1
|
Howroyd F, Chacko C, MacDuff A, Gautam N, Pouchet B, Tunnicliffe B, Weblin J, Gao-Smith F, Ahmed Z, Duggal NA, Veenith T. Ventilator-associated pneumonia: pathobiological heterogeneity and diagnostic challenges. Nat Commun 2024; 15:6447. [PMID: 39085269 PMCID: PMC11291905 DOI: 10.1038/s41467-024-50805-z] [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: 03/08/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
Ventilator-associated pneumonia (VAP) affects up to 20% of critically ill patients and induces significant antibiotic prescription pressure, accounting for half of all antibiotic use in the ICU. VAP significantly increases hospital length of stay and healthcare costs yet is also associated with long-term morbidity and mortality. The diagnosis of VAP continues to present challenges and pitfalls for the currently available clinical, radiological and microbiological diagnostic armamentarium. Biomarkers and artificial intelligence offer an innovative potential direction for ongoing future research. In this Review, we summarise the pathobiological heterogeneity and diagnostic challenges associated with VAP.
Collapse
Affiliation(s)
- Fiona Howroyd
- Therapy Services, University Hospitals Birmingham NHS Foundation Trust, Mindelsohn Way, Birmingham, UK.
- Institute of Inflammation and Ageing, The University of Birmingham, Edgbaston, Birmingham, UK.
| | - Cyril Chacko
- Department of Critical Care Medicine and Anaesthesia, The Royal Wolverhampton NHS Trust, Wolverhampton, UK
- Institute of Acute Care, Royal Wolverhampton Hospital and University of Wolverhampton, Wolverhampton, UK
| | - Andrew MacDuff
- Department of Critical Care Medicine and Anaesthesia, The Royal Wolverhampton NHS Trust, Wolverhampton, UK
- Institute of Acute Care, Royal Wolverhampton Hospital and University of Wolverhampton, Wolverhampton, UK
| | - Nandan Gautam
- Critical Care Department, University Hospitals Birmingham NHS Foundation Trust, Mindelsohn Way, Birmingham, UK
| | - Brian Pouchet
- Critical Care Department, University Hospitals Birmingham NHS Foundation Trust, Mindelsohn Way, Birmingham, UK
| | - Bill Tunnicliffe
- Critical Care Department, University Hospitals Birmingham NHS Foundation Trust, Mindelsohn Way, Birmingham, UK
| | - Jonathan Weblin
- Therapy Services, University Hospitals Birmingham NHS Foundation Trust, Mindelsohn Way, Birmingham, UK
| | - Fang Gao-Smith
- Institute of Inflammation and Ageing, The University of Birmingham, Edgbaston, Birmingham, UK
| | - Zubair Ahmed
- Institute of Inflammation and Ageing, The University of Birmingham, Edgbaston, Birmingham, UK.
| | - Niharika A Duggal
- Institute of Inflammation and Ageing, The University of Birmingham, Edgbaston, Birmingham, UK.
| | - Tonny Veenith
- Department of Critical Care Medicine and Anaesthesia, The Royal Wolverhampton NHS Trust, Wolverhampton, UK.
- Institute of Acute Care, Royal Wolverhampton Hospital and University of Wolverhampton, Wolverhampton, UK.
| |
Collapse
|
2
|
McGinniss JE, Graham-Wooten J, Whiteside SA, Fitzgerald AS, Khatib LA, Ma KC, DiBardino DM, Haas AR, Bushman FD, Fuchs BD, Collman RG. Microbiome Profiling Demonstrates Concordance of Endotracheal Tube Aspirates With Direct Lower Airway Sampling in Intubated Patients. Chest 2024; 165:1415-1420. [PMID: 38211701 PMCID: PMC11177094 DOI: 10.1016/j.chest.2024.01.007] [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: 05/30/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Endotracheal aspirates (ETAs) are widely used for microbiologic studies of the respiratory tract in intubated patients. However, they involve sampling through an established endotracheal tube using suction catheters, both of which can acquire biofilms that may confound results. RESEARCH QUESTION Does standard clinical ETA in intubated patients accurately reflect the authentic lower airway bacterial microbiome? STUDY DESIGN AND METHODS Comprehensive quantitative bacterial profiling using 16S rRNA V1-V2 gene sequencing was applied to compare bacterial populations captured by standard clinical ETA vs contemporaneous gold standard samples acquired directly from the lower airways through a freshly placed sterile tracheostomy tube. The study included 13 patients undergoing percutaneous tracheostomy following prolonged (median, 15 days) intubation. Metrics of bacterial composition, diversity, and relative quantification were applied to samples. RESULTS Pre-tracheostomy ETAs closely resembled the gold standard immediate post-tracheostomy airway microbiomes in bacterial composition and community features of diversity and quantification. Endotracheal tube and suction catheter biofilms also resembled cognate ETA and fresh tracheostomy communities. INTERPRETATION Unbiased molecular profiling shows that standard clinical ETA sampling has good concordance with the authentic lower airway microbiome in intubated patients.
Collapse
Affiliation(s)
- John E McGinniss
- Pulmonary, Allergy and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Jevon Graham-Wooten
- Pulmonary, Allergy and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Samantha A Whiteside
- Pulmonary, Allergy and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ayannah S Fitzgerald
- Pulmonary, Allergy and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Layla A Khatib
- Pulmonary, Allergy and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Kevin C Ma
- Pulmonary, Allergy and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - David M DiBardino
- Pulmonary, Allergy and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Andrew R Haas
- Pulmonary, Allergy and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Fredric D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Barry D Fuchs
- Pulmonary, Allergy and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ronald G Collman
- Pulmonary, Allergy and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA.
| |
Collapse
|
3
|
Fernández-Barat L, Torres A. Microbiota Profiling in Endotracheal Aspirates: Are There Differences When Obtained Through Endotracheal Tubes or Tracheostomy Tubes? Chest 2024; 165:1284-1285. [PMID: 38852961 DOI: 10.1016/j.chest.2024.02.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 06/11/2024] Open
Affiliation(s)
- Laia Fernández-Barat
- Ciberes (CB06/06/0028)-Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain.
| | - Antoni Torres
- Ciberes (CB06/06/0028)-Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain; Respiratory and Intensive Care Unit, University of Barcelona, Hospital Clinic of Barcelona, Villarroel, Spain
| |
Collapse
|
4
|
Akata K, Yamasaki K, Nemoto K, Ikegami H, Kawaguchi T, Noguchi S, Kawanami T, Fukuda K, Mukae H, Yatera K. Sarcoidosis Associated with Enlarged Mediastinal Lymph Nodes with the Detection of Streptococcus gordonii and Cutibacterium acnes Using a Clone Library Method. Intern Med 2024; 63:299-304. [PMID: 37258161 PMCID: PMC10864086 DOI: 10.2169/internalmedicine.1887-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/25/2023] [Indexed: 06/02/2023] Open
Abstract
A 77-year-old Japanese woman with mediastinal lymphadenopathy and uveitis was diagnosed with sarcoidosis. The bacterial flora in biopsied samples from mediastinal lymph nodes was analyzed using a clone library method with Sanger sequencing of the 16S rRNA gene, and Streptococcus gordonii (52 of 71 clones) and Cutibacterium acnes (19 of 71 clones) were detected. No previous study has conducted a bacterial floral analysis using the Sanger method for the mediastinal lymph node in sarcoidosis, making this case report the first to document the presence of S. gordonii and C. acnes in the mediastinal lymph node of a patient with sarcoidosis.
