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Zhang L, Xu J, Li Y, Meng F, Wang W. Smoking on the risk of acute respiratory distress syndrome: a systematic review and meta-analysis. Crit Care 2024; 28:122. [PMID: 38616271 PMCID: PMC11017665 DOI: 10.1186/s13054-024-04902-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/03/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND The relationship between smoking and the risk of acute respiratory distress syndrome (ARDS) has been recognized, but the conclusions have been inconsistent. This systematic review and meta-analysis investigated the association between smoking and ARDS risk in adults. METHODS The PubMed, EMBASE, Cochrane Library, and Web of Science databases were searched for eligible studies published from January 1, 2000, to December 31, 2023. We enrolled adult patients exhibiting clinical risk factors for ARDS and smoking condition. Outcomes were quantified using odds ratios (ORs) for binary variables and mean differences (MDs) for continuous variables, with a standard 95% confidence interval (CI). RESULTS A total of 26 observational studies involving 36,995 patients were included. The meta-analysis revealed a significant association between smoking and an increased risk of ARDS (OR 1.67; 95% CI 1.33-2.08; P < 0.001). Further analysis revealed that the associations between patient-reported smoking history and ARDS occurrence were generally similar to the results of all the studies (OR 1.78; 95% CI 1.38-2.28; P < 0.001). In contrast, patients identified through the detection of tobacco metabolites (cotinine, a metabolite of nicotine, and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), a metabolite of tobacco products) showed no significant difference in ARDS risk (OR 1.19; 95% CI 0.69-2.05; P = 0.53). The smoking group was younger than the control group (MD - 7.15; 95% CI - 11.58 to - 2.72; P = 0.002). Subgroup analysis revealed that smoking notably elevated the incidence of ARDS with extrapulmonary etiologies (OR 1.85; 95% CI 1.43-2.38; P < 0.001). Publication bias did not affect the integrity of our conclusions. Sensitivity analysis further reinforced the reliability of our aggregated outcomes. CONCLUSIONS There is a strong association between smoking and elevated ARDS risk. This emphasizes the need for thorough assessment of patients' smoking status, urging healthcare providers to vigilantly monitor individuals with a history of smoking, especially those with additional extrapulmonary risk factors for ARDS.
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Affiliation(s)
- Lujia Zhang
- Institute of Respiratory and Critical Care Medicine, The First Hospital of China Medical University, No. 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China
| | - Jiahuan Xu
- Institute of Respiratory and Critical Care Medicine, The First Hospital of China Medical University, No. 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China
| | - Yue Li
- Institute of Respiratory and Critical Care Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Fanqi Meng
- Institute of Respiratory and Critical Care Medicine, The First Hospital of China Medical University, No. 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China
| | - Wei Wang
- Institute of Respiratory and Critical Care Medicine, The First Hospital of China Medical University, No. 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.
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Zheng L, Liu C, Wang H, Zhang J, Mao L, Dong X, Hu S, Li N, Pi D, Qiu J, Xu F, Chen C, Zou Z. Intact lung tissue and bronchoalveolar lavage fluid are both suitable for the evaluation of murine lung microbiome in acute lung injury. Microbiome 2024; 12:56. [PMID: 38494479 PMCID: PMC10946114 DOI: 10.1186/s40168-024-01772-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/30/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Accumulating clinical evidence suggests that lung microbiome is closely linked to the progression of pulmonary diseases; however, it is still controversial which specimen type is preferred for the evaluation of lung microbiome. METHODS AND RESULTS To address this issue, we established a classical acute lung injury (ALI) mice model by intratracheal instillation of lipopolysaccharides (LPS). We found that the bacterial DNA obtained from the bronchoalveolar lavage fluid (BALF), intact lung tissue [Lung(i)], lung tissue after perfused [Lung(p)], and feces of one mouse were enough for 16S rRNA sequencing, except the BALF of mice treated with phosphate buffer saline (PBS), which might be due to the biomass of lung microbiome in the BALF were upregulated in the mice treated with LPS. Although the alpha diversity among the three specimens from lungs had minimal differences, Lung(p) had higher sample-to-sample variation compared with BALF and Lung(i). Consistently, PCoA analysis at phylum level indicated that BALF was similar to Lung(i), but not Lung(p), in the lungs of mice treated with LPS, suggesting that BALF and Lung(i) were suitable for the evaluation of lung microbiome in ALI. Importantly, Actinobacteria and Firmicutes were identified as the mostly changed phyla in the lungs and might be important factors involved in the gut-lung axis in ALI mice. Moreover, Actinobacteria and Proteobacteria might play indicative roles in the severity of lung injury. CONCLUSION This study shows both Lung(i) and BALF are suitable for the evaluation of murine lung microbiome in ALI, and several bacterial phyla, such as Actinobacteria, may serve as potential biomarkers for the severity of ALI. Video Abstract.
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Affiliation(s)
- Lijun Zheng
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Chengjun Liu
- Department of Pediatric Intensive Care Unit, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Hongjing Wang
- Department of Health Laboratory Technology, School of Public Health, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Jun Zhang
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
- Research Center for Environment and Human Health, School of Public Health, Chongqing, 400016, People's Republic of China
| | - Lejiao Mao
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Xiaomei Dong
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Siyao Hu
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Na Li
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Dandan Pi
- Department of Pediatric Intensive Care Unit, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Jingfu Qiu
- Department of Health Laboratory Technology, School of Public Health, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Feng Xu
- Department of Pediatric Intensive Care Unit, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Chengzhi Chen
- Department of Occupational and Environmental Health, School of Public Health, Chongqing Medical University, Chongqing, 400016, People's Republic of China
- Research Center for Environment and Human Health, School of Public Health, Chongqing, 400016, People's Republic of China
| | - Zhen Zou
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
- Research Center for Environment and Human Health, School of Public Health, Chongqing, 400016, People's Republic of China.
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Ziaka M, Exadaktylos A. Pathophysiology of acute lung injury in patients with acute brain injury: the triple-hit hypothesis. Crit Care 2024; 28:71. [PMID: 38454447 PMCID: PMC10918982 DOI: 10.1186/s13054-024-04855-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 03/01/2024] [Indexed: 03/09/2024] Open
Abstract
It has been convincingly demonstrated in recent years that isolated acute brain injury (ABI) may cause severe dysfunction of peripheral extracranial organs and systems. Of all potential target organs and systems, the lung appears to be the most vulnerable to damage after ABI. The pathophysiology of the bidirectional brain-lung interactions is multifactorial and involves inflammatory cascades, immune suppression, and dysfunction of the autonomic system. Indeed, the systemic effects of inflammatory mediators in patients with ABI create a systemic inflammatory environment ("first hit") that makes extracranial organs vulnerable to secondary procedures that enhance inflammation, such as mechanical ventilation (MV), surgery, and infections ("second hit"). Moreover, accumulating evidence supports the knowledge that gut microbiota constitutes a critical superorganism and an organ on its own, potentially modifying various physiological functions of the host. Furthermore, experimental and clinical data suggest the existence of a communication network among the brain, gastrointestinal tract, and its microbiome, which appears to regulate immune responses, gastrointestinal function, brain function, behavior, and stress responses, also named the "gut-microbiome-brain axis." Additionally, recent research evidence has highlighted a crucial interplay between the intestinal microbiota and the lungs, referred to as the "gut-lung axis," in which alterations during critical illness could result in bacterial translocation, sustained inflammation, lung injury, and pulmonary fibrosis. In the present work, we aimed to further elucidate the pathophysiology of acute lung injury (ALI) in patients with ABI by attempting to develop the "double-hit" theory, proposing the "triple-hit" hypothesis, focused on the influence of the gut-lung axis on the lung. Particularly, we propose, in addition to sympathetic hyperactivity, blast theory, and double-hit theory, that dysbiosis and intestinal dysfunction in the context of ABI alter the gut-lung axis, resulting in the development or further aggravation of existing ALI, which constitutes the "third hit."
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Affiliation(s)
- Mairi Ziaka
- Clinic for Geriatric Medicine, Center for Geriatric Medicine and Rehabilitation, Kantonsspital Baselland, Bruderholz, Switzerland.
- Department of Emergency Medicine, Inselspital, University Hospital, University of Bern, Bern, Switzerland.
| | - Aristomenis Exadaktylos
- Department of Emergency Medicine, Inselspital, University Hospital, University of Bern, Bern, Switzerland
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4
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Zhang DW, Lu JL, Dong BY, Fang MY, Xiong X, Qin XJ, Fan XM. Gut microbiota and its metabolic products in acute respiratory distress syndrome. Front Immunol 2024; 15:1330021. [PMID: 38433840 PMCID: PMC10904571 DOI: 10.3389/fimmu.2024.1330021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/30/2024] [Indexed: 03/05/2024] Open
Abstract
The prevalence rate of acute respiratory distress syndrome (ARDS) is estimated at approximately 10% in critically ill patients worldwide, with the mortality rate ranging from 17% to 39%. Currently, ARDS mortality is usually higher in patients with COVID-19, giving another challenge for ARDS treatment. However, the treatment efficacy for ARDS is far from satisfactory. The relationship between the gut microbiota and ARDS has been substantiated by relevant scientific studies. ARDS not only changes the distribution of gut microbiota, but also influences intestinal mucosal barrier through the alteration of gut microbiota. The modulation of gut microbiota can impact the onset and progression of ARDS by triggering dysfunctions in inflammatory response and immune cells, oxidative stress, cell apoptosis, autophagy, pyroptosis, and ferroptosis mechanisms. Meanwhile, ARDS may also influence the distribution of metabolic products of gut microbiota. In this review, we focus on the impact of ARDS on gut microbiota and how the alteration of gut microbiota further influences the immune function, cellular functions and related signaling pathways during ARDS. The roles of gut microbiota-derived metabolites in the development and occurrence of ARDS are also discussed.
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Affiliation(s)
- Dong-Wei Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Inflammation & Allergic Diseases Research Unit, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Department of Respiratory and Critical Care Medicine, Liuzhou People’s Hospital, Guangxi Medical University, Liuzhou, Guangxi, China
- Key Laboratory of Diagnosis, Treatment and Research of Asthma and Chronic Obstructive Pulmonary Disease, Liuzhou, Guangxi, China
| | - Jia-Li Lu
- Department of Respiratory and Critical Care Medicine, Liuzhou People’s Hospital, Guangxi Medical University, Liuzhou, Guangxi, China
- Key Laboratory of Diagnosis, Treatment and Research of Asthma and Chronic Obstructive Pulmonary Disease, Liuzhou, Guangxi, China
| | - Bi-Ying Dong
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Inflammation & Allergic Diseases Research Unit, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Department of Respiratory and Critical Care Medicine, Liuzhou People’s Hospital, Guangxi Medical University, Liuzhou, Guangxi, China
- Key Laboratory of Diagnosis, Treatment and Research of Asthma and Chronic Obstructive Pulmonary Disease, Liuzhou, Guangxi, China
| | - Meng-Ying Fang
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Inflammation & Allergic Diseases Research Unit, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Xia Xiong
- Department of Dermatology, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Xue-Jun Qin
- Department of Respiratory and Critical Care Medicine, Liuzhou People’s Hospital, Guangxi Medical University, Liuzhou, Guangxi, China
- Key Laboratory of Diagnosis, Treatment and Research of Asthma and Chronic Obstructive Pulmonary Disease, Liuzhou, Guangxi, China
| | - Xian-Ming Fan
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Inflammation & Allergic Diseases Research Unit, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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5
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Wang H, Wang Y. What Makes the Gut-Lung Axis Working? From the Perspective of Microbiota and Traditional Chinese Medicine. Can J Infect Dis Med Microbiol 2024; 2024:8640014. [PMID: 38274122 PMCID: PMC10810697 DOI: 10.1155/2024/8640014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 01/27/2024]
Abstract
Background An increasing number of studies have proved that gut microbiota is involved in the occurrence and development of various lung diseases and can interact with the diseased lung. The concept of the gut-lung axis (GLA) provides a new idea for the subsequent clinical treatment of lung diseases through human microbiota. This review aims to summarize the microbiota in the lung and gut and the interaction between them from the perspectives of traditional Chinese medicine and modern medicine. Method We conducted a literature search by using the search terms "GLA," "gut microbiota," "spleen," and "Chinese medicine" in the databases PubMed, Web of Science, and CNKI. We then explored the mechanism of action of the gut-lung axis from traditional Chinese medicine and modern medicine. Results The lung and gut microbiota enable the GLA to function through immune regulation, while metabolites of the gut microbiota also play an important role. The spleen can improve the gut microbiota to achieve the regulation of the GLA. Conclusion Improving the gut microbiota through qi supplementation and spleen fortification provides a new approach to the clinical treatment of lung diseases by regulating the GLA. Currently, our understanding of the GLA is limited, and more research is needed to explain its working principle.
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Affiliation(s)
- Hui Wang
- Zhejiang Chinese Medical University, Hangzhou 310000, China
| | - Ying Wang
- Zhejiang Chinese Medical University, Hangzhou 310000, China
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6
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Zhou P, Zou Z, Wu W, Zhang H, Wang S, Tu X, Huang W, Chen C, Zhu S, Weng Q, Zheng S. The gut-lung axis in critical illness: microbiome composition as a predictor of mortality at day 28 in mechanically ventilated patients. BMC Microbiol 2023; 23:399. [PMID: 38110878 PMCID: PMC10726596 DOI: 10.1186/s12866-023-03078-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/20/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Microbial communities are of critical importance in the human host. The lung and gut microbial communities represent the most essential microbiota within the human body, collectively referred to as the gut-lung axis. However, the differentiation between these communities and their influence on clinical outcomes in critically ill patients remains uncertain. METHODS An observational cohort study was obtained in the intensive care unit (ICU) of an affiliated university hospital. Sequential samples were procured from two distinct anatomical sites, namely the respiratory and intestinal tracts, at two precisely defined time intervals: within 48 h and on day 7 following intubation. Subsequently, these samples underwent a comprehensive analysis to characterize microbial communities using 16S ribosomal RNA (rRNA) gene sequencing and to quantify concentrations of fecal short-chain fatty acids (SCFAs). The primary predictors in this investigation included lung and gut microbial diversity, along with indicator species. The primary outcome of interest was the survival status at 28 days following mechanical ventilation. RESULTS Sixty-two mechanically ventilated critically ill patients were included in this study. Compared to the survivors, the diversity of microorganisms was significantly lower in the deceased, with a significant contribution from the gut-originated fraction of lung microorganisms. Lower concentrations of fecal SCFAs were detected in the deceased. Multivariate Cox regression analysis revealed that not only lung microbial diversity but also the abundance of Enterococcaceae from the gut were correlated with day 28 mortality. CONCLUSION Critically ill patients exhibited lung and gut microbial dysbiosis after mechanical ventilation, as evidenced by a significant decrease in lung microbial diversity and the proliferation of Enterococcaceae in the gut. Levels of fecal SCFAs in the deceased served as a marker of imbalance between commensal and pathogenic flora in the gut. These findings emphasize the clinical significance of microbial profiling in predicting the prognosis of ICU patients.
