scholarly journals Community structure of environmental microorganisms associated with COVID-19 affected patients

Aerobiologia ◽  
2021 ◽  
Author(s):  
Weihua Zhang ◽  
Guoxin Mo ◽  
Jie Yang ◽  
Xingshuo Hu ◽  
Hujie Huang ◽  
...  
Keyword(s):  
Environmental Samples ◽  
Close Contact ◽  
Positive Pressure ◽  
Surface Samples ◽  
Medical Supplies ◽  
Positive Rate ◽  
The Face ◽  
General Wards ◽  
Generation Sequencing ◽  
Environmental Microbes

AbstractTo clarify the characteristics and distribution of hospital environmental microbiome associated with confirmed COVID-19 patients. Environmental samples with varying degrees of contamination which were associated with confirmed COVID-19 patients were collected, including 13 aerosol samples collected near eight patients in different wards, five swabs from one patient’s skin and his personal belongings, and two swabs from the surface of positive pressure respiratory protective hood and the face shield from a physician who had close contact with one patient. Metagenomic next-generation sequencing (mNGS) was used to analyze the composition of the microbiome. One of the aerosol samples (near patient 4) was detected positive for COVID-19, and others were all negative. The environmental samples collected in different wards possessed protean compositions and community structures, the dominant genera including Pseudomonas, Corynebacterium, Neisseria, Staphylococcus, Acinetobacter, and Cutibacterium. Top 10 of genera accounted for more than 76.72%. Genera abundance and proportion of human microbes and pathogens radiated outward from the patient, while the percentage of environmental microbes increased. The abundance of the pathogenic microorganism of medical supplies is significantly higher than other surface samples. The microbial compositions of the aerosol collected samples nearby the patients were mostly similar to those from the surfaces of the patient's skin and personal belongings, but the abundance varied greatly. The positive rate of COVID-19 RNA detected from aerosol around patients in general wards was quite low. The ward environment was predominantly inhabited by species closely related to admitted patients. The spread of hospital microorganisms via aerosol was influenced by the patients’ activity.

scholarly journals PIMBA: a PIpeline for MetaBarcoding Analysis

2021 ◽  
Author(s):  
Renato R. M. Oliveira ◽  
Raissa L S Silva ◽  
Gisele L. Nunes ◽  
Guilherme Oliveira
Keyword(s):  
Environmental Samples ◽  
Next Generation Sequencing Data ◽  
Ecological Studies ◽  
Sequencing Data ◽  
Monitoring Method ◽  
Computational Tools ◽  
Dna Metabarcoding ◽  
Reference Databases ◽  
User Friendly ◽  
Generation Sequencing

DNA metabarcoding is an emerging monitoring method capable of assessing biodiversity from environmental samples (eDNA). Advances in computational tools have been required due to the increase of Next-Generation Sequencing data. Tools for DNA metabarcoding analysis, such as MOTHUR, QIIME, Obitools, and mBRAVE have been widely used in ecological studies. However, some difficulties are encountered when there is a need to use custom databases. Here we present PIMBA, a PIpeline for MetaBarcoding Analysis, which allows the use of customized databases, as well as other reference databases used by the softwares mentioned here. PIMBA is an open-source and user-friendly pipeline that consolidates all analyses in just three command lines.

scholarly journals Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples

2017 ◽  
Vol 5 (33) ◽  
Author(s):  
Russell J. S. Orr ◽  
Stephane Rombauts ◽  
Yves Van de Peer ◽  
Kamran Shalchian-Tabrizi
Keyword(s):  
Environmental Samples ◽  
Draft Genome ◽  
New Genera ◽  
Freshwater Lakes ◽  
Genome Sequences ◽  
Surface Samples

ABSTRACT We report here the draft genome sequences of two Chitinophagaceae bacteria, IBVUCB1 and IBVUCB2, assembled from metagenomes of surface samples from freshwater lakes. The genomes are >99% complete and may represent new genera within the Chitinophagaceae family, indicating a larger diversity than currently identified.