Collapse
Affiliation(s)
- Kentaro Akata
- Division of Infection Control and Prevention, University of Occupational and Environmental Health, Japan
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Kei Yamasaki
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Kazuki Nemoto
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Hiroaki Ikegami
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Takako Kawaguchi
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Shingo Noguchi
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Toshinori Kawanami
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| | - Kazumasa Fukuda
- Department of Microbiology, University of Occupational and Environmental Health, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Kazuhiro Yatera
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan
| |
Collapse
|
5
|
Karakosta A, Bousvaros K, Margaritis A, Moschovi P, Mousafiri O, Fousekis F, Papathanakos G, Samara E, Tzimas P, Christodoulou D, Koulouras V, Baltayiannis G. High Prevalence of Small Intestinal Bacterial Overgrowth Syndrome in ICU Patients: An Observational Study. J Intensive Care Med 2024; 39:69-76. [PMID: 37489018 DOI: 10.1177/08850666231190284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Background: Small intestinal bacterial overgrowth (SIBO), although associated with potentially serious complications, has not been adequately studied in critically ill patients. The primary objective of this study was to assess the prevalence of SIBO in critically ill patients. Secondary outcomes included the assessment of its effect on ventilator-associated pneumonia (VAP), intensive care unit (ICU) length of stay (LOS), and all-cause in-hospital mortality rate. Methods: This prospective observational study was conducted in a mixed medical-surgical ICU. In 52 consecutive ICU patients, a noninvasive modified hydrogen breath test (HBT) with lactulose was employed for SIBO diagnosis. The HBT was conducted at predetermined time intervals (first day of admission; third, fifth, and seventh day of ICU stay). Patients with an abnormal HBT suggesting SIBO on the day of ICU admission were excluded from the study. Participants were classified as either positive or negative based on their HBT on the third, fifth, and/or seventh day. A comparative assessment of demographic data, APACHE II score, incidence of VAP, duration of ICU stay, and all-cause in-hospital mortality was conducted. Multivariate logistic regression analysis was performed to identify the predictive factors for SIBO. Results: The groups were homogeneous in terms of their baseline characteristics. The prevalence of SIBO was 36.5%. The all-cause in-hospital mortality was 34.6%. The presence of SIBO was associated with an increased incidence of VAP (P < .001) and a prolonged ICU length of stay (P < .033). All-cause in-hospital mortality was similar between the groups. Regarding the results of the multivariate logistic regression model, only age was identified as a statistically significant independent predictor of SIBO (OR 1.08, P = .018). Conclusions: The prevalence of SIBO in ICU patients appears to be increased. Both early diagnosis and effective treatment are of utmost importance, especially for critically ill patients since it appears to be associated with VAP and prolonged hospitalization.
Collapse
Affiliation(s)
- Agathi Karakosta
- Department of Anaesthesia and Postoperative Intensive Care, Faculty of Medicine, University of Ioannina, Ioannina, Greece
| | | | | | - Ploumi Moschovi
- Intensive Care Unit, General Hospital of Ioannina "G. Hatzikosta," Ioannina, Greece
| | - Ourania Mousafiri
- Intensive Care Unit, General Hospital of Ioannina "G. Hatzikosta," Ioannina, Greece
| | - Fotios Fousekis
- Department of Gastroenterology, Faculty of Medicine, University of Ioannina, Ioannina, Greece
| | | | - Evangelia Samara
- Department of Anaesthesia and Postoperative Intensive Care, Faculty of Medicine, University of Ioannina, Ioannina, Greece
| | - Petros Tzimas
- Department of Anaesthesia and Postoperative Intensive Care, Faculty of Medicine, University of Ioannina, Ioannina, Greece
| | - Dimitrios Christodoulou
- Department of Gastroenterology, Faculty of Medicine, University of Ioannina, Ioannina, Greece
| | - Vasilios Koulouras
- Intensive Care Unit, Faculty of Medicine, University of Ioannina, Ioannina, Greece
| | - Gerasimos Baltayiannis
- Department of Gastroenterology, Faculty of Medicine, University of Ioannina, Ioannina, Greece
| |
Collapse
|
6
|
Mazzolini R, Rodríguez-Arce I, Fernández-Barat L, Piñero-Lambea C, Garrido V, Rebollada-Merino A, Motos A, Torres A, Grilló MJ, Serrano L, Lluch-Senar M. Engineered live bacteria suppress Pseudomonas aeruginosa infection in mouse lung and dissolve endotracheal-tube biofilms. Nat Biotechnol 2023; 41:1089-1098. [PMID: 36658340 PMCID: PMC10421741 DOI: 10.1038/s41587-022-01584-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/21/2022] [Indexed: 01/21/2023]
Abstract
Engineered live bacteria could provide a new modality for treating lung infections, a major cause of mortality worldwide. In the present study, we engineered a genome-reduced human lung bacterium, Mycoplasma pneumoniae, to treat ventilator-associated pneumonia, a disease with high hospital mortality when associated with Pseudomonas aeruginosa biofilms. After validating the biosafety of an attenuated M. pneumoniae chassis in mice, we introduced four transgenes into the chromosome by transposition to implement bactericidal and biofilm degradation activities. We show that this engineered strain has high efficacy against an acute P. aeruginosa lung infection in a mouse model. In addition, we demonstrated that the engineered strain could dissolve biofilms formed in endotracheal tubes of patients with ventilator-associated pneumonia and be combined with antibiotics targeting the peptidoglycan layer to increase efficacy against Gram-positive and Gram-negative bacteria. We expect our M. pneumoniae-engineered strain to be able to treat biofilm-associated infections in the respiratory tract.
Collapse
Affiliation(s)
- Rocco Mazzolini
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Pulmobiotics Ltd, Barcelona, Spain
| | - Irene Rodríguez-Arce
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Agrobiotechnology, CSIC-Navarra Government, Navarra, Spain
| | - Laia Fernández-Barat
- Cellex Laboratory, CibeRes, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- Department of Pneumology, Thorax Institute, Hospital Clinic of Barcelona, SpainICREA, Barcelona, Spain
| | - Carlos Piñero-Lambea
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Pulmobiotics Ltd, Barcelona, Spain
| | - Victoria Garrido
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Agrobiotechnology, CSIC-Navarra Government, Navarra, Spain
| | - Agustín Rebollada-Merino
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Internal Medicine and Animal Surgery, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | - Anna Motos
- Cellex Laboratory, CibeRes, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- Department of Pneumology, Thorax Institute, Hospital Clinic of Barcelona, SpainICREA, Barcelona, Spain
| | - Antoni Torres
- Cellex Laboratory, CibeRes, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- Department of Pneumology, Thorax Institute, Hospital Clinic of Barcelona, SpainICREA, Barcelona, Spain
| | | | - Luis Serrano
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Maria Lluch-Senar
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Pulmobiotics Ltd, Barcelona, Spain.