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Affiliation(s)
- Piaopiao Zhou
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zhiqiang Zou
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Wenwei Wu
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Hui Zhang
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shuling Wang
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Xiaoyan Tu
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Weibin Huang
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Cunrong Chen
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shuaijun Zhu
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Qinyong Weng
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, China.
| | - Shixiang Zheng
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, China.
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7
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Zinter MS, Dvorak CC, Mayday MY, Reyes G, Simon MR, Pearce EM, Kim H, Shaw PJ, Rowan CM, Auletta JJ, Martin PL, Godder K, Duncan CN, Lalefar NR, Kreml EM, Hume JR, Abdel-Azim H, Hurley C, Cuvelier GDE, Keating AK, Qayed M, Killinger JS, Fitzgerald JC, Hanna R, Mahadeo KM, Quigg TC, Satwani P, Castillo P, Gertz SJ, Moore TB, Hanisch B, Abdel-Mageed A, Phelan R, Davis DB, Hudspeth MP, Yanik GA, Pulsipher MA, Sulaiman I, Segal LN, Versluys BA, Lindemans CA, Boelens JJ, DeRisi JL. Pulmonary microbiome and transcriptome signatures reveal distinct pathobiologic states associated with mortality in two cohorts of pediatric stem cell transplant patients. medRxiv 2023:2023.11.29.23299130. [PMID: 38077035 PMCID: PMC10705623 DOI: 10.1101/2023.11.29.23299130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Lung injury is a major determinant of survival after pediatric hematopoietic cell transplantation (HCT). A deeper understanding of the relationship between pulmonary microbes, immunity, and the lung epithelium is needed to improve outcomes. In this multicenter study, we collected 278 bronchoalveolar lavage (BAL) samples from 229 patients treated at 32 children's hospitals between 2014-2022. Using paired metatranscriptomes and human gene expression data, we identified 4 patient clusters with varying BAL composition. Among those requiring respiratory support prior to sampling, in-hospital mortality varied from 22-60% depending on the cluster (p=0.007). The most common patient subtype, Cluster 1, showed a moderate quantity and high diversity of commensal microbes with robust metabolic activity, low rates of infection, gene expression indicating alveolar macrophage predominance, and low mortality. The second most common cluster showed a very high burden of airway microbes, gene expression enriched for neutrophil signaling, frequent bacterial infections, and moderate mortality. Cluster 3 showed significant depletion of commensal microbes, a loss of biodiversity, gene expression indicative of fibroproliferative pathways, increased viral and fungal pathogens, and high mortality. Finally, Cluster 4 showed profound microbiome depletion with enrichment of Staphylococci and viruses, gene expression driven by lymphocyte activation and cellular injury, and the highest mortality. BAL clusters were modeled with a random forest classifier and reproduced in a geographically distinct validation cohort of 57 patients from The Netherlands, recapitulating similar cluster-based mortality differences (p=0.022). Degree of antibiotic exposure was strongly associated with depletion of BAL microbes and enrichment of fungi. Potential pathogens were parsed from all detected microbes by analyzing each BAL microbe relative to the overall microbiome composition, which yielded increased sensitivity for numerous previously occult pathogens. These findings support personalized interpretation of the pulmonary microenvironment in pediatric HCT, which may facilitate biology-targeted interventions to improve outcomes.
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Affiliation(s)
- Matt S Zinter
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Madeline Y Mayday
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Departments of Laboratory Medicine and Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Gustavo Reyes
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Miriam R Simon
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Emma M Pearce
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Hanna Kim
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Peter J Shaw
- The Children`s Hospital at Westmead, Sydney, Australia
| | - Courtney M Rowan
- Indiana University, Department of Pediatrics, Division of Critical Care Medicine, Indianapolis, IN, USA
| | - Jeffrey J Auletta
- Hematology/Oncology/BMT and Infectious Diseases, Nationwide Children's Hospital, Columbus, OH, USA
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Paul L Martin
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
| | - Kamar Godder
- Cancer and Blood Disorders Center, Nicklaus Children's Hospital, Miami, FL, USA
| | - Christine N Duncan
- Harvard Medical School, Boston, Massachusetts; Division of Pediatric Oncology, Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Nahal R Lalefar
- Division of Pediatric Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, University of California San Francisco, Oakland, CA, USA
| | - Erin M Kreml
- Department of Child Health, Division of Critical Care Medicine, University of Arizona, Phoenix, AZ, USA
| | - Janet R Hume
- University of Minnesota, Department of Pediatrics, Division of Critical Care Medicine, Minneapolis, MN, USA
| | - Hisham Abdel-Azim
- Department of Pediatrics, Division of Hematology/Oncology and Transplant and Cell Therapy, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Loma Linda University School of Medicine, Cancer Center, Children Hospital and Medical Center, Loma Linda, CA, USA
| | - Caitlin Hurley
- Division of Critical Care, Department of Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey D E Cuvelier
- CancerCare Manitoba, Manitoba Blood and Marrow Transplant Program, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Amy K Keating
- Center for Cancer and Blood Disorders, Children's Hospital Colorado and University of Colorado, Aurora, CO, USA
- Harvard Medical School, Boston, Massachusetts; Division of Pediatric Oncology, Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Muna Qayed
- Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, GA, USA
| | - James S Killinger
- Division of Pediatric Critical Care, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Julie C Fitzgerald
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Rabi Hanna
- Department of Pediatric Hematology, Oncology and Blood and Marrow Transplantation, Pediatric Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kris M Mahadeo
- Department of Pediatrics, Division of Hematology/Oncology, MD Anderson Cancer Center, Houston, TX, USA
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
| | - Troy C Quigg
- Pediatric Blood and Marrow Transplantation Program, Texas Transplant Institute, Methodist Children's Hospital, San Antonio, TX, USA
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Prakash Satwani
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Paul Castillo
- University of Florida, Gainesville, UF Health Shands Children's Hospital, Gainesville, FL, USA
| | - Shira J Gertz
- Department of Pediatrics, Division of Critical Care Medicine, Joseph M Sanzari Children's Hospital at Hackensack University Medical Center, Hackensack, NJ, USA
- Department of Pediatrics, St. Barnabas Medical Center, Livingston, NJ, USA
| | - Theodore B Moore
- Department of Pediatric Hematology-Oncology, Mattel Children's Hospital, University of California, Los Angeles, CA, USA
| | - Benjamin Hanisch
- Children's National Hospital, Washington, District of Columbia, USA
| | - Aly Abdel-Mageed
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Rachel Phelan
- Division of Pediatric Hematology/Oncology/BMT, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Dereck B Davis
- Department of Pediatrics, Hematology/Oncology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Michelle P Hudspeth
- Adult and Pediatric Blood & Marrow Transplantation, Pediatric Hematology/Oncology, Medical University of South Carolina Children's Hospital/Hollings Cancer Center, Charleston, SC, USA
| | - Greg A Yanik
- Pediatric Blood and Bone Marrow Transplantation, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Pulsipher
- Division of Hematology, Oncology, Transplantation, and Immunology, Primary Children's Hospital, Huntsman Cancer Institute, Spense Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, USA
| | - Imran Sulaiman
- Departments of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, NY, USA
| | - Leopoldo N Segal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, NY, USA
| | - Birgitta A Versluys
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Caroline A Lindemans
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, NY, USA
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Jaap J Boelens
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands
- Transplantation and Cellular Therapy, MSK Kids, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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8
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Montassier E, Kitsios GD, Radder JE, Le Bastard Q, Kelly BJ, Panzer A, Lynch SV, Calfee CS, Dickson RP, Roquilly A. Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia. Nat Med 2023; 29:2793-2804. [PMID: 37957375 DOI: 10.1038/s41591-023-02617-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/27/2023] [Indexed: 11/15/2023]
Abstract
Respiratory microbial dysbiosis is associated with acute respiratory distress syndrome (ARDS) and hospital-acquired pneumonia (HAP) in critically ill patients. However, we lack reproducible respiratory microbiome signatures that can increase our understanding of these conditions and potential treatments. Here, we analyze 16S rRNA sequencing data from 2,177 respiratory samples collected from 1,029 critically ill patients (21.7% with ARDS and 26.3% with HAP) and 327 healthy controls, sourced from 17 published studies. After data harmonization and pooling of individual patient data, we identified microbiota signatures associated with ARDS, HAP and prolonged mechanical ventilation. Microbiota signatures for HAP and prolonged mechanical ventilation were characterized by depletion of a core group of microbes typical of healthy respiratory samples, and the ARDS microbiota signature was distinguished by enrichment of potentially pathogenic respiratory microbes, including Pseudomonas and Staphylococcus. Using machine learning models, we identified clinically informative, three- and four-factor signatures that predicted ARDS, HAP and prolonged mechanical ventilation with relatively high accuracy (area under the curve of 0.751, 0.72 and 0.727, respectively). We validated the signatures in an independent prospective cohort of 136 patients on mechanical ventillation and found that patients with microbiome signatures associated with ARDS, HAP or prolonged mechanical ventilation had longer times to successful extubation than patients lacking these signatures (hazard ratios of 1.56 (95% confidence interval (CI) 1.07-2.27), 1.51 (95% CI 1.02-2.23) and 1.50 (95% CI 1.03-2.18), respectively). Thus, we defined and validated robust respiratory microbiome signatures associated with ARDS and HAP that may help to identify promising targets for microbiome therapeutic modulation in critically ill patients.
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Affiliation(s)
- Emmanuel Montassier
- Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes Université, Inserm, CHU Nantes, Nantes, France.
- Service des Urgences, Nantes Université, CHU Nantes, Nantes, France.
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josiah E Radder
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Brendan J Kelly
- Department of Medicine, Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA, USA
| | - Ariane Panzer
- Department of Medicine, Division of Gastroenterology, University of California, San Francisco, CA, USA
| | - Susan V Lynch
- Department of Medicine, Division of Gastroenterology, University of California, San Francisco, CA, USA
| | - Carolyn S Calfee
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Robert P Dickson
- Department of Internal Medicine, Division of Pulmonary and Critical Care 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 and Innovation, Ann Arbor, MI, USA
| | - Antoine Roquilly
- Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes Université, Inserm, CHU Nantes, Nantes, France.
- Service d'Anesthesie Réanimation, Nantes Université, CHU Nantes, Nantes, France.
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
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Wu J, Li C, Gao P, Zhang C, Zhang P, Zhang L, Dai C, Zhang K, Shi B, Liu M, Zheng J, Pan B, Chen Z, Zhang C, Liao W, Pan W, Fang W, Chen C. Intestinal microbiota links to allograft stability after lung transplantation: a prospective cohort study. Signal Transduct Target Ther 2023; 8:326. [PMID: 37652953 PMCID: PMC10471611 DOI: 10.1038/s41392-023-01515-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 05/17/2023] [Accepted: 05/28/2023] [Indexed: 09/02/2023] Open
Abstract
Whether the alternated microbiota in the gut contribute to the risk of allograft rejection (AR) and pulmonary infection (PI) in the setting of lung transplant recipients (LTRs) remains unexplored. A prospective multicenter cohort of LTRs was identified in the four lung transplant centers. Paired fecal and serum specimens were collected and divided into AR, PI, and event-free (EF) groups according to the diagnosis at sampling. Fecal samples were determined by metagenomic sequencing. And metabolites and cytokines were detected in the paired serum to analyze the potential effect of the altered microbiota community. In total, we analyzed 146 paired samples (AR = 25, PI = 43, and EF = 78). Notably, we found that the gut microbiome of AR followed a major depletion pattern with decreased 487 species and compositional diversity. Further multi-omics analysis showed depleted serum metabolites and increased inflammatory cytokines in AR and PI. Bacteroides uniformis, which declined in AR (2.4% vs 0.6%) and was negatively associated with serum IL-1β and IL-12, was identified as a driven specie in the network of gut microbiome of EF. Functionally, the EF specimens were abundant in probiotics related to mannose and cationic antimicrobial peptide metabolism. Furthermore, a support-vector machine classifier based on microbiome, metabolome, and clinical parameters highly predicted AR (AUPRC = 0.801) and PI (AUPRC = 0.855), whereby the microbiome dataset showed a particularly high diagnostic power. In conclusion, a disruptive gut microbiota showed a significant association with allograft rejection and infection and with systemic cytokines and metabolites in LTRs.
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Affiliation(s)
- Junqi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
| | - Chongwu Li
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
| | - Peigen Gao
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Pei Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
| | - Lei Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
| | - Chenyang Dai
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
| | - Kunpeng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
| | - Bowen Shi
- Department of Thoracic Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Mengyang Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Junmeng Zheng
- Department of Cardiovascular Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bo Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Zhan Chen
- Adfontes (Shanghai) Bio-technology Co., Ltd, Shanghai, China
| | - Chao Zhang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China.
| | - Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China.
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China.
