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Fisher CR, Masters TL, Johnson S, Greenwood-Quaintance KE, Chia N, Abdel MP, Patel R. Comparative transcriptomic analysis of Staphylococcus epidermidis associated with periprosthetic joint infection under in vivo and in vitro conditions. Int J Med Microbiol 2024; 315:151620. [PMID: 38579524 PMCID: PMC11214590 DOI: 10.1016/j.ijmm.2024.151620] [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: 08/22/2023] [Revised: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 04/07/2024] Open
Abstract
Staphylococcus epidermidis is part of the commensal microbiota of the skin and mucous membranes, though it can also act as a pathogen in certain scenarios, causing a range of infections, including periprosthetic joint infection (PJI). Transcriptomic profiling may provide insights into mechanisms by which S. epidermidis adapts while in a pathogenic compared to a commensal state. Here, a total RNA-sequencing approach was used to profile and compare the transcriptomes of 19 paired PJI-associated S. epidermidis samples from an in vivo clinical source and grown in in vitro laboratory culture. Genomic comparison of PJI-associated and publicly available commensal-state isolates were also compared. Of the 1919 total transcripts found, 145 were from differentially expressed genes (DEGs) when comparing in vivo or in vitro samples. Forty-two transcripts were upregulated and 103 downregulated in in vivo samples. Of note, metal sequestration-associated genes, specifically those related to staphylopine activity (cntA, cntK, cntL, and cntM), were upregulated in a subset of clinical in vivo compared to laboratory grown in vitro samples. About 70% of the total transcripts and almost 50% of the DEGs identified have not yet been annotated. There were no significant genomic differences between known commensal and PJI-associated S. epidermidis isolates, suggesting that differential genomics may not play a role in S. epidermidis pathogenicity. In conclusion, this study provides insights into phenotypic alterations employed by S epidermidis to adapt to infective and non-infected microenvironments, potentially informing future therapeutic targets for related infections.
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Affiliation(s)
- Cody R Fisher
- Mayo Clinic Graduate School of Biomedical Sciences, Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA; Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Thao L Masters
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kerryl E Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.
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Lopes N, Pereira RB, Correia A, Vilanova M, Cerca N, França A. Deletion of codY impairs Staphylococcus epidermidis biofilm formation, generation of viable but non-culturable cells and stimulates cytokine production in human macrophages. J Med Microbiol 2024; 73. [PMID: 38743043 DOI: 10.1099/jmm.0.001837] [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: 05/16/2024] Open
Abstract
Introduction. Staphylococcus epidermidis biofilms are one of the major causes of bloodstream infections related to the use of medical devices. The diagnosis of these infections is challenging, delaying their treatment and resulting in increased morbidity and mortality rates. As such, it is urgent to characterize the mechanisms employed by this bacterium to endure antibiotic treatments and the response of the host immune system, to develop more effective therapeutic strategies. In several bacterial species, the gene codY was shown to encode a protein that regulates the expression of genes involved in biofilm formation and immune evasion. Additionally, in a previous study, our group generated evidence indicating that codY is involved in the emergence of viable but non-culturable (VBNC) cells in S. epidermidis.Gap statement/Hypothesis. As such, we hypothesized that the gene codY has have an important role in this bacterium virulence.Aim. This study aimed to assess, for the first time, the impact of the deletion of the gene codY in S. epidermidis virulence, namely, in antibiotic susceptibility, biofilm formation, VBNC state emergence and in vitro host immune system response.Methodology. Using an allelic replacement strategy, we constructed and then characterized an S. epidermidis strain lacking codY, in regards to biofilm and VBNC cell formation, susceptibility to antibiotics as well as their role in the interaction with human blood and plasma. Additionally, we investigate whether the codY gene can impact the activation of innate immune cells by evaluating the production of both pro- and anti-inflammatory cytokines by THP-1 macrophages.Results. We demonstrated that the deletion of the gene codY resulted in biofilms with less c.f.u. counts and fewer VBNC cells. Furthermore, we show that although WT and mutant cells were similarly internalized in vitro by human macrophages, a stronger cytokine response was elicited by the mutant in a toll-like receptor 4-dependent manner.Conclusion. Our results indicate that codY contributes to S. epidermidis virulence, which in turn may have an impact on our ability to manage the biofilm-associated infections caused by this bacterium.