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain.
| |
Collapse
|
7
|
Belizário J, Garay-Malpartida M, Faintuch J. Lung microbiome and origins of the respiratory diseases. CURRENT RESEARCH IN IMMUNOLOGY 2023; 4:100065. [PMID: 37456520 PMCID: PMC10339129 DOI: 10.1016/j.crimmu.2023.100065] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
The studies on the composition of the human microbiomes in healthy individuals, its variability in the course of inflammation, infection, antibiotic therapy, diets and different pathological conditions have revealed their intra and inter-kingdom relationships. The lung microbiome comprises of major species members of the phylum Bacteroidetes, Firmicutes, Actinobacteria, Fusobacteria and Proteobacteria, which are distributed in ecological niches along nasal cavity, nasopharynx, oropharynx, trachea and in the lungs. Commensal and pathogenic species are maintained in equilibrium as they have strong relationships. Bacterial overgrowth after dysbiosis and/or imbalanced of CD4+ helper T cells, CD8+ cytotoxic T cells and regulatory T cells (Treg) populations can promote lung inflammatory reactions and distress, and consequently acute and chronic respiratory diseases. This review is aimed to summarize the latest advances in resident lung microbiome and its participation in most common pulmonary infections and pneumonia, community-acquired pneumonia (CAP), ventilator-associated pneumonia (VAP), immunodeficiency associated pneumonia, SARS-CoV-2-associated pneumonia, acute respiratory distress syndrome (ARDS) and chronic obstructive pulmonary disease (COPD). We briefly describe physiological and immunological mechanisms that selectively create advantages or disadvantages for relative growth of pathogenic bacterial species in the respiratory tract. At the end, we propose some directions and analytical methods that may facilitate the identification of key genera and species of resident and transient microbes involved in the respiratory diseases' initiation and progression.
Collapse
Affiliation(s)
- José Belizário
- School of Arts, Sciences and Humanities of the University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo, CEP 03828-000, Brazil
| | - Miguel Garay-Malpartida
- School of Arts, Sciences and Humanities of the University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo, CEP 03828-000, Brazil
| | - Joel Faintuch
- Department of Gastroenterology of the Clinics Hospital of the University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, São Paulo, CEP 05403-000, Brazil
| |
Collapse
|
8
|
Bustos IG, Martín-Loeches I, Acosta-González A, Chotirmall SH, Dickson RP, Reyes LF. Exploring the complex relationship between the lung microbiome and ventilator-associated pneumonia. Expert Rev Respir Med 2023; 17:889-901. [PMID: 37872770 DOI: 10.1080/17476348.2023.2273424] [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: 06/14/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023]
Abstract
INTRODUCTION Understanding the presence and function of a diverse lung microbiome in acute lung infections, particularly ventilator-associated pneumonia (VAP), is still limited, evidencing significant gaps in our knowledge. AREAS COVERED In this comprehensive narrative review, we aim to elucidate the contribution of the respiratory microbiome in the development of VAP by examining the current knowledge on the interactions among microorganisms. By exploring these intricate connections, we endeavor to enhance our understanding of the disease's pathophysiology and pave the way for novel ideas and interventions in studying the respiratory tract microbiome. EXPERT OPINION The conventional perception of lungs as sterile is deprecated since it is currently recognized the existence of a diverse microbial community within them. However, despite extensive research on the role of the respiratory microbiome in healthy lungs, respiratory chronic diseases and acute lung infections such as pneumonia are not fully understood. It is crucial to investigate further the relationship between the pathophysiology of VAP and the pulmonary microbiome, elucidating the mechanisms underlying the interactions between the microbiome, host immune response and mechanical ventilation for the development of VAP.
Collapse
Affiliation(s)
- Ingrid G Bustos
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Doctorado de Biociencias, Department of Engineering, Universidad de la Sabana, Chia, Colombia
| | - Ignacio Martín-Loeches
- Multidisciplinary Intensive Care Research Organization (MICRO), St James's Hospital, Dublin, Ireland
| | - Alejandro Acosta-González
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Bioprospection Research Group (GIBP), Department of Engineering, Universidad de La Sabana, Chia, Colombia
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research & Innovation, Ann Arbor, MI, USA
| | - Luis Felipe Reyes
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Critical Care Department, Clinica Universidad de La Sabana, Chia, Colombia
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| |
Collapse
|
9
|
Lluch-Senar M. From science to business: translating live biotherapeutic products to the clinic. NATURE REVIEWS BIOENGINEERING 2023; 1:1-2. [PMID: 37359770 PMCID: PMC10236387 DOI: 10.1038/s44222-023-00078-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
At Pulmobiotics, we engineer bacteria for the treatment of respiratory diseases. Here, we outline how we designed MycoChassis - an attenuated bacterium strain obtained by genome engineering of Mycoplasma pneumoniae (a human lung pathogen) - and discuss the challenges on the road to its clinical translation.
Collapse
Affiliation(s)
- Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Pulmobiotics S.L., Barcelona, Spain
| |
Collapse
|
10
|
Determining the most accurate 16S rRNA hypervariable region for taxonomic identification from respiratory samples. Sci Rep 2023; 13:3974. [PMID: 36894603 PMCID: PMC9998635 DOI: 10.1038/s41598-023-30764-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
16S rRNA gene profiling, which contains nine hypervariable regions (V1-V9), is the gold standard for identifying taxonomic units by high-throughput sequencing. Microbiome studies combine two or more region sequences (usually V3-V4) to increase the resolving power for identifying bacterial taxa. We compare the resolving powers of V1-V2, V3-V4, V5-V7, and V7-V9 to improve microbiome analyses in sputum samples from patients with chronic respiratory diseases. DNA were isolated from 33 human sputum samples, and libraries were created using a QIASeq screening panel intended for Illumina platforms (16S/ITS; Qiagen Hilden, Germany). The analysis included a mock community as a microbial standard control (ZymoBIOMICS). We used the Deblur algorithm to identify bacterial amplicon sequence variants (ASVs) at the genus level. Alpha diversity was significantly higher for V1-V2, V3-V4, and V5-V7 compared with V7-V9, and significant compositional dissimilarities in the V1-V2 and V7-V9 analyses versus the V3-V4 and V5-V7 analyses. A cladogram confirmed these compositional differences, with the latter two being very similar in composition. The combined hypervariable regions showed significant differences when discriminating between the relative abundances of bacterial genera. The area under the curve revealed that V1-V2 had the highest resolving power for accurately identifying respiratory bacterial taxa from sputum samples. Our study confirms that 16S rRNA hypervariable regions provide significant differences for taxonomic identification in sputum. Comparing the taxa of microbial community standard control with the taxa samples, V1-V2 combination exhibits the most sensitivity and specificity. Thus, while third generation full-length 16S rRNA sequencing platforms become more available, the V1-V2 hypervariable regions can be used for taxonomic identification in sputum.
