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  1. Article: Bacterial Adaptive Memory in Methicillin-Resistant

    Fernández-Barat, Laia / López-Aladid, Ruben / Vázquez, Nil / Cabrera, Roberto / Vila, Jordi / Ferrer, Miquel / Torres, Antoni

    Pathogens (Basel, Switzerland)

    2024  Volume 13, Issue 2

    Abstract: Objectives: To evaluate the expression dynamics of biofilm genes in methicillin-resistant : Methods: Biofilm was grown (24 h) in tryptic broth soy plus 0.25% glucose for a clinical MRSA isolate in planktonic state and after sessile growth named ETT- ... ...

    Abstract Objectives: To evaluate the expression dynamics of biofilm genes in methicillin-resistant
    Methods: Biofilm was grown (24 h) in tryptic broth soy plus 0.25% glucose for a clinical MRSA isolate in planktonic state and after sessile growth named ETT-MRSA (S2, S3, S4, S5, S6, S7). Gene expression of five biofilm-related genes (
    Results: The MRSA isolates retrieved from ETT were capable of producing biofilms dependent on
    Conclusions: MRSA loses its biofilm gene expression in vitro, by adaptive features across multiple generations, as evidenced by the progressive downregulation of
    Language English
    Publishing date 2024-02-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2695572-6
    ISSN 2076-0817
    ISSN 2076-0817
    DOI 10.3390/pathogens13020144
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  2. Article ; Online: Brewpitopes: a pipeline to refine B-cell epitope predictions during public health emergencies.

    Farriol-Duran, Roc / López-Aladid, Ruben / Porta-Pardo, Eduard / Torres, Antoni / Fernández-Barat, Laia

    Frontiers in immunology

    2023  Volume 14, Page(s) 1278534

    Abstract: The application of B-cell epitope identification to develop therapeutic antibodies and vaccine candidates is well established. However, the validation of epitopes is time-consuming and resource-intensive. To alleviate this, in recent years, multiple ... ...

    Abstract The application of B-cell epitope identification to develop therapeutic antibodies and vaccine candidates is well established. However, the validation of epitopes is time-consuming and resource-intensive. To alleviate this, in recent years, multiple computational predictors have been developed in the immunoinformatics community. Brewpitopes is a pipeline that curates bioinformatic B-cell epitope predictions obtained by integrating different state-of-the-art tools. We used additional computational predictors to account for subcellular location, glycosylation status, and surface accessibility of the predicted epitopes. The implementation of these sets of rational filters optimizes
    MeSH term(s) Humans ; Epitopes, B-Lymphocyte/genetics ; Epitopes, T-Lymphocyte ; Emergencies ; Public Health ; Viral Vaccines ; SARS-CoV-2
    Chemical Substances Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Viral Vaccines
    Language English
    Publishing date 2023-12-06
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2023.1278534
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  3. Article ; Online: The value of serology testing to manage SARS-CoV-2 infections.

    Fernández-Barat, Laia / López-Aladid, Ruben / Torres, Antoni

    The European respiratory journal

    2020  Volume 56, Issue 2

    MeSH term(s) Betacoronavirus ; COVID-19 ; Coronavirus Infections/epidemiology ; Humans ; Pandemics ; Pneumonia, Viral/epidemiology ; SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-08-27
    Publishing country England
    Document type Editorial ; Comment
    ZDB-ID 639359-7
    ISSN 1399-3003 ; 0903-1936
    ISSN (online) 1399-3003
    ISSN 0903-1936
    DOI 10.1183/13993003.02411-2020
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  4. Article ; Online: Pseudomonas aeruginosa in Bronchiectasis.

    Fernández-Barat, Laia / Alcaraz-Serrano, Victoria / Amaro, Rosanel / Torres, Antoni

    Seminars in respiratory and critical care medicine

    2021  Volume 42, Issue 4, Page(s) 587–594

    Abstract: Pseudomonas ... ...

