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10
Authors: Alsaud, Arwa E., et al
Published: Feb 2021
Authors: Alsaud, Arwa E., et al
Published: Feb 2021
COVID-19 has surfaced as a multi-organ disease predominantly affecting the respiratory system. Detection of the viral RNA through reverse transcriptase–PCR (RT-PCR) from a nasopharyngeal or throat sample is the preferred method of diagnosis. Recent evidence has suggested that COVID-19 patients can shed the SARS-CoV-2 for several weeks. Herein, we report six cases of COVID-19 who had persistently positive SARS-CoV-2 on repeat RT-PCR testing reaching up to 9 weeks. The spectrum of cases described ranges from asymptomatic infection to severe COVID-19 pneumonia. A full understanding of the virus’s transmission dynamics needs further research. Prolonged viral shedding currently has unclear implications on the management and isolation decisions—the role of the cycle threshold (Ct) value in guiding therapeutic decisions is yet to be clarified. More data on the relationship between Ct values and viral cultivation are needed, especially in patients with prolonged viral shedding, to understand the virus’s viability and infectivity.
5
From Paper: Sea foams are ephemeral hotspots for distinctive bacterial communities contrasting sea-surface microlayer and underlying surface water
Published: Feb 2021
From Paper: Sea foams are ephemeral hotspots for distinctive bacterial communities contrasting sea-surface microlayer and underlying surface water
Published: Feb 2021
Abstract The occurrence of foams at oceans’ Surfaces is patchy and generally short-lived but a detailed understanding of bacterial communities inhabiting sea foams is lacking. Here we investigated how marine foams differ from the sea-surface microlayer (SML), a <1 mm thick layer at the air-sea interface and underlying water from 1 m depth. Samples of sea foams, SML and underlying water collected from the North Sea and Timor Sea indicated that foams were often characterized by a high abundance of small eukaryotic phototrophic and prokaryotic cells as well as a high concentration of surface-active substances (SAS). Amplicon sequencing of 16S rRNA (gene) revealed distinctive foam bacterial communities compared to SML and underlying water, with high abundance of Gammaproteobacteria. Typical SML dwellers such as Pseudoalteromonas and Vibrio were highly abundant, active foam inhabitants and thus might enhance foam formation and stability by producing SAS. Despite a clear difference in the overall bacterial community composition between foam and SML, the presence of SML bacteria in foams supports previous assumptions that foam is strongly influenced by the SML. We conclude that active and abundant bacteria from interfacial habitats potentially contribute to foam formation and stability, carbon cycling and air-sea exchange processes in the ocean.
1
Authors: Harihara Subrahmaniam Muralidharan, Nidhi Shah, Jacquelyn S. Meisel, Mihai Pop
Published: Feb 2021
Authors: Harihara Subrahmaniam Muralidharan, Nidhi Shah, Jacquelyn S. Meisel, Mihai Pop
Published: Feb 2021
High-throughput sequencing has revolutionized the field of microbiology, however, reconstructing complete genomes of organisms from whole metagenomic shotgun sequencing data remains a challenge. Recovered genomes are often highly fragmented, due to uneven abundances of organisms, repeats within and across genomes, sequencing errors, and strain-level variation. To address the fragmented nature of metagenomic assemblies, scientists rely on a process called binning, which clusters together contigs inferred to originate from the same organism. Existing binning algorithms use oligonucleotide frequencies and contig abundance (coverage) within and across samples to group together contigs from the same organism. However, these algorithms often miss short contigs and contigs from regions with unusual coverage or DNA composition characteristics, such as mobile elements. Here, we propose that information from assembly graphs can assist current strategies for metagenomic binning. We use MetaCarvel, a metagenomic scaffolding tool, to construct assembly graphs where contigs are nodes and edges are inferred based on paired-end reads. We developed a tool, Binnacle, that extracts information from the assembly graphs and clusters scaffolds into comprehensive bins. Binnacle also provides wrapper scripts to integrate with existing binning methods. The Binnacle pipeline can be found on GitHub ( https://github.com/marbl/binnacle ). We show that binning graph-based scaffolds, rather than contigs, improves the contiguity and quality of the resulting bins, and captures a broader set of the genes of the organisms being reconstructed.