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Affiliation(s)
- Nathalie Lopes
- Laboratório de Investigação em Biofilmes Rosário Oliveira (LIBRO), Centro de Engenharia Biológica (CEB), Universidade do Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Renato B Pereira
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Alexandra Correia
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Manuel Vilanova
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Nuno Cerca
- Laboratório de Investigação em Biofilmes Rosário Oliveira (LIBRO), Centro de Engenharia Biológica (CEB), Universidade do Minho, Campus de Gualtar, Braga, 4710-057, Portugal
- LABBELS-Laboratório Associado, Braga, Guimarães, Portugal
| | - Angela França
- Laboratório de Investigação em Biofilmes Rosário Oliveira (LIBRO), Centro de Engenharia Biológica (CEB), Universidade do Minho, Campus de Gualtar, Braga, 4710-057, Portugal
- LABBELS-Laboratório Associado, Braga, Guimarães, Portugal
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França A, Cerca N. Gene Expression Quantification from Pathogenic Bacterial Biofilms by Quantitative PCR. Methods Mol Biol 2023; 2967:133-149. [PMID: 37608108 DOI: 10.1007/978-1-0716-3358-8_11] [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: 08/24/2023]
Abstract
Quantitative PCR (qPCR) is one of the most used techniques to quantify gene expression in bacterial biofilms due to its easiness, sensitivity, and robustness. However, several practical aspects need to be considered to obtain accurate and reliable results. Here, we describe a detailed and optimized protocol to quantify mRNA transcripts from bacterial biofilms using qPCR, including pieces of advice to improve RNA quality, which ultimately increases the accuracy, consistency, and relevance of gene expression data.
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Affiliation(s)
- Angela França
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal.
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal.
| | - Nuno Cerca
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
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Gaio V, Lima T, Vilanova M, Cerca N, França A. mazEF Homologue Has a Minor Role in Staphylococcus epidermidis 1457 Virulence Potential. Front Cell Infect Microbiol 2022; 11:803134. [PMID: 35096651 PMCID: PMC8792614 DOI: 10.3389/fcimb.2021.803134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus epidermidis biofilm cells are characterized by increased antimicrobial tolerance and improved ability to evade host immune system defenses. These features are, in part, due to the presence of viable but non-culturable (VBNC) cells. A previous study identified genes potentially involved in VBNC cells formation in S. epidermidis biofilms, among which SERP1682/1681 raised special interest due to their putative role as a toxin–antitoxin system of the mazEF family. Herein, we constructed an S. epidermidis mutant lacking the mazEF genes homologues and determined their role in (i) VBNC state induction during biofilm formation, (ii) antimicrobial susceptibility, (iii) survival in human blood and plasma, and (iv) activation of immune cells. Our results revealed that mazEF homologue did not affect the proportion of VBNC cells in S. epidermidis 1457, refuting the previous hypothesis that mazEF homologue could be linked with the emergence of VBNC cells in S. epidermidis biofilms. Additionally, mazEF homologue did not seem to influence key virulence factors on this strain, since its deletion did not significantly affect the mutant biofilm formation capacity, antimicrobial tolerance or the response by immune cells. Surprisingly, our data suggest that mazEF does not behave as a toxin–antitoxin system in S. epidermidis strain 1457, since no decrease in the viability and culturability of bacteria was found when only the mazF toxin homologue was being expressed.
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Affiliation(s)
- Vânia Gaio
- Laboratory of Research in Biofilms Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Tânia Lima
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Manuel Vilanova
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Nuno Cerca
- Laboratory of Research in Biofilms Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Angela França
- Laboratory of Research in Biofilms Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
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Hou H, Li Y, Jin Y, Chen S, Long J, Duan G, Yang H. The crafty opponent: the defense systems of Staphylococcus aureus and response measures. Folia Microbiol (Praha) 2022; 67:233-243. [PMID: 35149955 DOI: 10.1007/s12223-022-00954-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/29/2022] [Indexed: 11/29/2022]
Abstract
Staphylococcus aureus is a serious threat to public health. S. aureus infection can cause acute or long-term persistent infections that are often resistant to antibiotics and are associated with high morbidity and death. Understanding the defensive systems of S. aureus can help clinicians make the best use of antimicrobial drugs and can also help with antimicrobial stewardship. The mechanisms and clinical implications of S. aureus defense systems, as well as potential response systems, were discussed in this study. Because resistance to all currently available antibiotics is unavoidable, new medicines are always being developed. Alternative techniques, such as anti-virulence and bacteriophage therapies, are being researched and may become major tools in the fight against staphylococcal infections in the future, in addition to the development of new small compounds that affect cell viability.