    Abstract Pseudomonas aeruginosa
    MeSH term(s) Anti-Bacterial Agents/therapeutic use ; Bronchiectasis/drug therapy ; Humans ; Persistent Infection ; Pseudomonas Infections/drug therapy ; Pseudomonas aeruginosa ; Quality of Life
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2021-07-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1183617-9
    ISSN 1098-9048 ; 1069-3424
    ISSN (online) 1098-9048
    ISSN 1069-3424
    DOI 10.1055/s-0041-1730921
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  5. Article ; Online: Reconsidering ventilator-associated pneumonia from a new dimension of the lung microbiome.

    Fernández-Barat, Laia / López-Aladid, Ruben / Torres, Antoni

    EBioMedicine

    2020  Volume 60, Page(s) 102995

    Abstract: Complex microbial communities that reside in the lungs, skin and gut are now appreciated for their role in maintaining organ, tissue and immune homoeostasis. As lungs are currently seen as an ecosystem, the shift in paradigm calls for the consideration ... ...

    Abstract Complex microbial communities that reside in the lungs, skin and gut are now appreciated for their role in maintaining organ, tissue and immune homoeostasis. As lungs are currently seen as an ecosystem, the shift in paradigm calls for the consideration of new algorithms related to lung ecology in pulmonology. Evidence of lung microbiota does not solely challenge the traditional physiopathology of ventilator-associated pneumonia (VAP); indeed, it also reinforces the need to include molecular techniques in VAP diagnosis and accelerate the use of immunomodulatory drugs, including corticosteroids, and other supplements such as probiotics for VAP prevention and/or treatment. With that stated, both microbiome and virome, including phageome, can lead to new opportunities in further understanding the relationship between health and dysbiosis in VAP. Previous knowledge may be, however, reconsidered at a microbiome scale.
    MeSH term(s) Disease Management ; Disease Susceptibility ; Dysbiosis ; Gastrointestinal Microbiome ; Humans ; Microbiota ; Mouth/microbiology ; Pneumonia, Ventilator-Associated/diagnosis ; Pneumonia, Ventilator-Associated/etiology ; Pneumonia, Ventilator-Associated/prevention & control ; Pneumonia, Ventilator-Associated/therapy ; Respiratory Mucosa/microbiology ; Virome
    Keywords covid19
    Language English
    Publishing date 2020-09-16
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2851331-9
    ISSN 2352-3964
    ISSN (online) 2352-3964
    DOI 10.1016/j.ebiom.2020.102995
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  6. Article ; Online: Brewpitopes

    Roc Farriol-Duran / Ruben López-Aladid / Eduard Porta-Pardo / Antoni Torres / Laia Fernández-Barat

    Frontiers in Immunology, Vol

    a pipeline to refine B-cell epitope predictions during public health emergencies

    2023  Volume 14

    Abstract: The application of B-cell epitope identification to develop therapeutic antibodies and vaccine candidates is well established. However, the validation of epitopes is time-consuming and resource-intensive. To alleviate this, in recent years, multiple ... ...

    Abstract The application of B-cell epitope identification to develop therapeutic antibodies and vaccine candidates is well established. However, the validation of epitopes is time-consuming and resource-intensive. To alleviate this, in recent years, multiple computational predictors have been developed in the immunoinformatics community. Brewpitopes is a pipeline that curates bioinformatic B-cell epitope predictions obtained by integrating different state-of-the-art tools. We used additional computational predictors to account for subcellular location, glycosylation status, and surface accessibility of the predicted epitopes. The implementation of these sets of rational filters optimizes in vivo antibody recognition properties of the candidate epitopes. To validate Brewpitopes, we performed a proteome-wide analysis of SARS-CoV-2 with a particular focus on S protein and its variants of concern. In the S protein, we obtained a fivefold enrichment in terms of predicted neutralization versus the epitopes identified by individual tools. We analyzed epitope landscape changes caused by mutations in the S protein of new viral variants that were linked to observed immune escape evidence in specific strains. In addition, we identified a set of epitopes with neutralizing potential in four SARS-CoV-2 proteins (R1AB, R1A, AP3A, and ORF9C). These epitopes and antigenic proteins are conserved targets for viral neutralization studies. In summary, Brewpitopes is a powerful pipeline that refines B-cell epitope bioinformatic predictions during public health emergencies in a high-throughput capacity to facilitate the optimization of experimental validation of therapeutic antibodies and candidate vaccines.
    Keywords bioinformatics and computational biology ; immunology and infectious diseases ; vaccine development ; antibody therapeutics ; epitope prediction and antigenicity prediction ; Immunologic diseases. Allergy ; RC581-607
    Subject code 570
    Language English
    Publishing date 2023-12-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: The efficacy of telavancin in comparison with linezolid on endotracheal tube biofilm in pigs with methicillin-resistant Staphylococcus aureus pneumonia.

