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Cusumano JA, Kalogeropoulos AP, Le Provost M, Gallo NR, Levine SM, Inzana T, Papamanoli A. The emerging challenge of Enterococcus faecalis endocarditis after transcatheter aortic valve implantation: time for innovative treatment approaches. Clin Microbiol Rev 2024; 37:e0016823. [PMID: 39235238 PMCID: PMC11629618 DOI: 10.1128/cmr.00168-23] [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: 09/06/2024] Open
Abstract
SUMMARYInfective endocarditis (IE) is a life-threatening infection that has nearly doubled in prevalence over the last two decades due to the increase in implantable cardiac devices. Transcatheter aortic valve implantation (TAVI) is currently one of the most common cardiac procedures. TAVI usage continues to exponentially rise, inevitability increasing TAVI-IE. Patients with TAVI are frequently nonsurgical candidates, and TAVI-IE 1-year mortality rates can be as high as 74% without valve or bacterial biofilm removal. Enterococcus faecalis, a historically less common IE pathogen, is the primary cause of TAVI-IE. Treatment options are limited due to enterococcal intrinsic resistance and biofilm formation. Novel approaches are warranted to tackle current therapeutic gaps. We describe the existing challenges in treating TAVI-IE and how available treatment discovery approaches can be combined with an in silico "Living Heart" model to create solutions for the future.
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Affiliation(s)
- Jaclyn A. Cusumano
- Arnold & Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York, USA
| | - Andreas P. Kalogeropoulos
- Renaissance School of Medicine Division of Cardiology, Stony Brook University, Stony Brook, New York, USA
| | - Mathieu Le Provost
- School of Engineering, Computer Science and Artificial Intelligence, Long Island University, Brooklyn, New York, USA
| | - Nicolas R. Gallo
- Arnold & Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York, USA
- School of Engineering, Computer Science and Artificial Intelligence, Long Island University, Brooklyn, New York, USA
| | | | - Thomas Inzana
- College of Veterinary Medicine, Long Island University, Brooklyn, New York, USA
| | - Aikaterini Papamanoli
- Division of Infectious Diseases, Stony Brook University Medical Center, Stony Brook, New York, USA
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2
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Coppens B, Belpaire TE, Pešek J, Steenackers HP, Ramon H, Smeets B. Anomalous diffusion of nanoparticles in the spatially heterogeneous biofilm environment. iScience 2023; 26:106861. [PMID: 37260744 PMCID: PMC10227381 DOI: 10.1016/j.isci.2023.106861] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/20/2023] [Accepted: 05/08/2023] [Indexed: 06/02/2023] Open
Abstract
Biofilms contain extracellular polymeric substances (EPS) that provide structural support and restrict penetration of antimicrobial treatment. To overcome limited penetration, functionalized nanoparticles (NPs) have been suggested as carriers for antimicrobial delivery. Using microscopy, we evaluate the diffusion of nanoparticles in function of the structure of Salmonella biofilms. We observe anomalous diffusion and heterogeneous mobility of NPs resulting in distinct NPs distribution that depended on biofilm structure. Through Brownian dynamics modeling with spatially varying viscosity around bacteria, we demonstrated that spatial gradients in diffusivity generate viscous sinks that trap NPs near bacteria. This model replicates the characteristic diffusion signature and vertical distribution of NPs in the biofilm. From a treatment perspective, our work indicates that both biofilm structure and the level of EPS can impact NP drug delivery, where low levels of EPS might benefit delivery by immobilizing NPs closer to bacteria and higher levels hamper delivery due to shielding effects.
