scholarly journals Functional profiling of COVID-19 respiratory tract microbiomes

2020 ◽  
Author(s):  
Niina Haiminen ◽  
Filippo Utro ◽  
Ed Seabolt ◽  
Laxmi Parida
Keyword(s):  
Functional Analysis ◽  
Respiratory Tract ◽  
Lavage Fluid ◽  
Community Acquired Pneumonia ◽  
The Body ◽  
Sequencing Data ◽  
Host Interactions ◽  
Global Pandemic ◽  
Functional Profiling ◽  
Functional Features

ABSTRACTIn response to the ongoing global pandemic, progress has been made in understanding the molecular-level host interactions of the new coronavirus SARS-CoV-2 responsible for COVID-19. However, when the virus enters the body it interacts not only with the host but also with the micro-organisms already inhabiting the host. Understanding the virus-host-microbiome interactions can yield additional insights into the biological processes perturbed by viral invasion. With this aim we carry out a functional analysis of previously published RNA sequencing data of bronchoalveolar lavage fluid from eight COVID-19 patients, twenty-five community-acquired pneumonia patients, and twenty healthy controls. The resulting microbiome functional profiles and their top differentiating features clearly separate the cohorts. By examining the functional features in connection with their associated metabolic pathways, differentially abundant pathways are indicated, compared to both the community-acquired pneumonia and healthy cohorts. From this analysis, distinguishing signatures in COVID-19 respiratory tract microbiomes are identified, including decreased lipid and glycan metabolism pathways, and increased carbohydrate metabolism pathways. Here we present a framework for comparative functional analysis of microbiomes, the results from which can lead to new hypotheses on the host-microbiome interactions in healthy versus afflicted cohorts. The findings from this analysis call for further research on microbial functions and host-microbiome interactions during SARS-CoV-2 infection.

scholarly journals Functional profiling of COVID-19 respiratory tract microbiomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Niina Haiminen ◽  
Filippo Utro ◽  
Ed Seabolt ◽  
Laxmi Parida
Keyword(s):  
Respiratory Tract ◽  
Carbohydrate Metabolism ◽  
Lower Respiratory Tract ◽  
Viral Infections ◽  
Lavage Fluid ◽  
Degradation Pathway ◽  
Community Acquired Pneumonia ◽  
The Body ◽  
Sequencing Data ◽  
Functional Profiling

AbstractIn response to the ongoing global pandemic, characterizing the molecular-level host interactions of the new coronavirus SARS-CoV-2 responsible for COVID-19 has been at the center of unprecedented scientific focus. However, when the virus enters the body it also interacts with the micro-organisms already inhabiting the host. Understanding the virus-host-microbiome interactions can yield additional insights into the biological processes perturbed by viral invasion. Alterations in the gut microbiome species and metabolites have been noted during respiratory viral infections, possibly impacting the lungs via gut-lung microbiome crosstalk. To better characterize microbial functions in the lower respiratory tract during COVID-19 infection, we carry out a functional analysis of previously published metatranscriptome sequencing data of bronchoalveolar lavage fluid from eight COVID-19 cases, twenty-five community-acquired pneumonia patients, and twenty healthy controls. The functional profiles resulting from comparing the sequences against annotated microbial protein domains clearly separate the cohorts. By examining the associated metabolic pathways, distinguishing functional signatures in COVID-19 respiratory tract microbiomes are identified, including decreased potential for lipid metabolism and glycan biosynthesis and metabolism pathways, and increased potential for carbohydrate metabolism pathways. The results include overlap between previous studies on COVID-19 microbiomes, including decrease in the glycosaminoglycan degradation pathway and increase in carbohydrate metabolism. The results also suggest novel connections to consider, possibly specific to the lower respiratory tract microbiome, calling for further research on microbial functions and host-microbiome interactions during SARS-CoV-2 infection.

