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Gao S, Huang X, Zhou X, Dai X, Han J, Chen Y, Qiao H, Li Y, Zhou Y, Wang T, He H, Liu Q, Tang S. A comprehensive evaluation of risk factors for mortality, infection and colonization associated with CRGNB in adult solid organ transplant recipients: a systematic review and meta-analysis. Ann Med 2024; 56:2314236. [PMID: 38442299 PMCID: PMC10916923 DOI: 10.1080/07853890.2024.2314236] [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: 12/03/2023] [Accepted: 01/30/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND The burden of carbapenem-resistant gram-negative bacteria (CRGNB) among solid organ transplant (SOT) recipients has not been systematically explored. Here, we discern the risk factors associated with CRGNB infection and colonization in SOT recipients. METHODS This study included observational studies conducted among CRGNB-infected SOT patients, which reported risk factors associated with mortality, infection or colonization. Relevant records will be searched in PubMed, Embase and Web of Science for the period from the time of database construction to 1 March 2023. RESULTS A total of 23 studies with 13,511 participants were included, enabling the assessment of 27 potential risk factors. The pooled prevalence of 1-year mortality among SOT recipients with CRGNB was 44.5%. Prolonged mechanical ventilation, combined transplantation, reoperation and pre-transplantation CRGNB colonization are salient contributors to the occurrence of CRGNB infections in SOT recipients. Renal replacement therapy, post-LT CRGNB colonization, pre-LT liver disease and model for end-stage liver disease score increased the risk of infection. Re-transplantation, carbapenem use before transplantation and ureteral stent utilization increaesd risk of CRGNB colonization. CONCLUSION Our study demonstrated that SOT recipients with CRGNB infections had a higher mortality risk. Invasive procedure may be the main factor contribute to CRGNB infection.
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Affiliation(s)
- Siyu Gao
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xiaoli Huang
- Department of Infectious Diseases, Yichang Central People’s Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Xiaolin Zhou
- Department of Infectious Diseases, Yichang Central People’s Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Xiangcheng Dai
- Department of Infectious Diseases, Yichang Central People’s Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Jing Han
- Department of Infectious Diseases, Yichang Central People’s Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Yandong Chen
- Department of Infectious Diseases, Yichang Central People’s Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Hongliang Qiao
- Department of Urology, Yichang Central People’s Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Yi Li
- Department of Cardio-Thoracic Surgery, Yichang Central People’s Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Yifan Zhou
- Department of Infectious Diseases, Yichang Central People’s Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Ting Wang
- Department of Infectious Diseases, Yichang Central People’s Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Huiqing He
- National Health Commission of the People’s Republic of China, Yichang, China
| | - Qiang Liu
- Department of Infectious Diseases, Yichang Central People’s Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Shenjie Tang
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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Ren Y, Liang J, Li X, Deng Y, Cheng S, Wu Q, Song W, He Y, Zhu J, Zhang X, Zhou H, Yin J. Association between oral microbial dysbiosis and poor functional outcomes in stroke-associated pneumonia patients. BMC Microbiol 2023; 23:305. [PMID: 37875813 PMCID: PMC10594709 DOI: 10.1186/s12866-023-03057-8] [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] [Accepted: 10/11/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Despite advances in our understanding of the critical role of the microbiota in stroke patients, the oral microbiome has rarely been reported to be associated with stroke-associated pneumonia (SAP). We sought to profile the oral microbial composition of SAP patients and to determine whether microbiome temporal instability and special taxa are associated with pneumonia progression and functional outcomes. METHODS This is a prospective, observational, single-center cohort study that examined patients with acute ischemic stroke (AIS) who were admitted within 24 h of experiencing a stroke event. The patients were divided into three groups based on the occurrence of pneumonia and the use of mechanical ventilation: nonpneumonia group, SAP group, and ventilator-associated pneumonia (VAP) group. We collected oral swabs at different time points post-admission and analyzed the microbiota using 16 S rRNA high-throughput sequencing. The microbiota was then compared among the three groups. RESULTS In total, 104 nonpneumonia, 50 SAP and 10 VAP patients were included in the analysis. We found that SAP and VAP patients exhibited significant dynamic differences in the diversity and composition of the oral microbiota and that the magnitude of this dysbiosis and instability increased during hospitalization. Then, by controlling the potential effect of all latent confounding variables, we assessed the changes associated with pneumonia after stroke and explored patients with a lower abundance of Streptococcus were more likely to suffer from SAP. The logistic regression analysis revealed that an increase in specific taxa in the phylum Actinobacteriota was linked to a higher risk of poor outcomes. A model for SAP patients based on oral microbiota could accurately predict 30-day clinical outcomes after stroke onset. CONCLUSIONS We concluded that specific oral microbiota signatures could be used to predict illness development and clinical outcomes in SAP patients. We proposed the potential of the oral microbiota as a non-invasive diagnostic biomarker in the clinical management of SAP patients. CLINICAL TRIAL REGISTRATION NCT04688138. Registered 29/12/2020, https://clinicaltrials.gov/ct2/show/NCT04688138 .