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Affiliation(s)
- Bart Coppens
- Division of Mechatronics, Biostatistics, and Sensors, KU Leuven, 3001 Leuven, Belgium
| | - Tom E.R. Belpaire
- Division of Mechatronics, Biostatistics, and Sensors, KU Leuven, 3001 Leuven, Belgium
| | - Jiří Pešek
- Team SIMBIOTX, Inria Saclay, 91120 Palaiseau, France
| | | | - Herman Ramon
- Division of Mechatronics, Biostatistics, and Sensors, KU Leuven, 3001 Leuven, Belgium
| | - Bart Smeets
- Division of Mechatronics, Biostatistics, and Sensors, KU Leuven, 3001 Leuven, Belgium
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Zabiegaj D, Hajirasouliha F, Duilio A, Guido S, Caserta S, Kostoglou M, Petala M, Karapantsios T, Trybala A. Wetting/spreading on porous media and on deformable, soluble structured substrates as a model system for studying the effect of morphology on biofilms wetting and for assessing anti-biofilm methods. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2021.101426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Feng D, Neuweiler I, Nogueira R, Nackenhorst U. Modeling of Symbiotic Bacterial Biofilm Growth with an Example of the Streptococcus-Veillonella sp. System. Bull Math Biol 2021; 83:48. [PMID: 33760986 PMCID: PMC7990864 DOI: 10.1007/s11538-021-00888-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/11/2021] [Indexed: 02/07/2023]
Abstract
We present a multi-dimensional continuum mathematical model for modeling the growth of a symbiotic biofilm system. We take a dual-species namely, the Streptococcus-Veillonella sp. biofilm system as an example for numerical investigations. The presented model describes both the cooperation and competition between these species of bacteria. The coupled partial differential equations are solved by using an integrative finite element numerical strategy. Numerical examples are carried out for studying the evolution and distribution of the bio-components. The results demonstrate that the presented model is capable of describing the symbiotic behavior of the biofilm system. However, homogenized numerical solutions are observed locally. To study the homogenization behavior of the model, numerical investigations regarding on how random initial biomass distribution influences the homogenization process are carried out. We found that a smaller correlation length of the initial biomass distribution leads to faster homogenization of the solution globally, however, shows more fluctuated biomass profiles along the biofilm thickness direction. More realistic scenarios with bacteria in patches are also investigated numerically in this study.
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Affiliation(s)
- Dianlei Feng
- Institute of Fluid Mechanics and Environmental Physics in Civil Engineering, Leibniz Universität Hannover, Appelstraße 9a, 30167, Hannover, Germany.
| | - Insa Neuweiler
- Institute of Fluid Mechanics and Environmental Physics in Civil Engineering, Leibniz Universität Hannover, Appelstraße 9a, 30167, Hannover, Germany
| | - Regina Nogueira
- Institute for Sanitary Engineering and Waste Management, Gottfried Wilhelm Leibniz Universität Hannover, Welfengarten 1, 30163, Hannover, Germany
| | - Udo Nackenhorst
- Institute of Mechanics and Computational Mechanics, Leibniz Universität Hannover, Appelstraße 9a, 30167, Hannover, Germany
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5
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Abstract
Bacteria use intercellular signaling, or quorum sensing (QS), to share information and respond collectively to aspects of their surroundings. The autoinducers that carry this information are exposed to the external environment; consequently, they are affected by factors such as removal through fluid flow, a ubiquitous feature of bacterial habitats ranging from the gut and lungs to lakes and oceans. To understand how QS genetic architectures in cells promote appropriate population-level phenotypes throughout the bacterial life cycle requires knowledge of how these architectures determine the QS response in realistic spatiotemporally varying flow conditions. Here we develop and apply a general theory that identifies and quantifies the conditions required for QS activation in fluid flow by systematically linking cell- and population-level genetic and physical processes. We predict that when a subset of the population meets these conditions, cell-level positive feedback promotes a robust collective response by overcoming flow-induced autoinducer concentration gradients. By accounting for a dynamic flow in our theory, we predict that positive feedback in cells acts as a low-pass filter at the population level in oscillatory flow, allowing a population to respond only to changes in flow that occur over slow enough timescales. Our theory is readily extendable and provides a framework for assessing the functional roles of diverse QS network architectures in realistic flow conditions.