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Affiliation(s)
- Hongjie Hou
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Yang Li
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Yuefei Jin
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Shuaiyin Chen
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Jinzhao Long
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Guangcai Duan
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China.
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Gaio V, Lopes N, Cerca N, França A. codY and pdhA Expression Is Induced in Staphylococcus epidermidis Biofilm and Planktonic Populations With Higher Proportions of Viable but Non-Culturable Cells. Front Cell Infect Microbiol 2021; 11:771666. [PMID: 34869073 PMCID: PMC8634161 DOI: 10.3389/fcimb.2021.771666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus epidermidis biofilm cells can enter a physiological state known as viable but non-culturable (VBNC), where, despite being alive, they do not grow in conventional laboratory media. As such, the presence of VBNC cells impacts the diagnosis of S. epidermidis biofilm-associated infections. Previous transcriptomics analysis of S. epidermidis strain 9142 biofilms with higher proportions of VBNC cells suggested that the genes pdhA, codY and mazEF could be involved in the induction of the VBNC state. However, it was previously demonstrated that VBNC induction is strain-dependent. To properly assess the role of these genes in VBNC induction, the construction of mutant strains is necessary. Thus, herein, we assessed if VBNC cells could be induced in strain 1457, a strain amenable to genetic manipulation, and if the previously identified genes were involved in the modulation of the VBNC state in this strain. Furthermore, we evaluated the formation of VBNC cells on planktonic cultures. Our results showed that despite being commonly associated with biofilms, the proportion of VBNC cells can be modulated in both biofilm and planktonic cultures and that the expression of codY and pdhA was upregulated under VBNC inducing conditions in both phenotypes. Overall, our study revealed that the formation of VBNC cells in S. epidermidis is independent of the mode of growth and that the genes codY and pdhA seem to be relevant for the regulation of this physiological condition.
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Affiliation(s)
- Vânia Gaio
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
| | - Nathalie Lopes
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
| | - Nuno Cerca
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
| | - Angela França
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
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7
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Furusawa G, Diyana T, Lau NS. Metabolic strategies of dormancy of a marine bacterium Microbulbifer aggregans CCB-MM1: Its alternative electron transfer chain and sulfate-reducing pathway. Genomics 2021; 114:443-455. [PMID: 33689784 DOI: 10.1016/j.ygeno.2021.02.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/26/2021] [Accepted: 02/28/2021] [Indexed: 12/26/2022]
Abstract
Bacterial dormancy plays a crucial role in maintaining the functioning and diversity of microbial communities in natural environments. However, the metabolic regulations of the dormancy of bacteria in natural habitats, especially marine habitats, have remained largely unknown. A marine bacterium, Microbulbifer aggregans CCB-MM1 exhibits rod-to-coccus cell shape change during the dormant state. Therefore, to clarify the metabolic regulation of the dormancy, differential gene expression analysis based on RNA-Seq was performed between rod- (vegetative), intermediate, and coccus-shaped cells (dormancy). The RNA-Seq data revealed that one of two distinct electron transfer chains was upregulated in the dormancy. Dissimilatory sulfite reductase and soluble hydrogenase were also highly upregulated in the dormancy. In addition, induction of the dormancy of MM1 in the absence of MgSO4 was slower than that in the presence of MgSO4. These results indicate that the sulfate-reducing pathway plays an important role in entering the dormancy of MM1.