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Affiliation(s)
- Yueran Ren
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jingru Liang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiao Li
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yiting Deng
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Sanping Cheng
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Qiheng Wu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Wei Song
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yan He
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jiajia Zhu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaomei Zhang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Hongwei Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Jia Yin
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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3
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Powell J, Powell S, Mather MW, Beck L, Nelson A, Palmowski P, Porter A, Coxhead J, Hedley A, Scott J, Rostron AJ, Hellyer TP, Zaidi F, Davey T, Garnett JP, Agbeko R, Ward C, Stewart CJ, Taggart CC, Brodlie M, Simpson AJ. Tracheostomy in children is associated with neutrophilic airway inflammation. Thorax 2023; 78:1019-1027. [PMID: 36808087 PMCID: PMC10511973 DOI: 10.1136/thorax-2022-219557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/29/2022] [Indexed: 02/22/2023]
Abstract
BACKGROUND Tracheostomies in children are associated with significant morbidity, poor quality of life, excess healthcare costs and excess mortality. The underlying mechanisms facilitating adverse respiratory outcomes in tracheostomised children are poorly understood. We aimed to characterise airway host defence in tracheostomised children using serial molecular analyses. METHODS Tracheal aspirates, tracheal cytology brushings and nasal swabs were prospectively collected from children with a tracheostomy and controls. Transcriptomic, proteomic and metabolomic methods were applied to characterise the impact of tracheostomy on host immune response and the airway microbiome. RESULTS Children followed up serially from the time of tracheostomy up to 3 months postprocedure (n=9) were studied. A further cohort of children with a long-term tracheostomy were also enrolled (n=24). Controls (n=13) comprised children without a tracheostomy undergoing bronchoscopy. Long-term tracheostomy was associated with airway neutrophilic inflammation, superoxide production and evidence of proteolysis when compared with controls. Reduced airway microbial diversity was established pre-tracheostomy and sustained thereafter. CONCLUSIONS Long-term childhood tracheostomy is associated with a inflammatory tracheal phenotype characterised by neutrophilic inflammation and the ongoing presence of potential respiratory pathogens. These findings suggest neutrophil recruitment and activation as potential exploratory targets in seeking to prevent recurrent airway complications in this vulnerable group of patients.
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Affiliation(s)
- Jason Powell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Paediatric Otolaryngology, Great North Children's Hospital, Newcastle upon Tyne, UK
| | - Steven Powell
- Department of Paediatric Otolaryngology, Great North Children's Hospital, Newcastle upon Tyne, UK
| | - Michael W Mather
- Department of Paediatric Otolaryngology, Great North Children's Hospital, Newcastle upon Tyne, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Lauren Beck
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Nelson
- Department of Applied Science, Northumbria University, Newcastle upon Tyne, UK
| | - Pawel Palmowski
- Protein and Proteome Facility, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Porter
- Protein and Proteome Facility, Newcastle University, Newcastle upon Tyne, UK
| | - Jonathan Coxhead
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ann Hedley
- Bioinformatics Support Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Jonathan Scott
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Anthony J Rostron
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Thomas P Hellyer
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Fatima Zaidi
- Discovery and Translational Science, Metabolon, Morrisville, North Carolina, USA
| | - Tracey Davey
- Electron Microscopy Research Services, Newcastle University, Newcastle upon Tyne, UK
| | - James P Garnett
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel Agbeko
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Paediatric Intensive Care, Great North Children's Hospital, Newcastle upon Tyne, UK
| | - Chris Ward
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Malcolm Brodlie
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne, UK
| | - A John Simpson
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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4
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Pérez-Cobas AE, Ginevra C, Rusniok C, Jarraud S, Buchrieser C. The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia. Cell Rep Med 2023; 4:101167. [PMID: 37633274 PMCID: PMC10518590 DOI: 10.1016/j.xcrm.2023.101167] [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: 12/05/2022] [Revised: 06/18/2023] [Accepted: 08/02/2023] [Indexed: 08/28/2023]
Abstract
Bacterial pneumonia is a considerable problem worldwide. Here, we follow the inter-kingdom respiratory tract microbiome (RTM) of a unique cohort of 38 hospitalized patients (n = 97 samples) with pneumonia caused by Legionella pneumophila. The RTM composition is characterized by diversity drops early in hospitalization and ecological species replacement. RTMs with the highest bacterial and fungal loads show low diversity and pathogen enrichment, suggesting high biomass as a biomarker for secondary and/or co-infections. The RTM structure is defined by a "commensal" cluster associated with a healthy RTM and a "pathogen" enriched one, suggesting that the cluster equilibrium drives the microbiome to recovery or dysbiosis. Legionella biomass correlates with disease severity and co-morbidities, while clinical interventions influence the RTM dynamics. Fungi, archaea, and protozoa seem to contribute to progress of pneumonia. Thus, the interplay of the RTM equilibrium, the pathogen load dynamics, and clinical interventions play a critical role in patient recovery.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France.
