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Uberoi A, McCready-Vangi A, Grice EA. The wound microbiota: microbial mechanisms of impaired wound healing and infection. Nat Rev Microbiol 2024; 22:507-521. [PMID: 38575708 DOI: 10.1038/s41579-024-01035-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/06/2024]
Abstract
The skin barrier protects the human body from invasion by exogenous and pathogenic microorganisms. A breach in this barrier exposes the underlying tissue to microbial contamination, which can lead to infection, delayed healing, and further loss of tissue and organ integrity. Delayed wound healing and chronic wounds are associated with comorbidities, including diabetes, advanced age, immunosuppression and autoimmune disease. The wound microbiota can influence each stage of the multi-factorial repair process and influence the likelihood of an infection. Pathogens that commonly infect wounds, such as Staphylococcus aureus and Pseudomonas aeruginosa, express specialized virulence factors that facilitate adherence and invasion. Biofilm formation and other polymicrobial interactions contribute to host immunity evasion and resistance to antimicrobial therapies. Anaerobic organisms, fungal and viral pathogens, and emerging drug-resistant microorganisms present unique challenges for diagnosis and therapy. In this Review, we explore the current understanding of how microorganisms present in wounds impact the process of skin repair and lead to infection through their actions on the host and the other microbial wound inhabitants.
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Affiliation(s)
- Aayushi Uberoi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amelia McCready-Vangi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth A Grice
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Bényei ÉB, Nazeer RR, Askenasy I, Mancini L, Ho PM, Sivarajan GAC, Swain JEV, Welch M. The past, present and future of polymicrobial infection research: Modelling, eavesdropping, terraforming and other stories. Adv Microb Physiol 2024; 85:259-323. [PMID: 39059822 DOI: 10.1016/bs.ampbs.2024.04.002] [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: 07/28/2024]
Abstract
Over the last two centuries, great advances have been made in microbiology as a discipline. Much of this progress has come about as a consequence of studying the growth and physiology of individual microbial species in well-defined laboratory media; so-called "axenic growth". However, in the real world, microbes rarely live in such "splendid isolation" (to paraphrase Foster) and more often-than-not, share the niche with a plethora of co-habitants. The resulting interactions between species (and even between kingdoms) are only very poorly understood, both on a theoretical and experimental level. Nevertheless, the last few years have seen significant progress, and in this review, we assess the importance of polymicrobial infections, and show how improved experimental traction is advancing our understanding of these. A particular focus is on developments that are allowing us to capture the key features of polymicrobial infection scenarios, especially as those associated with the human airways (both healthy and diseased).
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Affiliation(s)
| | | | - Isabel Askenasy
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Leonardo Mancini
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Pok-Man Ho
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | | | - Jemima E V Swain
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom.
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Mahout M, Carlson RP, Simon L, Peres S. Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections. NPJ Syst Biol Appl 2024; 10:34. [PMID: 38565568 PMCID: PMC10987626 DOI: 10.1038/s41540-024-00360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Minimal Cut Sets (MCSs) identify sets of reactions which, when removed from a metabolic network, disable certain cellular functions. The traditional search for MCSs within genome-scale metabolic models (GSMMs) targets cellular growth, identifies reaction sets resulting in a lethal phenotype if disrupted, and retrieves a list of corresponding gene, mRNA, or enzyme targets. Using the dual link between MCSs and Elementary Flux Modes (EFMs), our logic programming-based tool aspefm was able to compute MCSs of any size from GSMMs in acceptable run times. The tool demonstrated better performance when computing large-sized MCSs than the mixed-integer linear programming methods. We applied the new MCSs methodology to a medically-relevant consortium model of two cross-feeding bacteria, Staphylococcus aureus and Pseudomonas aeruginosa. aspefm constraints were used to bias the computation of MCSs toward exchanged metabolites that could complement lethal phenotypes in individual species. We found that interspecies metabolite exchanges could play an essential role in rescuing single-species growth, for instance inosine could complement lethal reaction knock-outs in the purine synthesis, glycolysis, and pentose phosphate pathways of both bacteria. Finally, MCSs were used to derive a list of promising enzyme targets for consortium-level therapeutic applications that cannot be circumvented via interspecies metabolite exchange.
