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Gourari-Bouzouina K, Boucherit-Otmani Z, Halla N, Seghir A, Baba Ahmed-Kazi Tani ZZ, Boucherit K. Exploring the dynamics of mixed-species biofilms involving Candida spp. and bacteria in cystic fibrosis. Arch Microbiol 2024; 206:255. [PMID: 38734793 DOI: 10.1007/s00203-024-03967-9] [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] [Received: 01/30/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
Cystic fibrosis (CF) is an inherited disease that results from mutations in the gene responsible for the cystic fibrosis transmembrane conductance regulator (CFTR). The airways become clogged with thick, viscous mucus that traps microbes in respiratory tracts, facilitating colonization, inflammation and infection. CF is recognized as a biofilm-associated disease, it is commonly polymicrobial and can develop in biofilms. This review discusses Candida spp. and both Gram-positive and Gram-negative bacterial biofilms that affect the airways and cause pulmonary infections in the CF context, with a particular focus on mixed-species biofilms. In addition, the review explores the intricate interactions between fungal and bacterial species within these biofilms and elucidates the underlying molecular mechanisms that govern their dynamics. Moreover, the review addresses the multifaceted issue of antimicrobial resistance in the context of CF-associated biofilms. By synthesizing current knowledge and research findings, this review aims to provide insights into the pathogenesis of CF-related infections and identify potential therapeutic approaches to manage and combat these complex biofilm-mediated infections.
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Affiliation(s)
- Karima Gourari-Bouzouina
- Antibiotics Antifungal Laboratory, Physical Chemistry, Synthesis and Biological Activity (LapSab), Department of Biology, Faculty of Sciences, University of Tlemcen, BP 119, 13000, Tlemcen, Algeria.
| | - Zahia Boucherit-Otmani
- Antibiotics Antifungal Laboratory, Physical Chemistry, Synthesis and Biological Activity (LapSab), Department of Biology, Faculty of Sciences, University of Tlemcen, BP 119, 13000, Tlemcen, Algeria
| | - Noureddine Halla
- Laboratory of Biotoxicology, Pharmacognosy and Biological Recovery of Plants, Department of Biology, Faculty of Sciences, University of Moulay-Tahar, 20000, Saida, Algeria
| | - Abdelfettah Seghir
- Antibiotics Antifungal Laboratory, Physical Chemistry, Synthesis and Biological Activity (LapSab), Department of Biology, Faculty of Sciences, University of Tlemcen, BP 119, 13000, Tlemcen, Algeria
| | - Zahira Zakia Baba Ahmed-Kazi Tani
- Antibiotics Antifungal Laboratory, Physical Chemistry, Synthesis and Biological Activity (LapSab), Department of Biology, Faculty of Sciences, University of Tlemcen, BP 119, 13000, Tlemcen, Algeria
| | - Kebir Boucherit
- Antibiotics Antifungal Laboratory, Physical Chemistry, Synthesis and Biological Activity (LapSab), Department of Biology, Faculty of Sciences, University of Tlemcen, BP 119, 13000, Tlemcen, Algeria
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O’Toole GA. We have a community problem. J Bacteriol 2024; 206:e0007324. [PMID: 38529952 PMCID: PMC11025320 DOI: 10.1128/jb.00073-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Affiliation(s)
- George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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3
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Robertson SN, Romero M, Fenn S, Kohler Riedi PL, Cámara M. Development, characterization, and evaluation of a simple polymicrobial colony biofilm model for testing of antimicrobial wound dressings. J Appl Microbiol 2024; 135:lxae042. [PMID: 38366933 DOI: 10.1093/jambio/lxae042] [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: 08/15/2023] [Revised: 01/12/2024] [Accepted: 02/15/2024] [Indexed: 02/19/2024]
Abstract
Chronic wound infections are generally of polymicrobial nature with aerobic and anaerobic bacteria, as well as fungi frequently observed in them. Wound treatment involves a series of steps, including debridement of the wound, flushing, and often the use of multiple wound dressings many of which are antimicrobial. Yet, many wound dressings are tested versus single species of planktonic microbes, which fails to mirror the real-life presence of biofilms. AIMS Simple biofilm models are the first step to testing of any antimicrobial and wound dressing; therefore, the aim of this study was to develop and validate a simple polymicrobial colony biofilm wound model comprised of Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans on RPMI-1640 agar. The model was then used to evaluate the topical disinfectant chlorohexidine and four commercially available wound dressings using the polymicrobial model. The model used was as a starting point to mimic debridement in clinical care of wounds and the effectiveness of wound dressings evaluated afterwards. METHODS AND RESULTS Planktonic assessment using AATCC100-2004 demonstrated that all antimicrobial wound dressings reduced the planktonic microbial burden below the limit of detection; however, when challenged with polymicrobial colony biofilms, silver wound dressings showed limited effectiveness (1-2 log CFU reductions). In contrast, a single iodine releasing wound dressing showed potent antibiofilm activity reducing all species CFUs below the limit of detection (>6-10 log) depending on the species. A disrupted biofilm model challenge was performed to represent the debridement of a wound and wound silver-based wound dressings were found to be marginally more effective than in whole colony biofilm challenges while the iodine containing wound dressing reduced microbial recovery below the limit of detection. CONCLUSIONS In this model, silver dressings were ineffective versus the whole colony biofilms but showed some recovery of activity versus the disrupted colony biofilm. The iodine wound dressing reduced the viability of all species below the level of detection. This suggests that mode of action of wound dressing should be considered for the type of biofilm challenge as should the clinical use, e.g. debridement.