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10
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Leroue MK, Williamson KM, Curtin PC, Sontag MK, Wagner BD, Ambroggio L, Bixby M, Busgang SA, Murphy SE, Peterson LA, Vevang KR, Sipe CJ, Kirk Harris J, Reeder RW, Locandro C, Carpenter TC, Maddux AB, Simões EAF, Osborne CM, Robertson CE, Langelier C, Carcillo JA, Meert KL, Pollack MM, McQuillen PS, Mourani PM. Tobacco smoke exposure, the lower airways microbiome and outcomes of ventilated children. Pediatr Res 2023; 94:660-667. [PMID: 36750739 PMCID: PMC9903281 DOI: 10.1038/s41390-023-02502-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/18/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023]
Abstract
BACKGROUND Tobacco smoke exposure increases the risk and severity of lower respiratory tract infections in children, yet the mechanisms remain unclear. We hypothesized that tobacco smoke exposure would modify the lower airway microbiome. METHODS Secondary analysis of a multicenter cohort of 362 children between ages 31 days and 18 years mechanically ventilated for >72 h. Tracheal aspirates from 298 patients, collected within 24 h of intubation, were evaluated via 16 S ribosomal RNA sequencing. Smoke exposure was determined by creatinine corrected urine cotinine levels ≥30 µg/g. RESULTS Patients had a median age of 16 (IQR 568) months. The most common admission diagnosis was lower respiratory tract infection (53%). Seventy-four (20%) patients were smoke exposed and exhibited decreased richness and Shannon diversity. Smoke exposed children had higher relative abundances of Serratia spp., Moraxella spp., Haemophilus spp., and Staphylococcus aureus. Differences were most notable in patients with bacterial and viral respiratory infections. There were no differences in development of acute respiratory distress syndrome, days of mechanical ventilation, ventilator free days at 28 days, length of stay, or mortality. CONCLUSION Among critically ill children requiring prolonged mechanical ventilation, tobacco smoke exposure is associated with decreased richness and Shannon diversity and change in microbial communities. IMPACT Tobacco smoke exposure is associated with changes in the lower airways microbiome but is not associated with clinical outcomes among critically ill pediatric patients requiring prolonged mechanical ventilation. This study is among the first to evaluate the impact of tobacco smoke exposure on the lower airway microbiome in children. This research helps elucidate the relationship between tobacco smoke exposure and the lower airway microbiome and may provide a possible mechanism by which tobacco smoke exposure increases the risk for poor outcomes in children.
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Affiliation(s)
- Matthew K Leroue
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA.
| | - Kayla M Williamson
- Biostatistics and Informatics, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - Paul C Curtin
- CHEAR Data Center, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marci K Sontag
- Epidemiology, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - Brandie D Wagner
- Biostatistics and Informatics, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - Lilliam Ambroggio
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Moira Bixby
- CHEAR Data Center, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stefanie A Busgang
- CHEAR Data Center, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sharon E Murphy
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Lisa A Peterson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Karin R Vevang
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | | | - J Kirk Harris
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Ron W Reeder
- Pediatrics, University of Utah, Salt Lake City, UT, USA
| | | | - Todd C Carpenter
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Aline B Maddux
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Eric A F Simões
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
- Epidemiology, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - Christina M Osborne
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Charles E Robertson
- Medicine, Division of Infectious Diseases, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Charles Langelier
- Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Kathleen L Meert
- Pediatrics, Children's Hospital of Michigan, Central Michigan University, Detroit, MI, USA
| | | | | | - Peter M Mourani
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
- Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR, USA
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11
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Boopathi S, Priya PS, Haridevamuthu B, Nayak SPRR, Chandrasekar M, Arockiaraj J, Jia AQ. Expanding germ-organ theory: Understanding non-communicable diseases through enterobacterial translocation. Pharmacol Res 2023; 194:106856. [PMID: 37460001 DOI: 10.1016/j.phrs.2023.106856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/02/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Diverse microbial communities colonize different habitats of the human body, including gut, oral cavity, nasal cavity and tissues. These microbial communities are known as human microbiome, plays a vital role in maintaining the health. However, changes in the composition and functions of human microbiome can result in chronic low-grade inflammation, which can damage the epithelial cells and allows pathogens and their toxic metabolites to translocate into other organs such as the liver, heart, and kidneys, causing metabolic inflammation. This dysbiosis of human microbiome has been directly linked to the onset of several non-communicable diseases. Recent metabolomics studies have revealed that pathogens produce several uraemic toxins. These metabolites can serve as inter-kingdom signals, entering the circulatory system and altering host metabolism, thereby aggravating a variety of diseases. Interestingly, Enterobacteriaceae, a critical member of Proteobacteria, has been commonly associated with several non-communicable diseases, and the abundance of this family has been positively correlated with uraemic toxin production. Hence, this review provides a comprehensive overview of Enterobacterial translocation and their metabolites role in non-communicable diseases. This understanding may lead to the identification of novel biomarkers for each metabolic disease as well as the development of novel therapeutic drugs.
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Affiliation(s)
- Seenivasan Boopathi
- Hainan General Hospital, Hainan affiliated hospital of Hainan Medical University, Haikou 570311, China; Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur 603 203, Chengalpattu District, Tamil Nadu, India
| | - P Snega Priya
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur 603 203, Chengalpattu District, Tamil Nadu, India
| | - B Haridevamuthu
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur 603 203, Chengalpattu District, Tamil Nadu, India
| | - S P Ramya Ranjan Nayak
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur 603 203, Chengalpattu District, Tamil Nadu, India
| | - Munisamy Chandrasekar
- Department of Veterinary Clinical Medicine, Madras Veterinary College, Chennai, Tamil Nadu, India
| | - Jesu Arockiaraj
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur 603 203, Chengalpattu District, Tamil Nadu, India.
| | - Ai-Qun Jia
- Hainan General Hospital, Hainan affiliated hospital of Hainan Medical University, Haikou 570311, China.
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12
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Belizário J, Garay-Malpartida M, Faintuch J. Lung microbiome and origins of the respiratory diseases. Curr Res Immunol 2023; 4:100065. [PMID: 37456520 PMCID: PMC10339129 DOI: 10.1016/j.crimmu.2023.100065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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13
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Sun G, Liu W, Zheng Q, Shan Q, Hou H. Ratio of procalcitonin/Simpson's dominance index predicted the short-term prognosis of patients with severe bacterial pneumonia. Front Cell Infect Microbiol 2023; 13:1175747. [PMID: 37465762 PMCID: PMC10350521 DOI: 10.3389/fcimb.2023.1175747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Objective The aim of this study was to explore the predictive value of the ratio of procalcitonin (PCT) in serum to Simpson's dominance index (SDI) in bronchoalveolar lavage fluid (BALF), in short-term prognosis of patients with severe bacterial pneumonia (SBP). Methods This is a retrospective review of case materials of 110 patients with SBP who selected BALF metagenomic next-generation sequencing technique in the intensive care unit (ICU) of the Affiliated Hospital of Yangzhou University from January 2019 and July 2022. Based on the acute physiology and chronic health status score II, within 24 h after admission to the ICU, patients were divided into a non-critical group (n = 40) and a critical group (n = 70). Taking death caused by bacterial pneumonia as the endpoint event, the 28-day prognosis was recorded, and the patients were divided into a survival group (n = 76) and a death group (n = 34). The SDI, PCT, C-reactive protein (CRP), PCT/SDI, and CRP/SDI were compared and analyzed. Results Compared with the non-critical group, the critical group had a higher PCT level, a greater PCT/SDI ratio, a longer ventilator-assisted ventilation time (VAVT), and more deaths in 28 days. Compared with the survivors, the death group had a higher PCT level, a lower SDI level, and a greater PCT/SDI ratio. The SDI level was significantly negatively correlated with the VAVT (r = -0.675, p < 0.05), while the PCT level, ratio of PCT/SDI, and ratio of CRP/SDI were remarkably positively correlated with VAVT (r = 0.669, 0.749, and 0.718, respectively, p < 0.05). The receiver operating characteristic (ROC) curves analysis showed that the area under ROC curves of PCT/SDI predicting patient death within 28 days was 0.851, followed by PCT + SDI, PCT, SDI, and CRP/SDI (0.845, 0.811, 0.778, and 0.720, respectively). The sensitivity and specificity of PCT/SDI for predicting death were 94.1% and 65.8%, respectively, at the optimal value (11.56). Cox regression analysis displayed that PCT/SDI (HR = 1.562; 95% CI: 1.271 to 1.920; p = 0.039) and PCT (HR = 1.148; 95% CI: 1.105 to 1.314; p = 0.015) were independent predictors of death in patients. Conclusion The ratio of PCT/SDI was a more valuable marker in predicting the 28-day prognosis in patients with SBP.
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Affiliation(s)
- Guoxian Sun
- Department of Infection Control, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Weili Liu
- Department of Critical Care Unit, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Qingbin Zheng
- Department of Critical Care Unit, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Qing Shan
- Department of Infection Control, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Hongling Hou
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, China
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14
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Britton N, Yang H, Fitch A, Li K, Seyed K, Guo R, Qin S, Zhang Y, Bain W, Shah F, Biswas P, Choi W, Finkelman M, Zhang Y, Haggerty CL, Benos PV, Brooks MM, McVerry BJ, Methe B, Kitsios GD, Morris A. Respiratory Fungal Communities are Associated with Systemic Inflammation and Predict Survival in Patients with Acute Respiratory Failure. medRxiv 2023:2023.05.11.23289861. [PMID: 37292915 PMCID: PMC10246035 DOI: 10.1101/2023.05.11.23289861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rationale Disruption of respiratory bacterial communities predicts poor clinical outcomes in critical illness; however, the role of respiratory fungal communities (mycobiome) is poorly understood. Objectives We investigated whether mycobiota variation in the respiratory tract is associated with host-response and clinical outcomes in critically ill patients. Methods To characterize the upper and lower respiratory tract mycobiota, we performed rRNA gene sequencing (internal transcribed spacer) of oral swabs and endotracheal aspirates (ETA) from 316 mechanically-ventilated patients. We examined associations of mycobiome profiles (diversity and composition) with clinical variables, host-response biomarkers, and outcomes. Measurements and Main Results ETA samples with >50% relative abundance for C. albicans (51%) were associated with elevated plasma IL-8 and pentraxin-3 (p=0.05), longer time-to-liberation from mechanical ventilation (p=0.04) and worse 30-day survival (adjusted hazards ratio (adjHR): 1.96 [1.04-3.81], p=0.05). Using unsupervised clustering, we derived two clusters in ETA samples, with Cluster 2 (39%) showing lower alpha diversity (p<0.001) and higher abundance of C. albicans (p<0.001). Cluster 2 was significantly associated with the prognostically adverse hyperinflammatory subphenotype (odds ratio 2.07 [1.03-4.18], p=0.04) and predicted worse survival (adjHR: 1.81 [1.03-3.19], p=0.03). C. albicans abundance in oral swabs was also associated with the hyperinflammatory subphenotype and mortality. Conclusions Variation in respiratory mycobiota was significantly associated with systemic inflammation and clinical outcomes. C. albicans abundance emerged as a negative predictor in both the upper and lower respiratory tract. The lung mycobiome may play an important role in the biological and clinical heterogeneity among critically ill patients and represent a potential therapeutic target for lung injury in critical illness.
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Affiliation(s)
- Noel Britton
- Division of Pulmonary Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Haopu Yang
- School of Medicine, Tsinghua University, Beijing, China
| | - Adam Fitch
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Khaled Seyed
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
| | - Rui Guo
- Department of Critical Care Medicine, First Affiliated Hospital of Chongqing Medical University, China
| | - Shulin Qin
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Partha Biswas
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Wonseok Choi
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | - Yonglong Zhang
- Associates of Cape Cod Inc., East Falmouth, Massachusetts, USA
| | - Catherine L. Haggerty
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Panayiotis V. Benos
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
| | - Maria M. Brooks
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Barbara Methe
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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15
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Ramji HF, Hafiz M, Altaq HH, Hussain ST, Chaudry F. Acute Respiratory Distress Syndrome; A Review of Recent Updates and a Glance into the Future. Diagnostics (Basel) 2023; 13:diagnostics13091528. [PMID: 37174920 PMCID: PMC10177247 DOI: 10.3390/diagnostics13091528] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/15/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a rapidly progressive form of respiratory failure that accounts for 10% of admissions to the ICU and is associated with approximately 40% mortality in severe cases. Despite significant mortality and healthcare burden, the mainstay of management remains supportive care. The recent pandemic of SARS-CoV-2 has re-ignited a worldwide interest in exploring the pathophysiology of ARDS, looking for innovative ideas to treat this disease. Recently, many trials have been published utilizing different pharmacotherapy targets; however, the long-term benefits of these agents remain unknown. Metabolomics profiling and stem cell transplantation offer strong enthusiasm and may completely change the outlook of ARDS management in the near future.
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Affiliation(s)
- Husayn F Ramji
- University of Oklahoma College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Maida Hafiz
- Department of Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Hiba Hammad Altaq
- Department of Pulmonary, Critical Care & Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Syed Talal Hussain
- Department of Pulmonary, Critical Care & Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Fawad Chaudry
- Department of Pulmonary, Critical Care & Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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16
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Cicchinelli S, Rosa F, Manca F, Zanza C, Ojetti V, Covino M, Candelli M, Gasbarrini A, Franceschi F, Piccioni A. The Impact of Smoking on Microbiota: A Narrative Review. Biomedicines 2023; 11:biomedicines11041144. [PMID: 37189762 DOI: 10.3390/biomedicines11041144] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/03/2023] [Accepted: 03/13/2023] [Indexed: 05/17/2023] Open
Abstract
Cigarette smoke is a classic risk factor for many diseases. The microbiota has been recently indicated as a new, major player in human health. Its deregulation-dysbiosis-is considered a new risk factor for several illnesses. Some studies highlight a cross-interaction between these two risk factors-smoke and dysbiosis-that may explain the pathogenesis of some diseases. We searched the keywords "smoking OR smoke AND microbiota" in the title of articles on PubMed®, UptoDate®, and Cochrane®. We included articles published in English over the last 25 years. We collected approximately 70 articles, grouped into four topics: oral cavity, airways, gut, and other organs. Smoke may impair microbiota homeostasis through the same harmful mechanisms exerted on the host cells. Surprisingly, dysbiosis and its consequences affect not only those organs that are in direct contact with the smoke, such as the oral cavity or the airways, but also involve distant organs, such as the gut, heart, vessels, and genitourinary tract. These observations yield a deeper insight into the mechanisms implicated in the pathogenesis of smoke-related diseases, suggesting a role of dysbiosis. We speculate that modulation of the microbiota may help prevent and treat some of these illnesses.