1
Authors: Geffroy, Solène, et al
Published: Feb 2021
Authors: Geffroy, Solène, et al
Published: Feb 2021
Paralytic shellfish poisoning (PSP) is a human foodborne syndrome caused by the consumption of shellfish that accumulate paralytic shellfish toxins (PSTs, saxitoxin group). In PST-producing dinoflagellates such as Alexandrium spp., toxin synthesis is encoded in the nuclear genome via a gene cluster ( sxt ). Toxin production is supposedly associated with the presence of a 4th domain in the sxtA gene ( sxtA4 ), one of the core genes of the PST gene cluster. It is postulated that gene expression in dinoflagellates is partially constitutive, with both transcriptional and post-transcriptional processes potentially co-occurring. Therefore, gene structure and expression mode are two important features to explore in order to fully understand toxin production processes in dinoflagellates. In this study, we determined the intracellular toxin contents of twenty European Alexandrium minutum and Alexandrium pacificum strains that we compared with their genome size and sxtA4 gene copy numbers. We observed a significant correlation between the sxtA4 gene copy number and toxin content, as well as a moderate positive correlation between the sxtA4 gene copy number and genome size. The 18 toxic strains had several sxtA4 gene copies (9–187), whereas only one copy was found in the two observed non-toxin producing strains. Exploration of allelic frequencies and expression of sxtA4 mRNA in 11 A. minutum strains showed both a differential expression and specific allelic forms in the non-toxic strains compared with the toxic ones. Also, the toxic strains exhibited a polymorphic sxtA4 mRNA sequence between strains and between gene copies within strains. Finally, our study supported the hypothesis of a genetic determinism of toxin synthesis (i.e., the existence of several genetic isoforms of the sxtA4 gene and their copy numbers), and was also consistent with the hypothesis that constitutive gene expression and moderation by transcriptional and post-transcriptional regulation mechanisms are the cause of the observed variability in the production of toxins by A. minutum .
1
Authors: Sucheta J. Lakhani, Sanjay J. Mehta, Dipak M. Panjwani, Jitendra D. Lakhani
Published: Feb 2021
Authors: Sucheta J. Lakhani, Sanjay J. Mehta, Dipak M. Panjwani, Jitendra D. Lakhani
Published: Feb 2021
Hospital acquired infections caused by Non-fermentative gram-negative bacteria (NFGNB) have features that are of specific concern, detection of which is helpful for prevention and for better quality of healthcare in hospital premises. Present study was conducted to find out the nosocomial infections caused by NFGNB and its sensitivity pattern. Present microbiological study was carried out at C. U. Shah Medical College. Clinical samples which were included in this study were in accordance with inclusion criteria laid down in the research protocol, which were obtained during January 2018 to June 2020.Samples were collected and processed with the help of automated identification and antimicrobial susceptibility testing instrument i.e. Vitek – 2 as per standard guidelines. Statistical analysis was done by Microsoft Excel. Total 385 were classified as NFGNB from 1000 confirmed isolates causing Hospital acquired infection (HAI). Respiratory site infection was most common type of HAI i.e. 48%. While most common isolate was Pseudomonas sp.i.e. 42% followed by Acinetobacter baumannii i.e. 31%. Medicine ward showed maximum isolates i.e. 33%, followed by Surgery ward i.e. 23%. Maximum NFGNB isolates encountered from sputum sample i.e. 25% while blood shows only 6%. Trimethoprim/sulfamethoxazole and ciprofloxacinwere disclosedmaximum resistant. This study reports 385NFGNB isolates causing HAI. Such alarming resistance among NFGNB spreading the threat in medical care and epidemiology as they act as nosocomial pathogen. These isolated pathogens being the major cause of illness particularly in hospitalized patients.
2
Authors: Anggraini Alam, Sri Sudarwati, Dzulfikar Djalil Lukmanul Hakim, Sally Mahdiani
Published: Feb 2021
Authors: Anggraini Alam, Sri Sudarwati, Dzulfikar Djalil Lukmanul Hakim, Sally Mahdiani
Published: Feb 2021
We report a case of a 10-month infant with dual severe infection of COVID-19 and dengue fever who was admitted to the hospital with an influenza-like illness. The patient experienced severe conditions of COVID-19 and dengue fever with shock followed by disseminated intravascular coagulation. The standard of COVID-19 care was given coupled with fluid resuscitation and blood transfusion. The pitfalls of this case are how to differentiate the clinical manifestation of dengue fever in a patient with confirmed COVID-19; the difficulty to monitor the dengue course of illness of the patient in the COVID-19 isolation room; and to differentiate the severe dengue from the multisystem inflammatory syndrome-C when the patient was in critical condition. The infant recovered without sequale, but the management of new probable cases must be improved more thoroughly, especially during dengue peak period in tropical and developing countries such as Indonesia.
