scholarly journals Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children

2018 ◽  
Author(s):  
MS Zinter ◽  
CC Dvorak ◽  
MY Mayday ◽  
K Iwanaga ◽  
NP Ly ◽  
...  
Keyword(s):  
Pulmonary Disease ◽  
Pathogenic Bacteria ◽  
Alpha Diversity ◽  
Clinical Diagnostics ◽  
Reference Database ◽  
Metagenomic Sequencing ◽  
Dna Viruses ◽  
Cross Domain ◽  
Causes Of Disease ◽  
Increased Sensitivity

ABSTRACTRATIONALEDespite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant morbidity and mortality.OBJECTIVESTo develop a highly sensitive metagenomic next generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children.METHODSWe collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children’s hospitals from 2014-2016. Samples underwent mechanical homogenization, paired RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the NCBI nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort.MEASUREMENTS & MAIN RESULTSWe identified a rich cross-domain pulmonary microbiome containing bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median 0.58, IQR 0.33-0.62 vs. median 0.94, IQR 0.93-0.95, p<0.001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (p<0.001).CONCLUSIONSAn optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.

scholarly journals Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children

2018 ◽  
Vol 68 (11) ◽  
pp. 1847-1855 ◽  
Author(s):  
Matt S Zinter ◽  
Christopher C Dvorak ◽  
Madeline Y Mayday ◽  
Kensho Iwanaga ◽  
Ngoc P Ly ◽  
...  
Keyword(s):  
Pulmonary Disease ◽  
Pathogenic Bacteria ◽  
Alpha Diversity ◽  
Clinical Diagnostics ◽  
Reference Database ◽  
Metagenomic Sequencing ◽  
Dna Viruses ◽  
Cross Domain ◽  
Causes Of Disease ◽  
Increased Sensitivity

Abstract Background Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed to develop a highly sensitive metagenomic next-generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children. Methods We collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children’s hospitals from 2014–2016. Samples underwent mechanical homogenization, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the National Center for Biotechnology Information nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort. Results We identified a rich cross-domain pulmonary microbiome that contained bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median, 0.61; interquartile range [IQR], 0.33–0.72 vs median, 0.96; IQR, 0.94–0.96; P < .001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (P < .001). Conclusions An optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.

Some aspects of management of patients with occupational chronic obstructive pulmonary disease: the value of bronchoscopy

2020 ◽  
pp. 817-817
Author(s):  
M. L. Shteiner ◽  
A. V. Zhestkov ◽  
N. E. Lavrentieva
Keyword(s):  
Chronic Obstructive Pulmonary Disease ◽  
Pulmonary Disease ◽  
Biologically Active ◽  
Chronic Obstructive ◽  
Common Disease ◽  
Obstructive Pulmonary Disease ◽  
Production Factors ◽  
Causes Of Disease ◽  
Genetic And Environmental Factors ◽  
Active Substances

Chronic obstructive pulmonary disease is a common disease that could lead to death. Pathogenesis of COPD involves both genetic and environmental factors. Such unfavorable production factors as dust, smoke, toxic and biologically active substances are the causes of disease in 15% of cases.

scholarly journals Soil microbes and oxygen influence the changes in bacterial community composition during swine carcass decomposition

2021 ◽  
Author(s):  
Michelle Miguel ◽  
Seon Ho Kim ◽  
Sang Suk Lee ◽  
Yong Il Cho
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Community Composition ◽  
Soil Microbes ◽  
Close Association ◽  
Bacterial Community Composition ◽  
Alpha Diversity ◽  
Decomposition Process ◽  
Metagenomic Sequencing ◽  
Unsterilized Soil

Abstract Background Carcass decomposition is influenced by various factors such as temperature, humidity, microorganisms, invertebrates, and scavengers. Soil microbes play a significant role in the decomposition process. In this study, we investigated the changes in the bacterial community during carcass decomposition in soil with an intact microbial community and soil which was sterilized decomposed with and without oxygen access using 16s rRNA metagenomic sequencing. Results Based on the 16S rRNA metagenomic sequencing, a total of 988 operational taxonomic units (OTUs) representing 16 phyla and 533 genera were detected. The bacterial diversity varied across the based on the alpha diversity indices. The bacterial composition in the unsterilized soil – aerobic condition (U_A) and unsterilized soil – anaerobic condition (U_An) set-ups have higher alpha diversity than the other burial set-ups. Beta diversity analysis revealed a close association in the samples according to the burial type and decomposition day. Firmicutes was the dominant phylum across all samples regardless of the burial type and decomposition day. The bacterial community composition changed throughout the decomposition process in all burial set-up. Meanwhile, the genus Bacillus dominated the bacterial community towards the end of decomposition period. Conclusions Our results showed that bacterial community composition changed during carcass decomposition and was affected by the soil and oxygen access, with microorganisms belonging to phylum Firmicutes dominating the community.