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Affiliation(s)
- Mohit P Dalwadi
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom;
| | - Philip Pearce
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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An open-source robotic platform that enables automated monitoring of replicate biofilm cultivations using optical coherence tomography. NPJ Biofilms Microbiomes 2020; 6:18. [PMID: 32238809 PMCID: PMC7113294 DOI: 10.1038/s41522-020-0129-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/06/2020] [Indexed: 12/14/2022] Open
Abstract
The paper introduces a fully automated cultivation and monitoring tool to study biofilm development in replicate experiments operated in parallel. To gain a fundamental understanding of the relation between cultivation conditions and biofilm characteristics (e.g., structural, mechanical) a monitoring setup allowing for the standardization of methods is required. Optical coherence tomography (OCT) is an imaging modality ideal for biofilms since it allows for the monitoring of structure in real time. By integrating an OCT device into the open-source robotic platform EvoBot, a fully automated monitoring platform for investigating biofilm development in several flow cells at once was realized. Different positioning scenarios were tested and revealed that the positioning accuracy is within the optical resolution of the OCT. On that account, a reliable and accurate monitoring of biofilm development by means of OCT has become possible. With this robotic platform, reproducible biofilm experiments including a statistical analysis are achievable with only a small investment of operator time. Furthermore, a number of structural parameters calculated within this study confirmed the necessity to perform replicate biofilm cultivations.
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Conrad JC, Poling-Skutvik R. Confined Flow: Consequences and Implications for Bacteria and Biofilms. Annu Rev Chem Biomol Eng 2018; 9:175-200. [DOI: 10.1146/annurev-chembioeng-060817-084006] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria overwhelmingly live in geometrically confined habitats that feature small pores or cavities, narrow channels, or nearby interfaces. Fluid flows through these confined habitats are ubiquitous in both natural and artificial environments colonized by bacteria. Moreover, these flows occur on time and length scales comparable to those associated with motility of bacteria and with the formation and growth of biofilms, which are surface-associated communities that house the vast majority of bacteria to protect them from host and environmental stresses. This review describes the emerging understanding of how flow near surfaces and within channels and pores alters physical processes that control how bacteria disperse, attach to surfaces, and form biofilms. This understanding will inform the development and deployment of technologies for drug delivery, water treatment, and antifouling coatings and guide the structuring of bacterial consortia for production of chemicals and pharmaceuticals.
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Affiliation(s)
- Jacinta C. Conrad
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
| | - Ryan Poling-Skutvik
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
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Majumdar S, Pal S. Information transmission in microbial and fungal communication: from classical to quantum. J Cell Commun Signal 2018; 12:491-502. [PMID: 29476316 PMCID: PMC5910326 DOI: 10.1007/s12079-018-0462-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 02/08/2018] [Indexed: 01/05/2023] Open
Abstract
Microbes have their own communication systems. Secretion and reception of chemical signaling molecules and ion-channels mediated electrical signaling mechanism are yet observed two special ways of information transmission in microbial community. In this article, we address the aspects of various crucial machineries which set the backbone of microbial cell-to-cell communication process such as quorum sensing mechanism (bacterial and fungal), quorum sensing regulated biofilm formation, gene expression, virulence, swarming, quorum quenching, role of noise in quorum sensing, mathematical models (therapy model, evolutionary model, molecular mechanism model and many more), synthetic bacterial communication, bacterial ion-channels, bacterial nanowires and electrical communication. In particular, we highlight bacterial collective behavior with classical and quantum mechanical approaches (including quantum information). Moreover, we shed a new light to introduce the concept of quantum synthetic biology and possible cellular quantum Turing test.
