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Cometta S, Hutmacher DW, Chai L. In vitro models for studying implant-associated biofilms - A review from the perspective of bioengineering 3D microenvironments. Biomaterials 2024; 309:122578. [PMID: 38692146 DOI: 10.1016/j.biomaterials.2024.122578] [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: 01/03/2024] [Revised: 04/01/2024] [Accepted: 04/13/2024] [Indexed: 05/03/2024]
Abstract
Biofilm research has grown exponentially over the last decades, arguably due to their contribution to hospital acquired infections when they form on foreign body surfaces such as catheters and implants. Yet, translation of the knowledge acquired in the laboratory to the clinic has been slow and/or often it is not attempted by research teams to walk the talk of what is defined as 'bench to bedside'. We therefore reviewed the biofilm literature to better understand this gap. Our search revealed substantial development with respect to adapting surfaces and media used in models to mimic the clinical settings, however many of the in vitro models were too simplistic, often discounting the composition and properties of the host microenvironment and overlooking the biofilm-implant-host interactions. Failure to capture the physiological growth conditions of biofilms in vivo results in major differences between lab-grown- and clinically-relevant biofilms, particularly with respect to phenotypic profiles, virulence, and antimicrobial resistance, and they essentially impede bench-to-bedside translatability. In this review, we describe the complexity of the biological processes at the biofilm-implant-host interfaces, discuss the prerequisite for the development and characterization of biofilm models that better mimic the clinical scenario, and propose an interdisciplinary outlook of how to bioengineer biofilms in vitro by converging tissue engineering concepts and tools.
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Affiliation(s)
- Silvia Cometta
- Max Planck Queensland Centre, Queensland University of Technology, Brisbane, QLD 4000, Australia; Faculty of Engineering, School of Mechanical, Medical and Process Engineering, Queensland University of Technology, Brisbane, QLD 4000, Australia; Australian Research Council (ARC) Training Centre for Multiscale 3D Imaging, Modelling, and Manufacturing (M3D Innovation), Queensland University of Technology, Brisbane, QLD 4000, Australia.
| | - Dietmar W Hutmacher
- Max Planck Queensland Centre, Queensland University of Technology, Brisbane, QLD 4000, Australia; Faculty of Engineering, School of Mechanical, Medical and Process Engineering, Queensland University of Technology, Brisbane, QLD 4000, Australia; Australian Research Council (ARC) Training Centre for Multiscale 3D Imaging, Modelling, and Manufacturing (M3D Innovation), Queensland University of Technology, Brisbane, QLD 4000, Australia; Australian Research Council Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology, Brisbane, QLD 4059, Australia.
| | - Liraz Chai
- Max Planck Queensland Centre, Queensland University of Technology, Brisbane, QLD 4000, Australia; The Hebrew University of Jerusalem, Institute of Chemistry, Jerusalem, 91904, Israel; The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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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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Guo X, He Y, Cheng Y, Liang J, Xu P, He W, Che J, Men J, Yuan Y, Yue T. The composition of Tibetan kefir grain TKG-Y and the antibacterial potential and milk fermentation ability of S. warneri KYS-164 screened from TKG-Y. Food Funct 2024; 15:5026-5040. [PMID: 38650522 DOI: 10.1039/d4fo00112e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
This study utilized high-throughput sequencing and SEM observation to elucidate the microbial composition of a Tibetan herder's homemade kefir grain named TKG-Y. Subsequently, S. warneri KYS-164 was isolated from TKG-Y, which can produce mixed protein substances with antibacterial activity, namely bacteriocin-like inhibitory substances (BLIS). BLIS can significantly reduce the growth rate of Escherichia coli 366-a, Staphylococcus aureus CICC 10384 and mixed strains at low concentrations (1 × MIC). The presence of the warnericin-centered gene cluster in KYS-164 may explain the antibacterial properties of the BLIS. Pepsin and an acidic environment can reduce the number of colonies of KYS-164 by 2.5 Log10 CFU mL-1 within 1 h, and reduce the antibacterial activity of BLIS by 21.48%. S. warneri KYS-164 showed no antibiotic resistance and biological toxicity after 80 subcultures, while BLIS produced by 40 generations of the strain retained their inhibitory efficacy against pathogenic bacteria. After 48-hour fermentation of milk with KYS-164, volatile compounds such as aldehydes, phenols, esters, and alcohols, giving it a floral, fruity, milky, oily, and nutty aroma, were released, enriching the sensory characteristics of dairy products. This study not only revealed the bacterial colony composition information of home-made kefir grain TKG-Y but also discovered and proved that S. warneri KYS-164 has the potential to inhibit bacteria and ferment dairy products. This will provide a basis for subsequent applied research on KYS-164.