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Affiliation(s)
- Maxime Mahout
- Université Paris-Saclay, CNRS, Laboratoire Interdisciplinaire des Sciences du Numérique, 91405, Orsay, France
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Laurent Simon
- Bordeaux-INP, Université Bordeaux, LaBRI, 33405, Talence Cedex, France
| | - Sabine Peres
- UMR CNRS 5558, Laboratoire de Biométrie et de Biologie Évolutive, Université Claude Bernard Lyon 1, 69100, Villeurbanne, France.
- INRIA Lyon Centre, 69100, Villeurbanne, France.
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Ji C, Guo W, Amir H. Experience of diagnosis and treatment of hard-to-heal wounds infected with Acinetobacter baumannii: a case study. J Wound Care 2024; 33:278-285. [PMID: 38573906 DOI: 10.12968/jowc.2024.33.4.278] [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: 04/06/2024]
Abstract
OBJECTIVE To explore the efficacy of 0.01% hypochlorous acid (HOCl) in the treatment of hard-to-heal wounds infected by multidrug-resistant Acinetobacter baumannii. METHOD We report a case of hard-to-heal wounds on a patient's forearms that were infected by Acinetobacter baumannii. The wounds were treated with 0.01% HOCl. We reviewed the relevant literature and discussed the definition, epidemiology and pathogenesis of hard-to-heal wounds infected by Acinetobacter baumannii. We also explored the safety and efficacy of 0.01% HOCl for the treatment of hard-to-heal wounds infected with Acinetobacter baumannii. RESULTS After 3-4 weeks of treatment with 0.01% HOCl, the pain and pruritus of the wounds was gradually alleviated, the infection was controlled and the granulation tissue was fresh. The ulcers also shrank and the nutritional condition of the patient improved. In the fifth week, the skin of the patient's right thigh was grafted to repair the wounds, which then healed within 18 days. During the three years of follow-up, the patient had no relapse. CONCLUSION In our case, the 0.01% HOCl seemed to effectively inactivate the bacterial biological biofilm. This helped to promote wound healing, and was non-toxic to the tissues. We consider low-concentration HOCl to be safe and effective for the treatment of hard-to-heal wounds infected with Acinetobacter baumannii.
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Affiliation(s)
- Chaochao Ji
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, China
| | - Wenyong Guo
- Institute of Basic Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hammad Amir
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, China
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, China
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Durand BARN, Pouget C, Magnan C, Molle V, Lavigne JP, Dunyach-Remy C. Bacterial Interactions in the Context of Chronic Wound Biofilm: A Review. Microorganisms 2022; 10:microorganisms10081500. [PMID: 35893558 PMCID: PMC9332326 DOI: 10.3390/microorganisms10081500] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 02/04/2023] Open
Abstract
Chronic wounds, defined by their resistance to care after four weeks, are a major concern, affecting millions of patients every year. They can be divided into three types of lesions: diabetic foot ulcers (DFU), pressure ulcers (PU), and venous/arterial ulcers. Once established, the classical treatment for chronic wounds includes tissue debridement at regular intervals to decrease biofilm mass constituted by microorganisms physiologically colonizing the wound. This particular niche hosts a dynamic bacterial population constituting the bed of interaction between the various microorganisms. The temporal reshuffle of biofilm relies on an organized architecture. Microbial community turnover is mainly associated with debridement (allowing transitioning from one major representant to another), but also with microbial competition and/or collaboration within wounds. This complex network of species and interactions has the potential, through diversity in antagonist and/or synergistic crosstalk, to accelerate, delay, or worsen wound healing. Understanding these interactions between microorganisms encountered in this clinical situation is essential to improve the management of chronic wounds.