Collapse
|
11
|
Alagna L, Mancabelli L, Magni F, Chatenoud L, Bassi G, Del Bianco S, Fumagalli R, Turroni F, Mangioni D, Migliorino GM, Milani C, Muscatello A, Nattino G, Picetti E, Pinciroli R, Rossi S, Tonetti T, Vargiolu A, Bandera A, Ventura M, Citerio G, Gori A. Changes in upper airways microbiota in ventilator-associated pneumonia. Intensive Care Med Exp 2023; 11:17. [PMID: 36862343 PMCID: PMC9981834 DOI: 10.1186/s40635-023-00496-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/03/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND The role of upper airways microbiota and its association with ventilator-associated pneumonia (VAP) development in mechanically ventilated (MV) patients is unclear. Taking advantage of data collected in a prospective study aimed to assess the composition and over-time variation of upper airway microbiota in patients MV for non-pulmonary reasons, we describe upper airway microbiota characteristics among VAP and NO-VAP patients. METHODS Exploratory analysis of data collected in a prospective observational study on patients intubated for non-pulmonary conditions. Microbiota analysis (trough 16S-rRNA gene profiling) was performed on endotracheal aspirates (at intubation, T0, and after 72 h, T3) of patients with VAP (cases cohort) and a subgroup of NO-VAP patients (control cohort, matched according to total intubation time). RESULTS Samples from 13 VAP patients and 22 NO-VAP matched controls were analyzed. At intubation (T0), patients with VAP revealed a significantly lower microbial complexity of the microbiota of the upper airways compared to NO-VAP controls (alpha diversity index of 84 ± 37 and 160 ± 102, in VAP and NO_VAP group, respectively, p-value < 0.012). Furthermore, an overall decrease in microbial diversity was observed in both groups at T3 as compared to T0. At T3, a loss of some genera (Prevotella 7, Fusobacterium, Neisseria, Escherichia-Shigella and Haemophilus) was found in VAP patients. In contrast, eight genera belonging to the Bacteroidetes, Firmicutes and Fusobacteria phyla was predominant in this group. However, it is unclear whether VAP caused dysbiosis or dysbiosis caused VAP. CONCLUSIONS In a small sample size of intubated patients, microbial diversity at intubation was less in patients with VAP compared to patients without VAP.
Collapse
Affiliation(s)
- Laura Alagna
- Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - Leonardo Mancabelli
- grid.10383.390000 0004 1758 0937Department of Medicine and Surgery, University of Parma, Parma, Italy ,grid.10383.390000 0004 1758 0937Interdepartmental Research Centre Microbiome Research Hub, University of Parma, Parma, Italy
| | - Federico Magni
- grid.415025.70000 0004 1756 8604Neurointensive Care Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Liliane Chatenoud
- grid.4527.40000000106678902Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | | | - Silvia Del Bianco
- grid.415025.70000 0004 1756 8604Neurointensive Care Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Roberto Fumagalli
- grid.7563.70000 0001 2174 1754School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Francesca Turroni
- grid.10383.390000 0004 1758 0937Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy ,grid.10383.390000 0004 1758 0937Interdepartmental Research Centre Microbiome Research Hub, University of Parma, Parma, Italy
| | - Davide Mangioni
- grid.414818.00000 0004 1757 8749Present Address: Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Guglielmo M. Migliorino
- grid.415025.70000 0004 1756 8604Infectious Diseases Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Christian Milani
- grid.10383.390000 0004 1758 0937Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy ,grid.10383.390000 0004 1758 0937Interdepartmental Research Centre Microbiome Research Hub, University of Parma, Parma, Italy
| | - Antonio Muscatello
- grid.414818.00000 0004 1757 8749Present Address: Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giovanni Nattino
- grid.4527.40000000106678902Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Edoardo Picetti
- grid.411482.aDepartment of Anesthesia and Intensive Care, Parma University Hospital, Parma, Italy
| | - Riccardo Pinciroli
- grid.7563.70000 0001 2174 1754School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Sandra Rossi
- grid.411482.aDepartment of Anesthesia and Intensive Care, Parma University Hospital, Parma, Italy
| | - Tommaso Tonetti
- grid.411482.aDepartment of Anesthesia and Intensive Care, Parma University Hospital, Parma, Italy
| | - Alessia Vargiolu
- grid.415025.70000 0004 1756 8604Neurointensive Care Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy ,grid.7563.70000 0001 2174 1754School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Alessandra Bandera
- grid.414818.00000 0004 1757 8749Present Address: Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Marco Ventura
- grid.10383.390000 0004 1758 0937Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy ,grid.10383.390000 0004 1758 0937Interdepartmental Research Centre Microbiome Research Hub, University of Parma, Parma, Italy
| | - Giuseppe Citerio
- grid.415025.70000 0004 1756 8604Neurointensive Care Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy ,grid.7563.70000 0001 2174 1754School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Andrea Gori
- grid.414818.00000 0004 1757 8749Present Address: Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| |
Collapse
|
12
|
Alves D, Grainha T, Pereira MO, Lopes SP. Antimicrobial materials for endotracheal tubes: A review on the last two decades of technological progress. Acta Biomater 2023; 158:32-55. [PMID: 36632877 DOI: 10.1016/j.actbio.2023.01.001] [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: 10/17/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023]
Abstract
Ventilator-associated pneumonia (VAP) is an unresolved problem in nosocomial settings, remaining consistently associated with a lack of treatment, high mortality, and prolonged hospital stay. The endotracheal tube (ETT) is the major culprit for VAP development owing to its early surface microbial colonization and biofilm formation by multiple pathogens, both critical events for VAP pathogenesis and relapses. To combat this matter, gradual research on antimicrobial ETT surface coating/modification approaches has been made. This review provides an overview of the relevance and implications of the ETT bioburden for VAP pathogenesis and how technological research on antimicrobial materials for ETTs has evolved. Firstly, certain main VAP attributes (definition/categorization; outcomes; economic impact) were outlined, highlighting the issues in defining/diagnosing VAP that often difficult VAP early- and late-onset differentiation, and that generate misinterpretations in VAP surveillance and discrepant outcomes. The central role of the ETT microbial colonization and subsequent biofilm formation as fundamental contributors to VAP pathogenesis was then underscored, in parallel with the uncovering of the polymicrobial ecosystem of VAP-related infections. Secondly, the latest technological developments (reported since 2002) on materials able to endow the ETT surface with active antimicrobial and/or passive antifouling properties were annotated, being further subject to critical scrutiny concerning their potentialities and/or constraints in reducing ETT bioburden and the risk of VAP while retaining/improving the safety of use. Taking those gaps/challenges into consideration, we discussed potential avenues that may assist upcoming advances in the field to tackle VAP rampant rates and improve patient care. STATEMENT OF SIGNIFICANCE: The use of the endotracheal tube (ETT) in patients requiring mechanical ventilation is associated with the development of ventilator-associated pneumonia (VAP). Its rapid surface colonization and biofilm formation are critical events for VAP pathogenesis and relapses. This review provides a comprehensive overview on the relevance/implications of the ETT biofilm in VAP, and on how research on antimicrobial ETT surface coating/modification technology has evolved over the last two decades. Despite significant technological advances, the limited number of gathered reports (46), highlights difficulty in overcoming certain hurdles associated with VAP (e.g., persistent colonization/biofilm formation; mechanical ventilation duration; hospital length of stay; VAP occurrence), which makes this an evolving, complex, and challenging matter. Challenges and opportunities in the field are discussed.
