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Chen CW, Ho CH. Substitutions in the nonactive site of the passenger domain on the activity of Haemophilus influenzae immunoglobulin A1 protease. Infect Immun 2024; 92:e0019324. [PMID: 38990045 PMCID: PMC11320935 DOI: 10.1128/iai.00193-24] [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: 04/29/2024] [Accepted: 06/22/2024] [Indexed: 07/12/2024] Open
Abstract
Immunoglobulin A1 (IgA1) protease is a critical virulence factor of Haemophilus influenzae that facilitates bacterial mucosal infection. This study investigates the effect of iga gene polymorphism on the enzymatic activity of H. influenzae IgA1 protease. The IgA1 protease activity was examined in the H. influenzae Rd KW20 strain and 51 isolates. Genetic variations in iga and deduced amino acid substitutions affecting IgA1 protease activity were assessed. Machine learning tools and functional complementation assays were used to analyze the effects of identified substitutions on the stability and activity of IgA1 protease, respectively. All 51 isolates exhibited similar iga expression levels. No igaB expression was detected. According to comparisons with the reference Rd KW20 strain, four substitutions in the protease domain, 26 in the nonprotease passenger domain, and two in the β-barrel domain were associated with the change in IgA1 protease activity. No substitutions in the catalytic site of IgA1 protease were observed. Logistic regression, receiver operating characteristic curves, Venn diagrams, and protein stability analyses revealed that the substitutions Asn352Lys, Pro353Ala, Lys356Asn, Gln916Lys, and Gly917Ser, which were located in the nonactive site of the passenger domain, were associated with decreases in IgA1 protease activity and stability, whereas Asn914Lys was associated with an increase in these events. Functional complementation assays revealed that the Asn914Lys substitution increased IgA1 protease activity in the Rd KW20 strain. This study identified substitutions in the nonactive site of the passenger domain that affect both the activity and stability of H. influenzae IgA1 protease.
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Affiliation(s)
- Chi-Wei Chen
- Graduate Degree Program of Smart Healthcare & Bioinformatics, College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan
- Department of Biomedical Engineering, College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan
| | - Cheng-Hsun Ho
- Department of Medical Laboratory Science, College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan
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2
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Kappler U, Henningham A, Nasreen M, Yamamoto A, Buultjens AH, Stinear TP, Sly P, Fantino E. Tolerance to Haemophilus influenzae infection in human epithelial cells: Insights from a primary cell-based model. PLoS Pathog 2024; 20:e1012282. [PMID: 38990812 PMCID: PMC11239077 DOI: 10.1371/journal.ppat.1012282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 05/22/2024] [Indexed: 07/13/2024] Open
Abstract
Haemophilus influenzae is a human respiratory pathogen and inhabits the human respiratory tract as its only niche. Despite this, the molecular mechanisms that allow H. influenzae to establish persistent infections of human epithelia are not well understood. Here, we have investigated how H. influenzae adapts to the host environment and triggers the host immune response using a human primary cell-based infection model that closely resembles human nasal epithelia (NHNE). Physiological assays combined with dualRNAseq revealed that NHNE from five healthy donors all responded to H. influenzae infection with an initial, 'unproductive' inflammatory response that included a strong hypoxia signature but did not produce pro-inflammatory cytokines. Subsequently, an apparent tolerance to large extracellular and intraepithelial burdens of H. influenzae developed, with NHNE transcriptional profiles resembling the pre-infection state. This occurred in parallel with the development of intraepithelial bacterial populations, and appears to involve interruption of NFκB signalling. This is the first time that large-scale, persistence-promoting immunomodulatory effects of H. influenzae during infection have been observed, and we were able to demonstrate that only infections with live, but not heat-killed H. influenzae led to immunomodulation and reduced expression of NFκB-controlled cytokines such as IL-1β, IL-36γ and TNFα. Interestingly, NHNE were able to re-activate pro-inflammatory responses towards the end of the 14-day infection, resulting in release of IL-8 and TNFα. In addition to providing first molecular insights into mechanisms enabling persistence of H. influenzae in the host, our data further indicate the presence of infection stage-specific gene expression modules, highlighting fundamental similarities between immune responses in NHNE and canonical immune cells, which merit further investigation.
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Affiliation(s)
- Ulrike Kappler
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Anna Henningham
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Marufa Nasreen
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Ayaho Yamamoto
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Andrew H. Buultjens
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Peter Sly
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Emmanuelle Fantino
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
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3
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Arleevskaya MI, Novikov AA, Valeeva AR, Korovina MO, Serdiuk IL, Popov VA, Carlé C, Renaudineau Y. At Early Rheumatoid Arthritis Stage, the Infectious Spectrum Is Driven by Non-Familial Factors and Anti-CCP Immunization. J Clin Med 2024; 13:2796. [PMID: 38792338 PMCID: PMC11122272 DOI: 10.3390/jcm13102796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/02/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Background/Objectives: Patients with rheumatoid arthritis (RA) are prone to develop infections. Methods: Accordingly, 195 untreated early (e)RA patients and 398 healthy controls were selected from women in Tatarstan's cohort to study infectious history in the anamnesis (four criteria) and in the previous year (16 criteria). Information about annual infections was collected face-to-face from year to year by a qualified rheumatologist/general practitioner and included the active use of information from medical records. Results: In the anamnesis, tuberculosis, and pneumonia, and in the previous year, respiratory tract infections, skin infections, and herpes simplex virus reactivation incidence were reported to be increased in eRA patients, as well as the event number and duration of acute and chronic tonsillitis. Moreover, more bacterial-suspected upper respiratory infections and urinary tract infections were retrieved in sporadic eRA patients as compared to familial eRA patients. An elevated immunization against CCP prevented respiratory tract infection in those with HSV exacerbation. Finally, associations were retrieved between infection (event number/delay) and RA indices: (i) chronic tonsillitis exacerbations with disease activity and health assessment (HAQ) in familial eRA; (ii) bacterial-suspected upper respiratory infections with the number of swollen and tender joints in sporadic eRA; and (iii) HSV exacerbation with inflammation in eRA patients with negative/low response against CCP. Here, we demonstrate the complex nature of the interplay of RA with specific infections. Conclusions: For the first time, differences in the patterns of annual trivial infections and their links with RA indices were found in cohorts of familial and sporadic cases of the disease. Additionally, for the first time, we identified a remarkable relationship between early RA and exacerbations of chronic tonsillitis, as well as tuberculosis in the patient's history. Altogether, this study supports the existence of a complex interplay between infections and RA at onset driven by familial status and the presence of anti-CCP Ab at elevated levels.
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Affiliation(s)
- Marina I. Arleevskaya
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (A.R.V.); (M.O.K.); (I.L.S.)
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Andrej A. Novikov
- Institute of Artificial Intelligence, Innopolis University, 420500 Innopolis, Russia;
| | - Anna R. Valeeva
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (A.R.V.); (M.O.K.); (I.L.S.)
- Institute of Environmental Sciences, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Marina O. Korovina
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (A.R.V.); (M.O.K.); (I.L.S.)
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Igor L. Serdiuk
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (A.R.V.); (M.O.K.); (I.L.S.)
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Vladimir A. Popov
- Institute of Physics, Kazan (Volga Region) Federal University, 420008 Kazan, Russia;
| | - Caroline Carlé
- Department of Immunology, Hôspital Purpan, INSERM U1291, CNRS U5051, Université Toulouse IIII, 31062 Toulouse, France; (C.C.); (Y.R.)
| | - Yves Renaudineau
- Department of Immunology, Hôspital Purpan, INSERM U1291, CNRS U5051, Université Toulouse IIII, 31062 Toulouse, France; (C.C.); (Y.R.)
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4
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Ariolli A, Canè M, Di Fede M, Tavarini S, Taddei AR, Buno KP, Delany I, Rossi Paccani S, Pezzicoli A. Modeling airway persistent infection of Moraxella catarrhalis and nontypeable Haemophilus influenzae by using human in vitro models. Front Cell Infect Microbiol 2024; 14:1397940. [PMID: 38751999 PMCID: PMC11094313 DOI: 10.3389/fcimb.2024.1397940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/12/2024] [Indexed: 05/18/2024] Open
Abstract
Non-typeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mcat) are two common respiratory tract pathogens often associated with acute exacerbations in Chronic Obstructive Pulmonary Disease (COPD) as well as with otitis media (OM) in children. Although there is evidence that these pathogens can adopt persistence mechanisms such as biofilm formation, the precise means through which they contribute to disease severity and chronicity remains incompletely understood, posing challenges for their effective eradication. The identification of potential vaccine candidates frequently entails the characterization of the host-pathogen interplay in vitro even though this approach is limited by the fact that conventional models do not permit long term bacterial infections. In the present work, by using air-liquid-interface (ALI) human airway in vitro models, we aimed to recreate COPD-related persistent bacterial infections. In particular, we explored an alternative use of the ALI system consisting in the assembly of an inverted epithelium grown on the basal part of a transwell membrane with the aim to enable the functionality of natural defense mechanisms such as mucociliary clearance and cellular extrusion that are usually hampered during conventional ALI infection experiments. The inversion of the epithelium did not affect tissue differentiation and considerably delayed NTHi or Mcat infection progression, allowing one to monitor host-pathogen interactions for up to three weeks. Notably, the use of these models, coupled with confocal and transmission electron microscopy, revealed unique features associated with NTHi and Mcat infection, highlighting persistence strategies including the formation of intracellular bacterial communities (IBCs) and surface-associated biofilm-like structures. Overall, this study demonstrates the possibility to perform long term host-pathogen investigations in vitro with the aim to define persistence mechanisms adopted by respiratory pathogens and individuate potential new vaccine targets.
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Affiliation(s)
- Andrea Ariolli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Martina Canè
- Department of Biology, University of Naples Federico II, Napoli, Italy
| | - Martina Di Fede
- GlaxoSmithKline Vaccines s.r.l., Preclinical R&D, Siena, Italy
| | - Simona Tavarini
- GlaxoSmithKline Vaccines s.r.l., Preclinical R&D, Siena, Italy
| | - Anna Rita Taddei
- Great Equipment Center-Section of Electron Microscopy, University of Tuscia, Viterbo, Italy
| | - Kevin Pete Buno
- GlaxoSmithKline Vaccines s.r.l., Preclinical R&D, Siena, Italy
| | - Isabel Delany
- GlaxoSmithKline Vaccines s.r.l., Preclinical R&D, Siena, Italy
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5
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Nasreen M, Ellis D, Hosmer J, Essilfie AT, Fantino E, Sly P, McEwan AG, Kappler U. The DmsABC S-oxide reductase is an essential component of a novel, hypochlorite-inducible system of extracellular stress defense in Haemophilus influenzae. Front Microbiol 2024; 15:1359513. [PMID: 38638903 PMCID: PMC11024254 DOI: 10.3389/fmicb.2024.1359513] [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: 12/21/2023] [Accepted: 03/11/2024] [Indexed: 04/20/2024] Open
Abstract
Defenses against oxidative damage to cell components are essential for survival of bacterial pathogens during infection, and here we have uncovered that the DmsABC S-/N-oxide reductase is essential for virulence and in-host survival of the human-adapted pathogen, Haemophilus influenzae. In several different infection models, H. influenzae ΔdmsA strains showed reduced immunogenicity as well as lower levels of survival in contact with host cells. Expression of DmsABC was induced in the presence of hypochlorite and paraquat, closely linking this enzyme to defense against host-produced antimicrobials. In addition to methionine sulfoxide, DmsABC converted nicotinamide- and pyrimidine-N-oxide, precursors of NAD and pyrimidine for which H. influenzae is an auxotroph, at physiologically relevant concentrations, suggesting that these compounds could be natural substrates for DmsABC. Our data show that DmsABC forms part of a novel, periplasmic system for defense against host-induced S- and N-oxide stress that also comprises the functionally related MtsZ S-oxide reductase and the MsrAB peptide methionine sulfoxide reductase. All three enzymes are induced following exposure of the bacteria to hypochlorite. MsrAB is required for physical resistance to HOCl and protein repair. In contrast, DmsABC was required for intracellular colonization of host cells and, together with MtsZ, contributed to resistance to N-Chlorotaurine. Our work expands and redefines the physiological role of DmsABC and highlights the importance of different types of S-oxide reductases for bacterial virulence.
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Affiliation(s)
- Marufa Nasreen
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
| | - Daniel Ellis
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
| | - Jennifer Hosmer
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
| | | | | | - Peter Sly
- Child Health Research Centre, South Brisbane, QLD, Australia
| | - Alastair G. McEwan
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
| | - Ulrike Kappler
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
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6
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Walsh D, Bevan J, Harrison F. How Does Airway Surface Liquid Composition Vary in Different Pulmonary Diseases, and How Can We Use This Knowledge to Model Microbial Infections? Microorganisms 2024; 12:732. [PMID: 38674677 PMCID: PMC11052052 DOI: 10.3390/microorganisms12040732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Growth environment greatly alters many facets of pathogen physiology, including pathogenesis and antimicrobial tolerance. The importance of host-mimicking environments for attaining an accurate picture of pathogen behaviour is widely recognised. Whilst this recognition has translated into the extensive development of artificial cystic fibrosis (CF) sputum medium, attempts to mimic the growth environment in other respiratory disease states have been completely neglected. The composition of the airway surface liquid (ASL) in different pulmonary diseases is far less well characterised than CF sputum, making it very difficult for researchers to model these infection environments. In this review, we discuss the components of human ASL, how different lung pathologies affect ASL composition, and how different pathogens interact with these components. This will provide researchers interested in mimicking different respiratory environments with the information necessary to design a host-mimicking medium, allowing for better understanding of how to treat pathogens causing infection in these environments.
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Affiliation(s)
- Dean Walsh
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.H.)
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7
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Malik S, Asghar M, Waheed Y. Outlining recent updates on influenza therapeutics and vaccines: A comprehensive review. Vaccine X 2024; 17:100452. [PMID: 38328274 PMCID: PMC10848012 DOI: 10.1016/j.jvacx.2024.100452] [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: 07/03/2023] [Revised: 12/27/2023] [Accepted: 01/29/2024] [Indexed: 02/09/2024] Open
Abstract
Influenza virus has presented a considerable healthcare challenge during the past years, particularly in vulnerable groups with compromised immune systems. Therapeutics and vaccination have always been in research annals since the spread of influenza. Efforts have been going on to develop an antiviral therapeutic approach that could assist in better disease management and reduce the overall disease complexity, resistance development, and fatality rates. On the other hand, vaccination presents a chance for effective, long-term, cost-benefit, and preventive response against the morbidity and mortality associated with the influenza. However, the issues of resistance development, strain mutation, antigenic variability, and inability to cure wide-spectrum and large-scale strains of the virus by available vaccines remain there. The article gathers the updated data for the therapeutics and available influenza vaccines, their mechanism of action, shortcomings, and trials under clinical experimentation. A methodological approach has been adopted to identify the prospective therapeutics and available vaccines approved and within the clinical trials against the influenza virus. Review contains influenza therapeutics, including traditional and novel antiviral drugs and inhibitor therapies against influenza virus as well as research trials based on newer drug combinations and latest technologies such as nanotechnology and organic and plant-based natural products. Most recent development of influenza vaccine has been discussed including some updates on traditional vaccination protocols and discussion on next-generation and upgraded novel technologies. This review will help the readers to understand the righteous approach for dealing with influenza virus infection and for deducing futuristic approaches for novel therapeutic and vaccine trials against Influenza.