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Affiliation(s)
- Benjamin A. R. N. Durand
- Bacterial Virulence and Chronic Infections, UMR 1047, Université Montpellier, INSERM, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France; (B.A.R.N.D.); (C.P.); (C.M.); (J.-P.L.)
| | - Cassandra Pouget
- Bacterial Virulence and Chronic Infections, UMR 1047, Université Montpellier, INSERM, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France; (B.A.R.N.D.); (C.P.); (C.M.); (J.-P.L.)
| | - Chloé Magnan
- Bacterial Virulence and Chronic Infections, UMR 1047, Université Montpellier, INSERM, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France; (B.A.R.N.D.); (C.P.); (C.M.); (J.-P.L.)
| | - Virginie Molle
- Laboratory of Pathogen Host Interactions, Université de Montpellier, CNRS, UMR 5235, 34000 Montpellier, France;
| | - Jean-Philippe Lavigne
- Bacterial Virulence and Chronic Infections, UMR 1047, Université Montpellier, INSERM, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France; (B.A.R.N.D.); (C.P.); (C.M.); (J.-P.L.)
| | - Catherine Dunyach-Remy
- Bacterial Virulence and Chronic Infections, UMR 1047, Université Montpellier, INSERM, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France; (B.A.R.N.D.); (C.P.); (C.M.); (J.-P.L.)
- Correspondence: ; Tel.: +33-466-683-202
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Schilrreff P, Alexiev U. Chronic Inflammation in Non-Healing Skin Wounds and Promising Natural Bioactive Compounds Treatment. Int J Mol Sci 2022; 23:ijms23094928. [PMID: 35563319 PMCID: PMC9104327 DOI: 10.3390/ijms23094928] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 12/14/2022] Open
Abstract
Chronic inflammation is one of the hallmarks of chronic wounds and is tightly coupled to immune regulation. The dysregulation of the immune system leads to continuing inflammation and impaired wound healing and, subsequently, to chronic skin wounds. In this review, we discuss the role of the immune system, the involvement of inflammatory mediators and reactive oxygen species, the complication of bacterial infections in chronic wound healing, and the still-underexplored potential of natural bioactive compounds in wound treatment. We focus on natural compounds with antioxidant, anti-inflammatory, and antibacterial activities and their mechanisms of action, as well as on recent wound treatments and therapeutic advancements capitalizing on nanotechnology or new biomaterial platforms.
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The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes. Microbiol Spectr 2022; 10:e0277721. [PMID: 35435739 PMCID: PMC9248897 DOI: 10.1128/spectrum.02777-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Two leading impediments to chronic wound healing are polymicrobial infection and biofilm formation. Recent studies have characterized the bacterial fraction of these microbiomes and have begun to elucidate compositional correlations to healing outcomes. However, the factors that drive compositional shifts are still being uncovered. The virome may play an important role in shaping bacterial community structure and function. Previous work on the skin virome determined that it was dominated by bacteriophages, viruses that infect bacteria. To characterize the virome, we enrolled 20 chronic wound patients presenting at an outpatient wound care clinic in a microbiome survey, collecting swab samples from healthy skin and chronic wounds (diabetic, venous, arterial, or pressure) before and after a single, sharp debridement procedure. We investigated the virome using a virus-like particle enrichment procedure, shotgun metagenomic sequencing, and a k-mer-based, reference-dependent taxonomic classification method. Taxonomic composition, diversity, and associations with covariates are presented. We find that the wound virome is highly diverse, with many phages targeting known pathogens, and may influence bacterial community composition and functionality in ways that impact healing outcomes. IMPORTANCE Chronic wounds are an increasing medical burden. These wounds are known to be rich in microbial content, including both bacteria and bacterial viruses (phages). The viruses may play an important role in shaping bacterial community structure and function. We analyzed the virome and bacterial composition of 20 patients with chronic wounds. The viruses found in wounds are highly diverse compared to normal skin, unlike the bacterial composition, where diversity is decreased. These data represent an initial look at this relatively understudied component of the chronic wound microbiome and may help inform future phage-based interventions.