Collapse
Affiliation(s)
- Diana Alves
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
| | - Tânia Grainha
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
| | - Maria Olívia Pereira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
| | - Susana Patrícia Lopes
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
| |
Collapse
|
13
|
Moda-Silva LS, Oliveira VC, Silva-Lovato CH, Fernández-Barat L, Watanabe E. Phage-based therapy: promising applicability in the control of oral dysbiosis and respiratory infections. Future Microbiol 2022; 17:1349-1352. [PMID: 36169344 DOI: 10.2217/fmb-2022-0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Letícia S Moda-Silva
- Department of Restorative Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Human Exposome & Infectious Diseases Network (HEID), Ribeirão Preto College of Nursing, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Viviane C Oliveira
- Department of Dental Materials & Prosthodontics, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Human Exposome & Infectious Diseases Network (HEID), Ribeirão Preto College of Nursing, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Cláudia H Silva-Lovato
- Department of Dental Materials & Prosthodontics, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Laia Fernández-Barat
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Evandro Watanabe
- Department of Restorative Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Human Exposome & Infectious Diseases Network (HEID), Ribeirão Preto College of Nursing, University of São Paulo, Ribeirão Preto, SP, Brazil
| |
Collapse
|
14
|
Cifuentes EA, Sierra MA, Yepes AF, Baldión AM, Rojas JA, Álvarez-Moreno CA, Anzola JM, Zambrano MM, Huertas MG. Endotracheal tube microbiome in hospitalized patients defined largely by hospital environment. Respir Res 2022; 23:168. [PMID: 35751068 PMCID: PMC9233342 DOI: 10.1186/s12931-022-02086-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
Background Studies of the respiratory tract microbiome primarily focus on airway and lung microbial diversity, but it is still unclear how these microbial communities may be affected by intubation and long periods in intensive care units (ICU), an aspect that today could aid in the understanding of COVID19 progression and disease severity. This study aimed to explore and characterize the endotracheal tube (ETT) microbiome by analyzing ETT-associated microbial communities. Methods This descriptive study was carried out on adult patients subjected to invasive mechanical ventilation from 2 to 21 days. ETT samples were obtained from 115 patients from ICU units in two hospitals. Bacteria isolated from endotracheal tubes belonging to the ESKAPE group were analyzed for biofilm formation using crystal violet quantification. Microbial profiles were obtained using Illumina sequencing of 16S rRNA gene. Results The ETT microbiome was mainly composed by the phyla Proteobacteria, Firmicutes and Bacteroidetes. Microbiome composition correlated with the ICU in which patients were hospitalized, while intubation time and diagnosis of ventilator-associated pneumonia (VAP) did not show any significant association. Conclusion These results suggest that the ICU environment, or medical practices, could be a key to microbial colonization and have a direct influence on the ETT microbiomes of patients that require mechanical ventilation. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02086-7.
Collapse
Affiliation(s)
| | - Maria A Sierra
- Corporación CorpoGen Research Center, Bogotá, Colombia.,Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | - Juan Manuel Anzola
- Corporación CorpoGen Research Center, Bogotá, Colombia.,Universidad Central, Bogotá, Colombia
| | - María Mercedes Zambrano
- Corporación CorpoGen Research Center, Bogotá, Colombia.,Universidad Central, Bogotá, Colombia
| | - Monica G Huertas
- Corporación CorpoGen Research Center, Bogotá, Colombia. .,Universidad Pedagógica y Tecnológica de Colombia, Tunja, Boyacá, Colombia.
| |
Collapse
|
15
|
Sieben NA, Dash S. A retrospective evaluation of multiple definitions for ventilator associated pneumonia (VAP) diagnosis in an Australian regional intensive care unit. Infect Dis Health 2022; 27:191-197. [PMID: 35637156 DOI: 10.1016/j.idh.2022.04.004] [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: 01/12/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Ventilator Associated Pneumonia is a common complication of invasively ventilated patients with significant and underestimated morbidity and mortality. Defining VAP cases is greatly varied as many definitions are used with varying success and sensitivity. This study evaluates VAP detection using four definitions in a regional Australian Intensive Care Unit (ICU). METHODS A cohort of patients admitted to ICU at the Mackay Base Hospital from April 1st 2020 to March 31st 2021, who had endo-tracheal intubation and mechanical ventilation for longer than 48 h were identified. Each patient was examined across four common definitions of VAP. Head-to-head analysis of definitions was pursued to determine the most suitable definition. The four definitions used included: An Australian VAP definition, the CDC VAP definition, the Mackay Base Hospital Local Protocol and a Physician Decision Arm. RESULTS 66 unique patients and 2 re-intubations were identified during the data collection window. The local protocol identified 8 cases of VAP. The Australian VAP definition identified 6 additional cases and 0 missed cases compared to the local protocol. The CDC definition missed 4 cases and identified 4 additional cases compared to the local protocol. Finally, the physician arm identified 10 cases including 8 additional cases and missed 6 cases. CONCLUSIONS VAP is an extremely difficult clinical condition to define and detect. Definitions have varied accuracy and suffer logistically for application to the individual patient. Refined criteria for diagnosis of VAP is greatly needed and its prevalence in intensive care units likely remains uncertain.