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Affiliation(s)
- Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia.
| | - Tarmizi Diyana
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
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RNA-based qPCR as a tool to quantify and to characterize dual-species biofilms. Sci Rep 2019; 9:13639. [PMID: 31541147 PMCID: PMC6754382 DOI: 10.1038/s41598-019-50094-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022] Open
Abstract
While considerable research has focused on studying individual-species, we now face the challenge of determining how interspecies interactions alter bacterial behaviours and pathogenesis. Pseudomonas aeruginosa and Staphylococcus aureus are often found to co-infect cystic-fibrosis patients. Curiously, their interaction is reported as competitive under laboratory conditions. Selecting appropriate methodologies is therefore critical to analyse multi-species communities. Herein, we demonstrated the major biases associated with qPCR quantification of bacterial populations and optimized a RNA-based qPCR able not only to quantify but also to characterize microbial interactions within dual-species biofilms composed by P. aeruginosa and S. aureus, as assessed by gene expression quantification. qPCR quantification was compared with flow-cytometry and culture-based quantification. Discrepancies between culture independent and culture dependent methods could be the result of the presence of viable but not-cultivable bacteria within the biofilm. Fluorescence microscopy confirmed this. A higher sensitivity to detect viable cells further highlights the potentialities of qPCR approach to quantify biofilm communities. By using bacterial RNA and an exogenous mRNA control, it was also possible to characterize bacterial transcriptomic profile, being this a major advantage of this method.
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9
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Morphophysiological responses of detached and adhered biofilms of Pseudomonas fluorescens to acidic electrolyzed water. Food Microbiol 2019; 82:89-98. [DOI: 10.1016/j.fm.2019.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 12/26/2022]
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10
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Sivaranjani M, Leskinen K, Aravindraja C, Saavalainen P, Pandian SK, Skurnik M, Ravi AV. Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach. Front Microbiol 2019; 10:150. [PMID: 30787919 PMCID: PMC6372523 DOI: 10.3389/fmicb.2019.00150] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/21/2019] [Indexed: 11/25/2022] Open
Abstract
Background: Alpha-mangostin (α-MG) is a natural xanthone reported to exhibit rapid bactericidal activity against Gram-positive bacteria, and may therefore have potential clinical application in healthcare sectors. This study sought to identify the impact of α-MG on Staphylococcus epidermidis RP62A through integrated advanced omic technologies. Methods: S. epidermidis was challenged with sub-MIC (0.875 μg/ml) of α-MG at various time points and the differential expression pattern of genes/proteins were analyzed in the absence and presence of α-MG using RNA sequencing and LC-MS/MS experiments. Bioinformatic tools were used to categorize the biological processes, molecular functions and KEGG pathways of differentially expressed genes/proteins. qRT-PCR was employed to validate the results obtained from these analyses. Results: Transcriptomic and proteomic profiling of α-MG treated cells indicated that genes/proteins affected by α-MG treatment were associated with diverse cellular functions. The greatest reduction in expression was observed in transcription of genes conferring cytoplasmic membrane integrity (yidC2, secA and mscL), cell division (ftsY and divlB), teichoic acid biosynthesis (tagG and dltA), fatty-acid biosynthesis (accB, accC, fabD, fabH, fabI, and fabZ), biofilm formation (icaA) and DNA replication and repair machinery (polA, polC, dnaE, and uvrA). Those with increased expression were involved in oxidative (katA and sodA) and cellular stress response (clpB, clpC, groEL, and asp23). The qRT-PCR analysis substantiated the results obtained from transcriptomic and proteomic profiling studies. Conclusion: Combining transcriptomic and proteomic methods provided comprehensive information about the antibacterial mode of action of α-MG. The obtained results suggest that α-MG targets S. epidermidis through multifarious mechanisms, and especially prompts that loss of cytoplasmic membrane integrity leads to rapid onset of bactericidal activity.