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Affiliation(s)
- Shiza Malik
- Bridging Health Foundation, Rawalpindi, Punjab 46000, Pakistan
| | - Muhammad Asghar
- Department of Biology, Lund University, Sweden
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Yasir Waheed
- Office of Research, Innovation, and Commercialization (ORIC), Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad 44000, Pakistan
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos 1401, Lebanon
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8
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Gil-Campillo C, González-Díaz A, Rapún-Araiz B, Iriarte-Elizaintzin O, Elizalde-Gutiérrez I, Fernández-Calvet A, Lázaro-Díez M, Martí S, Garmendia J. Imipenem heteroresistance but not tolerance in Haemophilus influenzae during chronic lung infection associated with chronic obstructive pulmonary disease. Front Microbiol 2023; 14:1253623. [PMID: 38179447 PMCID: PMC10765533 DOI: 10.3389/fmicb.2023.1253623] [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: 07/05/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024] Open
Abstract
Antibiotic resistance is a major Public Health challenge worldwide. Mechanisms other than resistance are described as contributors to therapeutic failure. These include heteroresistance and tolerance, which escape the standardized procedures used for antibiotic treatment decision-making as they do not involve changes in minimal inhibitory concentration (MIC). Haemophilus influenzae causes chronic respiratory infection and is associated with exacerbations suffered by chronic obstructive pulmonary disease (COPD) patients. Although resistance to imipenem is rare in this bacterial species, heteroresistance has been reported, and antibiotic tolerance cannot be excluded. Moreover, development of antibiotic heteroresistance or tolerance during within-host H. influenzae pathoadaptive evolution is currently unknown. In this study, we assessed imipenem resistance, heteroresistance and tolerance in a previously sequenced longitudinal collection of H. influenzae COPD respiratory isolates. The use of Etest, disc diffusion, population analysis profiling, tolerance disc (TD)-test methods, and susceptibility breakpoint criteria when available, showed a significant proportion of imipenem heteroresistance with differences in terms of degree among strains, absence of imipenem tolerance, and no specific trends among serial and clonally related strains could be established. Analysis of allelic variation in the ftsI, acrA, acrB, and acrR genes rendered a panel of polymorphisms only found in heteroresistant strains, but gene expression and genome-wide analyses did not show clear genetic traits linked to heteroresistance. In summary, a significant proportion of imipenem heteroresistance was observed among H. influenzae strains isolated from COPD respiratory samples over time. These data should be useful for making more accurate clinical recommendations to COPD patients.
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Affiliation(s)
- Celia Gil-Campillo
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Conexion Nanomedicina CSIC (NanomedCSIC), Madrid, Spain
| | - Aida González-Díaz
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Beatriz Rapún-Araiz
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
- Conexion Nanomedicina CSIC (NanomedCSIC), Madrid, Spain
| | - Oihane Iriarte-Elizaintzin
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Iris Elizalde-Gutiérrez
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Ariadna Fernández-Calvet
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - María Lázaro-Díez
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Sara Martí
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Junkal Garmendia
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Conexion Nanomedicina CSIC (NanomedCSIC), Madrid, Spain
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9
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Rapún-Araiz B, Sorzabal-Bellido I, Asensio-López J, Lázaro-Díez M, Ariz M, Sobejano de la Merced C, Euba B, Fernández-Calvet A, Cortés-Domínguez I, Burgui S, Toledo-Arana A, Ortiz-de-Solórzano C, Garmendia J. In vitro modeling of polyclonal infection dynamics within the human airways by Haemophilus influenzae differential fluorescent labeling. Microbiol Spectr 2023; 11:e0099323. [PMID: 37795992 PMCID: PMC10714817 DOI: 10.1128/spectrum.00993-23] [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: 03/08/2023] [Accepted: 08/22/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Genomic diversity of nontypeable H. influenzae strains confers phenotypic heterogeneity. Multiple strains of H. influenzae can be simultaneously isolated from clinical specimens, but we lack detailed information about polyclonal infection dynamics by this pathogen. A long-term barrier to our understanding of this host-pathogen interplay is the lack of genetic tools for strain engineering and differential labeling. Here, we present a novel plasmid toolkit named pTBH (toolbox for Haemophilus), with standardized modules for fluorescent or bioluminescent labeling, adapted to H. influenzae requirements but designed to be versatile so it can be utilized in other bacterial species. We present detailed experimental and quantitative image analysis methods, together with proof-of-principle examples, and show the ample possibilities of 3D microscopy, combined with quantitative image analysis, to model H. influenzae polyclonal infection lifestyles and unravel the co-habitation and co-infection dynamics of this respiratory pathogen.
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Grants
- RTI2018-094494-B-C22 Ministerio de Ciencia, Innovación y Universidades (MCIU)
- PDI2021-122409OB-C22 Ministerio de Ciencia, Innovación y Universidades (MCIU)
- RTI2018-096369-B-I00 Ministerio de Ciencia, Innovación y Universidades (MCIU)
- PID2021-125947OB-I00 Ministerio de Ciencia, Innovación y Universidades (MCIU)
- 875/2019 Sociedad Española de Neumología y Cirugía Torácica (SEPAR)
- PC150 Dirección General de Industria, Energia y Proyectos Estrategicos S3, Gobierno de Navarra (Department of Industry of the Government of Navarra)
- PC136 Dirección General de Industria, Energia y Proyectos Estrategicos S3, Gobierno de Navarra (Department of Industry of the Government of Navarra)
- PC151 Dirección General de Industria, Energia y Proyectos Estrategicos S3, Gobierno de Navarra (Department of Industry of the Government of Navarra)
- PC137 Dirección General de Industria, Energia y Proyectos Estrategicos S3, Gobierno de Navarra (Department of Industry of the Government of Navarra)
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Affiliation(s)
- Beatriz Rapún-Araiz
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
- Conexión Nanomedicina CSIC (NanomedCSIC), Mutilva, Spain
| | - Ioritz Sorzabal-Bellido
- Laboratorio de Sistemas Microfisiológicos y Biología Cuantitativa, Programa de Ingeniería Biomédica, Centro de Investigación Médica Aplicada (CIMA), Pamplona, Spain
| | - Javier Asensio-López
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
- Conexión Nanomedicina CSIC (NanomedCSIC), Mutilva, Spain
- Asociación de la Industria Navarra (AIN)-Gobierno de Navarra, Cordovilla, Spain
| | - María Lázaro-Díez
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
- Conexión Nanomedicina CSIC (NanomedCSIC), Mutilva, Spain
| | - Mikel Ariz
- Laboratorio de Sistemas Microfisiológicos y Biología Cuantitativa, Programa de Ingeniería Biomédica, Centro de Investigación Médica Aplicada (CIMA), Pamplona, Spain
| | - Carlos Sobejano de la Merced
- Laboratorio de Sistemas Microfisiológicos y Biología Cuantitativa, Programa de Ingeniería Biomédica, Centro de Investigación Médica Aplicada (CIMA), Pamplona, Spain
| | - Begoña Euba
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
- Conexión Nanomedicina CSIC (NanomedCSIC), Mutilva, Spain
| | - Ariadna Fernández-Calvet
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Ivan Cortés-Domínguez
- Laboratorio de Sistemas Microfisiológicos y Biología Cuantitativa, Programa de Ingeniería Biomédica, Centro de Investigación Médica Aplicada (CIMA), Pamplona, Spain
| | - Saioa Burgui
- Asociación de la Industria Navarra (AIN)-Gobierno de Navarra, Cordovilla, Spain
| | - Alejandro Toledo-Arana
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Carlos Ortiz-de-Solórzano
- Laboratorio de Sistemas Microfisiológicos y Biología Cuantitativa, Programa de Ingeniería Biomédica, Centro de Investigación Médica Aplicada (CIMA), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Oncológicas (CIBERONC), Madrid, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Junkal Garmendia
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
- Conexión Nanomedicina CSIC (NanomedCSIC), Mutilva, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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10
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Osorio-Aguilar Y, Gonzalez-Vazquez MC, Lozano-Zarain P, Martinez-Laguna Y, Baylon-Pacheco L, Rosales-Encina JL, Carabarin-Lima A, Rocha-Gracia RDC. The Enolase of the Haemophilus influenzae Mediates Binding to Collagens: An Extracellular Matrix Component. Int J Mol Sci 2023; 24:15499. [PMID: 37958487 PMCID: PMC10650631 DOI: 10.3390/ijms242115499] [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: 08/08/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
Enolase proteins play a significant role as moonlighting proteins. In their role as surface-associated enolase, they have multiple functions as they interact with extracellular matrix proteins. Type I and III collagens are the major constituents of this extracellular matrix, and collagen is one of the targets of interaction with the enolase of many pathogens, thereby helping the colonization process and promoting the subsequent invasion of the host. This work aimed to determine the participation of non-typeable H. influenzae enolase as a collagen-binding protein. In this study, through the use of in vitro tests it was demonstrated that recombinant enolase of non-typeable H. influenzae (rNTHiENO) strongly binds to type I collagen. Using molecular docking, the residues that could take part in the interaction of non-typeable H. influenzae enolase-type I collagen (NTHiENO-Cln I) and non-typeable H. influenzae enolase-type III collagen (NTHiENO-Cln III) were identified. However, in vitro assays show that NTHiENO has a better affinity to interact with Cln I, concerning type Cln III. The interaction of NTHiENO with collagen could play a significant role in the colonization process; this would allow H. influenzae to increase its virulence factors and strengthen its pathogenesis.
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Affiliation(s)
- Yesenia Osorio-Aguilar
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (Y.O.-A.); (P.L.-Z.); (Y.M.-L.)
| | - Maria Cristina Gonzalez-Vazquez
- Licenciatura en Biotecnología, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (M.C.G.-V.); (A.C.-L.)
| | - Patricia Lozano-Zarain
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (Y.O.-A.); (P.L.-Z.); (Y.M.-L.)
| | - Ygnacio Martinez-Laguna
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (Y.O.-A.); (P.L.-Z.); (Y.M.-L.)
| | - Lidia Baylon-Pacheco
- Departamento de Infectómica y Patogenesis Molecular, CINVESTAV-IPN, Avenida Instituto Politécnico Nacional No. 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, Mexico City 07360, Mexico; (L.B.-P.); (J.L.R.-E.)
| | - Jose Luis Rosales-Encina
- Departamento de Infectómica y Patogenesis Molecular, CINVESTAV-IPN, Avenida Instituto Politécnico Nacional No. 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, Mexico City 07360, Mexico; (L.B.-P.); (J.L.R.-E.)
| | - Alejandro Carabarin-Lima
- Licenciatura en Biotecnología, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (M.C.G.-V.); (A.C.-L.)
| | - Rosa del Carmen Rocha-Gracia
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (Y.O.-A.); (P.L.-Z.); (Y.M.-L.)
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11
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Euba B, Gil-Campillo C, Asensio-López J, López-López N, Sen-Kilic E, Díez-Martínez R, Burgui S, Barbier M, Garmendia J. In Vivo Genome-Wide Gene Expression Profiling Reveals That Haemophilus influenzae Purine Synthesis Pathway Benefits Its Infectivity within the Airways. Microbiol Spectr 2023; 11:e0082323. [PMID: 37195232 PMCID: PMC10269889 DOI: 10.1128/spectrum.00823-23] [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: 02/23/2023] [Accepted: 04/27/2023] [Indexed: 05/18/2023] Open
Abstract
Haemophilus influenzae is a human-adapted bacterial pathogen that causes airway infections. Bacterial and host elements associated with the fitness of H. influenzae within the host lung are not well understood. Here, we exploited the strength of in vivo-omic analyses to study host-microbe interactions during infection. We used in vivo transcriptome sequencing (RNA-seq) for genome-wide profiling of both host and bacterial gene expression during mouse lung infection. Profiling of murine lung gene expression upon infection showed upregulation of lung inflammatory response and ribosomal organization genes, and downregulation of cell adhesion and cytoskeleton genes. Transcriptomic analysis of bacteria recovered from bronchoalveolar lavage fluid samples from infected mice showed a significant metabolic rewiring during infection, which was highly different from that obtained upon bacterial in vitro growth in an artificial sputum medium suitable for H. influenzae. In vivo RNA-seq revealed upregulation of bacterial de novo purine biosynthesis, genes involved in non-aromatic amino acid biosynthesis, and part of the natural competence machinery. In contrast, the expression of genes involved in fatty acid and cell wall synthesis and lipooligosaccharide decoration was downregulated. Correlations between upregulated gene expression and mutant attenuation in vivo were established, as observed upon purH gene inactivation leading to purine auxotrophy. Likewise, the purine analogs 6-thioguanine and 6-mercaptopurine reduced H. influenzae viability in a dose-dependent manner. These data expand our understanding of H. influenzae requirements during infection. In particular, H. influenzae exploits purine nucleotide synthesis as a fitness determinant, raising the possibility of purine synthesis as an anti-H. influenzae target. IMPORTANCE In vivo-omic strategies offer great opportunities for increased understanding of host-pathogen interplay and for identification of therapeutic targets. Here, using transcriptome sequencing, we profiled host and pathogen gene expression during H. influenzae infection within the murine airways. Lung pro-inflammatory gene expression reprogramming was observed. Moreover, we uncovered bacterial metabolic requirements during infection. In particular, we identified purine synthesis as a key player, highlighting that H. influenzae may face restrictions in purine nucleotide availability within the host airways. Therefore, blocking this biosynthetic process may have therapeutic potential, as supported by the observed inhibitory effect of 6-thioguanine and 6-mercaptopurine on H. influenzae growth. Together, we present key outcomes and challenges for implementing in vivo-omics in bacterial airway pathogenesis. Our findings provide metabolic insights into H. influenzae infection biology, raising the possibility of purine synthesis as an anti-H. influenzae target and of purine analog repurposing as an antimicrobial strategy against this pathogen.