Efficient Half Face Detection System Based on Linear Binary Pattern

2020 ◽  
Vol 17 (5) ◽  
pp. 2342-2348
Author(s):  
Ashutosh Upadhyay ◽  
S. Vijayalakshmi
Keyword(s):  
Face Detection ◽  
Detection System ◽  
False Positive Rate ◽  
Computational Cost ◽  
Detection Algorithm ◽  
Data Set ◽  
Computation Cost ◽  
Face Features ◽  
Positive Rate ◽  
The Face

In the field of computer vision, face detection algorithms achieved accuracy to a great extent, but for the real time applications it remains a challenge to maintain the balance between the accuracy and efficiency i.e., to gain accuracy computational cost also increases to deal with the large data sets. This paper, propose half face detection algorithm to address the efficiency of the face detection algorithm. The full face detection algorithm consider complete face data set for training which incur more computation cost. To reduce the computation cost, proposed model captures the features of the half of the face by assuming that the human face is symmetric about the vertical axis passing through the nose and train the system using reduced half face features. The proposed algorithm extracts Linear Binary Pattern (LBP) features and train model using adaboost classifier. Algorithm performance is presented in terms of the accuracy i.e., True Positive Rate (TPR), False Positive Rate (FTR) and face recognition time complexity.

scholarly journals Clinical significance of IgM and IgG test for diagnosis of highly suspected COVID-19 infection

2020 ◽  
Author(s):  
Xingwang Jia ◽  
Pengjun Zhang ◽  
Yaping Tian ◽  
Junli Wang ◽  
Huadong Zeng ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Detection Method ◽  
Close Contact ◽  
Diagnostic Value ◽  
Negative Group ◽  
Nucleic Acid Test ◽  
Value Evaluation ◽  
Positive Rate ◽  
Acid Test ◽  
Positive Groups

AbstractQuick, simple and accurate diagnosis of suspected COVID-19 is very important for the screening and therapy of patients. Although several methods were performed in clinical practice, however, the IgM and IgG diagnostic value evaluation was little performed. 57 suspected COVID-19 infection patients were enrolled in our study. 24 patients with positive and 33 patients with negative nucleic acid test. The positive rate of COVID-19 nucleic acid was 42.10%. The positive detection rate of combination of IgM and IgG for patients with COVID-19 negative and positive nucleic acid test was 72.73% and 87.50%. The results were significantly higher than the nucleic acid or IgM, IgG single detection. hsCRP in the COVID-19 nucleic acid negative group showed significantly higher than the positive groups (P=0.0298). AST in the COVID-19 IgM negative group showed significantly lower than the positive groups (P=0.0365). We provided a quick, simple, accurate aided detection method for the suspected patients and on-site screening in close contact with the population.

scholarly journals Quantification of aerosol dispersal from suspected aerosol generating procedures

2021 ◽  
pp. 00206-2021
Author(s):  
Runar Strand-Amundsen ◽  
Christian Tronstad ◽  
Ole Elvebakk ◽  
Tormod Martinsen ◽  
Marius Dybwad ◽  
...  
Keyword(s):  
Test Chamber ◽  
Nasal Cannula ◽  
Low Flow ◽  
Positive Pressure ◽  
Productive Cough ◽  
Significant Drop ◽  
Non Invasive ◽  
Oxygen Treatment ◽  
The Face ◽  
Particle Sizer

BackgroundOxygen delivering modalities like humidified high-flow nasal cannula (HFNC) and non-invasive positive-pressure ventilation (NIV) are suspected of generating aerosols that may contribute to transmission of disease such as COVID-19. We sought to assess if these modalities lead to increased aerosol dispersal compared to the use of non-humidified low-flow nasal cannula oxygen treatment (LFNC).MethodsAerosol dispersal from 20 healthy volunteers using HFNC, LFNC and NIV oxygen treatment was measured in a controlled chamber. We investigated effects related to coughing and using a surgical facemask in combination with the oxygen delivering modalities. An aerodynamic particle sizer measured aerosol particles (APS3321, 0.3–20 µm) directly in front of the subjects, while a mesh of smaller particle sensors (SPS30, 0.3–10 µm) was distributed in the test chamber.ResultsNon-productive coughing led to significant increases in particle dispersal close to the face when using LFNC and HFNC but not when using NIV. HFNC or NIV did not lead to a statistically significant increase in aerosol dispersal compared to LFNC. With non-productive cough in a room without air changes, there was a significant drop in particle levels between 100 cm and 180 cm from the subjects.ConclusionsOur results indicate that using HFNC and NIV does not lead to increased aerosol dispersal compared to low-flow oxygen treatment, except in rare cases. For a subject with non-productive cough, NIV with double-limb circuit and non-vented mask may be a favourable choice to reduce the risk for aerosol spread.