| | - Christophe Ginevra
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Bron, France; Centre International de Recherche en Infectiologie, Université Lyon 1, UMR CNRS 5308, U1111 Inserm, École Normale Supérieure de Lyon, Lyon, France
| | - Christophe Rusniok
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France
| | - Sophie Jarraud
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Bron, France; Centre International de Recherche en Infectiologie, Université Lyon 1, UMR CNRS 5308, U1111 Inserm, École Normale Supérieure de Lyon, Lyon, France
| | - Carmen Buchrieser
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France.
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5
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Pérez-Cobas AE, Rodríguez-Beltrán J, Baquero F, Coque TM. Ecology of the respiratory tract microbiome. Trends Microbiol 2023; 31:972-984. [PMID: 37173205 DOI: 10.1016/j.tim.2023.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/05/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023]
Abstract
A thriving multi-kingdom microbial ecosystem inhabits the respiratory tract: the respiratory tract microbiome (RTM). In recent years, the contribution of the RTM to human health has become a crucial research aspect. However, research into the key ecological processes, such as robustness, resilience, and microbial interaction networks, has only recently started. This review leans on an ecological framework to interpret the human RTM and determine how the ecosystem functions and assembles. Specifically, the review illustrates the ecological RTM models and discusses microbiome establishment, community structure, diversity stability, and critical microbial interactions. Lastly, the review outlines the RTM responses to ecological disturbances, as well as the promising approaches for restoring ecological balance.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- 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.
| | - Jerónimo Rodríguez-Beltrán
- 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
| | - 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
| | - 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
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6
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Rosenboom I, Pust MM, Pirr S, Bakker A, Willers M, Davenport CF, Wiehlmann L, Viemann D, Tümmler B. Longitudinal development of the airway metagenome of preterm very low birth weight infants during the first two years of life. ISME COMMUNICATIONS 2023; 3:75. [PMID: 37474785 PMCID: PMC10359316 DOI: 10.1038/s43705-023-00285-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023]
Abstract
Preterm birth is accompanied with many complications and requires severe therapeutic regimens at the neonatal intensive care unit. The influence of the above-mentioned factors on the premature-born infants' respiratory metagenome or more generally its maturation is unknown. We therefore applied shotgun metagenome sequencing of oropharyngeal swabs to analyze the airway metagenome development of 24 preterm infants from one week postpartum to 15 months of age. Beta diversity analysis revealed a distinct clustering of airway microbial communities from hospitalized preterms and samples after hospital discharge. At nine and 15 months of age, the preterm infants lost their hospital-acquired individual metagenome signatures towards a common taxonomic structure. However, ecological network analysis and Random Forest classification of cross-sectional data revealed that by this age the preterm infants did not succeed in establishing the uniform and stable bacterial community structures that are characteristic for healthy full-term infants.
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Affiliation(s)
- Ilona Rosenboom
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Marie-Madlen Pust
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Sabine Pirr
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Alina Bakker
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Maike Willers
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Colin F Davenport
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Dorothee Viemann
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Translational Pediatrics, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Center for Infection Research, University Würzburg, Würzburg, Germany
| | - Burkhard Tümmler
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.
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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.
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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
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8
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Liu C, Wu K, Sun T, Chen B, Yi Y, Ren R, Xie L, Xiao K. Effect of invasive mechanical ventilation on the diversity of the pulmonary microbiota. Crit Care 2022; 26:252. [PMID: 35996150 PMCID: PMC9394019 DOI: 10.1186/s13054-022-04126-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/02/2022] [Indexed: 11/10/2022] Open
Abstract
Pulmonary microbial diversity may be influenced by biotic or abiotic conditions (e.g., disease, smoking, invasive mechanical ventilation (MV), etc.). Specially, invasive MV may trigger structural and physiological changes in both tissue and microbiota of lung, due to gastric and oral microaspiration, altered body posture, high O2 inhalation-induced O2 toxicity in hypoxemic patients, impaired airway clearance and ventilator-induced lung injury (VILI), which in turn reduce the diversity of the pulmonary microbiota and may ultimately lead to poor prognosis. Furthermore, changes in (local) O2 concentration can reduce the diversity of the pulmonary microbiota by affecting the local immune microenvironment of lung. In conclusion, systematic literature studies have found that invasive MV reduces pulmonary microbiota diversity, and future rational regulation of pulmonary microbiota diversity by existing or novel clinical tools (e.g., lung probiotics, drugs) may improve the prognosis of invasive MV treatment and lead to more effective treatment of lung diseases with precision.