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Affiliation(s)
- Begoña Euba
- Instituto de Agrobiotecnología (IDAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Celia Gil-Campillo
- Instituto de Agrobiotecnología (IDAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Mutilva, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Javier Asensio-López
- Instituto de Agrobiotecnología (IDAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Mutilva, Spain
- Asociación de la Industria Navarra (AIN)-Gobierno de Navarra, Cordovilla, Spain
| | - Nahikari López-López
- Instituto de Agrobiotecnología (IDAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Mutilva, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Emel Sen-Kilic
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | | | - Saioa Burgui
- Asociación de la Industria Navarra (AIN)-Gobierno de Navarra, Cordovilla, Spain
| | - Mariette Barbier
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | - Junkal Garmendia
- Instituto de Agrobiotecnología (IDAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Mutilva, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Conexión Nanomedicina-CSIC, Madrid, Spain
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12
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Murphy TF, Kirkham C, D’Mello A, Sethi S, Pettigrew MM, Tettelin H. Adaptation of Nontypeable Haemophilus influenzae in Human Airways in COPD: Genome Rearrangements and Modulation of Expression of HMW1 and HMW2. mBio 2023; 14:e0014023. [PMID: 36927061 PMCID: PMC10127715 DOI: 10.1128/mbio.00140-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/18/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a common debilitating disorder that is the third most common cause of death globally. Chronic lower airway infection by nontypeable Haemophilus influenzae (NTHi) in adults with COPD increases airway inflammation, causes increased symptoms, and accelerates progressive loss of lung function. Little is known about the mechanisms by which NTHi survives in COPD airways. To explore this question, the present study analyzes, in detail, 14 prospectively collected, serial isolates of a strain that persisted for 543 days in a patient with COPD, including analysis of four gap-free complete genomes. The NTHi genome underwent inversion of a ~400-kb segment three times during persistence. This inversion event resulted in switching of expression of the HMW1A and HMW2A adhesins as the inversion sites are in the promoter regions of HMW1 and HMW2. Regulation of the level of expression of HMW 1 and HMW2 in the human airways was controlled by the ~400-kb inversion and by 7-bp repeats in the HMW promoters. Analysis of knockout mutants of the persistent strain demonstrated that HMW1 and HMW2 proteins both function in the adherence of NTHi to human respiratory epithelial cells during persistence and that HMW1 also facilitates invasion of epithelial cells. An inverse relationship between biofilm formation and HMW1 expression was observed during persistence. This work advances understanding of the mechanisms of persistence of NTHi in COPD airways, which can inform the development of novel interventions to treat and prevent chronic NTHi infection in COPD. IMPORTANCE Nontypeable Haemophilus influenzae (NTHi) persists in the lower airways of adults with chronic obstructive pulmonary disease (COPD) for months to years, increasing airway inflammation that accelerates the progressive loss of lung function. Understanding the mechanisms of persistence in human airways by NTHi is critical in developing novel interventions. Here, in detail, we studied longitudinally collected sequential isolates of a strain of NTHi that persisted in an adult with COPD, including analysis of four gap-free genomes and knockout mutants to elucidate how the genome adapts in human airways. The NTHi genome underwent a genome rearrangement during persistence and this inversion impacted regulation of expression of key virulence phenotypes, including adherence to respiratory epithelial cells, invasion of epithelial cells and biofilm formation. These novel observations advance our understanding of the mechanisms of persistence of NTHi in the airways of adults with COPD.
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Affiliation(s)
- Timothy F. Murphy
- Division of Infectious Diseases, Department of Medicine, University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - Charmaine Kirkham
- Division of Infectious Diseases, Department of Medicine, University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - Adonis D’Mello
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sanjay Sethi
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University at Buffalo, The State University of New York, Buffalo, New York, USA
- Department of Medicine, Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
| | - Melinda M. Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
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13
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Mathieu E, Marquant Q, Chain F, Bouguyon E, Saint-Criq V, Le-Goffic R, Descamps D, Langella P, Tompkins TA, Binda S, Thomas M. An Isolate of Streptococcus mitis Displayed In Vitro Antimicrobial Activity and Deleterious Effect in a Preclinical Model of Lung Infection. Nutrients 2023; 15:nu15020263. [PMID: 36678133 PMCID: PMC9867278 DOI: 10.3390/nu15020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023] Open
Abstract
Microbiota studies have dramatically increased over these last two decades, and the repertoire of microorganisms with potential health benefits has been considerably enlarged. The development of next generation probiotics from new bacterial candidates is a long-term strategy that may be more efficient and rapid with discriminative in vitro tests. Streptococcus strains have received attention regarding their antimicrobial potential against pathogens of the upper and, more recently, the lower respiratory tracts. Pathogenic bacterial strains, such as non-typable Haemophilus influenzae (NTHi), Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus), are commonly associated with acute and chronic respiratory diseases, and it could be interesting to fight against pathogens with probiotics. In this study, we show that a Streptococcus mitis (S. mitis) EM-371 strain, isolated from the buccal cavity of a human newborn and previously selected for promising anti-inflammatory effects, displayed in vitro antimicrobial activity against NTHi, P. aeruginosa or S. aureus. However, the anti-pathogenic in vitro activity was not sufficient to predict an efficient protective effect in a preclinical model. Two weeks of treatment with S. mitis EM-371 did not protect against, and even exacerbated, NTHi lung infection.
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Affiliation(s)
- Elliot Mathieu
- Micalis Institute, Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, UMR1319, F-78350 Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, F-75571 Paris, France
- Correspondence:
| | - Quentin Marquant
- Université Paris-Saclay, INRAE, UVSQ, VIM, F-78350 Jouy-en-Josas, France
- Laboratoire VIM-Suresnes, Hôpital Foch, F-92150 Suresnes, France
| | - Florian Chain
- Micalis Institute, Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, UMR1319, F-78350 Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, F-75571 Paris, France
| | - Edwige Bouguyon
- Université Paris-Saclay, INRAE, UVSQ, VIM, F-78350 Jouy-en-Josas, France
| | - Vinciane Saint-Criq
- Micalis Institute, Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, UMR1319, F-78350 Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, F-75571 Paris, France
| | - Ronan Le-Goffic
- Université Paris-Saclay, INRAE, UVSQ, VIM, F-78350 Jouy-en-Josas, France
| | - Delphyne Descamps
- Université Paris-Saclay, INRAE, UVSQ, VIM, F-78350 Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, UMR1319, F-78350 Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, F-75571 Paris, France
| | | | - Sylvie Binda
- Lallemand Health Solutions, Montreal, QC H4P 2R2, Canada
| | - Muriel Thomas
- Micalis Institute, Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, UMR1319, F-78350 Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, F-75571 Paris, France
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14
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Monoclonal antibodies that target extracellular DNABII proteins or the type IV pilus of nontypeable Haemophilus influenzae (NTHI) worked additively to disrupt 2-genera biofilms. Biofilm 2022; 4:100096. [PMID: 36532267 PMCID: PMC9747592 DOI: 10.1016/j.bioflm.2022.100096] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The biofilm state is the preferred lifestyle of bacteria in nature. Within a biofilm, the resident bacteria are protected from environmental stresses, antibiotics and other antimicrobials, including those due to multiple immune effectors of their host during conditions of disease. Thereby, biofilms contribute significantly to pathogenicity, recalcitrance to clearance and chronicity/recurrence of bacterial diseases, including diseases of the respiratory tract. In the absence of highly effective, biofilm-targeted therapeutics, antibiotics are commonly prescribed to attempt to treat these diseases, however, in light of the canonical resistance of biofilm-resident bacteria to antibiotic-mediated killing, this ineffectual practice often fails to resolve the diseased condition and contributes significantly to the global threat of rising antimicrobial resistance. Nontypeable Haemophilus influenzae is a common respiratory tract disease co-pathogen, often present in partnership with other airway pathogens. Herein we aspired to determine whether either of two monoclonal antibodies we developed, one specific for NTHI [directed against the majority subunit (PilA) of the type IV pilus (T4P) of NTHI] and the other able to act agnostically on all bacteria tested to date (directed against a structural protein of the biofilm matrix, a DNABII protein), were able to disrupt 2-genera biofilms wherein NTHI co-partnered with another respiratory tract pathogen. These monoclonals were tested singly as well as when within an antibody cocktail. The monoclonal directed against the NTHI antigen PilA was only effective on single species NTHI biofilms and not on single species biofilms formed by other unrelated species. However, when NTHI co-partnered with any of 5 respiratory tract pathogens tested here (Burkholderia cenocepacia, Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae or Moraxella catarrhalis), this exclusively NTHI-directed monoclonal was able to disrupt these 2-genera biofilms. Conversely, the monoclonal antibody directed against protective epitopes of a DNABII protein, significantly disrupted all single species and 2-genera biofilms, which reflected the universal presence of this structural protein in all tested biofilm matrices. However, greatest release of both pathogens from a 2-genera biofilm was uniformly achieved by incubation with a 1:1 cocktail of both monoclonals. These data support the use of an approach wherein patients with respiratory tract disease could be treated with a therapeutic monoclonal antibody cocktail to release NTHI and its common co-pathogens from the protective biofilm to be killed by either traditional antibiotics and/or host immune effectors.
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15
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Airway Epithelial Cell Junctions as Targets for Pathogens and Antimicrobial Therapy. Pharmaceutics 2022; 14:pharmaceutics14122619. [PMID: 36559113 PMCID: PMC9786141 DOI: 10.3390/pharmaceutics14122619] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Intercellular contacts between epithelial cells are established and maintained by the apical junctional complexes (AJCs). AJCs conserve cell polarity and build epithelial barriers to pathogens, inhaled allergens, and environmental particles in the respiratory tract. AJCs consist of tight junctions (TJs) and adherens junctions (AJs), which play a key role in maintaining the integrity of the airway barrier. Emerging evidence has shown that different microorganisms cause airway barrier dysfunction by targeting TJ and AJ proteins. This review discusses the pathophysiologic mechanisms by which several microorganisms (bacteria and viruses) lead to the disruption of AJCs in airway epithelial cells. We present recent progress in understanding signaling pathways involved in the formation and regulation of cell junctions. We also summarize the potential chemical inhibitors and pharmacological approaches to restore the integrity of the airway epithelial barrier. Understanding the AJCs-pathogen interactions and mechanisms by which microorganisms target the AJC and impair barrier function may further help design therapeutic innovations to treat these infections.
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16
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Brown MA, Jabeen M, Bharj G, Hinks TSC. Non-typeable Haemophilus influenzae airways infection: the next treatable trait in asthma? Eur Respir Rev 2022; 31:220008. [PMID: 36130784 PMCID: PMC9724834 DOI: 10.1183/16000617.0008-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 07/04/2022] [Indexed: 11/05/2022] Open
Abstract
Asthma is a complex, heterogeneous condition that affects over 350 million people globally. It is characterised by bronchial hyperreactivity and airways inflammation. A subset display marked airway neutrophilia, associated with worse lung function, higher morbidity and poor response to treatment. In these individuals, recent metagenomic studies have identified persistent bacterial infection, particularly with non-encapsulated strains of the Gram-negative bacterium Haemophilus influenzae. Here we review knowledge of non-typeable H. influenzae (NTHi) in the microbiology of asthma, the immune consequences of mucosal NTHi infection, various immune evasion mechanisms, and the clinical implications of NTHi infection for phenotyping and targeted therapies in neutrophilic asthma. Airway neutrophilia is associated with production of neutrophil chemokines and proinflammatory cytokines in the airways, including interleukin (IL)-1β, IL-6, IL-8, IL-12, IL-17A and tumour necrosis factor. NTHi adheres to and invades the lower respiratory tract epithelium, inducing the NLR family pyrin domain containing 3 (NLRP3) and absent in melanoma 2 (AIM2) inflammasomes. NTHi reduces expression of tight-junction proteins, impairing epithelial integrity, and can persist intracellularly. NTHi interacts with rhinoviruses synergistically via upregulation of intracellular cell adhesion molecule 1 and promotion of a neutrophilic environment, to which NTHi is adapted. We highlight the clinical relevance of this emerging pathogen and its relevance for the efficacy of long-term macrolide therapy in airways diseases, we identify important unanswered questions and we propose future directions for research.
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Affiliation(s)
- Mary Ashley Brown
- Respiratory Medicine Unit and National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), Experimental Medicine Division, Nuffield Dept of Medicine, University of Oxford, Oxford, UK
| | - Maisha Jabeen
- Respiratory Medicine Unit and National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), Experimental Medicine Division, Nuffield Dept of Medicine, University of Oxford, Oxford, UK
| | - Gurpreet Bharj
- Respiratory Medicine Unit and National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), Experimental Medicine Division, Nuffield Dept of Medicine, University of Oxford, Oxford, UK
- Mammalian Genetics Unit, MRC Harwell Institute, Oxford, UK
| | - Timothy S C Hinks
- Respiratory Medicine Unit and National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), Experimental Medicine Division, Nuffield Dept of Medicine, University of Oxford, Oxford, UK
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17
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Hall-Stoodley L, McCoy KS. Biofilm aggregates and the host airway-microbial interface. Front Cell Infect Microbiol 2022; 12:969326. [PMID: 36081767 PMCID: PMC9445362 DOI: 10.3389/fcimb.2022.969326] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Biofilms are multicellular microbial aggregates that can be associated with host mucosal epithelia in the airway, gut, and genitourinary tract. The host environment plays a critical role in the establishment of these microbial communities in both health and disease. These host mucosal microenvironments however are distinct histologically, functionally, and regarding nutrient availability. This review discusses the specific mucosal epithelial microenvironments lining the airway, focusing on: i) biofilms in the human respiratory tract and the unique airway microenvironments that make it exquisitely suited to defend against infection, and ii) how airway pathophysiology and dysfunctional barrier/clearance mechanisms due to genetic mutations, damage, and inflammation contribute to biofilm infections. The host cellular responses to infection that contribute to resolution or exacerbation, and insights about evaluating and therapeutically targeting airway-associated biofilm infections are briefly discussed. Since so many studies have focused on Pseudomonas aeruginosa in the context of cystic fibrosis (CF) or on Haemophilus influenzae in the context of upper and lower respiratory diseases, these bacteria are used as examples. However, there are notable differences in diseased airway microenvironments and the unique pathophysiology specific to the bacterial pathogens themselves.
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Affiliation(s)
- Luanne Hall-Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, United States
- *Correspondence: Luanne Hall-Stoodley,
| | - Karen S. McCoy
- Division of Pulmonary Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
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18
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Wu X, Wei X, Li X, Deng J, Zhang J. Diversity of fungi and bacteria in bronchoalveolar lavage fluid during development of chronic obstructive pulmonary disease. Jpn J Infect Dis 2022; 75:560-568. [PMID: 35908874 DOI: 10.7883/yoken.jjid.2022.153] [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: 11/17/2022]
Abstract
The dynamic changes in microbiome during chronic obstructive pulmonary disease (COPD) exacerbations remains unclear. Using 16S ribosomal DNA and fungal internal transcribed spacer DNA sequencing, we described the composition and changes in the bacterial and fungal microbiota of bronchoalveolar lavage fluid (BALF) samples from 15 COPD patients and 7 non-COPD patients. In COPD patients, the dominant bacteria phyla were Proteobacteria, Firmicutes, Bacteroidete and Actinobacteria. The most abundant fungal phyla were Ascomycota and Basidiomycota. In terms of the genera of the bacteria and fungi, the numbers of Veillonella, Prevotella-7, Haemophilus, and Aspergillus were significantly more in COPD compared with the non-COPD patients. In addition, after the progression of COPD, the relative abundances of fungal genera of Aspergillus, Mortierella, Grifola, Thermoascus, Russula, and Thermomyces and the bacteria genera of Proteobacteria increased significantly. Existing analyses demonstrate changes in the diversity of bacterial and fungal communities, which appeared to be related to COPD. Our results demonstrated the potential utility of the microbiota as possible biomarkers for disease progression and provided therapeutic targets for COPD.