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Affiliation(s)
| | - Katarzyna Leskinen
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Päivi Saavalainen
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki, Helsinki, Finland
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, Helsinki, Finland
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Magana M, Sereti C, Ioannidis A, Mitchell CA, Ball AR, Magiorkinis E, Chatzipanagiotou S, Hamblin MR, Hadjifrangiskou M, Tegos GP. Options and Limitations in Clinical Investigation of Bacterial Biofilms. Clin Microbiol Rev 2018; 31:e00084-16. [PMID: 29618576 PMCID: PMC6056845 DOI: 10.1128/cmr.00084-16] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacteria can form single- and multispecies biofilms exhibiting diverse features based upon the microbial composition of their community and microenvironment. The study of bacterial biofilm development has received great interest in the past 20 years and is motivated by the elegant complexity characteristic of these multicellular communities and their role in infectious diseases. Biofilms can thrive on virtually any surface and can be beneficial or detrimental based upon the community's interplay and the surface. Advances in the understanding of structural and functional variations and the roles that biofilms play in disease and host-pathogen interactions have been addressed through comprehensive literature searches. In this review article, a synopsis of the methodological landscape of biofilm analysis is provided, including an evaluation of the current trends in methodological research. We deem this worthwhile because a keyword-oriented bibliographical search reveals that less than 5% of the biofilm literature is devoted to methodology. In this report, we (i) summarize current methodologies for biofilm characterization, monitoring, and quantification; (ii) discuss advances in the discovery of effective imaging and sensing tools and modalities; (iii) provide an overview of tailored animal models that assess features of biofilm infections; and (iv) make recommendations defining the most appropriate methodological tools for clinical settings.
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Affiliation(s)
- Maria Magana
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece
| | - Christina Sereti
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece
- Department of Microbiology, Thriassio General Hospital, Attiki, Greece
| | - Anastasios Ioannidis
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece
- Department of Nursing, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese, Sparta, Greece
| | - Courtney A Mitchell
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Anthony R Ball
- Gliese 623b, Mendon, Massachusetts, USA
- GAMA Therapeutics LLC, Pepperell, Massachusetts, USA
| | - Emmanouil Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens-Goudi, Greece
| | | | - Michael R Hamblin
- Harvard-MIT Division of Health Science and Technology, Cambridge, Massachusetts, USA
- Department of Dermatology, Harvard Medical School, Boston, Massachusetts, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - George P Tegos
- Gliese 623b, Mendon, Massachusetts, USA
- GAMA Therapeutics LLC, Pepperell, Massachusetts, USA
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Charlebois A, Jacques M, Archambault M. Comparative transcriptomic analysis of Clostridium perfringens biofilms and planktonic cells. Avian Pathol 2018; 45:593-601. [PMID: 27207477 DOI: 10.1080/03079457.2016.1189512] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Clostridium perfringens is an opportunistic pathogen that can cause food poisoning in humans and various enterotoxaemias in animal species. Recently, C. perfringens was shown to form biofilms, a structured community of bacterial cells enclosed in a self-produced extracellular matrix. However, very little is known on the subject and no information is available on gene expression in C. perfringens biofilms. To gain insights into the differences between free-living C. perfringens cells and those in biofilms, we used RNA sequencing. In total, 25.7% of genes showed differential expression in the two growth modes; about 12.8% of genes were up-regulated and about 12.9% were down-regulated in biofilms. We show that 772 genes were significantly differentially expressed between biofilms and planktonic cells from the supernatant of biofilms. Genes that were down-regulated in biofilm cells, relative to planktonic cells, included those involved in virulence, energy production, amino acid, nucleotide and carbohydrate metabolism, and in translation and ribosomal structure. Genes up-regulated in biofilm cells were mainly involved in amino acid and carbohydrate metabolism, transcription, inorganic ion metabolism and in defence mechanisms. This study provides new insights into the transcriptomic response of C. perfringens during biofilm formation.
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Affiliation(s)
- Audrey Charlebois
- a Faculté de médecine vétérinaire, Département de pathologie et microbiologie, Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA) , Université de Montréal , Saint-Hyacinthe , Canada
| | - Mario Jacques
- a Faculté de médecine vétérinaire, Département de pathologie et microbiologie, Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA) , Université de Montréal , Saint-Hyacinthe , Canada
| | - Marie Archambault
- a Faculté de médecine vétérinaire, Département de pathologie et microbiologie, Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA) , Université de Montréal , Saint-Hyacinthe , Canada
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Emelyanova EV, Souzina NE, Polivtseva VN, Reshetilov AN, Solyanikova IP. Survival and biodegradation activity of Gordonia polyisoprenivorans 135: Basics of a biosensor receptor. APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817050039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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O'Gara JP. Into the storm: Chasing the opportunistic pathogen Staphylococcus aureus from skin colonisation to life-threatening infections. Environ Microbiol 2017. [PMID: 28631399 DOI: 10.1111/1462-2920.13833] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Colonisation of the human skin by Staphylococcus aureus is a precursor for a variety of infections ranging from boils to sepsis and pneumonia. The rapid emergence of methicillin-resistant S. aureus following the clinical introduction of this antimicrobial drug and reports of resistance to all currently used anti-staphylococcal drugs has added to its formidable reputation. S. aureus survival on the skin and in vivo virulence is underpinned by a remarkable environmental adaptability, made possible by highly orchestrated regulation of gene expression and a capacity to undertake genome remodelling. Depending on the ecological or infection niche, controlled expression of a variety of adhesins can be initiated to facilitate adherence to extracellular matrix proteins, survival against desiccation or biofilm accumulation on implanted medical devices and host tissue. These adherence mechanisms complement toxin and enzyme production, immune evasion strategies, and antibiotic resistance and tolerance to collectively thwart efforts to develop reliable antimicrobial drug regimens and an effective S. aureus vaccine.