Functional analysis of chondroitin 4 sulfate constituting osseointegration

Impact ◽  
2019 ◽  
Vol 2019 (8) ◽  
pp. 18-20
Author(s):  
Shuhei Tsuchiya
Keyword(s):  
Functional Analysis ◽  
Extracellular Matrix ◽  
Dental Implants ◽  
Maxillofacial Surgery ◽  
The Body ◽  
Oral And Maxillofacial Surgery ◽  
Direct Connection ◽  
Tooth Replacement ◽  
Living Bone ◽  
Natural Tooth

Osseointegration can be defined as a direct connection, both structural and functional, between living bone and the surface of an artificial implant. Indeed, the word comes from the Greek term for 'bone' and 'to make whole'. In dentistry, once dental implants are placed, the body will react with osseointegration, enabling the implants to become a permanent part of the jaw. There are many benefits to this type of implant, compared with traditional tooth replacement options, not least that dental implants mimic the strength and functionality of a natural tooth. Dr Shuhei Tsuchiya is a researcher based in the Division of Oral and Maxillofacial Surgery at Nagoya University, Japan, who is interested in a range of areas, including regenerative medicine and the extracellular matrix. One of his key preoccupations, though, is shedding light on osseointegration. He and his team are working to unravel the mysteries of the mechanism.

Respiratory tract damage with bocavirus infection in children

2020 ◽  
Vol 19 (2) ◽  
pp. 14-18
Author(s):  
E. V. Sharipova ◽  
I. V. Babachenko ◽  
M. A. Shcherbatyh
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Clinical Manifestations ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Human Bocavirus ◽  
Long Time ◽  
Clinically Significant ◽  
Tract Infections ◽  
Tract Damage

Long time the main pathogens associated with the development of community-acquired pneumonia were bacteria. However, in recent years in the Russian Federation, like all over the world, the view of the damage of lower respiratory tract changed, including a unique approach to community-acquired pneumonia as a bacterial infection, and respiratory viruses have become seen as a direct cause of lower respiratory tract damage, or as part of a viral-bacterial co-infection. These studies became possible since the widespread introduction of PCR techniques in the clinical setting, identification of respiratory viruses has increased and new microorganisms such, one as human bocavirus have been discovered. Objective: to study the features of respiratory tract damage in acute bocavirus infection in children of different ages. Materials and methods: A retrospective analysis of 97 medical hospital documentation of children with acute bocavirus infection, detected confirmed by PCR in nasopharyngeal aspirate. Results: In this work, it was shown that human bocavirus spread throughout the year with an increase in the incidence of clinically significant forms in the autumnwinter period, including during the period of an increase in the incidence of influenza. HBoV infection requiring hospitals is most significant in the first three years of life. In 74.2% of hospitalized children, bocavirus infection occurs with lower respiratory tract infections in the form of bronchitis — 77.8%, pneumonia — 28.9% and rarely bronchiolitis and is complicated by the development of respiratory failure in 28.9% of cases. Changes in the blood test are non-specific, and the level of C-reactive protein in children with various clinical manifestations of HBoV infection generally does not exceed 50 mg / l. An x-ray of the chest organs does not objectively reflect the existing volume and nature of the inflammatory process in the lungs.

scholarly journals Respiratory tract infections in children with allergic asthma on allergen immunotherapy during influenza season

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuyun Li ◽  
Dongming Wang ◽  
Lili Zhi ◽  
Yunmei Zhu ◽  
Lan Qiao ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Allergic Asthma ◽  
Respiratory Tract Infections ◽  
Allergen Immunotherapy ◽  
Clinical Symptoms ◽  
Influenza Season ◽  
The Body ◽  
History Of ◽  
Tract Infections ◽  
Stage 1

AbstractTo describle how respiratory tract infections (RTIs) that occurred in children with allergic asthma (AA) on allergen immunotherapy (AIT) during an influenza season. Data including clinical symptoms and treatment history of children (those with AA on AIT and their siblings under 14 years old), who suffered from RTIs during an influenza season (Dec 1st, 2019–Dec 31st, 2019), were collected (by face to face interview and medical records) and analyzed. Children on AIT were divided into 2 groups: stage 1 (dose increasing stage) and stage 2 (dose maintenance stage). Their siblings were enrolled as control. During the study period, 49 children with AA on AIT (33 patients in stage 1 and 16 patients in stage 2) as well as 49 children without AA ( their siblings ) were included. There were no significant differences in occurrences of RTIs among the three groups (p > 0.05). Compared with children in the other two groups, patients with RTIs in stage 2 had less duration of coughing and needed less medicine. Children on AIT with maintenance doses had fewer symptoms and recovered quickly when they were attacked by RTIs, which suggested that AIT with dose maintenance may enhance disease resistance of the body.