1
Authors: Achan, Beatrice, et al
Published: Feb 2021
Authors: Achan, Beatrice, et al
Published: Feb 2021
Introduction. Drug resistant tuberculosis remains a worldwide problem that requires prompt diagnosis. Hypothesis/Gap statement. The WHO recommended direct, rapid Xpert MTB/RIF is prohibitively costly, therefore, there is a need to validate a rapid, affordable DST for use in low- and middle-income settings. Aim. The technical performance and time to results of a simple, direct microscopy-based slide DST (SDST) assay for diagnosis of rifampicin-resistant TB was evaluated in Uganda. Methodology. Sputum samples from 122 smear-positive re-treatment TB patients presenting to the TB treatment centre at Uganda’s National Referral Hospital, Mulago, Kampala, Uganda were examined. The sputum samples were tested by the direct SDST which was compared to the indirect Lowenstein Jensen Proportion Method (LJDST) method as the gold standard. The time to results was defined as the time from DST setting to results interpretation. The results were further analysed for sensitivity and specificity as well as agreement between LJDST and SDST for rifampicin resistance determination. Results. A total of 117 smear positive sputum samples with valid results for both tests were compared. The median time to results for SDST was 14 days with an interquartile range (IQR) of 10–14 days compared to 60 days with IQR of 60–75 days for LJDST. The number for rifampicin resistance by the gold standard LJDST was 26. The SDST had a sensitivity of 96 % (95 %; CI 81–99 %) and a specificity of 97.8 % (95 %; CI 93–100 %). The Positive Predictive and Negative Predictive values for SDST were 92.3 % (95 %; CI 76.8–99 %) and 98.9 % (95 %; CI 94–100 %), respectively. The kappa agreement between SDST and LJDST was 92.3 %. Conclusion. The SDST was found to be a rapid and accurate direct test for the detection of rifampicin resistance among retreatment TB cases in low-income settings.
1
Authors: R. Kalyani, N. Arvind, N. Suresh Kumar, Mahendra M Reddy, K. Dinesh
Published: Feb 2021
Authors: R. Kalyani, N. Arvind, N. Suresh Kumar, Mahendra M Reddy, K. Dinesh
Published: Feb 2021
Direct shedding of microbes by patients and health care workers results in contamination of Intensive care unit environment. Intensive care unit acquired infections due to microbial contamination is a major concern because the patient’s immunity is already compromised. To determine the rate of bacterial contamination on environmental surfaces of Intensive care unit and health care workers and to determine the antibiogram of the isolates. Air samples and swabs from healthcare workers, their accessories, surrounding environmental surfaces were collected randomly over a period of 2 months in Adult Intensive care units. Bacterial isolates were identified by standard microbiological techniques. Antibiotic sensitivity testing was performed by Kirby Bauer disc diffusion method and data analyzed by Statistical Product and Service Solutions 22 version software. A total of 208 samples were randomly collected over 2 months, of which 56 samples yielded positive bacterial growth. Of 56 growth, 12 isolates were detected from air sampling method and 44 isolates from swabs. Among 44 isolates identified from swabs, 10 were isolated from healthcare workers, 4 from health care worker’s accessories and 30 from environmental surfaces. Six different bacterial isolates were identified, Coagulase Negative Staphylococcus (24) and Micrococcus (15) were the major isolates followed by Non fermenters (6), Staphylococcus aureus(4), Bacillus species(4) and diphtheroids (3) The antimicrobial sensitivity pattern of these bacterial isolates were sensitive to commonly used antibacterial agents. Study results showed Intensive care unit staff and environmental surfaces as probable sources of bacterial contamination. Study highlights the importance of cleaning and disinfection process and educate the health care workers about the possible sources of infections within Intensive care unit.