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Affiliation(s)
- Sara Cicchinelli
- Department of Emergency, Ospedale SS. Filippo e Nicola, 67051 Avezzano, Italy
| | - Federico Rosa
- Department of Emergency Medicine, Fondazione Policlinico Universitario, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Federica Manca
- Department of Emergency Medicine, Fondazione Policlinico Universitario, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Christian Zanza
- Department of Anesthesia, Critical Care, and Emergency Medicine, Ospedale Michele e Pietro Ferrero, 12060 Cuneo, Italy
| | - Veronica Ojetti
- Department of Emergency Medicine, Fondazione Policlinico Universitario, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
- Department of Internal Medicine, Ospedale San Carlo di Nancy, 00165 Rome, Italy
| | - Marcello Covino
- Department of Emergency Medicine, Fondazione Policlinico Universitario, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Marcello Candelli
- Department of Emergency Medicine, Fondazione Policlinico Universitario, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Antonio Gasbarrini
- Department of Internal Medicine, Division of Gastroenterology, Fondazione Policlinico Universitario A. Gemelli, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Francesco Franceschi
- Department of Emergency Medicine, Fondazione Policlinico Universitario, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Andrea Piccioni
- Department of Emergency Medicine, Fondazione Policlinico Universitario, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
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17
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Nath S, Kitsios GD, Bos LDJ. Gut-lung crosstalk during critical illness. Curr Opin Crit Care 2023; 29:130-137. [PMID: 36762684 DOI: 10.1097/mcc.0000000000001015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
PURPOSE OF REVIEW Study of organ crosstalk in critical illness has uncovered complex biological communication between different organ systems, but the role of microbiota in organ crosstalk has received limited attention. We highlight the emerging understanding of the gut-lung axis, and how the largest biomass of the human body in the gut may affect lung physiology in critical illness. RECENT FINDINGS Disruption of healthy gut microbial communities and replacement by disease-promoting pathogens (pathobiome) generates a maladaptive transmitter of messages from the gut to the lungs, connected via the portal venous and the mesenteric lymphatic systems. Gut barrier impairment allows for microbial translocation (living organisms or cellular fragments) to the lungs. Host-microbiota interactions in the gut mucosa can also impact lung physiology through microbial metabolite secretion or host-derived messengers (hormones, cytokines or immune cells). Clinical examples like the prevention of ventilator-associated pneumonia by selective decontamination of the digestive tract show that the gut-lung axis can be manipulated therapeutically. SUMMARY A growing body of evidence supports the pathophysiological relevance of the gut-lung axis, yet we are only at the brink of understanding the therapeutic and prognostic relevance of the gut microbiome, metabolites and host-microbe interactions in critical illness.
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Affiliation(s)
- Sridesh Nath
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
| | - Georgios D Kitsios
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Acute Lung Injury Center of Excellence
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lieuwe D J Bos
- Intensive Care
- Laboratory of Experimental Intensive Care and Anesthesiology (LEICA), Amsterdam University Medical Centers, location AMC, University of Amsterdam, Amsterdam, The Netherlands
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18
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D'Alessandro VF, D'Alessandro-Gabazza CN, Yasuma T, Toda M, Takeshita A, Tomaru A, Tharavecharak S, Lasisi IO, Hess RY, Nishihama K, Fujimoto H, Kobayashi T, Cann I, Gabazza EC. Inhibition of a Microbiota-derived Peptide Ameliorates Established Acute Lung Injury. Am J Pathol 2023:S0002-9440(23)00113-X. [PMID: 36965776 PMCID: PMC10035802 DOI: 10.1016/j.ajpath.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 03/25/2023]
Abstract
Acute lung injury is a clinical syndrome characterized by a diffuse lung inflammation that commonly evolves into acute respiratory distress syndrome and respiratory failure. The lung microbiota is involved in the pathogenesis of acute lung injury. Corisin, a proapoptotic peptide derived from the lung microbiota, plays a role in acute lung injury and acute exacerbation of pulmonary fibrosis. Preventive therapeutic intervention with a monoclonal anticorisin antibody inhibits acute lung injury in mice. However, whether inhibition of corisin with the antibody ameliorates established acute lung injury is unknown. Here, the therapeutic effectiveness of the anticorisin antibody in already established acute lung injury in mice was assessed. Lipopolysaccharide was used to induce acute lung injury in mice. After causing acute lung injury, the mice were treated with a neutralizing anticorisin antibody. Mice treated with the antibody showed significant improvement in lung radiological and histopathological findings, decreased lung infiltration of inflammatory cells, reduced markers of lung tissue damage, and inflammatory cytokines in bronchoalveolar lavage fluid compared to untreated mice. In addition, the mice treated with anticorisin antibody showed significantly increased expression of antiapoptotic proteins with decreased caspase-3 activation in the lungs compared to control mice treated with an irrelevant antibody. In conclusion, these observations suggest that the inhibition of corisin is a novel and promising approach for treating established acute lung injury.
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Affiliation(s)
- Valeria Fridman D'Alessandro
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Corina N D'Alessandro-Gabazza
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan;; Center for Intractable Diseases, Mie University, Edobashi 2-174, Tsu, Mie 514-8507, Japan; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering), University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Taro Yasuma
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan;; Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Masaaki Toda
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Atsuro Takeshita
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan;; Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Atsushi Tomaru
- Department of Pulmonary and Critical care Medicine, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Suphachai Tharavecharak
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Isaiah O Lasisi
- School of Molecular and Cellular Biology, the University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Rebecca Y Hess
- School of Molecular and Cellular Biology, the University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Kota Nishihama
- Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Hajime Fujimoto
- Department of Pulmonary and Critical care Medicine, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Tetsu Kobayashi
- Department of Pulmonary and Critical care Medicine, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Isaac Cann
- School of Molecular and Cellular Biology, the University of Illinois at Urbana-Champaign, Urbana, IL, United States; Department of Animal Science, the University of Illinois at Urbana-Champaign, Urbana, IL, United States; Department of Microbiology, the University of Illinois at Urbana-Champaign, Urbana, IL, United States; Division of Nutritional Sciences, the University of Illinois at Urbana-Champaign, Urbana, IL, United States; Center for East Asian & Pacific Studies, the University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Esteban C Gabazza
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan;; Center for Intractable Diseases, Mie University, Edobashi 2-174, Tsu, Mie 514-8507, Japan; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering), University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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19
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Alsayed AR, Abed A, Khader HA, Al-Shdifat LMH, Hasoun L, Al-Rshaidat MMD, Alkhatib M, Zihlif M. Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment. Int J Mol Sci 2023; 24:4086. [PMID: 36835503 PMCID: PMC9966333 DOI: 10.3390/ijms24044086] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.
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Affiliation(s)
- Ahmad R. Alsayed
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931, Jordan
| | - Heba A. Khader
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Laith M. H. Al-Shdifat
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Luai Hasoun
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Mamoon M. D. Al-Rshaidat
- Laboratory for Molecular and Microbial Ecology (LaMME), Department of Biological Sciences, School of Sciences, The University of Jordan, Amman 11942, Jordan
| | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Roma, Italy
| | - Malek Zihlif
- Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan
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20
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Wang YH, Yan ZZ, Luo SD, Hu JJ, Wu M, Zhao J, Liu WF, Li C, Liu KX. Gut microbiota-derived succinate aggravates acute lung injury after intestinal ischaemia/reperfusion in mice. Eur Respir J 2023; 61:13993003.00840-2022. [PMID: 36229053 DOI: 10.1183/13993003.00840-2022] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 10/02/2022] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Acute lung injury (ALI) is a major cause of morbidity and mortality after intestinal ischaemia/reperfusion (I/R). The gut microbiota and its metabolic byproducts act as important modulators of the gut-lung axis. This study aimed to define the role of succinate, a key microbiota metabolite, in intestinal I/R-induced ALI progression. METHODS Gut and lung microbiota of mice subjected to intestinal I/R were analysed using 16S rRNA gene sequencing. Succinate level alterations were measured in germ-free mice or conventional mice treated with antibiotics. Succinate-induced alveolar macrophage polarisation and its effects on alveolar epithelial apoptosis were evaluated in succinate receptor 1 (Sucnr1)-deficient mice and in murine alveolar macrophages transfected with Sucnr1-short interfering RNA. Succinate levels were measured in patients undergoing cardiopulmonary bypass, including intestinal I/R. RESULTS Succinate accumulated in lungs after intestinal I/R, and this was associated with an imbalance of succinate-producing and succinate-consuming bacteria in the gut, but not the lungs. Succinate accumulation was absent in germ-free mice and was reversed by gut microbiota depletion with antibiotics, indicating that the gut microbiota is a source of lung succinate. Moreover, succinate promoted alveolar macrophage polarisation, alveolar epithelial apoptosis and lung injury during intestinal I/R. Conversely, knockdown of Sucnr1 or blockage of SUCNR1 in vitro and in vivo reversed the effects of succinate by modulating the phosphoinositide 3-kinase-AKT/hypoxia-inducible factor-1α pathway. Plasma succinate levels significantly correlated with intestinal I/R-related lung injury after cardiopulmonary bypass. CONCLUSION Gut microbiota-derived succinate exacerbates intestinal I/R-induced ALI through SUCNR1-dependent alveolar macrophage polarisation, identifying succinate as a novel target for gut-derived ALI in critically ill patients.
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Affiliation(s)
- Yi-Heng Wang
- Department of Anaesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Anaesthesiology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
- Yi-Heng Wang and Zheng-Zheng Yan contributed equally
| | - Zheng-Zheng Yan
- Department of Anaesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Yi-Heng Wang and Zheng-Zheng Yan contributed equally
| | - Si-Dan Luo
- Department of Anaesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jing-Juan Hu
- Department of Anaesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mei Wu
- Department of Anaesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jin Zhao
- Department of Anaesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wei-Feng Liu
- Department of Anaesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Cai Li
- Department of Anaesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Cai Li and Ke-Xuan Liu contributed equally to this article as lead authors and supervised the work
| | - Ke-Xuan Liu
- Department of Anaesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Cai Li and Ke-Xuan Liu contributed equally to this article as lead authors and supervised the work
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21
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Chanderraj R, Baker JM, Kay SG, Brown CA, Hinkle KJ, Fergle DJ, McDonald RA, Falkowski NR, Metcalf JD, Kaye KS, Woods RJ, Prescott HC, Sjoding MW, Dickson RP. In critically ill patients, anti-anaerobic antibiotics increase risk of adverse clinical outcomes. Eur Respir J 2023; 61:13993003.00910-2022. [PMID: 36229047 PMCID: PMC9909213 DOI: 10.1183/13993003.00910-2022] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/16/2022] [Indexed: 01/16/2023]
Abstract
BACKGROUND Critically ill patients routinely receive antibiotics with activity against anaerobic gut bacteria. However, in other disease states and animal models, gut anaerobes are protective against pneumonia, organ failure and mortality. We therefore designed a translational series of analyses and experiments to determine the effects of anti-anaerobic antibiotics on the risk of adverse clinical outcomes among critically ill patients. METHODS We conducted a retrospective single-centre cohort study of 3032 critically ill patients, comparing patients who did and did not receive early anti-anaerobic antibiotics. We compared intensive care unit outcomes (ventilator-associated pneumonia (VAP)-free survival, infection-free survival and overall survival) in all patients and changes in gut microbiota in a subcohort of 116 patients. In murine models, we studied the effects of anaerobe depletion in infectious (Klebsiella pneumoniae and Staphylococcus aureus pneumonia) and noninfectious (hyperoxia) injury models. RESULTS Early administration of anti-anaerobic antibiotics was associated with decreased VAP-free survival (hazard ratio (HR) 1.24, 95% CI 1.06-1.45), infection-free survival (HR 1.22, 95% CI 1.09-1.38) and overall survival (HR 1.14, 95% CI 1.02-1.28). Patients who received anti-anaerobic antibiotics had decreased initial gut bacterial density (p=0.00038), increased microbiome expansion during hospitalisation (p=0.011) and domination by Enterobacteriaceae spp. (p=0.045). Enterobacteriaceae were also enriched among respiratory pathogens in anti-anaerobic-treated patients (p<2.2×10-16). In murine models, treatment with anti-anaerobic antibiotics increased susceptibility to Enterobacteriaceae pneumonia (p<0.05) and increased the lethality of hyperoxia (p=0.0002). CONCLUSIONS In critically ill patients, early treatment with anti-anaerobic antibiotics is associated with increased mortality. Mechanisms may include enrichment of the gut with respiratory pathogens, but increased mortality is incompletely explained by infections alone. Given consistent clinical and experimental evidence of harm, the widespread use of anti-anaerobic antibiotics should be reconsidered.
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Affiliation(s)
- Rishi Chanderraj
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Medicine Service, Infectious Diseases Section, VA Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Jennifer M Baker
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stephen G Kay
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Brown
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Research on Innovation and Science, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kevin J Hinkle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel J Fergle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Roderick A McDonald
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicole R Falkowski
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Joseph D Metcalf
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Keith S Kaye
- Division of Infectious Diseases, Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Medicine Service, Infectious Diseases Section, VA Ann Arbor Healthcare System, Ann Arbor, MI, USA
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Hallie C Prescott
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI, USA
- VA Center for Clinical Management Research, Ann Arbor, MI, USA
| | - Michael W Sjoding
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, MI, USA
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, MI, USA
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22
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Hua LJ, Kong LX, Hu JN, Liu Q, Bao C, Liu C, Li ZL, Chen J, Xu SY. Perioperative Risk Factors for Post-operative Pneumonia after Type A Acute Aortic Dissection Surgery. Curr Med Sci 2023; 43:69-79. [PMID: 36334171 DOI: 10.1007/s11596-022-2659-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/18/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Type A acute aortic dissection (TAAAD) is a dangerous and complicated condition with a high death rate before hospital treatment. Patients who are fortunate to receive prompt surgical treatment still face high in-hospital mortality. A series of post-operative complications further affects the prognosis. Post-operative pneumonia (POP) also leads to great morbidity and mortality. This study aimed to identify the prevalence as well as the risk factors for POP in TAAAD patients and offer references for clinical decisions to further improve the prognosis of patients who survived the surgical procedure. METHODS The study enrolled 89 TAAAD patients who underwent surgical treatment in Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei province, China from December 2020 to July 2021 and analyzed the perioperative data and outcomes of these patients. Logistic regression analyses were used to identify the risk factors for POP. RESULTS In the study, 31.5% of patients developed POP. Patients with POP had higher proportions of severe oxygenation damage, pneumothorax, reintubation, tracheotomy, renal replacement therapy, arrhythmia, gastrointestinal bleeding, and longer duration of mechanical ventilation, fever, ICU stay, and length of stay (all with P<0.05). The in-hospital mortality was 2.3%. Smoking, preoperative white blood cells, and intraoperative transfusion were the independent risk factors for POP in TAAAD. CONCLUSION Patients who underwent TAAAD surgery suffered poorer outcomes when they developed POP. Furthermore, patients with risk factors should be treated with caution.