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Affiliation(s)
- Xin Wu
- Department of Respiratory and Critical Medicine, The First Affiliated Hospital of Guangxi Medical University, China.,Department of Respiratory Medicine, The Forth Affiliated Hospital of Guangxi Medical University, China
| | - Xuan Wei
- Department of Respiratory and Critical Medicine, The First Affiliated Hospital of Guangxi Medical University, China
| | - Xiaofeng Li
- Department of Respiratory and Critical Medicine, The First Affiliated Hospital of Guangxi Medical University, China
| | - Jiehua Deng
- Department of Respiratory and Critical Medicine, The First Affiliated Hospital of Guangxi Medical University, China
| | - Jianquan Zhang
- Department of Respiratory and Critical Medicine, The First Affiliated Hospital of Guangxi Medical University, China.,Department of Respiratory Medicine, The Eighth Affiliated Hospital, Sun Yat Sen University, China
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19
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Malvisi L, Yarraguntla A, Mortier MC, Osman K, Cleary DW, Sente B, Pascal TG, Weynants V, Clarke SC, Taddei L, Wilkinson TMA, Devaster JM, Devos N. Impact of bacterial strain acquisition in the lung of patients with COPD: the AERIS study. Infect Dis (Lond) 2022; 54:784-793. [PMID: 35794793 DOI: 10.1080/23744235.2022.2092648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Bacterial infections are associated with acute exacerbations of chronic obstructive pulmonary disease (AECOPD), but the mechanism is incompletely understood. METHOD In a COPD observational study (NCT01360398), sputum samples were collected monthly at the stable state and exacerbation. Post-hoc analyses of 1307 non-typeable Haemophilus influenzae (NTHi) isolates from 20 patients and 756 Moraxella catarrhalis isolates from 38 patients in one year of follow-up were conducted by multilocus sequence typing (MLST). All isolates came from cultured sputum samples that were analyzed for bacterial species presence, apparition (infection not detected at the preceding visit), or acquisition (first-time infection), with the first study visit as a baseline. Strain apparition or new strain acquisition was analyzed by MLST. The odds ratio (OR) of experiencing an exacerbation vs. stable state was estimated by conditional logistic regression modelling, stratified by patient. RESULTS The culture results confirmed a significant association with exacerbation only for NTHi species presence (OR 2.28; 95% confidence interval [CI]: 1.12-4.64) and strain apparition (OR 2.38; 95% CI: 1.08-5.27). For M. catarrhalis, although confidence intervals overlapped, the association with exacerbation for first-time species acquisition (OR 5.99; 2.75-13.02) appeared stronger than species presence (OR 3.67; 2.10-6.40), new strain acquisition (OR 2.94; 1.43-6.04), species apparition (OR 4.18; 2.29-7.63), and strain apparition (OR 2.78; 1.42-5.42). This may suggest that previous M. catarrhalis colonization may modify the risk of exacerbation associated with M. catarrhalis infection. CONCLUSIONS The results confirm that NTHi and M. catarrhalis infections are associated with AECOPD but suggest different dynamic mechanisms in triggering exacerbations.
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Affiliation(s)
| | | | | | - Karen Osman
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - David W Cleary
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,Southampton NIHR Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK
| | | | | | | | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK
| | | | - Tom M A Wilkinson
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,Southampton NIHR Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK.,Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK
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20
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Interrogation of Essentiality in the Reconstructed Haemophilus influenzae Metabolic Network Identifies Lipid Metabolism Antimicrobial Targets: Preclinical Evaluation of a FabH β-Ketoacyl-ACP Synthase Inhibitor. mSystems 2022; 7:e0145921. [PMID: 35293791 PMCID: PMC9040583 DOI: 10.1128/msystems.01459-21] [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] [Indexed: 11/20/2022] Open
Abstract
Expediting drug discovery to fight antibacterial resistance requires holistic approaches at system levels. In this study, we focused on the human-adapted pathogen Haemophilus influenzae, and by constructing a high-quality genome-scale metabolic model, we rationally identified new metabolic drug targets in this organism. Contextualization of available gene essentiality data within in silico predictions identified most genes involved in lipid metabolism as promising targets. We focused on the β-ketoacyl-acyl carrier protein synthase III FabH, responsible for catalyzing the first step in the FASII fatty acid synthesis pathway and feedback inhibition. Docking studies provided a plausible three-dimensional model of FabH in complex with the synthetic inhibitor 1-(5-(2-fluoro-5-(hydroxymethyl)phenyl)pyridin-2-yl)piperidine-4-acetic acid (FabHi). Validating our in silico predictions, FabHi reduced H. influenzae viability in a dose- and strain-dependent manner, and this inhibitory effect was independent of fabH gene expression levels. fabH allelic variation was observed among H. influenzae clinical isolates. Many of these polymorphisms, relevant for stabilization of the dimeric active form of FabH and/or activity, may modulate the inhibitory effect as part of a complex multifactorial process with the overall metabolic context emerging as a key factor tuning FabHi activity. Synergies with antibiotics were not observed and bacteria were not prone to develop resistance. Inhibitor administration during H. influenzae infection on a zebrafish septicemia infection model cleared bacteria without signs of host toxicity. Overall, we highlight the potential of H. influenzae metabolism as a source of drug targets, metabolic models as target-screening tools, and FASII targeting suitability to counteract this bacterial infection. IMPORTANCE Antimicrobial resistance drives the need of synergistically combined powerful computational tools and experimental work to accelerate target identification and drug development. Here, we present a high-quality metabolic model of H. influenzae and show its usefulness both as a computational framework for large experimental data set contextualization and as a tool to discover condition-independent drug targets. We focus on β-ketoacyl-acyl carrier protein synthase III FabH chemical inhibition by using a synthetic molecule with good synthetic and antimicrobial profiles that specifically binds to the active site. The mechanistic complexity of FabH inhibition may go beyond allelic variation, and the strain-dependent effect of the inhibitor tested supports the impact of metabolic context as a key factor driving bacterial cell behavior. Therefore, this study highlights the systematic metabolic evaluation of individual strains through computational frameworks to identify secondary metabolic hubs modulating drug response, which will facilitate establishing synergistic and/or more precise and robust antibacterial treatments.
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21
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Nontypeable Haemophilus influenzae Redox Recycling of Protein Thiols Promotes Resistance to Oxidative Killing and Bacterial Survival in Biofilms in a Smoke-Related Infection Model. mSphere 2022; 7:e0084721. [PMID: 35044805 PMCID: PMC8769201 DOI: 10.1128/msphere.00847-21] [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] [Indexed: 11/21/2022] Open
Abstract
Smoke exposure is a risk factor for community-acquired pneumonia, which is typically caused by host-adapted airway opportunists like nontypeable Haemophilus influenzae (NTHi). Genomic analyses of NTHi revealed homologs of enzymes with predicted roles in reduction of protein thiols, which can have key roles in oxidant resistance. Using a clinical NTHi isolate (NTHi 7P49H1), we generated isogenic mutants in which homologs of glutathione reductase (open reading frame NTHI 0251), thioredoxin-dependent thiol peroxidase (NTHI 0361), thiol peroxidase (NTHI 0907), thioredoxin reductase (NTHI 1327), and glutaredoxin/peroxiredoxin (NTHI 0705) were insertionally inactivated. Bacterial protein analyses revealed that protein oxidation after hydrogen peroxide treatment was elevated in all the mutant strains. Similarly, each of these mutants was less resistant to oxidative killing than the parental strain; these phenotypes were reversed by genetic complementation. Analysis of biofilm communities formed by the parental and mutant strains showed reduction in overall biofilm thickness and density and significant sensitization of bacteria within the biofilm structure to oxidative killing. Experimental respiratory infection of smoke-exposed mice with NTHi 7P49H1 showed significantly increased bacterial counts compared to control mice. Immunofluorescent staining of lung tissues showed NTHi communities on lung mucosae, interspersed with neutrophil extracellular traps; these bacteria had transcript profiles consistent with NTHi biofilms. In contrast, infection with the panel of NTHi mutants showed a significant decrease in bacterial load. Comparable results were observed in bactericidal assays with neutrophil extracellular traps in vitro. Thus, we conclude that thiol-mediated redox homeostasis is a determinant of persistence of NTHi within biofilm communities. IMPORTANCE Chronic bacterial respiratory infections are a significant problem for smoke-exposed individuals, especially those with chronic obstructive pulmonary disease (COPD). These infections often persist despite antibiotic use. Thus, the bacteria remain and contribute to the development of inflammation and other respiratory problems. Respiratory bacteria often form biofilms within the lungs; during growth in a biofilm, their antibiotic and oxidative stress resistance is incredibly heightened. It is well documented that redox homeostasis genes are upregulated during this phase of growth. Many common respiratory pathogens, such as NTHi and Streptococcus pneumoniae, are reliant on scavenging from the host the necessary components they need to maintain these redox systems. This work begins to lay the foundation for exploiting this requirement and thiol redox homeostasis pathways of these bacteria as a therapeutic target for managing chronic respiratory bacterial infections, which are resistant to traditional antibiotic treatments alone.
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22
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Rodríguez-Arce I, Morales X, Ariz M, Euba B, López-López N, Esparza M, Hood DW, Leiva J, Ortíz-de-Solórzano C, Garmendia J. Development and multimodal characterization of an elastase-induced emphysema mouse disease model for the COPD frequent bacterial exacerbator phenotype. Virulence 2021; 12:1672-1688. [PMID: 34252004 PMCID: PMC8276669 DOI: 10.1080/21505594.2021.1937883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/20/2021] [Accepted: 05/30/2021] [Indexed: 11/03/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) patients undergo infectious exacerbations whose frequency identifies a clinically meaningful phenotype. Mouse models have been mostly used to separately study both COPD and the infectious processes, but a reliable model of the COPD frequent exacerbator phenotype is still lacking. Accordingly, we first established a model of single bacterial exacerbation by nontypeable Haemophilus influenzae (NTHi) infection on mice with emphysema-like lesions. We characterized this single exacerbation model combining both noninvasive in vivo imaging and ex vivo techniques, obtaining longitudinal information about bacterial load and the extent of the developing lesions and host responses. Bacterial load disappeared 48 hours post-infection (hpi). However, lung recovery, measured using tests of pulmonary function and the disappearance of lung inflammation as revealed by micro-computed X-ray tomography, was delayed until 3 weeks post-infection (wpi). Then, to emulate the frequent exacerbator phenotype, we performed two recurrent episodes of NTHi infection on the emphysematous murine lung. Consistent with the amplified infectious insult, bacterial load reduction was now observed 96 hpi, and lung function recovery and disappearance of lesions on anatomical lung images did not happen until 12 wpi. Finally, as a proof of principle of the use of the model, we showed that azithromycin successfully cleared the recurrent infection, confirming this macrolide utility to ameliorate infectious exacerbation. In conclusion, we present a mouse model of recurrent bacterial infection of the emphysematous lung, aimed to facilitate investigating the COPD frequent exacerbator phenotype by providing complementary, dynamic information of both infectious and inflammatory processes.
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Affiliation(s)
- Irene Rodríguez-Arce
- Instituto De Agrobiotecnología, CSIC (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Xabier Morales
- Department of Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA), Laboratory of Preclinical Models and Analytical Tools, Pamplona, Spain
- Laboratory of Preclinical Models and Analytical Tools, Division of Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA), Pamplona, Spain
| | - Mikel Ariz
- Department of Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA), Laboratory of Preclinical Models and Analytical Tools, Pamplona, Spain
- Laboratory of Preclinical Models and Analytical Tools, Division of Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA), Pamplona, Spain
| | - Begoña Euba
- Instituto De Agrobiotecnología, CSIC (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Nahikari López-López
- Instituto De Agrobiotecnología, CSIC (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Maider Esparza
- Department of Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA), Laboratory of Preclinical Models and Analytical Tools, Pamplona, Spain
- Laboratory of Preclinical Models and Analytical Tools, Division of Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA), Pamplona, Spain
| | - Derek W. Hood
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, UK
| | - José Leiva
- Instituto De Investigación Sanitaria De Navarra (IdiSNA), Pamplona, Spain
- Servicio De Microbiología, Clínica Universidad De Navarra, Pamplona, Spain
| | - Carlos Ortíz-de-Solórzano
- Department of Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA), Laboratory of Preclinical Models and Analytical Tools, Pamplona, Spain
- Laboratory of Preclinical Models and Analytical Tools, Division of Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA), Pamplona, Spain
- Instituto De Investigación Sanitaria De Navarra (IdiSNA), Pamplona, Spain
| | - Junkal Garmendia
- Instituto De Agrobiotecnología, CSIC (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
- Centro De Investigación Biomédica En Red De Enfermedades Respiratorias (CIBERES), Madrid, Spain
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23
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Li K, Liu X, Zhang X, Liu Z, Yu Y, Zhao J, Wang L, Kong Y, Chen M. Identification microbial glycans substructure associate with disease and species. Carbohydr Polym 2021; 273:118595. [PMID: 34560996 DOI: 10.1016/j.carbpol.2021.118595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/01/2021] [Accepted: 08/18/2021] [Indexed: 11/27/2022]
Abstract
The microbial glycans mediate many significant biological acts, such as pathogen survival, host-microbe interactions, and immune evasion. The systematic study of microbial glycans structure remains challenging because of its high complexity and variability. In this study, we screened all the microbial glycans structures in the CSDB (Carbohydrate Structure Database), disassembled them into substructures, and calculated all the substructures' numbers. The results showed that a large number of glycan substructures are shared among different microorganisms. Further analysis showed that the glycan substructures appeared in specific bacterial groups may be related to the species and pathogenicity of microorganisms. Broadly, these findings provided an alternative approach or clue to discover the hidden information and the biological functions of glycans. The results can be used to detect broad-scope pathogen or prepare broad-spectrum vaccines.
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Affiliation(s)
- Kun Li
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoyu Liu
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Xunlian Zhang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Zhaoxi Liu
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Yue Yu
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China; School of Life Sciences, Shandong Normal University, Jinan, Shandong 250,000, China
| | - Jiayu Zhao
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Yun Kong
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Min Chen
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China.