1
Authors: Zou, Xiaohui, et al
Published: Feb 2021
Authors: Zou, Xiaohui, et al
Published: Feb 2021
Fibre is the viral protein that mediates the attachment and infection of adenovirus to the host cell. Fowl adenovirus 4 (FAdV-4) possesses two different fibre trimers on each penton capsomere, and roles of the separate fibres remain elusive. Here, we attempted to investigate the function of FAdV-4 fibres by using reverse genetics approaches. Adenoviral plasmids carrying fiber1 or fiber2 mutant genes were constructed and used to transfect chicken LMH cells. Fiber1-mutated recombinant virus could not be rescued. Such defective phenotype was complemented when a fiber1-bearing helper plasmid was included for co-transfection. The infection of fiber-intact FAdV-4 (FAdV4-GFP) to LMH cells could be blocked with purified fiber1 knob protein in a dose-dependent manner, while purifed fiber2 knob had no such function. On the contrary, fiber2-mutated FAdV-4, FAdV4XF2-GFP, was successfully rescued. The results of one-step growth curves showed that proliferative capacity of FAdV4XF2-GFP was 10 times lower than that of the control FAdV4-GFP. FAdV4XF2-GFP also caused fewer deaths of infected chicken embryos than FAdV4-GFP did, which resulted from poorer virus replication in vivo . These data illustrated that fiber1 mediated virus adsorption and was essential for FAdV-4, while fiber2 was dispensable although it significantly contributed to the virulence.
1
Authors: Nam, Da-eun, et al
Published: Feb 2021
Authors: Nam, Da-eun, et al
Published: Feb 2021
Plasminogen activator inhibitor-1 (PAI-1) is a critical factor that regulates protein synthesis and degradation. The increased PAI-1 levels are detectable in the serum of patients with chronic hepatitis C virus (HCV) liver disease. The differentiation state and motility of HCV-induced cancer stem-like cells (CSC) play a major role in severe liver disease progression. However, the role of PAI-1 in the pathological process of chronic liver diseases remains unknown. In this study, we determined how PAI-1 affects the differentiation of CSC state in hepatocytes upon HCV infection. We found that HCV infection induced the expression of PAI-1 while decreasing miR-30c expression in Huh7.5.1 cells. Similar results were obtained from isolated hepatocytes from humanized liver mice after HCV infection. Moreover, decreased miR-30c expression in HCV-infected hepatocytes was associated with the increased levels of PAI-1 mRNA and protein. Notably, the increased PAI-1 levels resulted in the activation of Protein Kinase B/AKT, a major mediator of cell proliferation, in HCV-infected hepatocytes along with the increased expression of CSC markers such as Human Differentiated Protein (CD) 133, Epithelial cell adhesion molecule (EpCAM), Octamer 4 (Oct4), Nanog, Cyclin D1, and MYC. Moreover, blockade of PAI-1 activity by miR-30c mimic and anti-PAI-1 mAb abrogated the AKT activation with decreased expression of CSC markers. Our findings suggest that HCV infection induces the CSC state via PAI-1-mediated AKT activation in hepatocytes. It implicates that the manipulation of PAI-1 activity could provide potential therapeutics to prevent the development of HCV-associated chronic liver diseases. IMPORTANCE The progression of chronic liver disease by HCV infection is considered a major risk factor for hepatocellular carcinoma (HCC), one of the major causes of death from cancer. Recent studies have demonstrated that increased CSC properties in HCV-infected hepatocytes are associated with the progression of HCC. Since proteins and miRNAs production by HCV-infected hepatocytes can play various roles in physiological processes, investigating these factors can potentially lead to new therapeutic targets. However, the mechanism of HCV associated progression of hepatocytes to CSC remains unclear. Here we identify the roles of PAI-1 and miR-30c in the progression of CSC during HCV infection in hepatocytes. Our data shows that increased secretion of PAI-1 following HCV infection promotes this CSC state and activation of AKT. We report that the inhibition of PAI-1 by miR-30c mimic reduces HCV associated CSC properties in hepatocytes. Taken together, targeting this interaction of secreted PAI-1 and miR-30c in HCV-infected hepatocytes may provide a potential therapeutic intervention against the progression to chronic liver diseases and HCC.
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