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Affiliation(s)
- Li-Juan Hua
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lu-Xia Kong
- Department of Respiratory and Critical Care Medicine, Taikang Tongji (Wuhan) Hospital, Wuhan, 430050, China
| | - Jian-Nan Hu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qian Liu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chen Bao
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chao Liu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zi-Ling Li
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jun Chen
- Department of Cardiovascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shu-Yun Xu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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23
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Chioma OS, Mallott EK, Chapman A, Van Amburg JC, Wu H, Shah-Gandhi B, Dey N, Kirkland ME, Blanca Piazuelo M, Johnson J, Bernard GR, Bodduluri SR, Davison S, Haribabu B, Bordenstein SR, Drake WP. Gut microbiota modulates lung fibrosis severity following acute lung injury in mice. Commun Biol 2022; 5:1401. [PMID: 36543914 DOI: 10.1038/s42003-022-04357-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Independent studies demonstrate the significance of gut microbiota on the pathogenesis of chronic lung diseases; yet little is known regarding the role of the gut microbiota in lung fibrosis progression. Here we show, using the bleomycin murine model to quantify lung fibrosis in C57BL/6 J mice housed in germ-free, animal biosafety level 1 (ABSL-1), or animal biosafety level 2 (ABSL-2) environments, that germ-free mice are protected from lung fibrosis, while ABSL-1 and ABSL-2 mice develop mild and severe lung fibrosis, respectively. Metagenomic analysis reveals no notable distinctions between ABSL-1 and ABSL-2 lung microbiota, whereas greater microbial diversity, with increased Bifidobacterium and Lactobacilli, is present in ABSL-1 compared to ABSL-2 gut microbiota. Flow cytometric analysis reveals enhanced IL-6/STAT3/IL-17A signaling in pulmonary CD4 + T cells of ABSL-2 mice. Fecal transplantation of ABSL-2 stool into germ-free mice recapitulated more severe fibrosis than transplantation of ABSL-1 stool. Lactobacilli supernatant reduces collagen 1 A production in IL-17A- and TGFβ1-stimulated human lung fibroblasts. These findings support a functional role of the gut microbiota in augmenting lung fibrosis severity.
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24
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Li W, Ma ZS. The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2. Microb Ecol 2022:1-10. [PMID: 36509943 PMCID: PMC9744668 DOI: 10.1007/s00248-022-02148-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/12/2022] [Indexed: 06/17/2023]
Abstract
The microbiome of upper respiratory tract (URT) acts as a gatekeeper to respiratory health of the host. However, little is still known about the impacts of SARS-CoV-2 infection on the microbial species composition and co-occurrence correlations of the URT microbiome, especially the relationships between SARS-CoV-2 and other microbes. Here, we characterized the URT microbiome based on RNA metagenomic-sequencing datasets from 1737 nasopharyngeal samples collected from COVID-19 patients. The URT-microbiome network consisting of bacteria, archaea, and RNA viruses was built and analyzed from aspects of core/periphery species, cluster composition, and balance between positive and negative interactions. It is discovered that the URT microbiome in the COVID-19 patients is enriched with Enterobacteriaceae, a gut associated family containing many pathogens. These pathogens formed a dense cooperative guild that seemed to suppress beneficial microbes collectively. Besides bacteria and archaea, 72 eukaryotic RNA viruses were identified in the URT microbiome of COVID-19 patients. Only five of these viruses were present in more than 10% of all samples, including SARS-CoV-2 and a bat coronavirus (i.e., BatCoV BM48-31) not detected in humans by routine means. SARS-CoV-2 was inhibited by a cooperative alliance of 89 species, but seems to cooperate with BatCoV BM48-31 given their statistically significant, positive correlations. The presence of cooperative bat-coronavirus partner of SARS-CoV-2 (BatCoV BM48-31), which was previously discovered in bat but not in humans to the best of our knowledge, is puzzling and deserves further investigation given their obvious implications. Possible microbial translocation mechanism from gut to URT also deserves future studies.
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Affiliation(s)
- Wendy Li
- Computational Biology and Medical Ecology Lab, State Key Laboratory for Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, China
| | - Zhanshan Sam Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory for Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China.
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25
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Yoon YM, Hrusch CL, Fei N, Barrón GM, Mills KAM, Hollinger MK, Velez TE, Leone VA, Chang EB, Sperling AI. Gut microbiota modulates bleomycin-induced acute lung injury response in mice. Respir Res 2022; 23:337. [PMID: 36496380 PMCID: PMC9741526 DOI: 10.1186/s12931-022-02264-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Airway instillation of bleomycin (BLM) in mice is a widely used, yet challenging, model for acute lung injury (ALI) with high variability in treatment scheme and animal outcomes among investigators. Whether the gut microbiota plays any role in the outcome of BLM-induced lung injury is currently unknown. METHODS Intratracheal instillation of BLM into C57BL/6 mice was performed. Fecal microbiomes were analyzed by 16s rRNA amplicon and metagenomic sequencing. Germ-free mice conventionalization and fecal microbiota transfer between SPF mice were performed to determine dominant commensal species that are associated with more severe BLM response. Further, lungs and gut draining lymph nodes of the mice were analyzed by flow cytometry to define immunophenotypes associated with the BLM-sensitive microbiome. RESULTS Mice from two SPF barrier facilities at the University of Chicago exhibited significantly different mortality and weight loss during BLM-induced lung injury. Conventionalizing germ-free mice with SPF microbiota from two different housing facilities recapitulated the respective donors' response to BLM. Fecal microbiota transfer from the facility where the mice had worse mortality into the mice in the facility with more survival rendered recipient mice more susceptible to BLM-induced weight loss in a dominant negative manner. BLM-sensitive phenotype was associated with the presence of Helicobacter and Desulfovibrio in the gut, decreased Th17-neutrophil axis during steady state, and augmented lung neutrophil accumulation during the acute phase of the injury response. CONCLUSION The composition of gut microbiota has significant impact on BLM-induced wasting and death suggesting a role of the lung-gut axis in lung injury.
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Affiliation(s)
- Young Me Yoon
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Cara L Hrusch
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Na Fei
- Section of Gastroenterology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Gabriel M Barrón
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kathleen A M Mills
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Maile K Hollinger
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Tania E Velez
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Box 800546, Charlottesville, VA, 22908-0546, USA
| | - Vanessa A Leone
- Section of Gastroenterology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Eugene B Chang
- Section of Gastroenterology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anne I Sperling
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Box 800546, Charlottesville, VA, 22908-0546, USA.
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26
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Zhu T, Jin J, Chen M, Chen Y. The impact of infection with COVID-19 on the respiratory microbiome: A narrative review. Virulence 2022; 13:1076-1087. [PMID: 35763685 PMCID: PMC9794016 DOI: 10.1080/21505594.2022.2090071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has affected millions of individuals with various implications. Consistent with the crucial role of the microbiome in determining health and disease in humans, various studies have investigated the gut and respiratory microbiome effect on the COVID-19. Microbiota dysbiosis might support the entry, replication, and establishment of SARS-CoV-2 infection by modulating various mechanisms. One of the main mechanisms that the modulation of respiratory microbiota composition during the COVID-19 infection affects the magnitude of the disease is changes in innate and acquired immune responses, including inflammatory markers and cytokines and B- and T-cells. The diversity of respiratory microbiota in COVID-19 patients is controversial; some studies reported low microbial diversity, while others found high diversity, suggesting the role of respiratory microbiota in this disease. Modulating microbiota diversity and profile by supplementations and nutrients can be applied prophylactic and therapeutic in combating COVID-19. Here, we discussed the lung microbiome dysbiosis during various lung diseases and its interaction with immune cells, focusing on COVID-19.
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Affiliation(s)
- Taiping Zhu
- Internal Medicine Department, Chun’an Maternal and Child Health Hospital, Hangzhou, Zhejiang, China
| | - Jun Jin
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - Minhua Chen
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital Hangzhou Medical College), Hangzhou, Zhejiang, China,CONTACT Minhua Chen
| | - Yingjun Chen
- Department of Infectious Diseases, Tiantai People’s Hospital of Zhejiang Province (Tiantai Branch of Zhejiang People’s Hospital), Taizhou, Zhejiang, China
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27
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Meng H, Wang S, Tang X, Guo J, Xu X, Wang D, Jin F, Zheng M, Yin S, He C, Han Y, Chen J, Han J, Ren C, Gao Y, Liu H, Wang Y, Jin R. Respiratory immune status and microbiome in recovered COVID-19 patients revealed by metatranscriptomic analyses. Front Cell Infect Microbiol 2022; 12:1011672. [PMID: 36483456 PMCID: PMC9724627 DOI: 10.3389/fcimb.2022.1011672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is currently a severe threat to global public health, and the immune response to COVID-19 infection has been widely investigated. However, the immune status and microecological changes in the respiratory systems of patients with COVID-19 after recovery have rarely been considered. We selected 72 patients with severe COVID-19 infection, 57 recovered from COVID-19 infection, and 65 with non-COVID-19 pneumonia, for metatranscriptomic sequencing and bioinformatics analysis. Accordingly, the differentially expressed genes between the infected and other groups were enriched in the chemokine signaling pathway, NOD-like receptor signaling pathway, phagosome, TNF signaling pathway, NF-kappa B signaling pathway, Toll-like receptor signaling pathway, and C-type lectin receptor signaling pathway. We speculate that IL17RD, CD74, and TNFSF15 may serve as disease biomarkers in COVID-19. Additionally, principal coordinate analysis revealed significant differences between groups. In particular, frequent co-infections with the genera Streptococcus, Veillonella, Gemella, and Neisseria, among others, were found in COVID-19 patients. Moreover, the random forest prediction model with differential genes showed a mean area under the curve (AUC) of 0.77, and KCNK12, IL17RD, LOC100507412, PTPRT, MYO15A, MPDZ, FLRT2, SPEG, SERPINB3, and KNDC1 were identified as the most important genes distinguishing the infected group from the recovered group. Agrobacterium tumefaciens, Klebsiella michiganensis, Acinetobacter pittii, Bacillus sp. FJAT.14266, Brevundimonas naejangsanensis, Pseudopropionibacterium propionicum, Priestia megaterium, Dialister pneumosintes, Veillonella rodentium, and Pseudomonas protegens were selected as candidate microbial markers for monitoring the recovery of COVID patients. These results will facilitate the diagnosis, treatment, and prognosis of COVID patients recovering from severe illness.
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Affiliation(s)
- Huan Meng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Shuang Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xiaomeng Tang
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jingjing Guo
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xinming Xu
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Dagang Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Fangfang Jin
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Mei Zheng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Shangqi Yin
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Chaonan He
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Ying Han
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jin Chen
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jinyu Han
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Chaobo Ren
- Translational R&D Center, Guangzhou Vision Medicals Co. LTD, Guangzhou, China
| | - Yantao Gao
- Translational R&D Center, Guangzhou Vision Medicals Co. LTD, Guangzhou, China
| | - Huifang Liu
- Translational R&D Center, Guangzhou Vision Medicals Co. LTD, Guangzhou, China
| | - Yajie Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China,*Correspondence: Yajie Wang, ; Ronghua Jin,
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, Beijing, China,*Correspondence: Yajie Wang, ; Ronghua Jin,
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28
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Yang W, Yuan Q, Li Z, Du Z, Wu G, Yu J, Hu J. Translocation and Dissemination of Gut Bacteria after Severe Traumatic Brain Injury. Microorganisms 2022; 10. [PMID: 36296362 DOI: 10.3390/microorganisms10102082] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 12/04/2022] Open
Abstract
Enterobacteriaceae are often found in the lungs of patients with severe Traumatic Brain Injury (sTBI). However, it is unknown whether these bacteria come from the gut microbiota. To investigate this hypothesis, the mice model of sTBI was used in this study. After sTBI, Chao1 and Simpson index peaking at 7 d in the lungs (p < 0.05). The relative abundance of Acinetobacter in the lungs increased to 16.26% at 7 d after sTBI. The chao1 index of gut microbiota increased after sTBI and peaked at 7 d (p < 0.05). Three hours after sTBI, the conditional pathogens such as Lachnoclostridium, Acinetobacter, Bacteroides and Streptococcus grew significantly. At 7 d and 14 d, the histology scores in the sTBI group were significantly higher than the control group (p < 0.05). The myeloperoxidase (MPO) activity increased at all-time points after sTBI and peaked at 7 d (p < 0.05). The LBP and sCD14 peaking 7 d after sTBI (p < 0.05). The Zonulin increased significantly at 3 d after sTBI and maintained the high level (p < 0.05). SourceTracker identified that the lung tissue microbiota reflects 49.69% gut source at 7 d after sTBI. In the small intestine, sTBI induced gastrointestinal dysfunction with increased apoptosis and decreasing antimicrobial peptides. There was a negative correlation between gut conditional pathogens and the expression level of antimicrobial peptides in Paneth cells. Our data indicate that gut bacteria translocated to the lungs after sTBI, and Paneth cells may regulate gut microbiota stability and translocation.
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29
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Merenstein C, Bushman FD, Collman RG. Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance. Microbiome 2022; 10:165. [PMID: 36195943 PMCID: PMC9532226 DOI: 10.1186/s40168-022-01342-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/02/2022] [Indexed: 06/16/2023]
Abstract
SARS-CoV-2 infection causes COVID-19 disease, which can result in consequences ranging from undetectable to fatal, focusing attention on the modulators of outcomes. The respiratory tract microbiome is thought to modulate the outcomes of infections such as influenza as well as acute lung injury, raising the question to what degree does the airway microbiome influence COVID-19? Here, we review the results of 56 studies examining COVID-19 and the respiratory tract microbiome, summarize the main generalizations, and point to useful avenues for further research. Although the results vary among studies, a few consistent findings stand out. The diversity of bacterial communities in the oropharynx typically declined with increasing disease severity. The relative abundance of Haemophilus and Neisseria also declined with severity. Multiple microbiome measures tracked with measures of systemic immune responses and COVID outcomes. For many of the conclusions drawn in these studies, the direction of causality is unknown-did an alteration in the microbiome result in increased COVID severity, did COVID severity alter the microbiome, or was some third factor the primary driver, such as medication use. Follow-up mechanistic studies can help answer these questions. Video Abstract.