Collapse
|
16
|
Sun YC, Wang CY, Wang HL, Yuan Y, Lu JH, Zhong L. Probiotic in the prevention of ventilator-associated pneumonia in critically ill patients: evidence from meta-analysis and trial sequential analysis of randomized clinical trials. BMC Pulm Med 2022; 22:168. [PMID: 35484547 PMCID: PMC9052689 DOI: 10.1186/s12890-022-01965-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Probiotic might have a role in the prevention of ventilator-associated pneumonia (VAP) among mechanically ventilated patients, but the efficacy and safety remained inconsistent. The aim of this systematic review and meta-analysis was to evaluate the efficacy and safety of probiotic (prebiotic, synbiotic) versus placebo in preventing VAP in critically ill patients undergoing mechanical ventilation. METHODS PubMed, Embase and the Cochrane library databases were searched to 10 October 2021 without language restriction for randomized or semi-randomized controlled trials evaluating probiotic (prebiotic, synbiotic) vs. placebo in prevention of VAP in critically ill mechanically ventilated patients. The pooled relative risk (RR) along with 95% confidence intervals (CI) were combined using a random-effects model. Furthermore, the trial sequential analysis (TSA) and subgroup analyses were performed. Statistical significance was regarded as P < 0.05. RESULTS Twenty-three trials involving 5543 patients were eligible for this meta-analysis. The combined RR of decreasing the risk of VAP by probiotic was 0.67 (0.56, 0.81) for all eligible studies, 0.69 (n = 5136; 95% CI = 0.57 to 0.84; P < 0.01) for adults studies and 0.55 (n = 407; 95%CI = 0.31 to 0.99; P = 0.046) for neonates/children studies. Additionally, the above-mentioned positive finding in 20 adults studies was verified by the results of TSA, subgroup analyses and cumulative meta-analysis. Ample evidences demonstrated a 31% decrease in RR of incidence of VAP was noted when prophylactic probiotic therapy was administrated among adult patients. Finally, there were no effects on the ICU/hospital/28-/90-day mortality, bacteremia, CRBSI, diarrhea, ICU-acquired infections, infectious complications, pneumonia, UTI and wound infection between two groups (P > 0.05 for all). CONCLUSIONS Based on the results of our study, the current evidences suggested that prophylactic administration of probiotic might be utilized as a preventive method for VAP in neonates/children and adults patients who required mechanical ventilation. However, further large, high-quality RCTs are warranted to assess the efficacy and safety of probiotic treatment in critically ill patients, especially for the neonates/children studies and the long-term consequences of this therapy.
Collapse
Affiliation(s)
- Yue-Chen Sun
- Department of Emergency, Huzhou Central Hospital, Affiliated Central Hospital HuZhou University, Huzhou, 313000, Zhejiang Province, China
| | - Chen-Yi Wang
- Department of Intensive Care Unit, Ningbo Yinzhou No. 2 Hospital, Ningbo, 315000, Zhejiang Province, China
| | - Hai-Li Wang
- Department of Obstetrics and Gynecology, Huzhou Central Hospital, Affiliated Central Hospital HuZhou University, Huzhou, 313000, Zhejiang Province, China
| | - Yao Yuan
- Department of Intensive Care Unit, Ningbo Yinzhou No. 2 Hospital, Ningbo, 315000, Zhejiang Province, China
| | - Jian-Hong Lu
- Department of Intensive Care Unit, Huzhou Central Hospital, Affiliated Central Hospital HuZhou University, No. 1558, North Sanhuan Road, Huzhou, 313000, Zhejiang Province, China
| | - Lei Zhong
- Department of Intensive Care Unit, Huzhou Central Hospital, Affiliated Central Hospital HuZhou University, No. 1558, North Sanhuan Road, Huzhou, 313000, Zhejiang Province, China.
| |
Collapse
|
17
|
Pérez-Cobas AE, Baquero F, de Pablo R, Soriano MC, Coque TM. Altered Ecology of the Respiratory Tract Microbiome and Nosocomial Pneumonia. Front Microbiol 2022; 12:709421. [PMID: 35222291 PMCID: PMC8866767 DOI: 10.3389/fmicb.2021.709421] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/21/2021] [Indexed: 12/23/2022] Open
Abstract
Nosocomial pneumonia is one of the most frequent infections in critical patients. It is primarily associated with mechanical ventilation leading to severe illness, high mortality, and prolonged hospitalization. The risk of mortality has increased over time due to the rise in multidrug-resistant (MDR) bacterial infections, which represent a global public health threat. Respiratory tract microbiome (RTM) research is growing, and recent studies suggest that a healthy RTM positively stimulates the immune system and, like the gut microbiome, can protect against pathogen infection through colonization resistance (CR). Physiological conditions of critical patients and interventions as antibiotics administration and mechanical ventilation dramatically alter the RTM, leading to dysbiosis. The dysbiosis of the RTM of ICU patients favors the colonization by opportunistic and resistant pathogens that can be part of the microbiota or acquired from the hospital environments (biotic or built ones). Despite recent evidence demonstrating the significance of RTM in nosocomial infections, most of the host-RTM interactions remain unknown. In this context, we present our perspective regarding research in RTM altered ecology in the clinical environment, particularly as a risk for acquisition of nosocomial pneumonia. We also reflect on the gaps in the field and suggest future research directions. Moreover, expected microbiome-based interventions together with the tools to study the RTM highlighting the "omics" approaches are discussed.
Collapse
Affiliation(s)
- Ana Elena Pérez-Cobas
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Raúl de Pablo
- Intensive Care Department, Ramón y Cajal University Hospital, Madrid, Spain
| | - María Cruz Soriano
- Intensive Care Department, Ramón y Cajal University Hospital, Madrid, Spain
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain.,CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
| |
Collapse
|
18
|
Critically ill patients with COVID-19 show lung fungal dysbiosis with reduced microbial diversity in Candida spp colonized patients. Int J Infect Dis 2022; 117:233-240. [PMID: 35150910 PMCID: PMC8828296 DOI: 10.1016/j.ijid.2022.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 02/03/2022] [Accepted: 02/06/2022] [Indexed: 12/16/2022] Open
Abstract
Background The COVID-19 pandemic has intensified interest in how the infection affects the lung microbiome of critically ill patients and how it contributes to acute respiratory distress syndrome (ARDS). We aimed to characterize the lower respiratory tract mycobiome of critically ill patients with COVID-19 in comparison to patients without COVID-19. Methods We performed an internal transcribed spacer 2 (ITS2) profiling with the Illumina MiSeq platform on 26 respiratory specimens from patients with COVID-19 as well as from 26 patients with non–COVID-19 pneumonia. Results Patients with COVID-19 were more likely to be colonized with Candida spp. ARDS was associated with lung dysbiosis characterized by a shift to Candida species colonization and a decrease of fungal diversity. We also observed higher bacterial phylogenetic distance among taxa in colonized patients with COVID-19. In patients with COVID-19 not colonized with Candida spp., ITS2 amplicon sequencing revealed an increase of Ascomycota unassigned spp. and 1 Aspergillus spp.–positive specimen. In addition, we found that corticosteroid therapy was frequently associated with positive Galactomannan cell wall component of Aspergillus spp. among patients with COVID-19. Conclusion Our study underpins that ARDS in patients with COVID-19 is associated with lung dysbiosis and that an increased density of Ascomycota unassigned spp. is present in patients not colonized with Candida spp.