scholarly journals AQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome

2017 ◽  
Author(s):  
Xiao-Tao Jiang ◽  
Ke Yu ◽  
Li-Guan Li ◽  
Xiao-Le Yin ◽  
An-Dong Li ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Experimental Design ◽  
Environmental Samples ◽  
Absolute Quantification ◽  
Relative Quantification ◽  
Quantification Method ◽  
Bioinformatic Approach ◽  
Per Gene ◽  
Generation Sequencing ◽  
Microbial Functional Gene

AbstractMetatranscriptome has become increasingly important along with the application of next generation sequencing in the studies of microbial functional gene activity in environmental samples. However, the quantification of target active gene is hindered by the current relative quantification methods, especially when tracking the sharp environmental change. Great needs are here for an easy-to-perform method to obtain the absolute quantification. By borrowing information from the parallel metagenome, an absolute quantification method for both metagenomic and metatranscriptomic data to per gene/cell/volume/gram level was developed. The effectiveness of AQMM was validated by simulated experiments and was demonstrated with a real experimental design of comparing activated sludge with and without foaming. Our method provides a novel bioinformatic approach to fast and accurately conduct absolute quantification of metagenome and metatranscriptome in environmental samples. The AQMM can be accessed from https://github.com/biofuture/aqmm.

scholarly journals Welcoming Wolves? Governing the Return of Large Carnivores in Traditional Pastoral Landscapes

2021 ◽  
Vol 2 ◽  
Author(s):  
Hanna L. Pettersson ◽  
Claire H. Quinn ◽  
George Holmes ◽  
Steven M. Sait ◽  
José Vicente López-Bao
Keyword(s):  
Close Contact ◽  
Situational Analysis ◽  
Apex Predators ◽  
Large Carnivore ◽  
Social Legitimacy ◽  
Social Ecological Systems ◽  
Local Livelihoods ◽  
The Social ◽  
Pastoral Landscapes ◽  
The Face

Wolf populations are recovering across Europe and readily recolonize most areas where humans allow their presence. Reintegrating wolves in human-dominated landscapes is a major challenge, particularly in places where memories and experience of coexistence have been lost. Despite the observed expansion trends, little has been done to prepare communities for the return of these apex predators, or to understand what fosters and perpetuates coexistence. In this study, we present a theoretical framework for resilient coexistence based on four conditions: Effective institutions, large carnivore persistence, social legitimacy, and low levels of risk and vulnerability, nested within the social-ecological systems (SES) concept. To empirically show how the conditions can be manifested and interconnected, and how this knowledge could be used to improve local coexistence capacities, the framework is applied in a case study of human–wolf relations in Spain. We examined three traditionally pastoral landscapes at different states of cohabitation with wolves: uninterrupted presence, recent recolonization, and imminent return. We found that both the perceptions of wolves and the capacity to coexist with them diverged across these states, and that this was largely determined by a diversity of vulnerabilities that have not been recognized or addressed within current management regimes, such as economic precarity and weak legitimacy for governing institutions. Our results illustrate the importance of working in close contact with communities to understand local needs and enhance adaptive capacities in the face of rural transitions, beyond those directly related to wolves. The framework complements emerging tools for coexistence developed by researchers and practitioners, which offer guidance on the process of situational analysis, planning, and resource allocation needed to balance large carnivore conservation with local livelihoods.