scholarly journals Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1372
Author(s):  
Himansu Kumar ◽  
Yu Jang ◽  
Kwangmin Kim ◽  
Junhyung Park ◽  
Min Jung ◽  
...  
Keyword(s):  
16S Rrna ◽  
Crop Production ◽  
Pathogenic Bacteria ◽  
Storage Time ◽  
Pig Slurry ◽  
Metagenomic Sequencing ◽  
Bacterial Populations ◽  
Linear Discriminant ◽  
Kegg Pathways ◽  
Microbial Biomarkers

Traditionally slurry is used as source of nitrogen, phosphorous, and potassium in bio fertilizers to improve crop production. However, poorly managed slurry causes a hazardous effect to the environment by producing greenhouse gases, causing the eutrophication of water bodies, and polluting the groundwater. It has been largely reported that the microbial presence in slurry causing a diverse effect on its storage and disposal system. However, the diversity of bacterial populations in pig slurries remains largely unexplored. Here we report the bacterial diversity present in the slurry from slurry pits, and the effect of storage time on bacterial population. We collected 42 samples from three different pig slurry pits, as three replicates from each one until the 14th week. We used the 16S rRNA, Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) protocols for the metagenomic downstream analysis. Taxonomic annotation using the Greengenes metagenomic database indicated that on an average 76.2% Firmicutes, 14.4% Bacteroidetes, 4.9% Proteobacteria, etc. microbial populations were present. Comparative microbial analysis showed that the population of Firmicutes decreased from the first to the 14th week, whereas the population of Bacteroidetes increased from the first to the 14th week. Through principal coordinate analysis (PCoA), (linear discriminant analysis effect size (LEfSe), and Pearson’s correlation analysis, we found microbial biomarkers according to the storage time point. All bacterial populations were well clustered according to the early, middle, and last weeks of storage. LEfSe showed that Actinobacteria, Lachnospiraceae, Ruminococcaceae, and Bacteroidia are dominantly present in first, seventh, ninth, and 14th week, respectively. Lachnospiraceae and Ruminococcaceae are ubiquitous gastrointestinal non-pathogenic bacteria. KEGG pathways, such as membrane transport, carbohydrate and amino acid metabolism, genetic replication and repair, were significant among all samples. Such a KEGG pathway may indicate the association between the host organism’s metabolic activity and the microbes present in the gastro intestinal tract (GIT).

scholarly journals Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients

2020 ◽  
Vol 22 (2) ◽  
pp. 196-207 ◽  
Author(s):  
Sander van Boheemen ◽  
Anneloes L. van Rijn ◽  
Nikos Pappas ◽  
Ellen C. Carbo ◽  
Ruben H.P. Vorderman ◽  
...  
Keyword(s):  
Pediatric Patients ◽  
Metagenomic Sequencing ◽  
Dna Viruses ◽  
Combined Detection ◽  
Rna And Dna

scholarly journals Regulation of Brucella abortusCatalase

2000 ◽  
Vol 68 (7) ◽  
pp. 3861-3866 ◽  
Author(s):  
Jeong-a Kim ◽  
Zengyu Sha ◽  
John E. Mayfield
Keyword(s):  
Oxidative Stress ◽  
Hydrogen Peroxide ◽  
Pathogenic Bacteria ◽  
Sublethal Concentration ◽  
Subsequent Exposure ◽  
Catalase Peroxidase ◽  
Increased Sensitivity ◽  
Analysis Survival ◽  
Hostile Environments

ABSTRACT All aerobic organisms have mechanisms that protect against oxidative compounds. Catalase, peroxidase, superoxide dismutase, glutathione, and thioredoxin are widely distributed in many taxa and constitute elements of a nearly ubiquitous antioxidant metabolic strategy. Interestingly, the regulatory mechanisms that control these elements are rather different depending on the nature of the oxidative stress and the organism. Catalase is well documented to play an important role in protecting cells from oxidative stress. In particular, pathogenic bacteria seem to use this enzyme as a defensive tool against attack by the host. To investigate the significance of catalase in hostile environments, we made catalase deletion mutations in two different B. abortus strains and used two-dimensional gel analysis, survival tests, and adaptation experiments to explore the behavior and role of catalase under several oxidative stress conditions. These studies show that B. abortus strains that do not express catalase activity exhibit increased sensitivity to hydrogen peroxide. We also demonstrate that catalase expression is regulated in this species, and that preexposure to a sublethal concentration of hydrogen peroxide allows B. abortus to adapt so as to survive subsequent exposure to higher concentrations of hydrogen peroxide.