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24
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Lukacik P, Owen CD, Harris G, Bolla JR, Picaud S, Alibay I, Nettleship JE, Bird LE, Owens RJ, Biggin PC, Filippakopoulos P, Robinson CV, Walsh MA. The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif. PLoS One 2021; 16:e0256070. [PMID: 34653190 PMCID: PMC8519434 DOI: 10.1371/journal.pone.0256070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/29/2021] [Indexed: 12/04/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a significant pathogen in respiratory disease and otitis media. Important for NTHi survival, colonization and persistence in vivo is the Sap (sensitivity to antimicrobial peptides) ABC transporter system. Current models propose a direct role for Sap in heme and antimicrobial peptide (AMP) transport. Here, the crystal structure of SapA, the periplasmic component of Sap, in a closed, ligand bound conformation, is presented. Phylogenetic and cavity volume analysis predicts that the small, hydrophobic SapA central ligand binding cavity is most likely occupied by a hydrophobic di- or tri- peptide. The cavity is of insufficient volume to accommodate heme or folded AMPs. Crystal structures of SapA have identified surface interactions with heme and dsRNA. Heme binds SapA weakly (Kd 282 μM) through a surface exposed histidine, while the dsRNA is coordinated via residues which constitute part of a conserved motif (estimated Kd 4.4 μM). The RNA affinity falls within the range observed for characterized RNA/protein complexes. Overall, we describe in molecular-detail the interactions of SapA with heme and dsRNA and propose a role for SapA in the transport of di- or tri-peptides.
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Affiliation(s)
- Petra Lukacik
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - C. David Owen
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Gemma Harris
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Jani Reddy Bolla
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Sarah Picaud
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom
| | - Irfan Alibay
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Joanne E. Nettleship
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Louise E. Bird
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Raymond J. Owens
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Martin A. Walsh
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
- * E-mail:
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25
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Ruan R, Deng X, Dong X, Wang Q, Lv X, Si C. Microbiota Emergencies in the Diagnosis of Lung Diseases: A Meta-Analysis. Front Cell Infect Microbiol 2021; 11:709634. [PMID: 34621687 PMCID: PMC8490768 DOI: 10.3389/fcimb.2021.709634] [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: 05/14/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022] Open
Abstract
Although many studies have reported that microbiota emergencies are deeply involved in the occurrence and subsequent progression of lung diseases, the present diagnosis of lung disease depends on microbiota markers, which is still poorly understood. Therefore, a meta-analysis was performed to confirm lung microbiota markers for the diagnosis of lung diseases. Literature databases were searched following the inclusion and exclusion criteria. There are 6 studies including 1347 patients and 26 comparisons to be enrolled, and then the diagnostic effect was evaluated using Stata 14.0 and Meta-disc 1.4 software. The pooled sensitivity (SEN), specificity (SPE), diagnostic likelihood ratio positive (DLR+), diagnostic likelihood ratio negative (DLR-), and diagnostic OR (DOR), as well as area under the curve (AUC) of microbiota markers in the diagnosis of lung diseases were 0.90 (95% CI: 0.83-0.94), 0.89 (95% CI: 0.76-0.95), 7.86 (95% CI: 3.39-18.21), 0.12 (95% CI: 0.06-0.21), 22.254 (95% CI: 12.83-39.59.14), and 0.95 (95% CI: 0.93-0.97), respectively. Subgroup analysis revealed that research based on Caucasian, adult, BAL fluid, PCR, pneumonia obtained higher AUC values. The microbiota markers have shown potential diagnosis value for lung diseases. But further large-scale clinical studies are still needed to verify and replicate the diagnostic value of lung microbiota markers.
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Affiliation(s)
- Renyu Ruan
- College of Undergradute, Jiangsu Food & Pharmaceutical Science College, Huaian, China
| | - Xiangmin Deng
- College of Pharmacy and Traditional Chinese Medicine, Jiangsu College of Nursing, Huaian, China
| | - Xiaoyan Dong
- College of Pharmacy and Traditional Chinese Medicine, Jiangsu College of Nursing, Huaian, China
| | - Qi Wang
- College of Pharmacy, Harbin Medical University-Daqing, Da Qing, China
| | - Xiaoling Lv
- Department of Nutrition, Zhejiang Hospital, Hangzhou, China
| | - Caijuan Si
- Department of Nutrition, Zhejiang Hospital, Hangzhou, China
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26
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Ackland J, Heinson AI, Cleary DW, Christodoulides M, Wilkinson TMA, Staples KJ. Dual RNASeq Reveals NTHi-Macrophage Transcriptomic Changes During Intracellular Persistence. Front Cell Infect Microbiol 2021; 11:723481. [PMID: 34497778 PMCID: PMC8419319 DOI: 10.3389/fcimb.2021.723481] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a pathobiont which chronically colonises the airway of individuals with chronic respiratory disease and is associated with poor clinical outcomes. It is unclear how NTHi persists in the airway, however accumulating evidence suggests that NTHi can invade and persist within macrophages. To better understand the mechanisms of NTHi persistence within macrophages, we developed an in vitro model of NTHi intracellular persistence using human monocyte-derived macrophages (MDM). Dual RNA Sequencing was used to assess MDM and NTHi transcriptomic regulation occurring simultaneously during NTHi persistence. Analysis of the macrophage response to NTHi identified temporally regulated transcriptomic profiles, with a specific 'core' profile displaying conserved expression of genes across time points. Gene list enrichment analysis identified enrichment of immune responses in the core gene set, with KEGG pathway analysis revealing specific enrichment of intracellular immune response pathways. NTHi persistence was facilitated by modulation of bacterial metabolic, stress response and ribosome pathways. Levels of NTHi genes bioC, mepM and dps were differentially expressed by intracellular NTHi compared to planktonic NTHi, indicating that the transcriptomic adaption was distinct between the two different NTHi lifestyles. Overall, this study provides crucial insights into the transcriptomic adaptations facilitating NTHi persistence within macrophages. Targeting these reported pathways with novel therapeutics to reduce NTHi burden in the airway could be an effective treatment strategy given the current antimicrobial resistance crisis and lack of NTHi vaccines.
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Affiliation(s)
- Jodie Ackland
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ashley I Heinson
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - David W Cleary
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Myron Christodoulides
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Tom M A Wilkinson
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom.,Wessex Investigational Sciences Hub, Southampton General Hospital, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Karl J Staples
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom.,Wessex Investigational Sciences Hub, Southampton General Hospital, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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27
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Weeks JR, Staples KJ, Spalluto CM, Watson A, Wilkinson TMA. The Role of Non-Typeable Haemophilus influenzae Biofilms in Chronic Obstructive Pulmonary Disease. Front Cell Infect Microbiol 2021; 11:720742. [PMID: 34422683 PMCID: PMC8373199 DOI: 10.3389/fcimb.2021.720742] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/15/2021] [Indexed: 11/13/2022] Open
Abstract
Non-typeable Haemophilus influenzae (NTHi) is an ubiquitous commensal-turned-pathogen that colonises the respiratory mucosa in airways diseases including Chronic Obstructive Pulmonary Disease (COPD). COPD is a progressive inflammatory syndrome of the lungs, encompassing chronic bronchitis that is characterised by mucus hypersecretion and impaired mucociliary clearance and creates a static, protective, humid, and nutrient-rich environment, with dysregulated mucosal immunity; a favourable environment for NTHi colonisation. Several recent large COPD cohort studies have reported NTHi as a significant and recurrent aetiological pathogen in acute exacerbations of COPD. NTHi proliferation has been associated with increased hospitalisation, disease severity, morbidity and significant lung microbiome shifts. However, some cohorts with patients at different severities of COPD do not report that NTHi is a significant aetiological pathogen in their COPD patients, indicating other obligate pathogens including Moraxella catarrhalis, Streptococcus pneumoniae and Pseudomonas aeruginosa as the cause. NTHi is an ubiquitous organism across healthy non-smokers, healthy smokers and COPD patients from childhood to adulthood, but it currently remains unclear why NTHi becomes pathogenic in only some cohorts of COPD patients, and what behaviours, interactions and adaptations are driving this susceptibility. There is emerging evidence that biofilm-phase NTHi may play a significant role in COPD. NTHi displays many hallmarks of the biofilm lifestyle and expresses key biofilm formation-promoting genes. These include the autoinducer-mediated quorum sensing system, epithelial- and mucus-binding adhesins and expression of a protective, self-produced polymeric substance matrix. These NTHi biofilms exhibit extreme tolerance to antimicrobial treatments and the immune system as well as expressing synergistic interspecific interactions with other lung pathogens including S. pneumoniae and M. catarrhalis. Whilst the majority of our understanding surrounding NTHi as a biofilm arises from otitis media or in-vitro bacterial monoculture models, the role of NTHi biofilms in the COPD lung is now being studied. This review explores the evidence for the existence of NTHi biofilms and their impact in the COPD lung. Understanding the nature of chronic and recurrent NTHi infections in acute exacerbations of COPD could have important implications for clinical treatment and identification of novel bactericidal targets.
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Affiliation(s)
- Jake R Weeks
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
| | - Karl J Staples
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, Southampton General Hospital, Southampton, United Kingdom
| | - C Mirella Spalluto
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, Southampton General Hospital, Southampton, United Kingdom
| | - Alastair Watson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, Southampton General Hospital, Southampton, United Kingdom.,Birmingham Medical School, University of Birmingham, Birmingham, United Kingdom
| | - Tom M A Wilkinson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, Southampton General Hospital, Southampton, United Kingdom
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Phase Variation in HMW1A Controls a Phenotypic Switch in Haemophilus influenzae Associated with Pathoadaptation during Persistent Infection. mBio 2021; 12:e0078921. [PMID: 34154422 PMCID: PMC8262952 DOI: 10.1128/mbio.00789-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Genetic variants arising from within-patient evolution shed light on bacterial adaptation during chronic infection. Contingency loci generate high levels of genetic variation in bacterial genomes, enabling adaptation to the stringent selective pressures exerted by the host. A significant gap in our understanding of phase-variable contingency loci is the extent of their contribution to natural infections. The human-adapted pathogen nontypeable Haemophilus influenzae (NTHi) causes persistent infections, which contribute to underlying disease progression. The phase-variable high-molecular-weight (HMW) adhesins located on the NTHi surface mediate adherence to respiratory epithelial cells and, depending on the allelic variant, can also confer high epithelial invasiveness or hyperinvasion. In this study, we characterize the dynamics of HMW-mediated hyperinvasion in living cells and identify a specific HMW binding domain shared by hyperinvasive NTHi isolates of distinct pathological origins. Moreover, we observed that HMW expression decreased over time by using a longitudinal set of persistent NTHi strains collected from chronic obstructive pulmonary disease (COPD) patients, resulting from increased numbers of simple-sequence repeats (SSRs) downstream of the functional P2hmw1A promoter, which is the one primarily driving HMW expression. Notably, the increased SSR numbers at the hmw1 promoter region also control a phenotypic switch toward lower bacterial intracellular invasion and higher biofilm formation, likely conferring adaptive advantages during chronic airway infection by NTHi. Overall, we reveal novel molecular mechanisms of NTHi pathoadaptation based on within-patient lifestyle switching controlled by phase variation.
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29
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Sialic Acid Protects Nontypeable Haemophilus influenzae from Natural IgM and Promotes Survival in Murine Respiratory Tract. Infect Immun 2021; 89:IAI.00676-20. [PMID: 33782153 DOI: 10.1128/iai.00676-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/12/2021] [Indexed: 11/20/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi), a common inhabitant of the human nasopharynx and upper airways, causes opportunistic respiratory tract infections that are frequently recurring and chronic. NTHi utilizes sialic acid from the host to evade antibacterial defenses and persist in mucosal tissues; however, the role of sialic acid scavenged by NTHi during infection is not fully understood. We previously showed that sialylation protects specific epitopes on NTHi lipooligosaccharide (LOS) targeted by bactericidal IgM in normal human serum. Here, we evaluated the importance of immune evasion mediated by LOS sialylation in the mouse respiratory tract using wild-type H. influenzae and an isogenic siaB mutant incapable of sialylating the LOS. Sialylation protected common NTHi glycan structures recognized by human and murine IgM and protected NTHi from complement-mediated killing directed by IgM against these structures. Protection from IgM binding by sialylated LOS correlated with decreased survival of the siaB mutant versus the wild type in the murine lung. Complement depletion with cobra venom factor increased survival of the siaB mutant in the nasopharynx but not in the lungs, suggesting differing roles of sialylation at these sites. Prior infection increased IgM against H. influenzae but not against sialic acid-protected epitopes, consistent with sialic acid-mediated immune evasion during infection. These results provide mechanistic insight into an NTHi evasive strategy against an immune defense conserved across host species, highlighting the potential of the mouse model for development of anti-infective strategies targeting LOS antigens of NTHi.
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30
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López-López N, Gil-Campillo C, Díez-Martínez R, Garmendia J. Learning from -omics strategies applied to uncover Haemophilus influenzae host-pathogen interactions: Current status and perspectives. Comput Struct Biotechnol J 2021; 19:3042-3050. [PMID: 34136102 PMCID: PMC8178019 DOI: 10.1016/j.csbj.2021.05.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 11/15/2022] Open
Abstract
Haemophilus influenzae has contributed to key bacterial genome sequencing hallmarks, as being not only the first bacterium to be genome-sequenced, but also starring the first genome-wide analysis of chromosomes directly transformed with DNA from a divergent genotype, and pioneering Tn-seq methodologies. Over the years, the phenomenal and constantly evolving development of -omic technologies applied to a whole range of biological questions of clinical relevance in the H. influenzae-host interplay, has greatly moved forward our understanding of this human-adapted pathogen, responsible for multiple acute and chronic infections of the respiratory tract. In this way, essential genes, virulence factors, pathoadaptive traits, and multi-layer gene expression regulatory networks with both genomic and epigenomic complexity levels are being elucidated. Likewise, the unstoppable increasing whole genome sequencing information underpinning H. influenzae great genomic plasticity, mainly when referring to non-capsulated strains, poses major challenges to understand the genomic basis of clinically relevant phenotypes and even more, to clearly highlight potential targets of clinical interest for diagnostic, therapeutic or vaccine development. We review here how genomic, transcriptomic, proteomic and metabolomic-based approaches are great contributors to our current understanding of the interactions between H. influenzae and the human airways, and point possible strategies to maximize their usefulness in the context of biomedical research and clinical needs on this human-adapted bacterial pathogen.
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Affiliation(s)
- Nahikari López-López
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Celia Gil-Campillo
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | | | - Junkal Garmendia
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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31
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Pinto AM, Silva MD, Pastrana LM, Bañobre-López M, Sillankorva S. The clinical path to deliver encapsulated phages and lysins. FEMS Microbiol Rev 2021; 45:6204673. [PMID: 33784387 DOI: 10.1093/femsre/fuab019] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/26/2021] [Indexed: 02/06/2023] Open
Abstract
The global emergence of multidrug-resistant pathogens is shaping the current dogma regarding the use of antibiotherapy. Many bacteria have evolved to become resistant to conventional antibiotherapy, representing a health and economic burden for those afflicted. The search for alternative and complementary therapeutic approaches has intensified and revived phage therapy. In recent decades, the exogenous use of lysins, encoded in phage genomes, has shown encouraging effectiveness. These two antimicrobial agents reduce bacterial populations; however, many barriers challenge their prompt delivery at the infection site. Encapsulation in delivery vehicles provides targeted therapy with a controlled compound delivery, surpassing chemical, physical and immunological barriers that can inactivate and eliminate them. This review explores phages and lysins' current use to resolve bacterial infections in the respiratory, digestive, and integumentary systems. We also highlight the different challenges they face in each of the three systems and discuss the advances towards a more expansive use of delivery vehicles.