Comparison of the BAX System PCR Method to Brazil's Official Method for the Detection of Salmonella in Food, Water, and Environmental Samples

2008 ◽  
Vol 71 (12) ◽  
pp. 2442-2447 ◽  
Author(s):  
INGRID BOESCHE TOMAZELLI ◽  
JOSINETE BARROS de FREITAS ◽  
LEANIA MARIA FABBI ◽  
TEREZINHA AGNESE FILIPINI ◽  
CLÁUDIA MARIA da SILVA ◽  
...  
Keyword(s):  
Environmental Samples ◽  
Limit Of Detection ◽  
False Positive Rate ◽  
False Negative ◽  
False Negative Rate ◽  
Reference Method ◽  
Culture Method ◽  
Official Method ◽  
Positive Rate ◽  
Pcr Method

A two-stage study compared the BAX system PCR method with the reference culture method used by the Brazilian Ministry of Agriculture and Food Supply for the detection of Salmonella in food, water, and environmental samples. In stage 1, fish matrix samples (n = 258) were spiked at several levels with Salmonella and a combination of Salmonella and non-Salmonella competitive organisms. Replicates were analyzed by the BAX system PCR method and the reference method with comparable results (sensitivity ≥ 97.5%, specificity ≥ 83.3%) from both methods at the limit of detection. In stage 2, a total of 1,988 samples with 70 product types were analyzed with both methods. Five laboratories were involved in this study, and the samples used were from routine analyses. The BAX system PCR method was shown to be comparable to the reference method, with a limit of detection of 1.0 to 2.0 CFU/25 g of sample. Analysis of the results obtained in stage 2 and in the combination of stages 1 and 2 for the BAX system showed the following performance: sensitivity ≥ 99.0%, specificity ≥ 97.2%, false-negative rate ≤ 1.1%, and false-positive rate ≤ 2.8%. Therefore, the BAX system appears to be equivalent to the reference method, with ≥ 97.3% agreement.

scholarly journals Displacement ventilation: a viable ventilation strategy for makeshift hospitals and public buildings to contain COVID-19 and other airborne diseases

2020 ◽  
Vol 7 (9) ◽  
pp. 200680
Author(s):  
Rajesh K. Bhagat ◽  
P. F. Linden
Keyword(s):  
Negative Pressure ◽  
Natural Ventilation ◽  
Public Spaces ◽  
Positive Pressure ◽  
Air Conditioner ◽  
Displacement Ventilation ◽  
Link Type ◽  
Building Ventilation ◽  
High Level ◽  
General Wards

The SARS-CoV-2 virus has so far infected more than 31 million people around the world, and its impact is being felt by all. Patients with diseases such as COVID-19 should ideally be treated in negative pressure isolation rooms. However, due to the overwhelming demand for hospital beds, patients have been treated in general wards, hospital corridors and makeshift hospitals. Adequate building ventilation in hospitals and public spaces is a crucial factor to contain the disease (Escombe et al. 2007 PLoS Med. 4 ; Escombe et al. 2019 BMC Infect. Dis. 19 , 88 ( doi:10.1186/s12879-019-3717-9 ); Morawska & Milton 2020 Clin. Infect. Dis . ciaa939. ( doi:10.1093/cid/ciaa939 )), to exit lockdown safely, and reduce the chance of subsequent waves of outbreaks. A recently reported air-conditioner-induced COVID-19 outbreak caused by an asymptomatic patient, in a restaurant in Guangzhou, China (Lu et al. 2020 Emerg. Infect. Dis. 26 ) exposes our vulnerability to future outbreaks linked to ventilation in public spaces. We argue that displacement ventilation (either mechanical or natural ventilation), where air intakes are at low level and extracts are at high level, is a viable alternative to negative pressure isolation rooms, which are often not available on site in hospital wards and makeshift hospitals. Displacement ventilation produces negative pressure at the occupant level, which draws fresh air from outdoors, and positive pressure near the ceiling, which expels the hot and contaminated air out. We acknowledge that, in both developed and developing countries, many modern large structures lack the openings required for natural ventilation. This lack of openings can be supplemented by installing extract fans. We have also discussed and addressed the issue of the ‘lock-up effect’. We provide guidelines for such mechanically assisted, naturally ventilated makeshift hospitals.

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