scholarly journals SlyA, a MarR Family Transcriptional Regulator, Is Essential for Virulence in Dickeya dadantii 3937

2009 ◽  
Vol 191 (17) ◽  
pp. 5409-5418 ◽  
Author(s):  
M. Manjurul Haque ◽  
M. Shahinur Kabir ◽  
Luqman Qurata Aini ◽  
Hisae Hirata ◽  
Shinji Tsuyumu
Keyword(s):  
Pathogenic Bacteria ◽  
Pectate Lyase ◽  
Transcriptional Regulator ◽  
Polymyxin B ◽  
In Planta ◽  
Cationic Antimicrobial Peptide ◽  
Dickeya Dadantii ◽  
Increased Sensitivity ◽  
Gene Deletion Mutant ◽  
And Oxidative Stress

ABSTRACT SlyA, a MarR family transcriptional regulator, controls an assortment of biological functions in several animal-pathogenic bacteria. In order to elucidate the functions of SlyA in the phytopathogen Dickeya dadantii (formerly Erwinia chrysanthemi) 3937, a slyA gene deletion mutant (denoted ΔslyA) was constructed. The mutant exhibited increased sensitivity to sodium hypochlorite, the cationic antimicrobial peptide polymyxin B, and oxidative stress. The mutant showed reduced production of pectate lyase and exopolysaccharide and an inability to form a pellicle. The mutant lacking a functional slyA gene showed a significantly reduced ability to cause maceration of potato tubers. Accordingly, the mutant exhibited significantly reduced bacterial growth and failed to hyperinduce pectate lyase production in planta. Introduction of a plasmid containing slyA into the ΔslyA mutant caused all of these phenotypes to recover to wild-type levels. These results suggest that SlyA plays an important role in virulence to plants by positively regulating the expression of multiple pathogenicity-related traits of D. dadantii 3937.

scholarly journals Complex approach to assessment of functional status of patients with chronic obstructive pulmonary disease

2021 ◽  
Vol 9 (4) ◽  
pp. 553-558
Author(s):  
Aleksey V. Kosyakov ◽  
Keyword(s):  
Chronic Obstructive Pulmonary Disease ◽  
Heart Rate ◽  
Functional Status ◽  
Pulmonary Disease ◽  
Clinical Diagnostics ◽  
Chronic Obstructive ◽  
Walk Test ◽  
Obstructive Pulmonary Disease ◽  
6 Minute Walk Test ◽  
Minute Walk

BACKGROUND: Considering the economic costs of managing patients with chronic obstructive pulmonary disease (COPD), as well as the high mortality and disability rate, it is necessary to improve the diagnosis of the disease, to look for new approaches to assessing the functional status of patients. AIM: Is to study the functional status of patients with COPD. MATERIALS AND METHODS: A comprehensive approach was applied to assess the functional status of patients: the data of the 6-minute walk test (6MWT), heart rate variability (HRV) was studied, ergoreflex was assessed according to HRV data. 64 patients with COPD and 41 male volunteers without respiratory diseases older than 40 years were examined. Statistical processing of the obtained results was carried out using the licensed package of applied statistical programs Excel 2010 and Statistica 10. RESULTS: The group of patients with COPD and the respondents of the control group were comparable in terms of body mass index, heart rate, respiratory rate, index of indicators of activity of regulatory systems (p > 0.05). As expected, during the 6MWT, differences were obtained between the studied groups in terms of the distance covered (p < 0.01). Similarly, the results of the study of the function of external respiration showed a statistically significant difference in all the studied parameters (p < 0.01). The results obtained confirmed the presence of impaired respiratory function in the group of patients with COPD. Analysis of HRV values, when conducting a test with external peripheral vascular occlusion, confirmed ergoreflex hyperactivity in patients with COPD. CONCLUSION: The integration of methods for routine clinical diagnostics of patients condition (spirometry, 6-minute walk test, assessment of autonomic status) and the introduction of the study of ergoreflex activity made it possible to expand the understanding of the functional state of patients with COPD and is of great interest for further research.

Sign in / Sign up

Export Citation Format

Share Document