    Kiarostami, Kasra / Fernández-Barat, Laia / Battaglini, Denise / Motos, Anna / Bueno-Freire, Leticia / Soler-Comas, Alba / Bassi, Gianluigi Li / Torres, Antoni

    International journal of antimicrobial agents

    2023  Volume 63, Issue 2, Page(s) 107052

    Abstract: Background: The effect of systemic treatment of ventilator-associated pneumonia (VAP) with telavancin, a semisynthetic lipoglycopeptide with good penetration in vitro biofilms, has not been tested in vivo during mechanical ventilation. This study ... ...

    Abstract Background: The effect of systemic treatment of ventilator-associated pneumonia (VAP) with telavancin, a semisynthetic lipoglycopeptide with good penetration in vitro biofilms, has not been tested in vivo during mechanical ventilation. This study examined the efficacy of telavancin compared with linezolid against endotracheal tube (ETT) biofilms in a porcine model of methicillin-resistant Staphylococcus aureus (MRSA) VAP.
    Methods: VAP was induced in 18 pigs by instilling 10
    Results: All 18 pigs completed the study. MRSA was isolated in 100% of ETTs from the control and linezolid groups and in 67% from the telavancin group. Telavancin treatment presented a lower MRSA load compared to the control and linezolid treatments (telavancin median [interquartile range (IQR)] = 1.94 [0.00-5.45], linezolid 3.99 [3.22-4.68] and control 4.93 [4.41-5.15], P = 0.236). Telavancin treatment also resulted in the lowest biofilm thickness according to the SEM (4.04 [2.09-6.00], P < 0.001). We found a positive correlation between ETT and BAL load (rho = 0.511, P = 0.045).
    Conclusions: In our VAP model, systemic telavancin treatment reduced ETT MRSA occurrence, load, and biofilm thickness. Our findings may have a bearing on ICU patients' clinical outcomes.
    MeSH term(s) Animals ; Aminoglycosides ; Anti-Bacterial Agents/therapeutic use ; Anti-Bacterial Agents/pharmacology ; Biofilms ; Intubation, Intratracheal/methods ; Linezolid/pharmacology ; Linezolid/therapeutic use ; Lipoglycopeptides/therapeutic use ; Methicillin-Resistant Staphylococcus aureus ; Pneumonia, Staphylococcal/drug therapy ; Pneumonia, Ventilator-Associated/drug therapy ; Swine ; Vancomycin/pharmacology ; Vancomycin/therapeutic use ; Disease Models, Animal
    Chemical Substances Aminoglycosides ; Anti-Bacterial Agents ; Linezolid (ISQ9I6J12J) ; Lipoglycopeptides ; telavancin (XK134822Z0) ; Vancomycin (6Q205EH1VU)
    Language English
    Publishing date 2023-12-09
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1093977-5
    ISSN 1872-7913 ; 0924-8579
    ISSN (online) 1872-7913
    ISSN 0924-8579
    DOI 10.1016/j.ijantimicag.2023.107052
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    Zs.A 3368: Show issues Location:
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    Zs.MO 500: Show issues

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  8. Article ; Online: Reconsidering ventilator-associated pneumonia from a new dimension of the lung microbiome

    Laia Fernández-Barat / Ruben López-Aladid / Antoni Torres

    EBioMedicine, Vol 60, Iss , Pp 102995- (2020)

    2020  

    Abstract: Complex microbial communities that reside in the lungs, skin and gut are now appreciated for their role in maintaining organ, tissue and immune homoeostasis. As lungs are currently seen as an ecosystem, the shift in paradigm calls for the consideration ... ...