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Affiliation(s)
- Sarangam Majumdar
- Dipartimento di Ingegneria Scienze Informatiche e Matematica, Università degli Studi di L’ Aquila, Via Vetoio – Loc. Coppito, 67010 L’ Aquila, Italy
| | - Sukla Pal
- Theoretical Physics Division, Physical Research Laboratory, Navrangpura, Ahmedabad, Gujarat 380009 India
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Ghasemi M, Hense BA, Eberl HJ, Kuttler C. Simulation-Based Exploration of Quorum Sensing Triggered Resistance of Biofilms to Antibiotics. Bull Math Biol 2018; 80:1736-1775. [PMID: 29691717 DOI: 10.1007/s11538-018-0433-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 04/13/2018] [Indexed: 11/28/2022]
Abstract
We present a mathematical model of biofilm response to antibiotics, controlled by a quorum sensing system that confers increased resistance. The model is a highly nonlinear system of partial differential equations that we investigate in computer simulations. Our results suggest that an adaptive, quorum sensing-controlled, mechanism to switch between modes of fast growth with little protection and protective modes of slow growth may confer benefits to biofilm populations. It enhances the formation of micro-niches in the inner regions of the biofilm in which bacteria are not easily reached by antibiotics. Whereas quorum sensing inhibitors can delay the onset of increased resistance, their advantage is lost after up-regulation. This emphasizes the importance of timing for treatment of biofilms with antibiotics.
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Affiliation(s)
- Maryam Ghasemi
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, N1G2W1, Canada.
| | - Burkhard A Hense
- Institute for Computational Biology, Helmholtz Zentrum München, 85764, Oberschleissheim, Germany
| | - Hermann J Eberl
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Christina Kuttler
- Zentrum Mathematik, TU München, Boltzmannstr. 3, 85748, Garching, Germany
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Jayathilake PG, Jana S, Rushton S, Swailes D, Bridgens B, Curtis T, Chen J. Extracellular Polymeric Substance Production and Aggregated Bacteria Colonization Influence the Competition of Microbes in Biofilms. Front Microbiol 2017; 8:1865. [PMID: 29021783 PMCID: PMC5623813 DOI: 10.3389/fmicb.2017.01865] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 09/12/2017] [Indexed: 11/25/2022] Open
Abstract
The production of extracellular polymeric substance (EPS) is important for the survival of biofilms. However, EPS production is costly for bacteria and the bacterial strains that produce EPS (EPS+) grow in the same environment as non-producers (EPS-) leading to competition between these strains for nutrients and space. The outcome of this competition is likely to be dependent on factors such as initial attachment, EPS production rate, ambient nutrient levels and quorum sensing. We use an Individual-based Model (IbM) to study the competition between EPS+ and EPS- strains by varying the nature of initial colonizers which can either be in the form of single cells or multicellular aggregates. The microbes with EPS+ characteristics obtain a competitive advantage if they initially colonize the surface as smaller aggregates and are widely spread-out between the cells of EPS-, when both are deposited on the substratum. Furthermore, the results show that quorum sensing-regulated EPS production may significantly reduce the fitness of EPS producers when they initially deposit as aggregates. The results provide insights into how the distribution of bacterial aggregates during initial colonization could be a deciding factor in the competition among different strains in biofilms.
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Affiliation(s)
| | - Saikat Jana
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Steve Rushton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David Swailes
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ben Bridgens
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tom Curtis
- Centre for Synthetic Biology and the Bioeconomy, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jinju Chen
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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11
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Continuum and discrete approach in modeling biofilm development and structure: a review. J Math Biol 2017; 76:945-1003. [PMID: 28741178 DOI: 10.1007/s00285-017-1165-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 07/04/2017] [Indexed: 12/21/2022]
Abstract
The scientific community has recognized that almost 99% of the microbial life on earth is represented by biofilms. Considering the impacts of their sessile lifestyle on both natural and human activities, extensive experimental activity has been carried out to understand how biofilms grow and interact with the environment. Many mathematical models have also been developed to simulate and elucidate the main processes characterizing the biofilm growth. Two main mathematical approaches for biomass representation can be distinguished: continuum and discrete. This review is aimed at exploring the main characteristics of each approach. Continuum models can simulate the biofilm processes in a quantitative and deterministic way. However, they require a multidimensional formulation to take into account the biofilm spatial heterogeneity, which makes the models quite complicated, requiring significant computational effort. Discrete models are more recent and can represent the typical multidimensional structural heterogeneity of biofilm reflecting the experimental expectations, but they generate computational results including elements of randomness and introduce stochastic effects into the solutions.
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