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Kim M, Sung J, Chia N. Resource-allocation constraint governs structure and function of microbial communities in metabolic modeling. Metab Eng 2022; 70:12-22. [PMID: 34990848 DOI: 10.1016/j.ymben.2021.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/01/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
Abstract
Predictive modeling tools for assessing microbial communities are important for realizing transformative capabilities of microbiomes in agriculture, ecology, and medicine. Constraint-based community-scale metabolic modeling is unique in its potential for making mechanistic predictions regarding both the structure and function of microbial communities. However, accessing this potential requires an understanding of key physicochemical constraints, which are typically considered on a per-species basis. What is needed is a means of incorporating global constraints relevant to microbial ecology into community models. Resource-allocation constraint, which describes how limited resources should be distributed to different cellular processes, sets limits on the efficiency of metabolic and ecological processes. In this study, we investigate the implications of resource-allocation constraints in community-scale metabolic modeling through a simple mechanism-agnostic implementation of resource-allocation constraints directly at the flux level. By systematically performing single-, two-, and multi-species growth simulations, we show that resource-allocation constraints are indispensable for predicting the structure and function of microbial communities. Our findings call for a scalable workflow for implementing a mechanistic version of resource-allocation constraints to ultimately harness the full potential of community-scale metabolic modeling tools.
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Affiliation(s)
- Minsuk Kim
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA; Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jaeyun Sung
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA; Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, MN, 55905, USA; Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA; Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, MN, 55905, USA.
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Nogales J, Garmendia J. Bacterial metabolism and pathogenesis intimate intertwining: time for metabolic modelling to come into action. Microb Biotechnol 2022; 15:95-102. [PMID: 34672429 PMCID: PMC8719832 DOI: 10.1111/1751-7915.13942] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/25/2021] [Indexed: 11/26/2022] Open
Abstract
We take a snapshot of the recent understanding of bacterial metabolism and the bacterial-host metabolic interplay during infection, and highlight key outcomes and challenges for the practical implementation of bacterial metabolic modelling computational tools in the pathogenesis field.
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Affiliation(s)
- Juan Nogales
- Department of Systems BiologyCentro Nacional de BiotecnologíaCSICMadridSpain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
| | - Junkal Garmendia
- Instituto de AgrobiotecnologíaConsejo Superior de Investigaciones Científicas (IdAB‐CSIC)‐Gobierno de NavarraMutilvaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES)MadridSpain
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Verbanic S, Shen Y, Lee J, Deacon JM, Chen IA. Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds. NPJ Biofilms Microbiomes 2020; 6:21. [PMID: 32358500 PMCID: PMC7195478 DOI: 10.1038/s41522-020-0130-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/24/2020] [Indexed: 02/06/2023] Open
Abstract
Chronic wounds represent a large and growing disease burden. Infection and biofilm formation are two of the leading impediments of wound healing, suggesting an important role for the microbiome of these wounds. Debridement is a common and effective treatment for chronic wounds. We analyzed the bacterial content of the wound surface from 20 outpatients with chronic wounds before and immediately after debridement, as well as healthy skin. Given the large variation observed among different wounds, we introduce a Bayesian statistical method that models patient-to-patient variability and identify several genera that were significantly enriched in wounds vs. healthy skin. We found no difference between the microbiome of the original wound surface and that exposed by a single episode of sharp debridement, suggesting that this debridement did not directly alter the wound microbiome. However, we found that aerobes and especially facultative anaerobes were significantly associated with wounds that did not heal within 6 months. The facultative anaerobic genus Enterobacter was significantly associated with lack of healing. The results suggest that an abundance of facultative anaerobes is a negative prognostic factor in the chronic wound microbiome, possibly due to the increased robustness of such communities to different metabolic environments.
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Affiliation(s)
- Samuel Verbanic
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, USA
| | - Yuning Shen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Juhee Lee
- Department of Statistics, University of California, Santa Cruz, CA, USA
| | - John M Deacon
- Goleta Valley Cottage Hospital, Ridley-Tree Center for Wound Management, Santa Barbara, CA, USA
| | - Irene A Chen
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, USA. .,Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA. .,Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA.
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