    Abstract Complex microbial communities that reside in the lungs, skin and gut are now appreciated for their role in maintaining organ, tissue and immune homoeostasis. As lungs are currently seen as an ecosystem, the shift in paradigm calls for the consideration of new algorithms related to lung ecology in pulmonology. Evidence of lung microbiota does not solely challenge the traditional physiopathology of ventilator-associated pneumonia (VAP); indeed, it also reinforces the need to include molecular techniques in VAP diagnosis and accelerate the use of immunomodulatory drugs, including corticosteroids, and other supplements such as probiotics for VAP prevention and/or treatment.With that stated, both microbiome and virome, including phageome, can lead to new opportunities in further understanding the relationship between health and dysbiosis in VAP. Previous knowledge may be, however, reconsidered at a microbiome scale.
    Keywords Ventilator-associated pneumonia ; Next-generation sequencing ; Microbiota ; Endotracheal tubes ; Mycobiome ; Virome ; Medicine ; R ; Medicine (General) ; R5-920
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Biofilms in ventilator-associated pneumonia.

    Fernández-Barat, Laia / Torres, Antoni

    Future microbiology

    2016  Volume 11, Page(s) 1599–1610

    Abstract: Biofilms develop rapidly following endotracheal intubation and represent a persistent source of unnecessary pathogens in the critically ill patient. Overall, the imbalance in the lung microbiome caused by an endotracheal tube and its role in biofilm ... ...

    Abstract Biofilms develop rapidly following endotracheal intubation and represent a persistent source of unnecessary pathogens in the critically ill patient. Overall, the imbalance in the lung microbiome caused by an endotracheal tube and its role in biofilm formation and in ventilator-associated pneumonia is still unclear. Although endotracheal tube-biofilm preventive measures are being tested, no outcome impact has ever been demonstrated, and therefore no approach has been clinically recommended. Nonetheless, an accurate description of the actual biofilm morphology in vivo could be useful to implement effective preventive measures. The combined use of in vitro biofilm models, in vivo animal models and clinical research is vitally important to the attainment of a comprehensive understanding of biofilms in ventilator-associated pneumonia in the near future.
    MeSH term(s) Animals ; Bacteria/genetics ; Bacteria/isolation & purification ; Bacterial Physiological Phenomena ; Biofilms ; Equipment Contamination ; Humans ; Pneumonia, Ventilator-Associated/microbiology ; Ventilators, Mechanical/microbiology
    Language English
    Publishing date 2016-12
    Publishing country England
    Document type Journal Article ; Review
    ISSN 1746-0921
    ISSN (online) 1746-0921
    DOI 10.2217/fmb-2016-0040
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  10. Article ; Online: Phage-based therapy: promising applicability in the control of oral dysbiosis and respiratory infections.

    Moda-Silva, Letícia S / Oliveira, Viviane C / Silva-Lovato, Cláudia H / Fernández-Barat, Laia / Watanabe, Evandro

    Future microbiology

    2022  Volume 17, Page(s) 1349–1352

    MeSH term(s) Humans ; Dysbiosis/therapy ; Phage Therapy ; Respiratory Tract Infections/therapy ; Bacteriophages
    Language English
    Publishing date 2022-09-28
    Publishing country England
    Document type Editorial ; Research Support, Non-U.S. Gov't
    ZDB-ID 2254620-0
    ISSN 1746-0921 ; 1746-0913
    ISSN (online) 1746-0921
    ISSN 1746-0913
    DOI 10.2217/fmb-2022-0149
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