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Affiliation(s)
- James P O'Gara
- Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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15
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Hardy L, Cerca N, Jespers V, Vaneechoutte M, Crucitti T. Bacterial biofilms in the vagina. Res Microbiol 2017; 168:865-874. [PMID: 28232119 DOI: 10.1016/j.resmic.2017.02.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 02/05/2017] [Accepted: 02/13/2017] [Indexed: 01/21/2023]
Abstract
A bacterial biofilm is a structured community of bacteria in a self-produced extracellular matrix, adherent to an inert surface or biological tissue. The involvement of biofilm in a bacterial infection implies that the infection is difficult to treat and that the patient will probably experience relapses of the condition. In bacterial vaginosis (BV), the lactobacilli concentration decreases, while the bacterial load of other (facultative) anaerobic bacteria increases. A hallmark of BV is the presence of clue cells, now known as the result of a polymicrobial biofilm formed in vaginal epithelial cells. Current knowledge of the individual roles of bacterial species involved in polymicrobial BV biofilms or interactions between these species are not fully known. In addition, knowledge of the composition matrix and triggers of biofilm formation is still lacking. Bacteria are able to attach to the surface of indwelling medical devices and cover these surfaces with biofilm. Vaginally inserted devices, such as tampons, intra-uterine devices and vaginal rings, can also be colonized by bacteria and be subjected to biofilm formation. This might hamper release of active product in case of drug-releasing devices such as vaginal rings, or promote the presence of unfavorable bacteria in the vagina. This paper reviews current knowledge of biofilms in the vaginal environment.
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Affiliation(s)
- Liselotte Hardy
- HIV and Sexual Health Unit, Department of Public Health, Institute of Tropical Medicine, Nationalestraat 155, Antwerp, Belgium; Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, University of Ghent, De Pintelaan 185, Ghent, Belgium; STI Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Nationalestraat 155, Antwerp, Belgium.
| | - Nuno Cerca
- Laboratory of Research in Biofilms Rosário Oliveira, Centre of Biological Engineering, University of Minho, Rua da Universidade, 4704-553 Braga, Portugal.
| | - Vicky Jespers
- HIV and Sexual Health Unit, Department of Public Health, Institute of Tropical Medicine, Nationalestraat 155, Antwerp, Belgium.
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, University of Ghent, De Pintelaan 185, Ghent, Belgium.
| | - Tania Crucitti
- STI Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Nationalestraat 155, Antwerp, Belgium.