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Affiliation(s)
- Shaun N Robertson
- National Biofilms Innovation Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, NG7 2RD Nottingham, United Kingdom
| | - Manuel Romero
- National Biofilms Innovation Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, NG7 2RD Nottingham, United Kingdom
- Department of Microbiology and Parasitology, Faculty of Biology-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
- Aquatic One Health Research Center (ARCUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Samuel Fenn
- National Biofilms Innovation Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, NG7 2RD Nottingham, United Kingdom
- Schools of Microbiology and Medicine, University College Cork, and APC Microbiome Ireland, Cork T12 TP07, Ireland
| | | | - Miguel Cámara
- National Biofilms Innovation Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, NG7 2RD Nottingham, United Kingdom
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Nazeer RR, Wang M, Welch M. More than just a gel: the extracellular matrixome of Pseudomonas aeruginosa. Front Mol Biosci 2023; 10:1307857. [PMID: 38028553 PMCID: PMC10679415 DOI: 10.3389/fmolb.2023.1307857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Armed with an arsenal of protein secretion systems, antibiotic efflux pumps, and the occasional proclivity for explosive self-destruction, Pseudomonas aeruginosa has become a model for the study of bacterial pathogenesis and biofilm formation. There is accruing evidence to suggest that the biofilm matrix-the bioglue that holds the structure together-acts not only in a structural capacity, but is also a molecular "net" whose function is to capture and retain certain secreted products (including proteins and small molecules). In this perspective, we argue that the biofilm matrixome is a distinct extracellular compartment, and one that is differentiated from the bulk secretome. Some of the points we raise are deliberately speculative, but are becoming increasingly accessible to experimental investigation.
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Affiliation(s)
| | | | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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On YY, Figueroa W, Fan C, Ho PM, Bényei ÉB, Weimann A, Ruis C, Floto AR, Welch M. Impact of transient acquired hypermutability on the inter- and intra-species competitiveness of Pseudomonas aeruginosa. THE ISME JOURNAL 2023; 17:1931-1939. [PMID: 37666975 PMCID: PMC10579334 DOI: 10.1038/s41396-023-01503-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/06/2023]
Abstract
Once acquired, hypermutation is unrelenting, and in the long-term, leads to impaired fitness due to its cumulative impact on the genome. This raises the question of why hypermutators arise so frequently in microbial ecosystems. In this work, we explore this problem by examining how the transient acquisition of hypermutability affects inter- and intra-species competitiveness, and the response to environmental insults such as antibiotic challenge. We do this by engineering Pseudomonas aeruginosa to allow the expression of an important mismatch repair gene, mutS, to be experimentally controlled over a wide dynamic range. We show that high levels of mutS expression induce genomic stasis (hypomutation), whereas lower levels of induction lead to progressively higher rates of mutation. Whole-genome sequence analyses confirmed that the mutational spectrum of the inducible hypermutator is similar to the distinctive profile associated with mutS mutants obtained from the airways of people with cystic fibrosis (CF). The acquisition of hypermutability conferred a distinct temporal fitness advantage over the wild-type P. aeruginosa progenitor strain, in both the presence and the absence of an antibiotic selection pressure. However, over a similar time-scale, acquisition of hypermutability had little impact on the population dynamics of P. aeruginosa when grown in the presence of a competing species (Staphylococcus aureus). These data indicate that in the short term, acquired hypermutability primarily confers a competitive intra-species fitness advantage.