Collapse
|
19
|
de Castilhos J, Zamir E, Hippchen T, Rohrbach R, Schmidt S, Hengler S, Schumacher H, Neubauer M, Kunz S, Müller-Esch T, Hiergeist A, Gessner A, Khalid D, Gaiser R, Cullin N, Papagiannarou SM, Beuthien-Baumann B, Krämer A, Bartenschlager R, Jäger D, Müller M, Herth F, Duerschmied D, Schneider J, Schmid RM, Eberhardt JF, Khodamoradi Y, Vehreschild MJGT, Teufel A, Ebert MP, Hau P, Salzberger B, Schnitzler P, Poeck H, Elinav E, Merle U, Stein-Thoeringer CK. Severe Dysbiosis and Specific Haemophilus and Neisseria Signatures as Hallmarks of the Oropharyngeal Microbiome in Critically Ill Coronavirus Disease 2019 (COVID-19) Patients. Clin Infect Dis 2021; 75:e1063-e1071. [PMID: 34694375 PMCID: PMC8586732 DOI: 10.1093/cid/ciab902] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND At the entry site of respiratory virus infections, the oropharyngeal microbiome has been proposed as a major hub integrating viral and host immune signals. Early studies suggested that infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are associated with changes of the upper and lower airway microbiome, and that specific microbial signatures may predict coronavirus disease 2019 (COVID-19) illness. However, the results are not conclusive, as critical illness can drastically alter a patient's microbiome through multiple confounders. METHODS To study oropharyngeal microbiome profiles in SARS-CoV-2 infection, clinical confounders, and prediction models in COVID-19, we performed a multicenter, cross-sectional clinical study analyzing oropharyngeal microbial metagenomes in healthy adults, patients with non-SARS-CoV-2 infections, or with mild, moderate, and severe COVID-19 (n = 322 participants). RESULTS In contrast to mild infections, patients admitted to a hospital with moderate or severe COVID-19 showed dysbiotic microbial configurations, which were significantly pronounced in patients treated with broad-spectrum antibiotics, receiving invasive mechanical ventilation, or when sampling was performed during prolonged hospitalization. In contrast, specimens collected early after admission allowed us to segregate microbiome features predictive of hospital COVID-19 mortality utilizing machine learning models. Taxonomic signatures were found to perform better than models utilizing clinical variables with Neisseria and Haemophilus species abundances as most important features. CONCLUSIONS In addition to the infection per se, several factors shape the oropharyngeal microbiome of severely affected COVID-19 patients and deserve consideration in the interpretation of the role of the microbiome in severe COVID-19. Nevertheless, we were able to extract microbial features that can help to predict clinical outcomes.
Collapse
Affiliation(s)
- Juliana de Castilhos
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany,Vale do Rio dos Sinos University (UNISINOS), Sao Leopoldo, Brazil
| | - Eli Zamir
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Theresa Hippchen
- Department of Gastroenterology and Infectious Diseases, University Clinic Heidelberg, Heidelberg, Germany
| | - Roman Rohrbach
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Sabine Schmidt
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Silvana Hengler
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Hanna Schumacher
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Melanie Neubauer
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Sabrina Kunz
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - Tonia Müller-Esch
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Clinic Regensburg, Regensburg, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Clinic Regensburg, Regensburg, Germany
| | - Dina Khalid
- Department of Virology, University Clinic Heidelberg, Heidelberg, Germany
| | - Rogier Gaiser
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Nyssa Cullin
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Stamatia M Papagiannarou
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | | | - Alwin Krämer
- German Cancer Research Center (DKFZ), Research Division Molecular Hematology/Oncology, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany,German Cancer Research Center (DKFZ), Research Division Virus-associated Carcinogenesis, Heidelberg
| | - Dirk Jäger
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Michael Müller
- Thoraxklinik and Translational Lung Research Center, Heidelberg University, Heidelberg, Germany
| | - Felix Herth
- Thoraxklinik and Translational Lung Research Center, Heidelberg University, Heidelberg, Germany
| | - Daniel Duerschmied
- Department of Internal Medicine III, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jochen Schneider
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Roland M Schmid
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Johann F Eberhardt
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Andreas Teufel
- Department of Medicine II, Section of Hepatology, University Medical Center Mannheim, University of Heidelberg, Mannheim, and Center for Preventive Medicine and Digital Health Baden-Württemberg, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias P Ebert
- Department of Medicine II, Section of Hepatology, University Medical Center Mannheim, University of Heidelberg, Mannheim, and Center for Preventive Medicine and Digital Health Baden-Württemberg, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Peter Hau
- Wilhelm Sander-NeuroOncology Unit and Department of Neurology, University Clinic Regensburg, Regensburg, Germany
| | - Bernd Salzberger
- Department of Infectious Disease, University Clinic Regensburg, Regensburg, Germany
| | - Paul Schnitzler
- Department of Virology, University Clinic Heidelberg, Heidelberg, Germany
| | - Hendrik Poeck
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany,National Center for Tumor Diseases (NCT) WERA
| | - Eran Elinav
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany,Weizmann Institute of Science, Rehovot, Israel
| | - Uta Merle
- Department of Gastroenterology and Infectious Diseases, University Clinic Heidelberg, Heidelberg, Germany
| | - Christoph K Stein-Thoeringer
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany,National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany,Corresponding author: Christoph K. Stein-Thoeringer, MD, Microbiome and Cancer Research Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany,
| |
Collapse
|
20
|
Ikegami H, Noguchi S, Fukuda K, Akata K, Yamasaki K, Kawanami T, Mukae H, Yatera K. Refinement of microbiota analysis of specimens from patients with respiratory infections using next-generation sequencing. Sci Rep 2021; 11:19534. [PMID: 34599245 PMCID: PMC8486753 DOI: 10.1038/s41598-021-98985-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have been applied in bacterial flora analysis. However, there is no standardized protocol, and the optimal clustering threshold for estimating bacterial species in respiratory infection specimens is unknown. This study was conducted to investigate the optimal threshold for clustering 16S ribosomal RNA gene sequences into operational taxonomic units (OTUs) by comparing the results of NGS technology with those of the Sanger method, which has a higher accuracy of sequence per single read than NGS technology. This study included 45 patients with pneumonia with aspiration risks and 35 patients with lung abscess. Compared to Sanger method, the concordance rates of NGS technology (clustered at 100%, 99%, and 97% homology) with the predominant phylotype were 78.8%, 71.3%, and 65.0%, respectively. With respect to the specimens dominated by the Streptococcus mitis group, containing several important causative agents of pneumonia, Bray Curtis dissimilarity revealed that the OTUs obtained at 100% clustering threshold (versus those obtained at 99% and 97% thresholds; medians of 0.35, 0.69, and 0.71, respectively) were more similar to those obtained by the Sanger method, with statistical significance (p < 0.05). Clustering with 100% sequence identity is necessary when analyzing the microbiota of respiratory infections using NGS technology.