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Affiliation(s)
- Ana Mafalda Pinto
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal.,INL - International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga, Braga 4715-330, Portugal
| | - Maria Daniela Silva
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal.,INL - International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga, Braga 4715-330, Portugal
| | - Lorenzo M Pastrana
- INL - International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga, Braga 4715-330, Portugal
| | - Manuel Bañobre-López
- INL - International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga, Braga 4715-330, Portugal
| | - Sanna Sillankorva
- INL - International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga, Braga 4715-330, Portugal
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32
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Page LK, Staples KJ, Spalluto CM, Watson A, Wilkinson TMA. Influence of Hypoxia on the Epithelial-Pathogen Interactions in the Lung: Implications for Respiratory Disease. Front Immunol 2021; 12:653969. [PMID: 33868294 PMCID: PMC8044850 DOI: 10.3389/fimmu.2021.653969] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/09/2021] [Indexed: 12/11/2022] Open
Abstract
Under normal physiological conditions, the lung remains an oxygen rich environment. However, prominent regions of hypoxia are a common feature of infected and inflamed tissues and many chronic inflammatory respiratory diseases are associated with mucosal and systemic hypoxia. The airway epithelium represents a key interface with the external environment and is the first line of defense against potentially harmful agents including respiratory pathogens. The protective arsenal of the airway epithelium is provided in the form of physical barriers, and the production of an array of antimicrobial host defense molecules, proinflammatory cytokines and chemokines, in response to activation by receptors. Dysregulation of the airway epithelial innate immune response is associated with a compromised immunity and chronic inflammation of the lung. An increasing body of evidence indicates a distinct role for hypoxia in the dysfunction of the airway epithelium and in the responses of both innate immunity and of respiratory pathogens. Here we review the current evidence around the role of tissue hypoxia in modulating the host-pathogen interaction at the airway epithelium. Furthermore, we highlight the work needed to delineate the role of tissue hypoxia in the pathophysiology of chronic inflammatory lung diseases such as asthma, cystic fibrosis, and chronic obstructive pulmonary disease in addition to novel respiratory diseases such as COVID-19. Elucidating the molecular mechanisms underlying the epithelial-pathogen interactions in the setting of hypoxia will enable better understanding of persistent infections and complex disease processes in chronic inflammatory lung diseases and may aid the identification of novel therapeutic targets and strategies.
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Affiliation(s)
- Lee K. Page
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
| | - Karl J. Staples
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, Southampton Centre for Biomedical Research, Southampton General Hospital, Southampton, United Kingdom
| | - C. Mirella Spalluto
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, Southampton Centre for Biomedical Research, Southampton General Hospital, Southampton, United Kingdom
| | - Alastair Watson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, Southampton Centre for Biomedical Research, Southampton General Hospital, Southampton, United Kingdom
- Birmingham Medical School, University of Birmingham, Birmingham, United Kingdom
| | - Tom M. A. Wilkinson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, Southampton Centre for Biomedical Research, Southampton General Hospital, Southampton, United Kingdom
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33
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Malvisi L, Taddei L, Yarraguntla A, Wilkinson TMA, Arora AK. Sputum sample positivity for Haemophilus influenzae or Moraxella catarrhalis in acute exacerbations of chronic obstructive pulmonary disease: evaluation of association with positivity at earlier stable disease timepoints. Respir Res 2021; 22:67. [PMID: 33627095 PMCID: PMC7903661 DOI: 10.1186/s12931-021-01653-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/07/2021] [Indexed: 12/04/2022] Open
Abstract
Background Infection with Haemophilus influenzae (Hi) or Moraxella catarrhalis (Mcat) is a risk factor for exacerbation in chronic obstructive pulmonary disease (COPD). The ability to predict Hi- or Mcat-associated exacerbations may be useful for interventions developed to reduce exacerbation frequency. Methods In a COPD observational study, sputum samples were collected at monthly stable-state visits and at exacerbation during two years of follow-up. Bacterial species (Hi, Mcat) were identified by culture and quantitative PCR assay. Post-hoc analyses were conducted to assess: (1) first Hi- or Mcat-positive exacerbations given presence or absence of Hi or Mcat at the screening visit (stable-state timepoint); (2) first Hi- or Mcat-positive exacerbations given presence or absence of Hi or Mcat at stable timepoints within previous 90 days; (3) second Hi- or Mcat-positive exacerbations given presence or absence of Hi or Mcat at stable timepoints within previous 90 days. Percentages and risk ratios (RRs) with 95% confidence intervals were calculated. Results PCR results for analyses 1, 2 and 3 (samples from 84, 88 and 83 subjects, respectively) showed that the risk of an Hi- or Mcat-positive exacerbation is significantly higher if sputum sample was Hi- or Mcat-positive than if Hi- or Mcat-negative at previous stable timepoints (apart from Mcat in analysis 3); RRs ranged from 2.1 to 3.2 for Hi and 1.9 to 2.6 for Mcat.For all analyses, the percentage of Hi- or Mcat-positive exacerbations given previous Hi- or Mcat-positive stable timepoints was higher than the percentage of Hi- or Mcat-positive exacerbations if Hi- or Mcat-negative at previous stable timepoints. Percentage of Hi- or Mcat-positive exacerbations given previous Hi- or Mcat-negative stable timepoints was 26.3%–37.0% for Hi and 17.6%–19.7% for Mcat. Conclusions Presence of Hi or Mcat at a stable timepoint was associated with a higher risk of a subsequent Hi- or Mcat-associated exacerbation compared with earlier absence. However, a large percentage of Hi- or Mcat-associated exacerbations was not associated with Hi/Mcat detection at an earlier timepoint. This suggests that administration of an intervention to reduce these exacerbations should be independent of bacterial presence at baseline. Trial Registrationhttps://clinicaltrials.gov/; NCT01360398, registered May 25, 2011
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Affiliation(s)
| | | | | | - Tom M A Wilkinson
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,Southampton NIHR Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK.,Wessex Investigational Sciences Hub, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
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34
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Haemophilin-Producing Strains of Haemophilus haemolyticus Protect Respiratory Epithelia from NTHi Colonisation and Internalisation. Pathogens 2021; 10:pathogens10010029. [PMID: 33401487 PMCID: PMC7823694 DOI: 10.3390/pathogens10010029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/17/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a significant respiratory tract pathogen responsible for infections that collectively pose a substantial health and socioeconomic burden. The clinical course of these infections is largely dictated by NTHi interactions with host respiratory epithelia, and thus, approaches that disrupt colonisation and invasion may have significant therapeutic potential. Survival, successful host–cell interactions, and pathogenesis are reliant on NTHi’s ability to sequester host-derived haem. Previously, we demonstrated the therapeutic potential of exploiting this haem-dependence using a closely related competitor bacterium, Haemophilus haemolyticus (Hh). Hh strains capable of producing the novel haem-binding protein haemophilin (Hpl) possessed potent inhibitory activity by restricting NTHi access to haem in a broth co-culture environment. Here, we extend this work to cell culture models that more closely represent the human respiratory epithelium and show that Hh strains with high levels of hpl expression protect epithelial cell line monolayers against adhesion and invasion by NTHi. Inhibitory activity was dependent on the level of Hpl production, which was stimulated by NTHi challenge and nasopharyngeal cell exposure. Provided these protective benefits translate to in vivo applications, Hpl-producing Hh may have probiotic utility against NTHi infections by inhibiting requisite nasopharyngeal colonisation.
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35
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Mokrzan EM, Ahearn CP, Buzzo JR, Novotny LA, Zhang Y, Goodman SD, Bakaletz LO. Nontypeable Haemophilus influenzae newly released (NRel) from biofilms by antibody-mediated dispersal versus antibody-mediated disruption are phenotypically distinct. Biofilm 2020; 2:100039. [PMID: 33447823 PMCID: PMC7798465 DOI: 10.1016/j.bioflm.2020.100039] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/02/2020] [Accepted: 11/12/2020] [Indexed: 02/08/2023] Open
Abstract
Biofilms contribute significantly to the chronicity and recurrence of bacterial diseases due to the fact that biofilm-resident bacteria are highly recalcitrant to killing by host immune effectors and antibiotics. Thus, antibody-mediated release of bacteria from biofilm residence into the surrounding milieu supports a powerful strategy to resolve otherwise difficult-to-treat biofilm-associated diseases. In our prior work, we revealed that antibodies directed against two unique determinants of nontypeable Haemophilus influenzae (NTHI) [e.g. the Type IV pilus (T4P) or a bacterial DNABII DNA-binding protein, a species-independent target that provides structural integrity to bacterial biofilms] release biofilm-resident bacteria via discrete mechanisms. Herein, we now show that the phenotype of the resultant newly released (or NRel) NTHI is dependent upon the specific mechanism of release. We used flow cytometry, proteomic profiles, and targeted transcriptomics to demonstrate that the two NRel populations were significantly different not only from planktonically grown NTHI, but importantly, from each other despite genetic identity. Moreover, each NRel population had a distinct, significantly increased susceptibility to killing by either a sulfonamide or β-lactam antibiotic compared to planktonic NTHI, an observation consistent with their individual proteomes and further supported by relative differences in targeted gene expression. The distinct phenotypes of NTHI released from biofilms by antibodies directed against specific epitopes of T4P or DNABII binding proteins provide new opportunities to develop targeted therapeutic strategies for biofilm eradication and disease resolution.
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Affiliation(s)
- Elaine M Mokrzan
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Christian P Ahearn
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - John R Buzzo
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Laura A Novotny
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Yan Zhang
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH, USA.,The Ohio State University Comprehensive Cancer Center (OSUCCC - James), Columbus, OH, USA
| | - Steven D Goodman
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
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Beech AS, Lea S, Kolsum U, Wang Z, Miller BE, Donaldson GC, Wedzicha JA, Brightling CE, Singh D. Bacteria and sputum inflammatory cell counts; a COPD cohort analysis. Respir Res 2020; 21:289. [PMID: 33131502 PMCID: PMC7603729 DOI: 10.1186/s12931-020-01552-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/20/2020] [Indexed: 01/08/2023] Open
Abstract
Background There is evidence that bacterial colonisation in chronic obstructive pulmonary disease (COPD) is associated with increased neutrophilic airway inflammation. This study tested the hypothesis that different bacterial phyla and species cause different inflammatory profiles in COPD patients. Methods Sputum was analysed by quantitative polymerase chain reaction (qPCR) to quantify bacterial load and 16S rRNA gene sequencing to identify taxonomic composition. Sputum differential cell counts (DCC) and blood DCC were obtained at baseline and 6 months. Patients were categorised into five groups based on bacterial load defined by genome copies/ml of ≥ 1 × 104, no colonisation and colonisation by Haemophilus influenzae (H. influenzae), Moraxella catarrhalis (M. catarrhalis), Streptococcus pneumoniae (S. pneumoniae), or > 1 potentially pathogenic microorganism (PPM). Results We observed an increase in sputum neutrophil (%), blood neutrophil (%) and neutrophil–lymphocyte ratio (NLR) in patients colonised with H. influenzae (82.6, 67.1, and 3.29 respectively) compared to those without PPM colonisation at baseline (69.5, 63.51 and 2.56 respectively) (p < 0.05 for all analyses), with similar findings at 6 months. The bacterial load of H. influenzae and Haemophilus determined by qPCR and 16s rRNA gene sequencing respectively, and sputum neutrophil % were positively correlated between baseline and 6 months visits (p < 0.0001, 0.0150 and 0.0002 with r = 0.53, 0.33 and 0.44 respectively). Conclusions These results demonstrate a subgroup of COPD patients with persistent H. influenzae colonisation that is associated with increased airway and systemic neutrophilic airway inflammation, and less eosinophilic airway inflammation.
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Affiliation(s)
- Augusta S Beech
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK. .,Medicines Evaluation Unit, University of Manchester, Manchester University NHS Foundation Trust, Southmoor Road, Manchester, M23 9QZ, UK.
| | - Simon Lea
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Umme Kolsum
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Bruce E Miller
- Medical Innovation, Value Evidence and Outcomes, GSK R&D, Collegeville, PA, USA
| | - Gavin C Donaldson
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | | | - Dave Singh
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.,Medicines Evaluation Unit, University of Manchester, Manchester University NHS Foundation Trust, Southmoor Road, Manchester, M23 9QZ, UK
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Liu J, Ran Z, Wang F, Xin C, Xiong B, Song Z. Role of pulmonary microorganisms in the development of chronic obstructive pulmonary disease. Crit Rev Microbiol 2020; 47:1-12. [PMID: 33040638 DOI: 10.1080/1040841x.2020.1830748] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic obstructive respiratory disease characterized by irreversible airway limitation and persistent respiratory symptoms. The main clinical symptoms of COPD are dyspnoea, chronic cough, and sputum. COPD is often accompanied by other respiratory diseases, which can cause worsening of the disease. COPD patients with dyspnoea and aggravation of cough and sputum symptoms represent acute exacerbations of COPD (AECOPD). There is mounting evidence suggesting that dysbiosis of pulmonary microbiota participates in the disease. However, investigations of dysbiosis of pulmonary microbiota and the disease are still in initial phases. To screen, diagnose, and treat this respiratory disease, integrating data from different studies can improve our understanding of the occurrence and development of COPD and AECOPD. In this review, COPD epidemiology and the primary triggering mechanism are explored. Emerging knowledge regarding the association of inflammation, caused by pulmonary microbiome imbalance, and changes in lung microbiome flora species involved in the development of the disease are also highlighted. These data will further our understanding of the pathogenesis of COPD and AECOPD and may yield novel strategies for the use of pulmonary microbiota as a potential therapeutic intervention.
