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.

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 Results of Detecting SARS-CoV-2 and Other Pathogens of Community-Acquired Pneumonia by PCR in the Tyumen Region

2020 ◽  
pp. 146-149
Author(s):  
I. V. Bakshtanovskaya ◽  
T. F. Stepanova ◽  
G. V. Sharukho ◽  
A. N. Letyushev ◽  
K. B. Stepanova ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Respiratory Tract ◽  
Mycoplasma Pneumoniae ◽  
Causative Agent ◽  
Lower Respiratory Tract ◽  
Viral Infections ◽  
Respiratory Infections ◽  
Bacterial Pathogens ◽  
Community Acquired Pneumonia ◽  
Respiratory Viral Infections

The aim of this work was to identify the causative agent of community-acquired pneumonia and coinfection using PCR study of biomaterial from patients.Materials and methods. PCR testing of 268 samples from 258 patients was carried out to identify RNA/DNA of viral and bacterial pathogens of respiratory infections.Results and discussion. In 43.3 % of samples SARS-CoV-2 RNA was detected, in 4.5 % – RNA/DNA of acute respiratory viral infections pathogens, in one sample – DNA of Mycoplasma pneumoniae. Co-infection was detected only in patients of the anti-tuberculosis dispensary (SARS-CoV-2 and Mycobacterium tuberculosis). In the examined patients with pneumonia, SARS-CoV-2 RNA was significantly more often detected in biomaterial from the lower respiratory tract (52 %) than in respiratory smears (8.5 %). In the first week from the onset of the disease, 19.2 % of positive samples were found, in the second – 56.5 %. 

scholarly journals Respiratory viral infections in the lower respiratory tract failure (Literature review)

2021 ◽  
Vol 13 (4) ◽  
pp. 5-13
Author(s):  
I. V. Babachenko ◽  
E. A. Kozyrev ◽  
E. V. Sharipova ◽  
E. D. Orlova ◽  
N. S. Tian
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Viral Infections ◽  
Community Acquired Pneumonia ◽  
Laboratory Diagnostics ◽  
Bacterial Strains ◽  
Lower Respiratory Tract Disease ◽  
Coronavirus Infection ◽  
Tract Disease

The sharp increase in viral pneumonia against the background of the pandemic of the new coronavirus infection SARS-CoV-2 requires more attention to the study of the role of viruses in damage to the lower respiratory tract, including their etiological significance in the development of community-acquired pneumonia. Modern possibilities of laboratory diagnostics make it possible not only to identify and study respiratory viruses, but also to help differentiate active viral infections as a cause of lower respiratory tract disease from virus carriers. The review describes the epidemiological and clinical features of the most relevant or less studied pneumotropic viral infections in children (respiratory syncytial, adenovirus, bocavirus, metapneumovirus), including their role in the etiology of pneumonia in children. Understanding the viral etiology of pneumonia in children will reduce the antibacterial load, which will help to reduce the side effects of chemotherapy and slow the emergence of antimicrobialresistant bacterial strains.

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.

A One Health Approach to Simple Liquid Sample Handling for Respiratory Based -Omics Analysis; Tracheal Wash and Bronchoalveolar Lavage Fluid

2021 ◽  
Author(s):  
Anna E. Karagianni ◽  
Samantha L. Eaton ◽  
Dominic Kurian ◽  
Eugenio Cillán-Garcia ◽  
Jonathan Twynam-Perkins ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Bronchoalveolar Lavage ◽  
Airway Inflammation ◽  
Lower Respiratory Tract ◽  
Bronchoalveolar Lavage Fluid ◽  
Lavage Fluid ◽  
Lower Airway ◽  
Simple Liquid ◽  
Sample Handling ◽  
Sequential Screening