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Affiliation(s)
- Xing Guo
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, China.
| | - Yining He
- School of Food and Advanced Technology, Massey University, Palmerston North, 4442, New Zealand
| | - Yifan Cheng
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, China.
| | - Jingyimei Liang
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, China.
- College of Analytical Chemistry and Food Science, Universidade de Vigo, Vigo, 36310, Spain
| | - Pandi Xu
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, China.
| | - Wenwen He
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, China.
| | - Jiayin Che
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, China.
| | - Jiexing Men
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, China.
| | - Yahong Yuan
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, China.
| | - Tianli Yue
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, 710069, China.
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Lichtenberg M, Coenye T, Parsek MR, Bjarnsholt T, Jakobsen TH. What's in a name? Characteristics of clinical biofilms. FEMS Microbiol Rev 2023; 47:fuad050. [PMID: 37656883 PMCID: PMC10503651 DOI: 10.1093/femsre/fuad050] [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: 06/10/2023] [Revised: 08/06/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023] Open
Abstract
In vitro biofilms are communities of microbes with unique features compared to individual cells. Biofilms are commonly characterized by physical traits like size, adhesion, and a matrix made of extracellular substances. They display distinct phenotypic features, such as metabolic activity and antibiotic tolerance. However, the relative importance of these traits depends on the environment and bacterial species. Various mechanisms enable biofilm-associated bacteria to withstand antibiotics, including physical barriers, physiological adaptations, and changes in gene expression. Gene expression profiles in biofilms differ from individual cells but, there is little consensus among studies and so far, a 'biofilm signature transcriptome' has not been recognized. Additionally, the spatial and temporal variability within biofilms varies greatly depending on the system or environment. Despite all these variable conditions, which produce very diverse structures, they are all noted as biofilms. We discuss that clinical biofilms may differ from those grown in laboratories and found in the environment and discuss whether the characteristics that are commonly used to define and characterize biofilms have been shown in infectious biofilms. We emphasize that there is a need for a comprehensive understanding of the specific traits that are used to define bacteria in infections as clinical biofilms.
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Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Matthew R Parsek
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., WA 98195 Seattle, United States
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital, Ole Maaløes vej 26, 2100 Copenhagen, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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Feng Y, Ming T, Zhou J, Lu C, Wang R, Su X. The Response and Survival Mechanisms of Staphylococcus aureus under High Salinity Stress in Salted Foods. Foods 2022; 11:foods11101503. [PMID: 35627073 PMCID: PMC9140498 DOI: 10.3390/foods11101503] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/11/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
Staphylococcus aureus (S. aureus) has a strong tolerance to high salt stress. It is a major reason as to why the contamination of S. aureus in salted food cannot be eradicated. To elucidate its response and survival mechanisms, changes in the morphology, biofilm formation, virulence, transcriptome, and metabolome of S. aureus were investigated. IsaA positively regulates and participates in the formation of biofilm. Virulence was downregulated to reduce the depletion of nonessential cellular functions. Inositol phosphate metabolism was downregulated to reduce the conversion of functional molecules. The MtsABC transport system was downregulated to reduce ion transport and signaling. Aminoacyl-tRNA biosynthesis was upregulated to improve cellular homeostasis. The betaine biosynthesis pathway was upregulated to protect the active structure of proteins and nucleic acids. Within a 10% NaCl concentration, the L-proline content was upregulated to increase osmotic stability. In addition, 20 hub genes were identified through an interaction analysis. The findings provide theoretical support for the prevention and control of salt-tolerant bacteria in salted foods.
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Affiliation(s)
- Ying Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (Y.F.); (T.M.); (J.Z.); (C.L.); (X.S.)
- College of Life Sciences, Tonghua Normal University, Tonghua 134000, China
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Tinghong Ming
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (Y.F.); (T.M.); (J.Z.); (C.L.); (X.S.)
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (Y.F.); (T.M.); (J.Z.); (C.L.); (X.S.)
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Chenyang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (Y.F.); (T.M.); (J.Z.); (C.L.); (X.S.)
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Rixin Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
- Correspondence: ; Tel.: +86-574-8760-8368
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (Y.F.); (T.M.); (J.Z.); (C.L.); (X.S.)