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Affiliation(s)
- Jiexing Liu
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Zhuonan Ran
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Fen Wang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, PR China
| | - Caiyan Xin
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, PR China
| | - Bin Xiong
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Zhangyong Song
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, PR China.,Molecular Biotechnology Platform, Public Center of Experimental Technology, Southwest Medical University, Luzhou, PR China
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Pehote G, Vij N. Autophagy Augmentation to Alleviate Immune Response Dysfunction, and Resolve Respiratory and COVID-19 Exacerbations. Cells 2020; 9:cells9091952. [PMID: 32847034 PMCID: PMC7565665 DOI: 10.3390/cells9091952] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/18/2022] Open
Abstract
The preservation of cellular homeostasis requires the synthesis of new proteins (proteostasis) and organelles, and the effective removal of misfolded or impaired proteins and cellular debris. This cellular homeostasis involves two key proteostasis mechanisms, the ubiquitin proteasome system and the autophagy–lysosome pathway. These catabolic pathways have been known to be involved in respiratory exacerbations and the pathogenesis of various lung diseases, such as chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), idiopathic pulmonary fibrosis (IPF), acute lung injury (ALI), acute respiratory distress syndrome (ARDS), and coronavirus disease-2019 (COVID-19). Briefly, proteostasis and autophagy processes are known to decline over time with age, cigarette or biomass smoke exposure, and/or influenced by underlying genetic factors, resulting in the accumulation of misfolded proteins and cellular debris, elevating apoptosis and cellular senescence, and initiating the pathogenesis of acute or chronic lung disease. Moreover, autophagic dysfunction results in an impaired microbial clearance, post-bacterial and/or viral infection(s) which contribute to the initiation of acute and recurrent respiratory exacerbations as well as the progression of chronic obstructive and restrictive lung diseases. In addition, the autophagic dysfunction-mediated cystic fibrosis transmembrane conductance regulator (CFTR) immune response impairment further exacerbates the lung disease. Recent studies demonstrate the therapeutic potential of novel autophagy augmentation strategies, in alleviating the pathogenesis of chronic obstructive or restrictive lung diseases and exacerbations such as those commonly seen in COPD, CF, ALI/ARDS and COVID-19.
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Affiliation(s)
- Garrett Pehote
- Michigan State University College of Osteopathic Medicine, East Lansing, MI 48823, USA;
| | - Neeraj Vij
- Department of Pediatrics and Pulmonary Medicine, the Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- PRECISION THERANOSTICS INC, Baltimore, MD 21202, USA
- VIJ BIOTECH, Baltimore, MD 21202, USA
- Correspondence: or ; Tel.: +1-240-623-0757
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Nontypeable Haemophilus influenzae Type IV Pilus Mediates Augmented Adherence to Rhinovirus-Infected Human Airway Epithelial Cells. Infect Immun 2020; 88:IAI.00248-20. [PMID: 32540869 DOI: 10.1128/iai.00248-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
Human rhinovirus (hRV) is frequently detected in the upper respiratory tract, and symptomatic infection is associated with an increased nasopharyngeal bacterial load, with subsequent development of secondary bacterial diseases. Nontypeable Haemophilus influenzae (NTHI) is a commensal bacterial species of the human nasopharynx; however, in the context of prior or concurrent upper respiratory tract viral infection, this bacterium commonly causes multiple diseases throughout the upper and lower respiratory tracts. The present study was conducted to determine the mechanism(s) by which hRV infection promotes the development of NTHI-induced diseases. We showed that hRV infection of polarized primary human airway epithelial cells resulted in increased adherence of NTHI, due in part to augmented expression of CEACAM1 and ICAM1, host cell receptors to which NTHI binds via engagement of multiple adhesins. Antibody blockade of these host cell receptors significantly reduced NTHI adherence. With a specific focus on the NTHI type IV pilus (T4P), which we have previously shown binds to ICAM1, an essential adhesin and virulence determinant, we next showed that T4P-directed antibody blockade significantly reduced NTHI adherence to hRV-infected airway cells and, further, that expression of this adhesin was required for the enhanced adherence observed. Collectively, these data provide a mechanism by which "the common cold" promotes diseases due to NTHI, and they add further support for the use of PilA (the majority subunit of T4P) as a vaccine antigen, since antibodies directed against PilA are expected to limit the notably increased bacterial load associated with hRV coinfection and thereby to prevent secondary NTHI-induced diseases of the respiratory tract.
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Wang Z, Liu H, Wang F, Yang Y, Wang X, Chen B, Stampfli MR, Zhou H, Shu W, Brightling CE, Liang Z, Chen R. A Refined View of Airway Microbiome in Chronic Obstructive Pulmonary Disease at Species and Strain-Levels. Front Microbiol 2020; 11:1758. [PMID: 32849386 PMCID: PMC7406711 DOI: 10.3389/fmicb.2020.01758] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022] Open
Abstract
Little is known about the underlying airway microbiome diversity in chronic obstructive pulmonary disease (COPD) at in-depth taxonomic levels. Here we present the first insights on the COPD airway microbiome at species and strain-levels. The full-length 16S rRNA gene was characterized from sputum in 98 COPD patients and 27 age-matched healthy controls, using the Pacific Biosciences sequencing platform. Individual species within the same genus exhibited reciprocal relationships with COPD and disease severity. Species dominant in health can be taken over by another species within the same genus but with potentially increasing pathogenicity in severe COPD patients. Ralstonia mannitolilytica, an opportunistic pathogen, was significantly increased in frequent exacerbators (fold-change = 4.94, FDR P = 0.005). There were distinct patterns of interaction between bacterial species and host inflammatory mediators according to neutrophilic or eosinophilic inflammations, two major airway inflammatory phenotypes in COPD. Haemophilus influenzae, Moraxella catarrhalis, Pseudomonas aeruginosa, and Neisseria meningitidis were associated with enhanced Th1, Th17 and pro-inflammatory mediators, while a group of seven species including Tropheryma whipplei were specifically associated with Th2 mediators related to eosinophilia. We developed an automated pipeline to assign strain-level taxonomy leveraging bacterial intra-genomic 16S allele frequency. Using this pipeline we further resolved three non-typeable H. influenzae strains PittEE, PittGG and 86-028NP with reasonable precision and uncovered strain-level variation related to airway inflammation. In particular, 86-028NP and PittGG strains exhibited inverse associations with Th2 chemokines CCL17 and CCL13, suggesting their abundances may inversely predict eosinophilic inflammation. A systematic comparison of 16S hypervariable regions indicated V1V3 instead of the commonly used V4 region was the best surrogate for airway microbiome. The full-length 16S data augmented the power of functional inference, which slightly better recapitulated the actual metagenomes. This led to the unique identification of butyrate-producing and nitrate reduction pathways as depleted in COPD. Our analysis uncovered finer-scale airway microbial diversity that was previously underappreciated, thus enabled a refined view of the airway microbiome in COPD.
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Affiliation(s)
- Zhang Wang
- Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Haiyue Liu
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Fengyan Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuqiong Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaojuan Wang
- Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Boxuan Chen
- Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Martin R. Stampfli
- Department of Medicine, Firestone Institute for Respiratory Health at St. Joseph’s Healthcare, McMaster University, Hamilton, ON, Canada
| | - Hongwei Zhou
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Wensheng Shu
- Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Christopher E. Brightling
- Institute for Lung Health, NIHR Leicester Biomedical Research Centre, Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Zhenyu Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rongchang Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Pulmonary and Critical Care Department, Shenzhen Institute of Respiratory Diseases, Shenzhen People’s Hospital, Shenzhen, China
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Nontypeable Haemophilus influenzae Responds to Virus-Infected Cells with a Significant Increase in Type IV Pilus Expression. mSphere 2020; 5:5/3/e00384-20. [PMID: 32461275 PMCID: PMC7253600 DOI: 10.1128/msphere.00384-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHI) is the predominant bacterial causative agent of many chronic and recurrent diseases of the upper and lower respiratory tracts. NTHI-induced chronic rhinosinusitis, otitis media, and exacerbations of cystic fibrosis and chronic obstructive pulmonary disease often develop during or just after an upper respiratory tract viral infection. We have developed a vaccine candidate immunogen for NTHI-induced diseases that targets the majority subunit (PilA) of the type IV twitching pilus (T4P), which NTHI uses to adhere to respiratory tract epithelial cells and that also plays a role in disease. Here, we showed that NTHI cocultured with virus-infected respiratory tract epithelial cells express significantly more of the vaccine-targeted T4P than NTHI that encounters mock-infected (healthy) cells. These results strongly suggest that a vaccine strategy that targets the NTHI T4P will be effective under the most common predisposing condition: when the human host has a respiratory tract virus infection. Nontypeable Haemophilus influenzae (NTHI) colonizes the human nasopharynx, but when the host immune response is dysregulated by upper respiratory tract (URT) virus infection, NTHI can gain access to more distal airway sites and cause disease. The NTHI type IV pilus (T4P) facilitates adherence, benign colonization, and infection, and its majority subunit PilA is in clinical trials as a vaccinogen. To further validate the strategy of immunization with PilA against multiple NTHI-induced diseases, it is important to demonstrate T4P expression under microenvironmental conditions that predispose to NTHI infection of the airway. Because URT infection commonly facilitates NTHI-induced diseases, we examined the influence of ongoing virus infection of respiratory tract epithelial cells on NTHI T4P expression in vitro. Polarized primary human airway epithelial cells (HAEs) were sequentially inoculated with one of three common URT viruses, followed by NTHI. Use of a reporter construct revealed that NTHI upregulated pilA promoter activity when cultured with HAEs infected with adenovirus (AV), respiratory syncytial virus (RSV), or rhinovirus (RV) versus that in mock-infected HAEs. Consistent with these results, pilA expression and relative PilA/pilin abundance, as assessed by quantitative reverse transcription-PCR (qRT-PCR) and immunoblot, respectively, were also significantly increased when NTHI was cultured with virus-infected HAEs. Collectively, our data strongly suggest that under conditions of URT virus infection, PilA vaccinogen induction of T4P-directed antibodies is likely to be highly effective against multiple NTHI-induced diseases by interfering with T4P-mediated adherence. We hypothesize that this outcome could thereby limit or prevent the increased load of NTHI in the nasopharynx that characteristically precedes these coinfections. IMPORTANCE Nontypeable Haemophilus influenzae (NTHI) is the predominant bacterial causative agent of many chronic and recurrent diseases of the upper and lower respiratory tracts. NTHI-induced chronic rhinosinusitis, otitis media, and exacerbations of cystic fibrosis and chronic obstructive pulmonary disease often develop during or just after an upper respiratory tract viral infection. We have developed a vaccine candidate immunogen for NTHI-induced diseases that targets the majority subunit (PilA) of the type IV twitching pilus (T4P), which NTHI uses to adhere to respiratory tract epithelial cells and that also plays a role in disease. Here, we showed that NTHI cocultured with virus-infected respiratory tract epithelial cells express significantly more of the vaccine-targeted T4P than NTHI that encounters mock-infected (healthy) cells. These results strongly suggest that a vaccine strategy that targets the NTHI T4P will be effective under the most common predisposing condition: when the human host has a respiratory tract virus infection.
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In Vitro Anti-NTHi Activity of Haemophilin-Producing Strains of Haemophilus haemolyticus. Pathogens 2020; 9:pathogens9040243. [PMID: 32218184 PMCID: PMC7238096 DOI: 10.3390/pathogens9040243] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/18/2020] [Accepted: 03/22/2020] [Indexed: 12/21/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a leading causative organism of opportunistic respiratory tract infections. However, there are currently no effective vaccination strategies, and existing treatments are compromised by antibiotic resistance. We previously characterized Haemophilus haemolyticus (Hh) strains capable of producing haemophilin (HPL), a heme-binding protein that restricts NTHi growth by limiting its access to an essential growth factor, heme. Thus, these strains may have utility as a probiotic therapy against NTHi infection by limiting colonization, migration and subsequent infection in susceptible individuals. Here, we assess the preliminary feasibility of this approach by direct in vitro competition assays between NTHi and Hh strains with varying capacity to produce HPL. Subsequent changes in NTHi growth rate and fitness, in conjunction with HPL expression analysis, were employed to assess the NTHi-inhibitory capacity of Hh strains. HPL-producing strains of Hh not only outcompeted NTHi during short-term and extended co-culture, but also demonstrated a growth advantage compared with Hh strains unable to produce the protein. Additionally, HPL expression levels during competition correlated with the NTHi-inhibitory phenotype. HPL-producing strains of Hh demonstrate significant probiotic potential against NTHi colonization in the upper respiratory tract, however, further investigations are warranted to demonstrate a range of other characteristics that would support the eventual development of a probiotic.
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López-López N, Euba B, Hill J, Dhouib R, Caballero L, Leiva J, Hosmer J, Cuesta S, Ramos-Vivas J, Díez-Martínez R, Schirra HJ, Blank LM, Kappler U, Garmendia J. Haemophilus influenzae Glucose Catabolism Leading to Production of the Immunometabolite Acetate Has a Key Contribution to the Host Airway-Pathogen Interplay. ACS Infect Dis 2020; 6:406-421. [PMID: 31933358 DOI: 10.1021/acsinfecdis.9b00359] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by abnormal inflammatory responses and impaired airway immunity, which provides an opportunistic platform for nontypeable Haemophilus influenzae (NTHi) infection. Clinical evidence supports that the COPD airways present increased concentrations of glucose, which may facilitate proliferation of pathogenic bacteria able to use glucose as a carbon source. NTHi metabolizes glucose through respiration-assisted fermentation, leading to the excretion of acetate, formate, and succinate. We hypothesized that such specialized glucose catabolism may be a pathoadaptive trait playing a pivotal role in the NTHi airway infection. To find out whether this is true, we engineered and characterized bacterial mutant strains impaired to produce acetate, formate, or succinate by inactivating the ackA, pflA, and frdA genes, respectively. While the inactivation of the pflA and frdA genes only had minimal physiological effects, the inactivation of the ackA gene affected acetate production and led to reduced bacterial growth, production of lactate under low oxygen tension, and bacterial attenuation in vivo. Moreover, bacterially produced acetate was able to stimulate the expression of inflammatory genes by cultured airway epithelial cells. These results back the notion that the COPD lung supports NTHi growth on glucose, enabling production of fermentative end products acting as immunometabolites at the site of infection. Thus, glucose catabolism may contribute not only to NTHi growth but also to bacterially driven airway inflammation. This information has important implications for developing nonantibiotic antimicrobials, given that airway glucose homeostasis modifying drugs could help prevent microbial infections associated with chronic lung disease.