Abstract Airway inflammation is highly prevalent in horses, with the majority of non-infectious cases being defined as equine asthma. Currently, cytological analysis of airway derived samples is the principal method of assessing lower airway inflammation. Samples can be obtained by tracheal wash (TW) or by lavage of the lower respiratory tract (bronchoalveolar lavage fluid; BALF). Although BALF cytology carries significant diagnostic advantages over TW cytology, sample acquisition is invasive, making it prohibitive for routine and sequential-screening of airway health. The aim of this study was to establish a robust protocol to isolate macrophages, protein and RNA for molecular characterisation of TW samples and demonstrate the applicability of sample handling to rodent and human pediatric bronchoalveolar lavage fluid isolates. TW samples provided a good quality and yield of both RNA and protein for downstream transcriptomic/proteomic analyses. The sample handling methodologies were successfully applicable to BALF for rodent and human research. TW samples represent a rich source of airway cells, and molecular analysis to facilitate and study airway inflammation, based on both transcriptomic and proteomic analysis. This study provides a necessary methodological platform for future transcriptomic and/or proteomic studies on equine lower respiratory tract secretions and BALF samples from humans and mice.

Bacterial etiology of lower respiratory tract infection:a surveillance report from a Chinese large teaching hospital from 2015 to 2019

2020 ◽  
Author(s):  
zhen zhang ◽  
lei tian
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Bacterial Resistance ◽  
Lavage Fluid ◽  
Resistance Rate ◽  
Large Teaching Hospital ◽  
High Incidence ◽  
Positive Rate ◽  
Surveillance Report ◽  
Tract Infections

Abstract Background Sputum is the most common specimen type of lower respiratory tract in China, but its cultivation result is easily confused by the bacteria colonized in the oral cavity and pharynx. It is very difficult to evaluate the clinical significance of sputum culture results both for clinicians and microbiologists. Bronchoscope alveolus lavage fluid(BALF)is a good specimen, which can accurately reflect the situation of lower respiratory tract infections (LRIs). Methods The accumulated data of BALF culture and antimicrobial susceptibility test in our hospital from January 2015 to October 2019 were reviewed and analyzed. Results The positive rate of BALF culture in our hospital was 18.3% (3467/18935) in 2015–2019. The most common pathogens were Klebsiella pneumoniae (18.1%, 627/3467), Pseudomonas aeruginosa (16.9%, 587/3467) and Acinetobacter baumannii (14.0%, 485/3467). For the eight most common pathogens, 40–70 years old was the highest age of distribution, but for Escherichia coli and Streptococcus pneumoniae, 0–5 years old was also the higher age of distribution. The antibiotic resistance rate of K. pneumoniae to imipenem and meropenem was 30.6% and 30.8%, respectively. The sensitivity of P. aeruginosa to antibiotics other than minocycline and ticarcillin clavulanic acid was all more than 60%. However, the resistance rate of A. baumannii to antibiotics other than tegacyclin and minocycline was all more than 80%. Conclusions 40–70 years old was the high incidence age of lower respiratory tract bacterial infection. K. pneumoniae resistant to carbapenems (CR-K. pneumoniae) and A. baumannii were a great challenge to clinical treatment and bacterial resistance control.

scholarly journals Vaccine Effectiveness Against Influenza-Associated Lower Respiratory Tract Infections in Hospitalized Adults, Louisville, Kentucky, 2010–2013

2020 ◽  
Vol 7 (7) ◽  
Author(s):  
Eric J Chow ◽  
Melissa A Rolfes ◽  
Ruth L Carrico ◽  
Stephen Furmanek ◽  
Julio A Ramirez ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Community Acquired Pneumonia ◽  
Vaccine Effectiveness ◽  
Self Report ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
Radiographic Findings ◽  
History Of ◽  
Tract Infections