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Affiliation(s)
- Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Ronald G. Collman
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
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30
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Hashimoto Y, Eguchi A, Wei Y, Shinno-Hashimoto H, Fujita Y, Ishima T, Chang L, Mori C, Suzuki T, Hashimoto K. Antibiotic-induced microbiome depletion improves LPS-induced acute lung injury via gut-lung axis. Life Sci 2022; 307:120885. [PMID: 35981631 DOI: 10.1016/j.lfs.2022.120885] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/02/2022] [Accepted: 08/11/2022] [Indexed: 12/01/2022]
Abstract
AIMS Acute lung injury (ALI) is an acute inflammatory disorder. However, the precise mechanisms underlying the pathology of ALI remain elusive. An increasing evidence suggests the role of the gut-microbiota axis in the pathology of lung injury. This study aimed to investigate whether antibiotic-induced microbiome depletion could affect ALI in mice after lipopolysaccharide (LPS) administration. MAIN METHODS The effects of antibiotic cocktail (ABX) on ALI in the mice after intratracheally administration of LPS (5 mg/kg) were examined. Furthermore, 16s rRNA analysis and measurement of short-chain fatty acids in feces samples and metabolomics analysis of blood samples were performed. KEY FINDINGS LPS significantly increased the interleukin-6 (IL-6) levels in the bronchoalveolar lavage fluid (BALF) of water-treated mice. Interestingly, an ABX significantly attenuated the LPS-induced increase in IL-6 in BALF and lung injury scores. Furthermore, ABX and/or LPS treatment markedly altered the α- and β-diversity of the gut microbiota. There were significant differences in the α- and β-diversity of the water + LPS group and ABX + LPS group. LEfSe analysis identified Enterococusfaecalis, Clostriumtertium, and Bacteroidescaecimyris as potential microbial markers for ABX + LPS group. Untargeted metabolomics analysis identified several plasma metabolites responsible for discriminating water + LPS group from ABX + LPS group. There were correlations between the relative abundance of the microbiome and plasma metabolites. Integrative network analysis showed correlations between IL-6 levels in BALF and several gut microbes (or plasma metabolites). SIGNIFICANCE These data suggest that ABX-induced microbiome depletion could protect against LPS-induced ALI via the gut-microbiota-lung axis.
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Affiliation(s)
- Yaeko Hashimoto
- Department of Respirology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan; Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan.
| | - Akifumi Eguchi
- Department of Sustainable Health Science, Chiba University Center for Preventive Medical Sciences, Chiba 263-8522, Japan
| | - Yan Wei
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Hiroyo Shinno-Hashimoto
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan; Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Yuko Fujita
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Tamaki Ishima
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Lijia Chang
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Chisato Mori
- Department of Sustainable Health Science, Chiba University Center for Preventive Medical Sciences, Chiba 263-8522, Japan; Department of Bioenvironmental Medicine, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Takuji Suzuki
- Department of Respirology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Kenji Hashimoto
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan.
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31
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Zhang P, Liu B, Zheng W, Chen Y, Wu Z, Lu Y, Ma J, Lu W, Zheng M, Wu W, Meng Z, Wu J, Zheng Y, Zhang X, Zhang S, Huang Y. Pulmonary Microbial Composition in Sepsis-Induced Acute Respiratory Distress Syndrome. Front Mol Biosci 2022; 9:862570. [PMID: 35813824 PMCID: PMC9262094 DOI: 10.3389/fmolb.2022.862570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Acute respiratory distress syndrome (ARDS) is an unresolved challenge in the field of respiratory and critical care, and the changes in the lung microbiome during the development of ARDS and their clinical diagnostic value remain unclear. This study aimed to explore the role of the lung microbiome in disease progression in patients with sepsis-induced ARDS and potential therapeutic targets.Methods: Patients with ARDS were divided into two groups according to the initial site of infection, intrapulmonary infection (ARDSp, 111 cases) and extrapulmonary infection (ARDSexp, 45 cases), and a total of 28 patients with mild pulmonary infections were enrolled as the control group. In this study, we sequenced the DNA in the bronchoalveolar lavage fluid collected from patients using metagenomic next-generation sequencing (mNGS) to analyze the changes in the lung microbiome in patients with different infectious site and prognosis and before and after antibiotic treatment.Results: The Shannon–Wiener index indicated a statistically significant reduction in microbial diversity in the ARDSp group compared with the ARDSexp and control groups. The ARDSp group was characterized by a reduction in microbiome diversity, mainly in the normal microbes of the lung, whereas the ARDSexp group was characterized by an increase in microbiome diversity, mainly in conditionally pathogenic bacteria and intestinal microbes. Further analysis showed that an increase in Bilophila is a potential risk factor for death in ARDSexp. An increase in Escherichia coli, Staphylococcus aureus, Candida albicans, enteric microbes, or conditional pathogens may be risk factors for death in ARDSp. In contrast, Hydrobacter may be a protective factor in ARDSp.Conclusion: Different initial sites of infection and prognoses are likely to affect the composition and diversity of the pulmonary microbiome in patients with septic ARDS. This study provides insights into disease development and exploration of potential therapeutic targets.
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Affiliation(s)
- Peng Zhang
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
| | - Baoyi Liu
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
| | - Weihao Zheng
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
| | - Yantang Chen
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
| | - Zhentao Wu
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
| | - Yuting Lu
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
| | - Jie Ma
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
| | - Wenjie Lu
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
| | - Mingzhu Zheng
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
| | - Wanting Wu
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
| | - Zijie Meng
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
| | - Jinhua Wu
- Department of Clinical Laboratory, Jiangmen Central Hospital, Jiangmen, China
| | - Yan Zheng
- Department of Research and Development, Guangdong Research Institute of Genetic Diagnostic and Engineering Technologies for Thalassemia, Hybribio Limited, Guangzhou, China
| | - Xin Zhang
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, China
- Collaborative Innovation Center for Antitumor Active Substance Research and Development, Guangdong Medical University, Zhanjiang, China
- *Correspondence: Xin Zhang, ; Shuang Zhang, ; Yanming Huang,
| | - Shuang Zhang
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
- *Correspondence: Xin Zhang, ; Shuang Zhang, ; Yanming Huang,
| | - Yanming Huang
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
- Department of Respiratory and Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
- *Correspondence: Xin Zhang, ; Shuang Zhang, ; Yanming Huang,
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32
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Diamond JM. Don't Inhale: Acute Respiratory Distress Syndrome Risk and Tobacco Exposure in Patients with Sepsis. Am J Respir Crit Care Med 2022; 205:866-867. [PMID: 35130469 PMCID: PMC9838625 DOI: 10.1164/rccm.202201-0034ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Joshua M Diamond
- Pulmonary, Allergy, and Critical Care Division Perelman School of Medicine at the University of Pennsylvania Philadelphia, Pennsylvania
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Abstract
Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are common acute and severe cases of the respiratory system with complicated pathogenesis and high mortality. Sepsis is the leading indirect cause of ALI/ARDS in the intensive care unit (ICU). The pathogenesis of septic ALI/ARDS is complex and multifactorial. In the development of sepsis, the disruption of the intestinal barrier function, the alteration of gut microbiota, and the translocation of the intestinal microbiome can lead to systemic and local inflammatory responses, which further alter the immune homeostasis in the systemic environment. Disruption of homeostasis may promote and propagate septic ALI/ARDS. In turn, when ALI occurs, elevated levels of inflammatory cytokines and the shift of the lung microbiome may lead to the dysregulation of the intestinal microbiome and the disruption of the intestinal mucosal barrier. Thus, the interaction between the lung and the gut can initiate and potentiate sepsis-induced ALI/ARDS. The gut–lung crosstalk may be a promising potential target for intervention. This article reviews the underlying mechanism of gut-lung crosstalk in septic ALI/ARDS.
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Affiliation(s)
- Xin Zhou
- Department of ICU/Emergency, Wuhan University, Wuhan Third Hospital, Wuhan, China
| | - Youxia Liao
- Department of ICU/Emergency, Wuhan University, Wuhan Third Hospital, Wuhan, China
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Wang H, Wang H, Sun Y, Ren Z, Zhu W, Li A, Cui G. Potential Associations Between Microbiome and COVID-19. Front Med (Lausanne) 2022; 8:785496. [PMID: 35004750 PMCID: PMC8727742 DOI: 10.3389/fmed.2021.785496] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has plunged the world into a major crisis. The disease is characterized by strong infectivity, high morbidity, and high mortality. It is still spreading in some countries. Microbiota and their metabolites affect human physiological health and diseases by participating in host digestion and nutrition, promoting metabolic function, and regulating the immune system. Studies have shown that human microecology is associated with many diseases, including COVID-19. In this research, we first reviewed the microbial characteristics of COVID-19 from the aspects of gut microbiome, lung microbime, and oral microbiome. We found that significant changes take place in both the gut microbiome and airway microbiome in patients with COVID-19 and are characterized by an increase in conditional pathogenic bacteria and a decrease in beneficial bacteria. Then, we summarized the possible microecological mechanisms involved in the progression of COVID-19. Intestinal microecological disorders in individuals may be involved in the occurrence and development of COVID-19 in the host through interaction with ACE2, mitochondria, and the lung-gut axis. In addition, fecal bacteria transplantation (FMT), prebiotics, and probiotics may play a positive role in the treatment of COVID-19 and reduce the fatal consequences of the disease.
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Affiliation(s)
- Huifen Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haiyu Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Sun
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weiwei Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangying Cui
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Fromentin M, Ricard JD, Roux D. Lung Microbiome in Critically Ill Patients. Life (Basel) 2021; 12:life12010007. [PMID: 35054400 PMCID: PMC8778861 DOI: 10.3390/life12010007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/11/2022] Open
Abstract
The historical hypothesis of sterility of the lungs was invalidated over a decade ago when studies demonstrated the existence of sparse but very diverse bacterial populations in the normal lung and the association between pulmonary dysbiosis and chronic respiratory diseases. Under mechanical ventilation, dysbiosis occurs rapidly with a gradual decline in diversity over time and the progressive predominance of a bacterial pathogen (mainly Proteobacteria) when lung infection occurs. During acute respiratory distress syndrome, an enrichment in bacteria of intestinal origin, mainly Enterobacteriaceae, is observed. However, the role of this dysbiosis in the pathogenesis of ventilator-associated pneumonia and acute respiratory distress syndrome is not yet fully understood. The lack of exploration of other microbial populations, viruses (eukaryotes and prokaryotes) and fungi is a key issue. Further analysis of the interaction between these microbial kingdoms and a better understanding of the host−microbiome interaction are necessary to fully elucidate the role of the microbiome in the pathogenicity of acute diseases. The validation of a consensual and robust methodology in order to make the comparison of the different studies relevant is also required. Filling these different gaps should help develop preventive and therapeutic strategies for both acute respiratory distress syndrome and ventilator-associated pneumonia.
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Affiliation(s)
- Mélanie Fromentin
- Anesthesiology and Intensive Care Department, AP-HP, Hôpital Cochin, 75014 Paris, France;
- UMR1137 IAME, Université de Paris, INSERM, 75018 Paris, France;
| | - Jean-Damien Ricard
- UMR1137 IAME, Université de Paris, INSERM, 75018 Paris, France;
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, 92700 Colombes, France
| | - Damien Roux
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, 92700 Colombes, France
- Institut Necker-Enfants Malades, Université de Paris, INSERM U1151, CNRS UMR 8253, 75015 Paris, France
- Correspondence: ; Tel.: +33-1-47-60-63-29
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36
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Bello S, Vengoechea JJ, Ponce-Alonso M, Figueredo AL, Mincholé E, Rezusta A, Gambó P, Pastor JM, Del Campo R. Core Microbiota in Central Lung Cancer With Streptococcal Enrichment as a Possible Diagnostic Marker. Arch Bronconeumol 2021; 57:681-689. [PMID: 35699005 DOI: 10.1016/j.arbr.2020.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/04/2020] [Indexed: 06/15/2023]
Abstract
BACKGROUND Dysbiosis in lung cancer has been underexplored. The aim of this study was to define the bacterial and fungal microbiota of the bronchi in central lung cancer and to compare it with that of the oral and intestinal compartments. METHODS Twenty-five patients with central lung cancer and sixteen controls without antimicrobial intake during the previous month were recruited. Bacterial and fungal distribution was determined by massive sequencing of bronchial biopsies and saliva and faecal samples. Complex computational analysis was performed to define the core lung microbiota. RESULTS Affected and contralateral bronchi of patients have almost identical microbiota dominated by Streptococcus, whereas Pseudomonas was the dominant genera in controls. Oral and pulmonary ecosystems were significantly more similar in patients, probably due to microaspirations. Streptococcal abundance in the bronchi differentiated patients from controls according to a ROC curve analysis (90.9% sensitivity, 83.3% specificity, AUC=0.897). The saliva of patients characteristically showed a greater abundance of Streptococcus, Rothia, Gemella and Lactobacillus. The mycobiome of controls (Candida) was significantly different from that of patients (Malassezia). Cancer patients' bronchial mycobiome was similar to their saliva, but different from their contralateral bronchi. CONCLUSIONS The central lung cancer microbiome shows high levels of Streptococcus, and differs significantly in its composition from that of control subjects. Changes are not restricted to tumour tissue, and seem to be the consequence of microaspirations from the oral cavity. These findings could be useful in the screening and even diagnosis of this disease.