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Affiliation(s)
| | - Begoña Euba
- Instituto de Agrobiotecnologı́a, CSIC-Gobierno Navarra, 31192 Mutilva, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
| | - Julian Hill
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Rabeb Dhouib
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Lucı́a Caballero
- Instituto de Agrobiotecnologı́a, CSIC-Gobierno Navarra, 31192 Mutilva, Spain
| | - José Leiva
- Servicio de Microbiologı́a, Clı́nica Universidad de Navarra, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Jennifer Hosmer
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Sergio Cuesta
- Instituto de Agrobiotecnologı́a, CSIC-Gobierno Navarra, 31192 Mutilva, Spain
| | - José Ramos-Vivas
- Servicio Microbiologı́a, Hospital Universitario Marqués de Valdecilla and Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain
- Red Española de Investigación en Patologı́a Infecciosa (REIPI), ISCIII, Madrid, Spain
| | - Roberto Díez-Martínez
- Telum Therapeutics, Centro Europeo de Empresas e Innovación de Navarra (CEIN), 31110 Noáin, Spain
| | - Horst Joachim Schirra
- Centre for Advanced Imaging, The University of Queensland, 4072 St Lucia, Queensland, Australia
| | - Lars M. Blank
- Institute of Applied Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Junkal Garmendia
- Instituto de Agrobiotecnologı́a, CSIC-Gobierno Navarra, 31192 Mutilva, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
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Baddal B. Characterization of biofilm formation and induction of apoptotic DNA fragmentation by nontypeable Haemophilus influenzae on polarized human airway epithelial cells. Microb Pathog 2020; 141:103985. [PMID: 31968224 DOI: 10.1016/j.micpath.2020.103985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 10/25/2022]
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a common airway commensal and opportunistic pathogen that persists within biofilm communities in vivo. Biofilm studies so far are mainly based on assays on plastic surfaces. The aim of this work was to investigate the capacity of clinical NTHi strains to form biofilm structures on polarized Calu-3 human airway epithelial cells and primary normal human bronchial epithelial cells and to characterize the biofilm architecture. Formation of adherent NTHi biofilms post colonization of host cells at multiple time-points was evaluated using confocal laser scanning microscopy and electron microscopy. NTHi biofilms were analyzed in terms of biofilm height and presence of extracellular matrix components, and their apoptotic effects on epithelial cells were measured by TUNEL assay. Strain Fi176 was observed to form robust biofilms on airway epithelia over time, while disrupting the integrity of Calu-3 monolayer by 72 h of co-culture. NTHi biofilms were observed to induce apoptotic DNA fragmentation in host cells at 24 h post infection. Biofilm formation on cell monolayers by Fi176ΔpilA strain was markedly reduced compared to WT strain. Biofilm inhibition and disruption assays by crystal violet staining indicated that DNA and proteins are part of NTHi biofilms in vitro. Our findings highlight critical stages of NTHi pathogenesis following host colonization and provide useful biofilm models for future antimicrobial drug discovery investigations.
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Affiliation(s)
- Buket Baddal
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, 99138, Nicosia, Cyprus; Microbial Pathogenesis Research Group, DESAM Institute, Near East University, Nicosia, Cyprus.
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Murphy TF, Brauer AL, Pettigrew MM, LaFontaine ER, Tettelin H. Persistence of Moraxella catarrhalis in Chronic Obstructive Pulmonary Disease and Regulation of the Hag/MID Adhesin. J Infect Dis 2020; 219:1448-1455. [PMID: 30496439 DOI: 10.1093/infdis/jiy680] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/26/2018] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Persistence of bacterial pathogens in the airways has profound consequences on the course and pathogenesis of chronic obstructive pulmonary disease (COPD). Patients with COPD continuously acquire and clear strains of Moraxella catarrhalis, a major pathogen in COPD. Some strains are cleared quickly and some persist for months to years. The mechanism of the variability in duration of persistence is unknown. METHODS Guided by genome sequences of selected strains, we studied the expression of Hag/MID, hag/mid gene sequences, adherence to human cells, and autoaggregation in longitudinally collected strains of M. catarrhalis from adults with COPD. RESULTS Twenty-eight of 30 cleared strains of M. catarrhalis expressed Hag/MID whereas 17 of 30 persistent strains expressed Hag/MID upon acquisition by patients. All persistent strains ceased expression of Hag/MID during persistence. Expression of Hag/MID in human airways was regulated by slipped-strand mispairing. Virulence-associated phenotypes (adherence to human respiratory epithelial cells and autoaggregation) paralleled Hag/MID expression in airway isolates. CONCLUSIONS Most strains of M. catarrhalis express Hag/MID upon acquisition by adults with COPD and all persistent strains shut off expression during persistence. These observations suggest that Hag/MID is important for initial colonization by M. catarrhalis and that cessation of expression facilitates persistence in COPD airways.
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Affiliation(s)
- Timothy F Murphy
- Division of Infectious Diseases, Department of Medicine, The State University of New York, Buffalo.,Department of Microbiology and Immunology, The State University of New York, Buffalo.,Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo
| | - Aimee L Brauer
- Division of Infectious Diseases, Department of Medicine, The State University of New York, Buffalo.,Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo
| | - Melinda M Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
| | - Eric R LaFontaine
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore
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Preclinical Evaluation of the Antimicrobial-Immunomodulatory Dual Action of Xenohormetic Molecules against Haemophilus influenzae Respiratory Infection. Biomolecules 2019; 9:biom9120891. [PMID: 31861238 PMCID: PMC6995536 DOI: 10.3390/biom9120891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by abnormal inflammation and impaired airway immunity, providing an opportunistic platform for nontypeable Haemophilus influenzae (NTHi) infection. In this context, therapies targeting not only overactive inflammation without significant adverse effects, but also infection are of interest. Increasing evidence suggests that polyphenols, plant secondary metabolites with anti-inflammatory and antimicrobial properties, may be protective. Here, a Cistus salviifolius plant extract containing quercetin, myricetin, and punicalagin was shown to reduce NTHi viability. Analysis of these polyphenols revealed that quercetin has a bactericidal effect on NTHi, does not display synergies, and that bacteria do not seem to develop resistance. Moreover, quercetin lowered NTHi airway epithelial invasion through a mechanism likely involving inhibition of Akt phosphorylation, and reduced the expression of bacterially-induced proinflammatory markers il-8, cxcl-1, il-6, pde4b, and tnfα. We further tested quercetin’s effect on NTHi murine pulmonary infection, showing a moderate reduction in bacterial counts and significantly reduced expression of proinflammatory genes, compared to untreated mice. Quercetin administration during NTHi infection on a zebrafish septicemia infection model system showed a bacterial clearing effect without signs of host toxicity. In conclusion, this study highlights the therapeutic potential of the xenohormetic molecule quercetin against NTHi infection.
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D'Mello A, Ahearn CP, Murphy TF, Tettelin H. ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates. BMC Genomics 2019; 20:981. [PMID: 31842745 PMCID: PMC6916091 DOI: 10.1186/s12864-019-6195-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/16/2019] [Indexed: 12/24/2022] Open
Abstract
Background Reverse vaccinology accelerates the discovery of potential vaccine candidates (PVCs) prior to experimental validation. Current programs typically use one bacterial proteome to identify PVCs through a filtering architecture using feature prediction programs or a machine learning approach. Filtering approaches may eliminate potential antigens based on limitations in the accuracy of prediction tools used. Machine learning approaches are heavily dependent on the selection of training datasets with experimentally validated antigens (positive control) and non-protective-antigens (negative control). The use of one or few bacterial proteomes does not assess PVC conservation among strains, an important feature of vaccine antigens. Results We present ReVac, which implements both a panoply of feature prediction programs without filtering out proteins, and scoring of candidates based on predictions made on curated positive and negative control PVCs datasets. ReVac surveys several genomes assessing protein conservation, as well as DNA and protein repeats, which may result in variable expression of PVCs. ReVac’s orthologous clustering of conserved genes, identifies core and dispensable genome components. This is useful for determining the degree of conservation of PVCs among the population of isolates for a given pathogen. Potential vaccine candidates are then prioritized based on conservation and overall feature-based scoring. We present the application of ReVac, applied to 69 Moraxella catarrhalis and 270 non-typeable Haemophilus influenzae genomes, prioritizing 64 and 29 proteins as PVCs, respectively. Conclusion ReVac’s use of a scoring scheme ranks PVCs for subsequent experimental testing. It employs a redundancy-based approach in its predictions of features using several prediction tools. The protein’s features are collated, and each protein is ranked based on the scoring scheme. Multi-genome analyses performed in ReVac allow for a comprehensive overview of PVCs from a pan-genome perspective, as an essential pre-requisite for any bacterial subunit vaccine design. ReVac prioritized PVCs of two human respiratory pathogens, identifying both novel and previously validated PVCs.
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Affiliation(s)
- Adonis D'Mello
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Christian P Ahearn
- Department of Microbiology and Immunology, University at Buffalo, the State University of New York, Buffalo, NY, USA.,Clinical and Translational Research Center, University at Buffalo, the State University of New York, Buffalo, NY, USA
| | - Timothy F Murphy
- Department of Microbiology and Immunology, University at Buffalo, the State University of New York, Buffalo, NY, USA.,Clinical and Translational Research Center, University at Buffalo, the State University of New York, Buffalo, NY, USA.,Division of Infectious Disease, Department of Medicine, University at Buffalo, the State University of New York, Buffalo, NY, 14203, USA
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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Rodríguez-Arce I, Al-Jubair T, Euba B, Fernández-Calvet A, Gil-Campillo C, Martí S, Törnroth-Horsefield S, Riesbeck K, Garmendia J. Moonlighting of Haemophilus influenzae heme acquisition systems contributes to the host airway-pathogen interplay in a coordinated manner. Virulence 2019; 10:315-333. [PMID: 30973092 PMCID: PMC6550540 DOI: 10.1080/21505594.2019.1596506] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/18/2019] [Accepted: 03/12/2019] [Indexed: 01/30/2023] Open
Abstract
Nutrient iron sequestration is the most significant form of nutritional immunity and causes bacterial pathogens to evolve strategies of host iron scavenging. Cigarette smoking contains iron particulates altering lung and systemic iron homeostasis, which may enhance colonization in the lungs of patients suffering chronic obstructive pulmonary disease (COPD) by opportunistic pathogens such as nontypeable. NTHi is a heme auxotroph, and the NTHi genome contains multiple heme acquisition systems whose role in pulmonary infection requires a global understanding. In this study, we determined the relative contribution to NTHi airway infection of the four heme-acquisition systems HxuCBA, PE, SapABCDFZ, and HbpA-DppBCDF that are located at the bacterial outer membrane or the periplasm. Our computational studies provided plausible 3D models for HbpA, SapA, PE, and HxuA interactions with heme. Generation and characterization of single mutants in the hxuCBA, hpe, sapA, and hbpA genes provided evidence for participation in heme binding-storage and inter-bacterial donation. The hxuA, sapA, hbpA, and hpe genes showed differential expression and responded to heme. Moreover, HxuCBA, PE, SapABCDFZ, and HbpA-DppBCDF presented moonlighting properties related to resistance to antimicrobial peptides or glutathione import, together likely contributing to the NTHi-host airway interplay, as observed upon cultured airway epithelia and in vivo lung infection. The observed multi-functionality was shown to be system-specific, thus limiting redundancy. Together, we provide evidence for heme uptake systems as bacterial factors that act in a coordinated and multi-functional manner to subvert nutritional- and other sources of host innate immunity during NTHi airway infection.
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Affiliation(s)
| | - Tamim Al-Jubair
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Begoña Euba
- Instituto de Agrobiotecnología, CSIC-Gobierno, Navarra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | | | | | - Sara Martí
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento Microbiología, Hospital Universitari Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain
| | - Susanna Törnroth-Horsefield
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Junkal Garmendia
- Instituto de Agrobiotecnología, CSIC-Gobierno, Navarra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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49
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Vaca DJ, Thibau A, Schütz M, Kraiczy P, Happonen L, Malmström J, Kempf VAJ. Interaction with the host: the role of fibronectin and extracellular matrix proteins in the adhesion of Gram-negative bacteria. Med Microbiol Immunol 2019; 209:277-299. [PMID: 31784893 PMCID: PMC7248048 DOI: 10.1007/s00430-019-00644-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/14/2019] [Indexed: 01/03/2023]
Abstract
The capacity of pathogenic microorganisms to adhere to host cells and avoid clearance by the host immune system is the initial and most decisive step leading to infections. Bacteria have developed different strategies to attach to diverse host surface structures. One important strategy is the adhesion to extracellular matrix (ECM) proteins (e.g., collagen, fibronectin, laminin) that are highly abundant in connective tissue and basement membranes. Gram-negative bacteria express variable outer membrane proteins (adhesins) to attach to the host and to initiate the process of infection. Understanding the underlying molecular mechanisms of bacterial adhesion is a prerequisite for targeting this interaction by “anti-ligands” to prevent colonization or infection of the host. Future development of such “anti-ligands” (specifically interfering with bacteria-host matrix interactions) might result in the development of a new class of anti-infective drugs for the therapy of infections caused by multidrug-resistant Gram-negative bacteria. This review summarizes our current knowledge about the manifold interactions of adhesins expressed by Gram-negative bacteria with ECM proteins and the use of this information for the generation of novel therapeutic antivirulence strategies.
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Affiliation(s)
- Diana J Vaca
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University Frankfurt am Main, Paul-Ehrlich-Str. 40, 60596, Frankfurt, Germany
| | - Arno Thibau
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University Frankfurt am Main, Paul-Ehrlich-Str. 40, 60596, Frankfurt, Germany
| | - Monika Schütz
- Institute for Medical Microbiology and Infection Control, University Hospital, Eberhard Karls-University, Tübingen, Germany
| | - Peter Kraiczy
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University Frankfurt am Main, Paul-Ehrlich-Str. 40, 60596, Frankfurt, Germany
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
| | - Volkhard A J Kempf
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University Frankfurt am Main, Paul-Ehrlich-Str. 40, 60596, Frankfurt, Germany.
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50
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Expression of the Nontypeable Haemophilus influenzae Type IV Pilus Is Stimulated by Coculture with Host Respiratory Tract Epithelial Cells. Infect Immun 2019; 87:IAI.00704-19. [PMID: 31548326 DOI: 10.1128/iai.00704-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 09/13/2019] [Indexed: 12/22/2022] Open
Abstract
The type IV pilus (Tfp) of nontypeable Haemophilus influenzae (NTHI) mediates adherence, colonization, motility, and biofilm formation, and the major protein subunit, PilA, is a promising vaccine candidate. Thus, it is crucial to understand how Tfp expression is regulated within the microenvironments of the human nasopharynx, which NTHI colonizes asymptomatically, and the more distal regions of the respiratory tract where NTHI-induced diseases occur. Here, we examined the effects of coculture of NTHI with human airway epithelial cells and heme availability on Tfp expression at temperatures typical of the human nasopharynx (34°C) or warmer anatomical sites during infection (37°C). Tfp expression was estimated by pilA promoter activity, pilA gene expression, and relative abundances of PilA and pilin protein. The results revealed that at both temperatures, NTHI cocultured with airway epithelial cells demonstrated significantly greater expression of pilA, PilA/pilin protein, and likely, fully assembled Tfp than NTHI cultured on an abiotic surface. Because NTHI is a heme auxotroph, we hypothesized that availability of heme from host cells might be a signal for Tfp expression. Thereby, we cultured NTHI in iron-limited medium, and we observed that supplementation with heme significantly increased pilA promoter activity. Collectively, our data suggested that NTHI Tfp expression was stimulated by soluble factor(s) released by epithelial cells, which are present in all microenvironments of the respiratory tract. The expression of this target antigen under conditions that mimic the human airway strongly supports the rationale for the use of PilA as a vaccine immunogen to prevent NTHI-induced diseases of the respiratory tract.
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