scholarly journals A deep learning integrated radiomics model for identification of coronavirus disease 2019 using computed tomography

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiaoguo Zhang ◽  
Dawei Wang ◽  
Jiang Shao ◽  
Song Tian ◽  
Weixiong Tan ◽  
...  
Keyword(s):  
Deep Learning ◽  
Ct Images ◽  
Community Acquired Pneumonia ◽  
Machine Learning Algorithms ◽  
Multi Layer Perceptron ◽  
Selection Methods ◽  
Medical Centers ◽  
Global Pandemic ◽  
Diagnostic Time ◽  
Logistic Regression Classifier

AbstractSince its first outbreak, Coronavirus Disease 2019 (COVID-19) has been rapidly spreading worldwide and caused a global pandemic. Rapid and early detection is essential to contain COVID-19. Here, we first developed a deep learning (DL) integrated radiomics model for end-to-end identification of COVID-19 using CT scans and then validated its clinical feasibility. We retrospectively collected CT images of 386 patients (129 with COVID-19 and 257 with other community-acquired pneumonia) from three medical centers to train and externally validate the developed models. A pre-trained DL algorithm was utilized to automatically segment infected lesions (ROIs) on CT images which were used for feature extraction. Five feature selection methods and four machine learning algorithms were utilized to develop radiomics models. Trained with features selected by L1 regularized logistic regression, classifier multi-layer perceptron (MLP) demonstrated the optimal performance with AUC of 0.922 (95% CI 0.856–0.988) and 0.959 (95% CI 0.910–1.000), the same sensitivity of 0.879, and specificity of 0.900 and 0.887 on internal and external testing datasets, which was equivalent to the senior radiologist in a reader study. Additionally, diagnostic time of DL-MLP was more efficient than radiologists (38 s vs 5.15 min). With an adequate performance for identifying COVID-19, DL-MLP may help in screening of suspected cases.

scholarly journals EXPRESS: Retrospective study of clinical characteristics and viral etiologies of patients with viral pneumonia in Beijing

2021 ◽  
pp. 204589402110110
Author(s):  
Xiang Zhao ◽  
Yao Meng ◽  
Duo Li ◽  
Zhaomin Feng ◽  
Weijuan Huang ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Influenza A ◽  
Clinical Characteristics ◽  
Ebola Virus ◽  
Treatment Strategies ◽  
Lavage Fluid ◽  
Viral Pneumonia ◽  
Chip Technology ◽  
Viral Influenza ◽  
Simplex Virus

Aims: The virus is common in patients with viral pneumonia. However, the viral etiology and clinical features of patients with viral pneumonia in China remain unclear. The main purpose of this study was to analyze the viral causes and epidemiology of patients with viral pneumonia in Beijing, which can significantly improve the pertinence and accuracy of clinical treatment of the disease. Methods: Firstly, 1,539 respiratory specimens of pneumonia (oropharyngeal swabs, nasopharyngeal swabs, saliva samples and bronchoalveolar lavage fluid) were collected from 19 hospitals in Beijing from September 2015 to August 2018. Then, TaqMan low-density microfluidic chip technology was used to detect viral pneumonia specimens in 1,539 respiratory tract specimens of pneumonia, and determine the types of viral bacteria in them. Lastly, the analysis of demographic, clinical and etiological data of patients with viral pneumonia was performed. Results: The results showed that among the 1,539 respiratory tract specimens with pneumonia, 760 were detected as viral pneumonia specimens, with a positive rate of 49.4%. Among which, 467 were infected with mono-viral and 293 were infected with multi-viral. Influenza A virus (Flu A), mycoplasma pneumoniae (MPn), ebola virus (EBV) and herpes simplex virus type 1 (HSV-1) were the major viral components in the samples of these patients. Furthermore, these viral species were significantly associated with sample sources, onset season and certain clinical characteristics. Discussion: Our findings may provide corresponding treatment strategies for viral pneumonia patients infected with specific viruses.