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16
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Waters EM, Rowe SE, O'Gara JP, Conlon BP. Convergence of Staphylococcus aureus Persister and Biofilm Research: Can Biofilms Be Defined as Communities of Adherent Persister Cells? PLoS Pathog 2016; 12:e1006012. [PMID: 28033390 PMCID: PMC5199038 DOI: 10.1371/journal.ppat.1006012] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Elaine M. Waters
- Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Sarah E. Rowe
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - James P. O'Gara
- Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- * E-mail: (JPO); (BPC)
| | - Brian P. Conlon
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (JPO); (BPC)
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17
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Viable But Not Culturable (VBNC) state of Brettanomyces bruxellensis in wine: New insights on molecular basis of VBNC behaviour using a transcriptomic approach. Food Microbiol 2016; 59:196-204. [DOI: 10.1016/j.fm.2016.06.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/20/2016] [Accepted: 06/08/2016] [Indexed: 11/23/2022]
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18
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Chronic Biofilm Infection in Breast Implants Is Associated with an Increased T-Cell Lymphocytic Infiltrate. Plast Reconstr Surg 2015; 135:1057e-1059e. [DOI: 10.1097/prs.0000000000001254] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Dharmaprakash A, Thandavarayan R, Joseph I, Thomas S. Development of broad-spectrum antibiofilm drugs: strategies and challenges. Future Microbiol 2015; 10:1035-48. [DOI: 10.2217/fmb.15.14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
ABSTRACT The severity of many chronic bacterial infections is mainly due to the biofilm mode of life adapted by pathogenic bacteria. The bacteria in biofilm-stage exhibit high resistance to host immune responses and antimicrobials, which complicates the treatment process and results in life threatening conditions. Most of the chronic infections are polymicrobial in nature. In order to combat the polymicrobial biofilm infections and to increase the efficiency of antimicrobials, there is an urgent need for broad-spectrum antibiofilm drugs. This review discusses the clinical needs and current status of broad-spectrum antibiofilm drugs with special emphasis on prospective strategies and hurdles in the process of new drug discovery.
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Affiliation(s)
- Akhilandeswarre Dharmaprakash
- Cholera & Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram – 695 014, Kerala, India
| | | | - Iype Joseph
- Pathogen Biology Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram – 695 014, Kerala, India
| | - Sabu Thomas
- Cholera & Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram – 695 014, Kerala, India
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20
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Carvalhais V, Cerveira F, Vilanova M, Cerca N, Vitorino R. An immunoproteomic approach for characterization of dormancy within Staphylococcus epidermidis biofilms. Mol Immunol 2015; 65:429-35. [PMID: 25749707 DOI: 10.1016/j.molimm.2015.02.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 02/19/2015] [Indexed: 01/02/2023]
Abstract
Virulence of Staphylococcus epidermidis is mainly attributed to surface colonization and biofilm formation in indwelling medical devices. Physiological heterogeneity of biofilms may influence host immune response and sensitivity to antibiotics. Dormant cells, among others, contribute to biofilm heterogeneity. The aim of this study was to identify immunogenic proteins of S. epidermidis biofilms associated with dormancy mechanism, by using two-dimensional electrophoresis (2-DE) immunoblotting and mass spectrometry (MS). A total of 19 bacterial proteins, recognized by human serum samples, were identified. These proteins were mainly involved in small molecule metabolic biological processes. Catalytic activity and ion binding were the most representative molecular functions. CodY and GpmA proteins were more reactive to sera when biofilm dormancy was induced, while FtnA and ClpP were more reactive when dormancy was prevented. This is the first work that identifies differences in immunoreactive proteins within bacterial biofilms with induced or prevented dormancy. Considering the importance of dormancy within biofilms, further evaluation of these proteins can provide insights into the mechanisms related to dormancy and help to improve current understanding on how dormancy affects the host immune response.
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Affiliation(s)
- Virginia Carvalhais
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Frederico Cerveira
- Anatomia Patológica, Centro Hospitalar Baixo-Vouga, Avenida Artur Ravara, 3814-501 Aveiro, Portugal
| | - Manuel Vilanova
- IBMC - Instituto de Biologia Molecular e Celular, Rua do Campo Alegre 83, Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Rua de Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Nuno Cerca
- CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Rui Vitorino
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; iBiMED, Institute for Biomedical Research, University of Aveiro, Aveiro, Portugal.
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Proteomic profile of dormancy within Staphylococcus epidermidis biofilms using iTRAQ and label-free strategies. Appl Microbiol Biotechnol 2015; 99:2751-62. [PMID: 25672847 DOI: 10.1007/s00253-015-6434-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 12/16/2014] [Accepted: 01/25/2015] [Indexed: 12/12/2022]
Abstract
Staphylococcus epidermidis is an important nosocomial bacterium among carriers of indwelling medical devices, since it has a strong ability to form biofilms. The presence of dormant bacteria within a biofilm is one of the factors that contribute to biofilm antibiotic tolerance and immune evasion. Here, we provide a detailed characterization of the quantitative proteomic profile of S. epidermidis biofilms with different proportions of dormant bacteria. A total of 427 and 409 proteins were identified by label-free and label-based quantitative methodologies, respectively. From these, 29 proteins were found to be differentially expressed between S. epidermidis biofilms with prevented and induced dormancy. Proteins overexpressed in S. epidermidis with prevented dormancy were associated with ribosome synthesis pathway, which reflects the metabolic state of dormant bacteria. In the opposite, underexpressed proteins were related to catalytic activity and ion binding, with involvement in purine, arginine, and proline metabolism. Additionally, GTPase activity seems to be enhanced in S. epidermidis biofilm with induced dormancy. The role of magnesium in dormancy modulation was further investigated with bioinformatics tool based in predicted interactions. The main molecular function of proteins, which strongly interact with magnesium, was nucleic acid binding. Different proteomic strategies allowed to obtain similar results and evidenced that prevented dormancy led to an expression of a markedly different repertoire of proteins in comparison to the one of dormant biofilms.