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Affiliation(s)
- Salvador Bello
- Department of Pulmonary Medicine, Miguel Servet University Hospital, CIBERES, Instituto de Investigación Sanitaria (ISS) Aragón, Zaragoza, Spain.
| | - José J Vengoechea
- Department of Pulmonary Medicine, Miguel Servet University Hospital, CIBERES, Instituto de Investigación Sanitaria (ISS) Aragón, Zaragoza, Spain
| | - Manuel Ponce-Alonso
- Department of Microbiology, Ramón y Cajal Health Investigation Institute (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Ana L Figueredo
- Department of Pulmonary Medicine, Miguel Servet University Hospital, CIBERES, Instituto de Investigación Sanitaria (ISS) Aragón, Zaragoza, Spain
| | - Elisa Mincholé
- Department of Pulmonary Medicine, Miguel Servet University Hospital, CIBERES, Instituto de Investigación Sanitaria (ISS) Aragón, Zaragoza, Spain
| | - Antonio Rezusta
- Department of Microbiology, Miguel Servet University Hospital, Instituto de Investigación Sanitaria (ISS) Aragón, Zaragoza, Spain
| | - Paula Gambó
- Department of Pathology, Miguel Servet University Hospital, Instituto de Investigación Sanitaria (ISS) Aragón, Zaragoza, Spain
| | | | - Rosa Del Campo
- Department of Microbiology, Ramón y Cajal Health Investigation Institute (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain; University Alfonso X El Sabio, Villanueva de la Cañada, Madrid, Spain
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37
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Tourelle KM, Boutin S, Weigand MA, Schmitt FCF. Sepsis and the Human Microbiome. Just Another Kind of Organ Failure? A Review. J Clin Med 2021; 10:jcm10214831. [PMID: 34768350 PMCID: PMC8585089 DOI: 10.3390/jcm10214831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 01/05/2023] Open
Abstract
Next-generation sequencing (NGS) has been further optimised during the last years and has given us new insights into the human microbiome. The 16S rDNA sequencing, especially, is a cheap, fast, and reliable method that can reveal significantly more microorganisms compared to culture-based diagnostics. It might be a useful method for patients suffering from severe sepsis and at risk of organ failure because early detection and differentiation between healthy and harmful microorganisms are essential for effective therapy. In particular, the gut and lung microbiome in critically ill patients have been probed by NGS. For this review, an iterative approach was used. Current data suggest that an altered microbiome with a decreased alpha-diversity compared to healthy individuals could negatively influence the individual patient’s outcome. In the future, NGS may not only contribute to the diagnosis of complications. Patients at risk could also be identified before surgery or even during their stay in an intensive care unit. Unfortunately, there is still a lack of knowledge to make precise statements about what constitutes a healthy microbiome, which patients exactly have an increased perioperative risk, and what could be a possible therapy to strengthen the microbiome. This work is an iterative review that presents the current state of knowledge in this field.
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Affiliation(s)
- Kevin M. Tourelle
- Department of Anesthesiology, Heidelberg University Hospital, 420, Im Neuenheimer Feld, 69120 Heidelberg, Germany; (K.M.T.); (M.A.W.)
| | - Sebastien Boutin
- Department of Infectious Disease, Medical Microbiology and Hygiene, University Hospital, 324, Im Neuenheimer Feld, 69120 Heidelberg, Germany;
| | - Markus A. Weigand
- Department of Anesthesiology, Heidelberg University Hospital, 420, Im Neuenheimer Feld, 69120 Heidelberg, Germany; (K.M.T.); (M.A.W.)
| | - Felix C. F. Schmitt
- Department of Anesthesiology, Heidelberg University Hospital, 420, Im Neuenheimer Feld, 69120 Heidelberg, Germany; (K.M.T.); (M.A.W.)
- Correspondence:
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38
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Abstract
The acute respiratory distress syndrome (ARDS) remains a major cause of morbidity and mortality in the intensive care unit. Improving outcomes depends on not only evidence-based care once ARDS has already developed but also preventing ARDS incidence. Several environmental exposures have now been shown to increase the risk of ARDS and related adverse outcomes. How environmental factors impact the risk of developing ARDS is a growing and important field of research that should inform the care of individual patients as well as public health policy.
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Affiliation(s)
- Katherine D Wick
- Department of Anesthesia, University of California, San Francisco, 513 Parnassus Avenue, HSE 760, San Francisco, CA 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Michael A Matthay
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, 505 Parnassus Avenue, M-917, San Francisco, CA 94143, USA; Department of Anesthesia, University of California, San Francisco, 505 Parnassus Avenue, M-917, San Francisco, CA 94143, USA.
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39
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Affiliation(s)
- Pratik Sinha
- Division of Clinical and Translational Research, Department of Anesthesia, Washington University School of Medicine, 660 S. Euclid Avenue, Campus Box 8054, St Louis, MO 63110, USA.
| | - Lieuwe D Bos
- Department of Respiratory Medicine, Infection and Immunity, Amsterdam University Medical Center, AMC, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands
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40
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Abstract
The healthy lung was long thought of as sterile, but recent advances using molecular sequencing approaches have detected bacteria at low levels. Healthy lung bacteria largely reflect communities present in the upper respiratory tract that enter the lung via microaspiration, which is balanced by mechanical and immune clearance and likely involves limited local replication. The nature and dynamics of the lung microbiome, therefore, differ from those of ecological niches with robust self-sustaining microbial communities. Aberrant populations (dysbiosis) have been demonstrated in many pulmonary diseases not traditionally considered microbial in origin, and potential pathways of microbe-host crosstalk are emerging. The question now is whether and how dysbiotic microbiota contribute to initiation or perpetuation of injury. The fungal microbiome and virome are less well studied. This Review highlights features of the lung microbiome, unique considerations in studying it, examples of dysbiosis in selected disease, emerging concepts in lung microbiome-host interactions, and critical areas for investigation.
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41
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Du S, Wu X, Li B, Wang Y, Shang L, Huang X, Xia Y, Yu D, Lu N, Liu Z, Wang C, Liu X, Xiong Z, Zou X, Lu B, Liu Y, Zhan Q, Cao B. Clinical factors associated with composition of lung microbiota and important taxa predicting clinical prognosis in patients with severe community-acquired pneumonia. Front Med 2021. [PMID: 34302613 DOI: 10.1007/s11684-021-0856-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 04/15/2021] [Indexed: 12/28/2022]
Abstract
Few studies have described the key features and prognostic roles of lung microbiota in patients with severe community-acquired pneumonia (SCAP). We prospectively enrolled consecutive SCAP patients admitted to ICU. Bronchoscopy was performed at bedside within 48 h of ICU admission, and 16S rRNA gene sequencing was applied to the collected bronchoalveolar lavage fluid. The primary outcome was clinical improvements defined as a decrease of 2 categories and above on a 7-category ordinal scale within 14 days following bronchoscopy. Sixty-seven patients were included. Multivariable permutational multivariate analysis of variance found that positive bacteria lab test results had the strongest independent association with lung microbiota (R2 = 0.033; P = 0.018), followed by acute kidney injury (AKI; R2 = 0.032; P = 0.011) and plasma MIP-1β level (R2 = 0.027; P = 0.044). Random forest identified that the families Prevotellaceae, Moraxellaceae, and Staphylococcaceae were the biomarkers related to the positive bacteria lab test results. Multivariable Cox regression showed that the increase in α-diversity and the abundance of the families Prevotellaceae and Actinomycetaceae were associated with clinical improvements. The positive bacteria lab test results, AKI, and plasma MIP-1β level were associated with patients’ lung microbiota composition on ICU admission. The families Prevotellaceae and Actinomycetaceae on admission predicted clinical improvements.
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42
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Alexander JL, Mullish BH. A Guide to the Gut Microbiome and its Relevance to Critical Care. ACTA ACUST UNITED AC 2021; 29:1106-1112. [PMID: 33104419 DOI: 10.12968/bjon.2020.29.19.1106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Although it is well-established that particular bacteria may cause gastroenteritis and other infections when present in the gut, it is only recently that scientists have made significant inroads into understanding the huge number of other bacteria and additional microbes that live within the gastrointestinal tract, referred to as the gut microbiome. In particular, it is now recognised that bacteria within the gut microbiome have a wide variety of roles in maintaining different aspects of human health, and that disturbances of these bacteria may potentially cause or contribute to a number of different medical conditions, including particular infections, certain cancers, and chronic conditions, including inflammatory bowel disease. Moreover, there is increasing awareness that these bacteria help determine how the body responds to medication, including antibiotics and chemotherapy. There has been growing interest in different approaches to alter the gut microbiome as a novel approach to medical therapy. This article provides an overview of the importance of the gut microbiome, with a particular focus on critical care.
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Affiliation(s)
- James L Alexander
- Clinical Lecturer and Honorary Specialty Registrar, Department of Metabolism, Digestion and Reproduction, Imperial College London, and Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London
| | - Benjamin H Mullish
- Clinical Lecturer and Honorary Specialty Registrar, Department of Metabolism, Digestion and Reproduction, Imperial College London, and Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London
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Hérivaux A, Willis JR, Mercier T, Lagrou K, Gonçalves SM, Gonçales RA, Maertens J, Carvalho A, Gabaldón T, Cunha C. Lung microbiota predict invasive pulmonary aspergillosis and its outcome in immunocompromised patients. Thorax 2021; 77:283-291. [PMID: 34172558 PMCID: PMC8867272 DOI: 10.1136/thoraxjnl-2020-216179] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 05/26/2021] [Indexed: 11/17/2022]
Abstract
Rationale Recent studies have revealed that the lung microbiota of critically ill patients is altered and predicts clinical outcomes. The incidence of invasive fungal infections, namely, invasive pulmonary aspergillosis (IPA), in immunocompromised patients is increasing, but the clinical significance of variations in lung bacterial communities is unknown. Objectives To define the contribution of the lung microbiota to the development and course of IPA. Methods and measurements We performed an observational cohort study to characterise the lung microbiota in 104 immunocompromised patients using bacterial 16S ribosomal RNA gene sequencing on bronchoalveolar lavage samples sampled on clinical suspicion of infection. Associations between lung dysbiosis in IPA and pulmonary immunity were evaluated by quantifying alveolar cytokines and chemokines and immune cells. The contribution of microbial signatures to patient outcome was assessed by estimating overall survival. Main results Patients diagnosed with IPA displayed a decreased alpha diversity, driven by a markedly increased abundance of the Staphylococcus, Escherichia, Paraclostridium and Finegoldia genera and a decreased proportion of the Prevotella and Veillonella genera. The overall composition of the lung microbiome was influenced by the neutrophil counts and associated with differential levels of alveolar cytokines. Importantly, the degree of bacterial diversity at the onset of IPA predicted the survival of infected patients. Conclusions Our results reveal the lung microbiota as an understudied source of clinical variation in patients at risk of IPA and highlight its potential as a diagnostic and therapeutic target in the context of respiratory fungal diseases.
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Affiliation(s)
- Anaïs Hérivaux
- Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Jesse R Willis
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Toine Mercier
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium.,Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.,Clinical Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Samuel M Gonçalves
- Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Relber A Gonçales
- Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Johan Maertens
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium.,Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain .,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal .,ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
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44
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Toni T, Alverdy J. Harnessing the Microbiome to Optimize Surgical Outcomes in the COVID-19 Era. Ann Surg Open 2021; 2:e056. [PMID: 36590034 PMCID: PMC9794001 DOI: 10.1097/as9.0000000000000056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 02/18/2021] [Indexed: 01/04/2023] Open
Abstract
In this era of testing uncertainties, changing guidelines, and incomplete knowledge, "clearing" patients for surgery in the time of SARS-COVID-19 has been met with various challenges. Efforts to increase patient fitness have long been at the forefront of surgical practicing guidelines, but the current climate requires a renewed sense of focus on these measures. It is essential to understand how dietary history, previous antibiotic exposure, and baseline microbiota can inform and optimize preoperative and postoperative management of the surgical patient in the time of COVID-19. This piece focuses on the clinical, molecular, and physiologic dynamics that occur in preparing patients for surgery during COVID-19, considering the physiologic stress inherent in the procedure itself and the importance of specialized perioperative management approaches. COVID-19 has created a renewed sense of urgency to maintain our discipline in implementing those practices that have long been confirmed to be beneficial to patient outcome. This practice, along with a renewed interest in understanding how the gut microbiome is affected by the confinement, social distancing, etc., due to the COVID pandemic, is ever more important. Therefore, here we discuss the microbiome's role as a defense against viral infection and its potential for reactivation during the process of surgery as the next frontier for surgical advancement.
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Affiliation(s)
- Tiffany Toni
- From the Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - John Alverdy
- From the Pritzker School of Medicine, University of Chicago, Chicago, IL
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45
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Baker JM, Hinkle KJ, McDonald RA, Brown CA, Falkowski NR, Huffnagle GB, Dickson RP. Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota. Microbiome 2021; 9:99. [PMID: 33952355 PMCID: PMC8101028 DOI: 10.1186/s40168-021-01055-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/22/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Low-biomass microbiome studies (such as those of the lungs, placenta, and skin) are vulnerable to contamination and sequencing stochasticity, which obscure legitimate microbial signal. While human lung microbiome studies have rigorously identified sampling strategies that reliably capture microbial signal from these low-biomass microbial communities, the optimal sampling strategy for characterizing murine lung microbiota has not been empirically determined. Performing accurate, reliable characterization of murine lung microbiota and distinguishing true microbial signal from noise in these samples will be critical for further mechanistic microbiome studies in mice. RESULTS Using an analytic approach grounded in microbial ecology, we compared bacterial DNA from the lungs of healthy adult mice collected via two common sampling approaches: homogenized whole lung tissue and bronchoalveolar lavage (BAL) fluid. We quantified bacterial DNA using droplet digital PCR, characterized bacterial communities using 16S rRNA gene sequencing, and systematically assessed the quantity and identity of bacterial DNA in both specimen types. We compared bacteria detected in lung specimens to each other and to potential source communities: negative (background) control specimens and paired oral samples. By all measures, whole lung tissue in mice contained greater bacterial signal and less evidence of contamination than did BAL fluid. Relative to BAL fluid, whole lung tissue exhibited a greater quantity of bacterial DNA, distinct community composition, decreased sample-to-sample variation, and greater biological plausibility when compared to potential source communities. In contrast, bacteria detected in BAL fluid were minimally different from those of procedural, reagent, and sequencing controls. CONCLUSIONS An ecology-based analytical approach discriminates signal from noise in this low-biomass microbiome study and identifies whole lung tissue as the preferred specimen type for murine lung microbiome studies. Sequencing, analysis, and reporting of potential source communities, including negative control specimens and contiguous biological sites, are crucial for biological interpretation of low-biomass microbiome studies, independent of specimen type. Video abstract.
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Affiliation(s)
- Jennifer M Baker
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA
| | - Kevin J Hinkle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA
| | - Roderick A McDonald
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA
| | - Christopher A Brown
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA
| | - Nicole R Falkowski
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA
| | - Gary B Huffnagle
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA
- Department of Molecular, Cellular, & Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Robert P Dickson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA.
- Michigan Center for Integrative Research in Critical Care, Ann Arbor, MI, USA.