Abstract Background Preventing severe complications of influenza such as hospitalization is a public health priority; however, estimates of influenza vaccine effectiveness (VE) against influenza-associated acute lower respiratory tract infection (LRTI) hospitalizations are limited. We examined influenza VE against influenza-associated LRTIs in hospitalized adult patients. Methods We retrospectively analyzed data from a randomized trial of oseltamivir treatment in adults hospitalized with LRTI in Louisville, Kentucky, from 2010 to 2013. Patients were systematically tested for influenza at the time of enrollment. We estimated VE as 1 – the adjusted odds ratio (aOR) of antecedent vaccination in influenza-positives vs negatives × 100%. Vaccination status was obtained by patient self-report. Using logistic regression adjusting for age, sex, season, timing of illness, history of chronic lung disease, and activities of daily living, we estimated VE against hospitalized influenza-associated LRTIs and community-acquired pneumonia (CAP) with radiographic findings of infiltrate. Results Of 810 patients with LRTI (median age, 62 years), 184 (23%) were influenza-positive and 57% had radiographically confirmed CAP. Among influenza-positives and -negatives, respectively, 61% and 69% were vaccinated. Overall, 29% were hospitalized in the prior 90 days and >80% had comorbidities. Influenza-negatives were more likely to have a history of chronic obstructive pulmonary disease than influenza-positives (59% vs 48%; P = .01), but baseline medical conditions were otherwise similar. Overall, VE was 35% (95% CI, 4% to 56%) against influenza-associated LRTI and 51% (95% CI, 13% to 72%) against influenza-associated radiographically confirmed CAP. Conclusions Vaccination reduced the risk of hospitalization for influenza-associated LRTI and radiographically confirmed CAP. Clinicians should maintain high rates of influenza vaccination to prevent severe influenza-associated complications.

scholarly journals Metapneumovirus infection in children

2020 ◽  
Vol 11 (5) ◽  
pp. 13-19
Author(s):  
Elena V. Sharipova ◽  
Irina V. Babachenko ◽  
Elizaveta D. Orlova
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Viral Infections ◽  
Clinical Symptoms ◽  
Hospitalized Children ◽  
Lower Respiratory Tract Infections ◽  
Nucleic Acid Isolation ◽  
Hmpv Infection ◽  
Tract Infections

Objective: to study the clinical features of metapneumovirus infection in children of different ages in a hospital. Materials and methods. A retrospective analysis of medical records of 142 patients aged 1 month to 14 years inclusive who were hospitalized in the period from January 2012 to April 2019. Metapneumovirus infection was confirmed by hMPV nucleic acid isolation by PCR in nasopharyngeal smears. Results. Metapneumovirus infection is detected among hospitalized children with acute respiratory viral infections in 4,4% of cases. In the age structure, 72,2% are children under 4 years old, and the maximum incidence rate is among children aged 3 years of life. The leading clinical symptoms are cough in 93,0% of cases and rhinitis in 96,5% of cases.In 88,2% of children, the disease proceeds with an increase in temperature 38 C, including in 34,6% 39,5 C and above. Symptoms of gastrointestinal dysfunction in the form of vomiting and diarrhea develop in 26,1% and 22,5% of children, respectively. 78,2% of patients requiring hospitalization suffer hMPV infection with damage to the lower respiratory tract, including in the form of bronchitis in 85,6% of cases and pneumonia in 14,4% of cases. The disease is complicated by the development of bronchial obstructive syndrome in 38,7% and acute respiratory failure in 22,3% of cases. ARF and BOS are significantly more likely to develop in children of the first 3 years of life 71,0% versus 29,0% in children of the older age group (p = 0.038) and 69,8% against 30,2% (p = 0.007), respectively. In a clinical blood test for hMPV infection, leukopenia and leukocytosis are detected only in 3,5% and 12,7% of cases, respectively, as well as an increase in ESR in 23,9% of children. The level of CRP in the 93,0% of children was less than 20 mg/l. Conclusions. Virological confirmation of metapneumovirus infection in hospitalized children with lower respiratory tract infections contributes to the formation of an adequate therapeutic tactic.

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