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22
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Cerca F, França Â, Pérez-Cabezas B, Carvalhais V, Ribeiro A, Azeredo J, Pier G, Cerca N, Vilanova M. Dormant bacteria within Staphylococcus epidermidis biofilms have low inflammatory properties and maintain tolerance to vancomycin and penicillin after entering planktonic growth. J Med Microbiol 2014; 63:1274-1283. [PMID: 25053799 DOI: 10.1099/jmm.0.073163-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Staphylococcus epidermidis is the most commonly isolated aetiological agent of nosocomial infections, mainly due to its ability to establish biofilms on indwelling medical devices. Detachment of bacteria from S. epidermidis biofilms and subsequent growth in the planktonic form is a hallmark of the pathogenesis of these infections leading to dissemination. Here we showed that S. epidermidis cells collected from biofilms cultured in conditions that promote cell viability present marked changes in their physiological status upon initiating a planktonic mode of growth. When compared to cells growing in biofilms, they displayed an increased SYBR green I staining intensity, increased transcription of the rpiA gene, decreased transcription of the icaA gene, as well as higher susceptibility to vancomycin and penicillin. When bacteria collected from biofilms with high proportions of dormant cells were subsequently cultured in the planktonic mode, a large proportion of cells maintained a low SYBR green I staining intensity and increased resistance to vancomycin and penicillin, a profile typical of dormant cells. This phenotype further associated with a decreased ability of these biofilm-derived cells to induce the production of pro-inflammatory cytokines by bone marrow-derived dendritic cells in vitro. These results demonstrated that cells detached from the biofilm maintain a dormant cell-like phenotype, having a low pro-inflammatory effect and decreased susceptibility to antibiotics, suggesting these cells may contribute to the recalcitrant nature of biofilm infections.
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Affiliation(s)
- Filipe Cerca
- IBMC - Instituto de Biologia Molecular e Celular, Rua do Campo Alegre 83, Porto, Portugal.,ICBAS-UP - Instituto de Ciências Biomédicas de Abel Salazar - Universidade do Porto, Rua de Jorge Viterbo Ferreira no. 228, 4050-313, Porto, Portugal
| | - Ângela França
- CEB, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Begoña Pérez-Cabezas
- IBMC - Instituto de Biologia Molecular e Celular, Rua do Campo Alegre 83, Porto, Portugal
| | - Virgínia Carvalhais
- CEB, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,ICBAS-UP - Instituto de Ciências Biomédicas de Abel Salazar - Universidade do Porto, Rua de Jorge Viterbo Ferreira no. 228, 4050-313, Porto, Portugal
| | - Adília Ribeiro
- IBMC - Instituto de Biologia Molecular e Celular, Rua do Campo Alegre 83, Porto, Portugal.,ICBAS-UP - Instituto de Ciências Biomédicas de Abel Salazar - Universidade do Porto, Rua de Jorge Viterbo Ferreira no. 228, 4050-313, Porto, Portugal
| | - Joana Azeredo
- CEB, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Gerald Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, MA 02115, USA
| | - Nuno Cerca
- CEB, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Manuel Vilanova
- IBMC - Instituto de Biologia Molecular e Celular, Rua do Campo Alegre 83, Porto, Portugal.,ICBAS-UP - Instituto de Ciências Biomédicas de Abel Salazar - Universidade do Porto, Rua de Jorge Viterbo Ferreira no. 228, 4050-313, Porto, Portugal
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