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46
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DeMerle KM, Angus DC, Baillie JK, Brant E, Calfee CS, Carcillo J, Chang CCH, Dickson R, Evans I, Gordon AC, Kennedy J, Knight JC, Lindsell CJ, Liu V, Marshall JC, Randolph AG, Scicluna BP, Shankar-Hari M, Shapiro NI, Sweeney TE, Talisa VB, Tang B, Thompson BT, Tsalik EL, van der Poll T, van Vught LA, Wong HR, Yende S, Zhao H, Seymour CW. Sepsis Subclasses: A Framework for Development and Interpretation. Crit Care Med 2021; 49:748-759. [PMID: 33591001 PMCID: PMC8627188 DOI: 10.1097/ccm.0000000000004842] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sepsis is defined as a dysregulated host response to infection that leads to life-threatening acute organ dysfunction. It afflicts approximately 50 million people worldwide annually and is often deadly, even when evidence-based guidelines are applied promptly. Many randomized trials tested therapies for sepsis over the past 2 decades, but most have not proven beneficial. This may be because sepsis is a heterogeneous syndrome, characterized by a vast set of clinical and biologic features. Combinations of these features, however, may identify previously unrecognized groups, or "subclasses" with different risks of outcome and response to a given treatment. As efforts to identify sepsis subclasses become more common, many unanswered questions and challenges arise. These include: 1) the semantic underpinning of sepsis subclasses, 2) the conceptual goal of subclasses, 3) considerations about study design, data sources, and statistical methods, 4) the role of emerging data types, and 5) how to determine whether subclasses represent "truth." We discuss these challenges and present a framework for the broader study of sepsis subclasses. This framework is intended to aid in the understanding and interpretation of sepsis subclasses, provide a mechanism for explaining subclasses generated by different methodologic approaches, and guide clinicians in how to consider subclasses in bedside care.
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Affiliation(s)
- Kimberley M DeMerle
- Department of Critical Care Medicine, The Clinical Research, Investigation, and Systems Modeling of Acute illness (CRISMA) Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Derek C Angus
- Department of Critical Care Medicine, The Clinical Research, Investigation, and Systems Modeling of Acute illness (CRISMA) Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - J Kenneth Baillie
- Anaesthesia, Critical Care, and Pain Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Emily Brant
- Department of Critical Care Medicine, The Clinical Research, Investigation, and Systems Modeling of Acute illness (CRISMA) Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Carolyn S Calfee
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA
| | - Joseph Carcillo
- Division of Pediatric Critical Care Medicine, Department of Critical Care Medicine, Children's Hospital of Pittsburgh, Pittsburgh, PA
| | - Chung-Chou H Chang
- Department of Critical Care Medicine, The Clinical Research, Investigation, and Systems Modeling of Acute illness (CRISMA) Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Robert Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Idris Evans
- Department of Critical Care Medicine, The Clinical Research, Investigation, and Systems Modeling of Acute illness (CRISMA) Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Anthony C Gordon
- Division of Anaesthetics, Pain Medicine, and Intensive Care, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jason Kennedy
- Department of Critical Care Medicine, The Clinical Research, Investigation, and Systems Modeling of Acute illness (CRISMA) Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Vincent Liu
- Kaiser Permanente Division of Research, Oakland, CA
| | - John C Marshall
- Keenan Research Centre for Biomedical Science, St Michael's Hospital, Toronto, ON, Canada
| | - Adrienne G Randolph
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA
| | - Brendon P Scicluna
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Manu Shankar-Hari
- Guy's and St Thomas' NHS Foundation Trust, ICU support Offices, St Thomas' Hospital, London, United Kingdom
- School of Immunology and Microbial Sciences, Kings College London, London, United Kingdom
| | - Nathan I Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | | | - Victor B Talisa
- Department of Critical Care Medicine, The Clinical Research, Investigation, and Systems Modeling of Acute illness (CRISMA) Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Benjamin Tang
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, NSW, Australia
| | - B Taylor Thompson
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Ephraim L Tsalik
- Department of Medicine, Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Lonneke A van Vught
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hector R Wong
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Cincinnati, OH
| | - Sachin Yende
- Department of Critical Care Medicine, The Clinical Research, Investigation, and Systems Modeling of Acute illness (CRISMA) Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Huiying Zhao
- Department of Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Christopher W Seymour
- Department of Critical Care Medicine, The Clinical Research, Investigation, and Systems Modeling of Acute illness (CRISMA) Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
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47
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Fromentin M, Ricard JD, Roux D. Respiratory microbiome in mechanically ventilated patients: a narrative review. Intensive Care Med 2021; 47:292-306. [PMID: 33559707 PMCID: PMC7871139 DOI: 10.1007/s00134-020-06338-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022]
Abstract
The respiratory microbiome has been less explored than the gut microbiome. Despite the speculated importance of dysbiosis of the microbiome in ventilator-associated pneumonia (VAP) and acute respiratory distress syndrome (ARDS), only few studies have been performed in invasively ventilated ICU patients. And only the results of small cohorts have been published. An overlap exists between bacterial populations observed in the lower respiratory tract and the oropharyngeal tract. The bacterial microbiota is characterized by relatively abundant bacteria difficult to cultivate by standard methods. Under mechanical ventilation, a dysbiosis occurs with a drop overtime in diversity. During VAP development, lung dysbiosis is characterized by a shift towards a dominant bacterial pathogen (mostly Proteobacteria) whereas enrichment of gut-associated bacteria mainly Enterobacteriaceae is the specific feature discriminating ARDS patients. However, the role of this dysbiosis in VAP and ARDS pathogenesis is not yet fully understood. A more in-depth analysis of the interplay between bacteria, virus and fungi and a better understanding of the host-microbiome interaction could provide a more comprehensive view of the role of the microbiome in VAP and ARDS pathogenesis. Priority should be given to validate a consensual and robust methodology for respiratory microbiome research and to conduct longitudinal studies. A deeper understanding of microbial interplay should be a valuable guide for care of ARDS and VAP preventive/therapeutic strategies. We present a review on the current knowledge and expose perspectives and potential clinical applications of respiratory microbiome research in mechanically ventilated patients.
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Affiliation(s)
- Mélanie Fromentin
- Anesthesiology and Intensive Care Department, AP-HP, Hôpital Cochin, 75014, Paris, France.,UMR1137 IAME, INSERM, Université de Paris, 75018, Paris, France
| | - Jean-Damien Ricard
- Médecine Intensive Réanimation, DMU ESPRIT, AP-HP, Hôpital Louis Mourier, 92700, Colombes, France.,UMR1137 IAME, INSERM, Université de Paris, 75018, Paris, France
| | - Damien Roux
- Médecine Intensive Réanimation, DMU ESPRIT, AP-HP, Hôpital Louis Mourier, 92700, Colombes, France. .,UMR1137 IAME, INSERM, Université de Paris, 75018, Paris, France.
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48
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Dumont-Leblond N, Veillette M, Racine C, Joubert P, Duchaine C. Development of a robust protocol for the characterization of the pulmonary microbiota. Commun Biol 2021; 4:164. [PMID: 33547364 PMCID: PMC7864980 DOI: 10.1038/s42003-021-01690-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
The lack of methodological standardization diminishes the validity of results obtained and the conclusions drawn when studying the lung microbiota. We report the validation of a complete 16S rRNA gene amplicon sequencing workflow, from patient recruitment to bioinformatics, tailored to the constrains of the pulmonary environment. We minimize the impact of contaminants and establish negative controls to track and account for them at every step. Enzymatic and mechanical homogenization combined to commercially available extraction kits allow for a fast and reliable extraction of bacterial DNA. The DNA extraction kits have a significant impact on the bacterial composition of the controls. The bacterial signatures of extracted cancerous and healthy human tissues from 5 patients are highly distinguishable from methodological controls. Our work expands our understanding of low microbial burdened environments analysis. This article is to be a starting point towards methodological standardization and the implementation of proper sampling procedures in the study of lung microbiota. Nathan Dumont-Leblond et al. present a protocol for lung microbiota analysis, including all steps from patient recruitment to bioinformatics. The data show how methodological variation, such as use of different DNA extraction kits, can impact the results and represent an important step toward methods standardization in the pulmonary microbiome field.
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Affiliation(s)
- Nathan Dumont-Leblond
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada.,Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada
| | - Marc Veillette
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - Christine Racine
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - Philippe Joubert
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval, Quebec City, QC, Canada
| | - Caroline Duchaine
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada. .,Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada.
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49
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Heijnen NFL, Hagens LA, Smit MR, Schultz MJ, van der Poll T, Schnabel RM, van der Horst ICC, Dickson RP, Bergmans DCJJ, Bos LDJ. Biological subphenotypes of acute respiratory distress syndrome may not reflect differences in alveolar inflammation. Physiol Rep 2021; 9:e14693. [PMID: 33547768 PMCID: PMC7865405 DOI: 10.14814/phy2.14693] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 12/12/2022] Open
Abstract
Biological subphenotypes have been identified in acute respiratory distress syndrome (ARDS) based on two parsimonious models: the "uninflamed" and "reactive" subphenotype (cluster-model) and "hypo-inflammatory" and "hyper-inflammatory" (latent class analysis (LCA) model). The distinction between the subphenotypes is mainly driven by inflammatory and coagulation markers in plasma. However, systemic inflammation is not specific for ARDS and it is unknown whether these subphenotypes also reflect differences in the alveolar compartment. Alveolar inflammation and dysbiosis of the lung microbiome have shown to be important mediators in the development of lung injury. This study aimed to determine whether the "reactive" or "hyper-inflammatory" biological subphenotype also had higher concentrations of inflammatory mediators and enrichment of gut-associated bacteria in the lung. Levels of alveolar inflammatory mediators myeloperoxidase (MPO), surfactant protein D (SPD), interleukin (IL)-1b, IL-6, IL-10, IL-8, interferon gamma (IFN-ƴ), and tumor necrosis factor-alpha (TNFα) were determined in the mini-BAL fluid. Key features of the lung microbiome were measured: bacterial burden (16S rRNA gene copies/ml), community diversity (Shannon Diversity Index), and community composition. No statistically significant differences between the "uninflamed" and "reactive" ARDS subphenotypes were found in a selected set of alveolar inflammatory mediators and key features of the lung microbiome. LCA-derived subphenotypes and stratification based on cause of ARDS (direct vs. indirect) showed similar profiles, suggesting that current subphenotypes may not reflect the alveolar host response. It is important for future research to elucidate the pulmonary biology within each subphenotype properly, which is arguably a target for intervention.
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Affiliation(s)
- Nanon F. L. Heijnen
- Department of Intensive CareMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Laura A. Hagens
- Department of Intensive CareAmsterdam University Medical CentersLocation Academic Medical CenterAmsterdamThe Netherlands
| | - Marry R. Smit
- Department of Intensive CareAmsterdam University Medical CentersLocation Academic Medical CenterAmsterdamThe Netherlands
| | - Marcus J. Schultz
- Department of Intensive CareAmsterdam University Medical CentersLocation Academic Medical CenterAmsterdamThe Netherlands
- Laboratory of Experimental Intensive Care and Anesthesiology (L·E·I·C·A)Academic Medical CentersLocation Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
- Mahidol‐Oxford Tropical Medicine Research Unit (MORU)Mahidol UniversityBangkokThailand
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Tom van der Poll
- Center for Experimental and Molecular MedicineAmsterdam University Medical CentersLocation Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
- Division of Infectious DiseasesAmsterdam University Medical CentersLocation Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Ronny M. Schnabel
- Department of Intensive CareMaastricht University Medical Center+MaastrichtThe Netherlands
| | | | - Robert P. Dickson
- Division of Pulmonary and Critical Care MedicineDepartment of Internal MedicineUniversity of Michigan Medical SchoolAnn ArborMIUSA
- Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn ArborMIUSA
- Michigan Center for Integrative Research in Critical CareAnn ArborMIUSA
| | | | - Lieuwe D. J. Bos
- Department of Intensive CareAmsterdam University Medical CentersLocation Academic Medical CenterAmsterdamThe Netherlands
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50
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Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A, McVerry BJ. Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients. Am J Respir Crit Care Med 2021; 202:1666-1677. [PMID: 32717152 DOI: 10.1164/rccm.201912-2441oc] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Rationale: Host inflammatory responses have been strongly associated with adverse outcomes in critically ill patients, but the biologic underpinnings of such heterogeneous responses have not been defined.Objectives: We examined whether respiratory tract microbiome profiles are associated with host inflammation and clinical outcomes of acute respiratory failure.Methods: We collected oral swabs, endotracheal aspirates (ETAs), and plasma samples from mechanically ventilated patients. We performed 16S ribosomal RNA gene sequencing to characterize upper and lower respiratory tract microbiota and classified patients into host-response subphenotypes on the basis of clinical variables and plasma biomarkers of innate immunity and inflammation. We derived diversity metrics and composition clusters with Dirichlet multinomial models and examined our data for associations with subphenotypes and clinical outcomes.Measurements and Main Results: Oral and ETA microbial communities from 301 mechanically ventilated subjects had substantial heterogeneity in α and β diversity. Dirichlet multinomial models revealed a cluster with low α diversity and enrichment for pathogens (e.g., high Staphylococcus or Pseudomonadaceae relative abundance) in 35% of ETA samples, associated with a hyperinflammatory subphenotype, worse 30-day survival, and longer time to liberation from mechanical ventilation (adjusted P < 0.05), compared with patients with higher α diversity and relative abundance of typical oral microbiota. Patients with evidence of dysbiosis (low α diversity and low relative abundance of "protective" oral-origin commensal bacteria) in both oral and ETA samples (17%, combined dysbiosis) had significantly worse 30-day survival and longer time to liberation from mechanical ventilation than patients without dysbiosis (55%; adjusted P < 0.05).Conclusions: Respiratory tract dysbiosis may represent an important, modifiable contributor to patient-level heterogeneity in systemic inflammatory responses and clinical outcomes.
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Affiliation(s)
- Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Center for Medicine and the Microbiome
| | - Haopu Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Department of Computational and Systems Biology, and.,Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Libing Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Center for Medicine and the Microbiome.,Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Shulin Qin
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Center for Medicine and the Microbiome
| | | | - Xiao-Hong Wang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center
| | - Katherine Fair
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center
| | - John Evankovich
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center
| | - Faraaz Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,School of Medicine, Tsinghua University, Beijing, China; and
| | - Kelvin Li
- Center for Medicine and the Microbiome
| | - Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Center for Medicine and the Microbiome
| | | | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Center for Medicine and the Microbiome.,Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Center for Medicine and the Microbiome
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