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Affiliation(s)
- Yue Yuan On
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Wendy Figueroa
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Catherine Fan
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
- Currently based at Epoch Biodesign, Oxford, UK
| | - Pok-Man Ho
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | | | - Aaron Weimann
- Heart Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Christopher Ruis
- Heart Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andres R Floto
- Heart Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
- Cambridge University Hospitals Trust, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
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Ho PM, Nazeer RR, Welch M. Therapeutic interventions alter ecological interactions among cystic fibrosis airway microbiota. Front Microbiol 2023; 14:1178131. [PMID: 37323900 PMCID: PMC10265647 DOI: 10.3389/fmicb.2023.1178131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/28/2023] [Indexed: 06/17/2023] Open
Abstract
The airways of people with cystic fibrosis (CF) often harbor a diverse microbiota and in recent years, much effort has been invested in cataloguing these. In spite of providing a wealth of insight, this cataloguing tells us little about how the organisms interact with one another in the CF airways. However, such relationships can be inferred using the theoretical framework of the Lotka-Volterra (LV) model. In the current work, we use a generalized Lotka-Volterra model to interrogate the nationwide data collected and curated by the UK CF Registry. This longitudinal dataset (covering the period 2008-2020) contains annual depositions that record the presence/absence of microbial taxa in each patient, their medication, and their CF genotype. Specifically, we wanted to identify trends in ecological relationships between the CF microbiota at a nationwide level, and whether these are potentially affected by medication. Our results show that some medications have a distinct influence on the microbial interactome, especially those that potentially influence the "gut-lung axis" or mucus viscosity. In particular, we found that patients treated with a combination of antimicrobial agents (targeting the airway microbiota), digestive enzymes (assisting in the assimilation of dietary fats and carbohydrates), and DNase (to reduce mucus viscosity) displayed a distinctly different airway interactome compared with patients treated separately with these medications.
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Affiliation(s)
| | | | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Barton TE, Frost F, Fothergill JL, Neill DR. Challenges and opportunities in the development of novel antimicrobial therapeutics for cystic fibrosis. J Med Microbiol 2022; 71. [PMID: 36748497 DOI: 10.1099/jmm.0.001643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Chronic respiratory infection is the primary driver of mortality in individuals with cystic fibrosis (CF). Existing drug screening models utilised in preclinical antimicrobial development are unable to mimic the complex CF respiratory environment. Consequently, antimicrobials showing promising activity in preclinical models often fail to translate through to clinical efficacy in people with CF. Model systems used in CF anti-infective drug discovery and development range from antimicrobial susceptibility testing in nutrient broth, through to 2D and 3D in vitro tissue culture systems and in vivo models. No single model fully recapitulates every key aspect of the CF lung. To improve the outcomes of people with CF (PwCF) it is necessary to develop a set of preclinical models that collectively recapitulate the CF respiratory environment to a high degree of accuracy. Models must be validated for their ability to mimic aspects of the CF lung and associated lung infection, through evaluation of biomarkers that can also be assessed following treatment in the clinic. This will give preclinical models greater predictive power for identification of antimicrobials with clinical efficacy. The landscape of CF is changing, with the advent of modulator therapies that correct the function of the CFTR protein, while antivirulence drugs and phage therapy are emerging alternative treatments to chronic infection. This review discusses the challenges faced in current antimicrobial development pipelines, including the advantages and disadvantages of current preclinical models and the impact of emerging treatments.
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Affiliation(s)
- Thomas E Barton
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, L69 7BE, UK
| | - Frederick Frost
- Adult Cystic Fibrosis Centre, Liverpool Heart & Chest Hospital NHS Foundation Trust, Liverpool, UK.,Liverpool Centre for Cardiovascular Sciences, University of Liverpool, Liverpool, UK
| | - Joanne L Fothergill
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, L69 7BE, UK
| | - Daniel R Neill
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, L69 7BE, UK
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O'Brien TJ, Figueroa W, Welch M. Decreased efficacy of antimicrobial agents in a polymicrobial environment. THE ISME JOURNAL 2022; 16:1694-1704. [PMID: 35304578 PMCID: PMC9213441 DOI: 10.1038/s41396-022-01218-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 12/20/2022]
Abstract
The airways of people with cystic fibrosis (CF) often harbour diverse polymicrobial communities. These airway infections can be impossible to resolve through antibiotic intervention, even though isolates of the individual species present are susceptible to the treatment when tested in vitro. In this work, we investigate how polymicrobial cultures comprised of key CF-associated pathogens respond to challenge with species-specific antimicrobial agents; colistin (targets Pseudomonas aeruginosa), fusidic acid (targets Staphylococcus aureus), and fluconazole (targets Candida albicans). We found that growth in a polymicrobial environment protects the target microorganism (sometimes by several orders of magnitude) from the effect(s) of the antimicrobial agent. This decreased antimicrobial efficacy was found to have both non-heritable (physiological) and heritable (genetic) components. Whole-genome sequencing of the colistin-resistant P. aeruginosa isolates revealed single nucleotide polymorphisms and indels in genes encoding lipopolysaccharide (LPS) biosynthesis and/or pilus biogenesis, indicating that a previously undescribed colistin resistance mechanism was in operation. This was subsequently confirmed through further genetic analyses. Our findings indicate that the polymicrobial nature of the CF airways is likely to have a significant impact on the clinical response to antimicrobial therapy.
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Affiliation(s)
| | - Wendy Figueroa
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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