Collapse
Affiliation(s)
- Hiroaki Ikegami
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan
| | - Shingo Noguchi
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan
| | - Kazumasa Fukuda
- Department of Microbiology, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | - Kentaro Akata
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan
| | - Kei Yamasaki
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan
| | - Toshinori Kawanami
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kazuhiro Yatera
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan.
| |
Collapse
|
21
|
Fernández-Barat L, Alcaraz-Serrano V, Amaro R, Torres A. Pseudomonas aeruginosa in Bronchiectasis. Semin Respir Crit Care Med 2021; 42:587-594. [PMID: 34261182 DOI: 10.1055/s-0041-1730921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Pseudomonas aeruginosa (PA) in patients with bronchiectasis (BE) is associated with a poor outcome and quality of life, and its presence is considered a marker of disease severity. This opportunistic pathogen is known for its ability to produce biofilms on biotic or abiotic surfaces and to survive environmental stress exerted by antimicrobials, inflammation, and nutrient or oxygen depletion. The presence of PA biofilms has been linked to chronic respiratory infection in cystic fibrosis but not in BE. There is considerable inconsistency in the reported infection/eradication rates of PA and chronic PA. In addition, inadequate antimicrobial treatment may potentiate the progression from intermittent to chronic infection and also the emergence of antibiotic resistance. A better comprehension of the pathophysiology of PA infections and its implications for BE is urgently needed. This can drive improvements in diagnostic accuracy, can move us toward a new consensus definition of chronic infection, can better define the follow-up of patients at risk of PA, and can achieve more successful eradication rates. In addition, the new technological advances regarding molecular diagnostics, -omics, and biomarkers require us to reconsider our traditional concepts.
Collapse
Affiliation(s)
- Laia Fernández-Barat
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,School of Medicine, University of Barcelona, Barcelona, Spain.,Department of Pneumology, Respiratory Institute, Hospital Clinic of Barcelona, Spain
| | - Victoria Alcaraz-Serrano
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,School of Medicine, University of Barcelona, Barcelona, Spain.,Department of Pneumology, Respiratory Institute, Hospital Clinic of Barcelona, Spain
| | - Rosanel Amaro
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,School of Medicine, University of Barcelona, Barcelona, Spain.,Department of Pneumology, Respiratory Institute, Hospital Clinic of Barcelona, Spain
| | - Antoni Torres
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,School of Medicine, University of Barcelona, Barcelona, Spain.,Department of Pneumology, Respiratory Institute, Hospital Clinic of Barcelona, Spain
| |
Collapse
|
22
|
Battaglini D, Robba C, Fedele A, Trancǎ S, Sukkar SG, Di Pilato V, Bassetti M, Giacobbe DR, Vena A, Patroniti N, Ball L, Brunetti I, Torres Martí A, Rocco PRM, Pelosi P. The Role of Dysbiosis in Critically Ill Patients With COVID-19 and Acute Respiratory Distress Syndrome. Front Med (Lausanne) 2021; 8:671714. [PMID: 34150807 PMCID: PMC8211890 DOI: 10.3389/fmed.2021.671714] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022] Open
Abstract
In late December 2019, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) quickly spread worldwide, and the syndrome it causes, coronavirus disease 2019 (COVID-19), has reached pandemic proportions. Around 30% of patients with COVID-19 experience severe respiratory distress and are admitted to the intensive care unit for comprehensive critical care. Patients with COVID-19 often present an enhanced immune response with a hyperinflammatory state characterized by a "cytokine storm," which may reflect changes in the microbiota composition. Moreover, the evolution to acute respiratory distress syndrome (ARDS) may increase the severity of COVID-19 and related dysbiosis. During critical illness, the multitude of therapies administered, including antibiotics, sedatives, analgesics, body position, invasive mechanical ventilation, and nutritional support, may enhance the inflammatory response and alter the balance of patients' microbiota. This status of dysbiosis may lead to hyper vulnerability in patients and an inappropriate response to critical circumstances. In this context, the aim of our narrative review is to provide an overview of possible interaction between patients' microbiota dysbiosis and clinical status of severe COVID-19 with ARDS, taking into consideration the characteristic hyperinflammatory state of this condition, respiratory distress, and provide an overview on possible nutritional strategies for critically ill patients with COVID-19-ARDS.
Collapse
Affiliation(s)
- Denise Battaglini
- Anesthesia and Intensive Care, Ospedale Policlinico San Martino, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) per l'Oncologia e le Neuroscienze, Genova, Italy
- Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Chiara Robba
- Anesthesia and Intensive Care, Ospedale Policlinico San Martino, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) per l'Oncologia e le Neuroscienze, Genova, Italy
- Department of Surgical Sciences and Integrated Diagnostics (DISC), Università degli Studi di Genova, Genova, Italy
| | - Andrea Fedele
- Anesthesia and Intensive Care, Ospedale Policlinico San Martino, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) per l'Oncologia e le Neuroscienze, Genova, Italy
| | - Sebastian Trancǎ
- Department of Anesthesia and Intensive Care II, Clinical Emergency County Hospital of Cluj, Iuliu Hatieganu, University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Anaesthesia and Intensive Care 1, Clinical Emergency County Hospital Cluj-Napoca, Cluj-Napoca, Romania
| | - Samir Giuseppe Sukkar
- Dietetics and Clinical Nutrition Unit, Ospedale Policlinico San Martino, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) per l'Oncologia e le Neuroscienze, Genova, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics (DISC), Università degli Studi di Genova, Genova, Italy
| | - Matteo Bassetti
- Clinica Malattie Infettive, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) per l'Oncologia e le Neuroscienze, Genova, Italy
- Dipartimento di Scienze della Salute (DISSAL), Università degli Studi di Genova, Genova, Italy
| | - Daniele Roberto Giacobbe
- Clinica Malattie Infettive, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) per l'Oncologia e le Neuroscienze, Genova, Italy
- Dipartimento di Scienze della Salute (DISSAL), Università degli Studi di Genova, Genova, Italy
| | - Antonio Vena
- Clinica Malattie Infettive, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) per l'Oncologia e le Neuroscienze, Genova, Italy
| | - Nicolò Patroniti
- Anesthesia and Intensive Care, Ospedale Policlinico San Martino, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) per l'Oncologia e le Neuroscienze, Genova, Italy
- Department of Surgical Sciences and Integrated Diagnostics (DISC), Università degli Studi di Genova, Genova, Italy
| | - Lorenzo Ball
- Anesthesia and Intensive Care, Ospedale Policlinico San Martino, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) per l'Oncologia e le Neuroscienze, Genova, Italy
- Department of Surgical Sciences and Integrated Diagnostics (DISC), Università degli Studi di Genova, Genova, Italy
| | - Iole Brunetti
- Anesthesia and Intensive Care, Ospedale Policlinico San Martino, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) per l'Oncologia e le Neuroscienze, Genova, Italy
| | - Antoni Torres Martí
- Department of Medicine, University of Barcelona, Barcelona, Spain
- Division of Animal Experimentation, Department of Pulmonology, Hospital Clinic, Barcelona, Spain
- Centro de Investigacion en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Institut d'investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Patricia Rieken Macedo Rocco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- COVID-19-Network, Ministry of Science, Technology, Innovation and Communication, Brasilia, Brazil
| | - Paolo Pelosi
- Anesthesia and Intensive Care, Ospedale Policlinico San Martino, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) per l'Oncologia e le Neuroscienze, Genova, Italy
- Department of Surgical Sciences and Integrated Diagnostics (DISC), Università degli Studi di Genova, Genova, Italy
| |
Collapse
|