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Affiliation(s)
- Chang Liu
- College of Pulmonary & Critical Care Medicine, 8th Medical Center, Chinese PLA General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Kang Wu
- College of Pulmonary & Critical Care Medicine, 8th Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Tianyu Sun
- College of Pulmonary & Critical Care Medicine, 8th Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Bin Chen
- MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Yaxing Yi
- MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Ruotong Ren
- MatriDx Biotechnology Co., Ltd, Hangzhou, China.
- Foshan Branch, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Lixin Xie
- College of Pulmonary & Critical Care Medicine, 8th Medical Center, Chinese PLA General Hospital, Beijing, China.
- School of Medicine, Nankai University, Tianjin, China.
| | - Kun Xiao
- College of Pulmonary & Critical Care Medicine, 8th Medical Center, Chinese PLA General Hospital, Beijing, China.
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9
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Ren L, Wang Y, Zhong J, Li X, Xiao Y, Li J, Yang J, Fan G, Guo L, Shen Z, Kang L, Shi L, Li Q, Li J, Di L, Li H, Wang C, Wang Y, Wang X, Zou X, Rao J, Zhang L, Wang J, Huang Y, Cao B, Wang J, Li M. Dynamics of the Upper Respiratory Tract Microbiota and Its Association with Mortality in COVID-19. Am J Respir Crit Care Med 2021; 204:1379-1390. [PMID: 34534435 PMCID: PMC8865718 DOI: 10.1164/rccm.202103-0814oc] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rationale Alteration of human respiratory microbiota had been observed in coronavirus disease (COVID-19). How the microbiota is associated with the prognosis in COVID-19 is unclear. Objectives To characterize the feature and dynamics of the respiratory microbiota and its associations with clinical features in patients with COVID-19. Methods We conducted metatranscriptome sequencing on 588 longitudinal oropharyngeal swab specimens collected from 192 patients with COVID-19 (including 39 deceased patients) and 95 healthy controls from the same geographic area. Meanwhile, the concentration of 27 cytokines and chemokines in plasma was measured for patients with COVID-19. Measurements and Main Results The upper respiratory tract (URT) microbiota in patients with COVID-19 differed from that in healthy controls, whereas deceased patients possessed a more distinct microbiota, both on admission and before discharge/death. The alteration of URT microbiota showed a significant correlation with the concentration of proinflammatory cytokines and mortality. Specifically, Streptococcus-dominated microbiota was enriched in recovered patients, and showed high temporal stability and resistance against pathogens. In contrast, the microbiota in deceased patients was more susceptible to secondary infections and became more deviated from the norm after admission. Moreover, the abundance of S. parasanguinis on admission was significantly correlated with prognosis in nonsevere patients (lower vs. higher abundance, odds ratio, 7.80; 95% CI, 1.70–42.05). Conclusions URT microbiota dysbiosis is a remarkable manifestation of COVID-19; its association with mortality suggests it may reflect the interplay between pathogens, symbionts, and the host immune status. Whether URT microbiota could be used as a biomarker for diagnosis and prognosis of respiratory diseases merits further investigation.
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Affiliation(s)
- Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, and.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yeming Wang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, and.,Department of Respiratory Medicine, Capital Medical University, Beijing, China
| | - Jiaxin Zhong
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xia Li
- Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Wuhan, China
| | - Yan Xiao
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, and.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Li
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, and Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jing Yang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guohui Fan
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, China
| | - Li Guo
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, and.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zijie Shen
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lu Kang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Leisheng Shi
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiong Li
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, and Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jizhou Li
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, and Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Lin Di
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, College of Chemistry, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Haibo Li
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, and.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Conghui Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, and
| | - Ying Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, and
| | - Xinming Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, and
| | - Xiaohui Zou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, and.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Jian Rao
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, and.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jianbin Wang
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, and Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, College of Chemistry, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Institute for Cell Analysis, Shenzhen Bay Laboratory, Guangdong, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, and.,Department of Respiratory Medicine, Capital Medical University, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China; and
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, and.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingkun Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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