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
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Teichmann P, Both A, Wolz C, Hornef MW, Rohde H, Yazdi AS, Burian M. The Staphylococcus epidermidis Transcriptional Profile During Carriage. Front Microbiol 2022; 13:896311. [PMID: 35558117 PMCID: PMC9087046 DOI: 10.3389/fmicb.2022.896311] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
The virulence factors of the opportunistic human pathogen Staphylococcus epidermidis have been a main subject of research. In contrast, limited information is available on the mechanisms that allow the bacterium to accommodate to the conditions during carriage, a prerequisite for pathogenicity. Here, we tested the hypothesis that the adaptation of S. epidermidis at different anatomical sites is reflected by differential gene regulation. We used qPCR to profile S. epidermidis gene expression in vivo in nose and skin swabs of 11 healthy individuals. Despite some heterogeneity between individuals, significant site-specific differences were detected. For example, expression of the S. epidermidis regulator sarA was found similarly in the nose and on the skin of all individuals. Also, genes encoding colonization and immune evasion factors (sdrG, capC, and dltA), as well as the sphingomyelinase encoding gene sph, were expressed at both anatomical sites. In contrast, expression of the global regulator agr was almost inactive in the nose but readily present on the skin. A similar site-specific expression profile was also identified for the putative chitinase-encoding SE0760. In contrast, expression of the autolysine-encoding gene sceD and the wall teichoic acid (WTA) biosynthesis gene tagB were more pronounced in the nose as compared to the skin. In summary, our analysis identifies site-specific gene expression patterns of S. epidermidis during colonization. In addition, the observed expression signature was significantly different from growth in vitro. Interestingly, the strong transcription of sphingomyelinase together with the low expression of genes encoding the tricarboxylic acid cycle (TCA) suggests very good nutrient supply in both anatomical niches, even on the skin where one might have suspected a rather lower nutrient supply compared to the nose.
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Affiliation(s)
- Pascâl Teichmann
- Department of Dermatology and Allergology, RWTH University Hospital Aachen, Aachen, Germany
| | - Anna Both
- Institute of Medical Microbiology, Virology and Hygiene, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH University Hospital Aachen, Aachen, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Amir S Yazdi
- Department of Dermatology and Allergology, RWTH University Hospital Aachen, Aachen, Germany
| | - Marc Burian
- Department of Dermatology and Allergology, RWTH University Hospital Aachen, Aachen, Germany
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Cho H, Masters T, Greenwood‐Quaintance KE, Johnson S, Jeraldo PR, Chia N, Pu M, Abdel MP, Patel R. Transcriptomic analysis of Streptococcus agalactiae periprosthetic joint infection. Microbiologyopen 2021; 10:e1256. [PMID: 34964296 PMCID: PMC8678771 DOI: 10.1002/mbo3.1256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 09/09/2021] [Accepted: 11/22/2021] [Indexed: 11/08/2022] Open
Abstract
Although Streptococcus agalactiae periprosthetic joint infection (PJI) is not as prevalent as staphylococcal PJI, invasive S. agalactiae infection is not uncommon. Here, RNA-seq was used to perform transcriptomic analysis of S. agalactiae PJI using fluid derived from sonication of explanted arthroplasties of subjects with S. agalactiae PJI, with results compared to those of S. agalactiae strain NEM316 grown in vitro. A total of 227 genes with outlier expression were found (164 upregulated and 63 downregulated) between PJI sonicate fluid and in vitro conditions. Functional enrichment analysis showed genes involved in mobilome and inorganic ion transport and metabolism to be most enriched. Genes involved in nickel, copper, and zinc transport, were upregulated. Among known virulence factors, cyl operon genes, encoding β-hemolysin/cytolysin, were consistently highly expressed in PJI versus in vitro. The data presented provide insight into S. agalactiae PJI pathogenesis and may be a resource for identification of novel PJI therapeutics or vaccines against invasive S. agalactiae infections.
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Affiliation(s)
- Hye‐Kyung Cho
- Division of Clinical Microbiology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Thao Masters
- Division of Clinical Microbiology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | | | - Stephen Johnson
- Department of Health Sciences ResearchMayo ClinicRochesterMinnesotaUSA
| | - Patricio R. Jeraldo
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
- Department of SurgeryMayo ClinicRochesterMinnesotaUSA
| | - Nicholas Chia
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
- Department of SurgeryMayo ClinicRochesterMinnesotaUSA
| | - Meng Pu
- Department of Medicine, Division of Gastroenterology and HepatologyMayo ClinicRochesterMinnesotaUSA
| | - Matthew P. Abdel
- Department of Orthopedic SurgeryMayo ClinicRochesterMinnesotaUSA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
- Division of Infectious Diseases, Department of MedicineMayo ClinicRochesterMinnesotaUSA
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