assay, scanning electron microscopy, fluorescent and absorption spectroscopies. The presence of Zr phthalocyanines was shown to modify the fibril formation. The morphology of fibrils formed in the presence of the Zr phthalocyanines differs from that of free insulin and depends on the structure of out-of-plane ligands. It is shown that free insulin mostly forms fibril clusters with the length of about 0.3-2.1 μm. The presence of Zr phthalocyanines leads to the formation of individual 0.4-2.8 μm-long fibrils with a reduced tendency to lateral aggregation and cluster formation (PcZr(L1)2), shorter 0.2-1.5 μm-long fibrils with the tendency to lateral aggregation without clusters (PcZr(L2)2), and fibril-like 0.2-1.0 μm-long structures (PcZr(L3)2). The strongest influence on fibrils morphology made by PcZr(L3)2 could be explained by the additional stacking of phenyl moiety of the ligand with aromatic amino acids in protein. The evidences of binding of studied Zr phthalocyanines to mature fibrils were shown by absorption spectroscopy (for PcZr(L1)2 and PcZr(L2)2) and fluorescent spectroscopy (for PcZr(L3)2). These complexes could be potentially used as external tools allowing the development of functional materials on protein fibrils basis.
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Affiliation(s)
- Svitlana Chernii
- Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine
| | - Yuriy Gerasymchuk
- Institute of Low Temperature and Structure Research, PAS, Wroclaw, Poland
| | | | - Damian Szymański
- Institute of Low Temperature and Structure Research, PAS, Wroclaw, Poland
| | - Iryna Tretyakova
- Institute of General and Inorganic Chemistry, NASU, Kyiv, Ukraine
| | - Anna Łukowiak
- Institute of Low Temperature and Structure Research, PAS, Wroclaw, Poland
| | - Vasyl Pekhnyo
- Institute of General and Inorganic Chemistry, NASU, Kyiv, Ukraine
| | - Sergiy Yarmoluk
- Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine
| | - Viktor Chernii
- Institute of General and Inorganic Chemistry, NASU, Kyiv, Ukraine
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