scholarly journals Evaluation of LBM415 (NVP PDF-713), a Novel Peptide Deformylase Inhibitor, for Treatment of Experimental Mycoplasma pneumoniae Pneumonia

2005 ◽  
Vol 49 (10) ◽  
pp. 4128-4136 ◽  
Author(s):  
Monica Fonseca-Aten ◽  
Christine M. Salvatore ◽  
Asunción Mejías ◽  
Ana M. Ríos ◽  
Susana Chávez-Bueno ◽  
...  
Keyword(s):  
Bronchoalveolar Lavage ◽  
Mycoplasma Pneumoniae ◽  
Bronchoalveolar Lavage Fluid ◽  
Lavage Fluid ◽  
Placebo Treatment ◽  
Community Acquired Pneumonia ◽  
Peptide Deformylase ◽  
Necrosis Factor Alpha ◽  
Days Of Therapy ◽  
Ifn Γ

ABSTRACT Mycoplasma pneumoniae is a major cause of community-acquired pneumonia. We evaluated the efficacy of LBM415, a novel peptide deformylase inhibitor antimicrobial agent, for the treatment of M. pneumoniae pneumonia in a mouse model. Eight-week-old BALB/c mice were intranasally inoculated once with 107 CFU of M. pneumoniae. Groups of mice were treated with LBM415 (50 mg/kg of body weight) or placebo subcutaneously daily for 13 days, starting 24 h after inoculation. Groups of mice were evaluated at the baseline; at days of treatment 1, 3, 6, and 13; and at 7 days after treatment. The MIC of LBM415 against M. pneumoniae was <0.005 μg/ml. LBM415-treated mice had significantly lower bronchoalveolar lavage fluid M. pneumoniae concentrations than placebo-treated mice on days 6 and 13 of treatment. Compared with placebo treatment, therapy with LBM415 significantly decreased lung histopathology scores at days 3, 6, and 13 of treatment and at 7 days after treatment. Airway obstruction was significantly lower in LBM415-treated mice than in placebo-treated mice on days 1, 3, and 6 of treatment and after 7 days of therapy, while airway hyperresponsiveness was significantly lower only on day 3 of therapy. The bronchoalveolar lavage fluid concentrations of tumor necrosis factor alpha, gamma interferon (IFN-γ), interleukin-6 (IL-6), IL-12, KC (functional IL-8), monocyte chemotactic protein 1, macrophage inflammatory protein 1α, monokine induced by IFN-γ, and IFN-inducible protein 10 were significantly reduced in LBM415-treated mice compared with the levels in placebo-treated mice. There were no differences in the bronchoalveolar lavage fluid concentrations of granulocyte-macrophage colony-stimulating factor, IL-1β, IL-2, IL-4, IL-5, and IL-10 between the two groups of mice. LBM415 therapy had beneficial microbiologic, histologic, respiratory, and immunologic effects on acute murine M. pneumoniae pneumonia.

Respiratory disease in foreign body aspiration in children

1927 ◽  
Vol 23 (11) ◽  
pp. 1145-1150
Author(s):  
G. M. Lopatin
Keyword(s):  
Foreign Body ◽  
Respiratory Tract ◽  
Respiratory Disease ◽  
Foreign Bodies ◽  
Foreign Body Aspiration ◽  
The Body ◽  
Different Parts

Aspiration of foreign bodies into the windpipe usually results in respiratory damage. This lesion may be of varying intensity and may be localized in different parts of the respiratory tract or lungs. Both the intensity and the localization of the lesion may depend on a number of reasons and above all on the location of the foreign body and its type, but also on the constitutional characteristics of the body and on many other causes. Aspirated foreign bodies are found in the trachea or larynx and almost as often in the bronchi.

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