ABSTRACT
Background. At the height of the novel coronavirus infection, the risk of fungal coinfection increases due to a decrease in the immune status of patients and massive antibacterial therapy, which leads to a complication in the course of the underlying disease and increases the risk of an unfavorable outcome. Therefore, it is necessary not only to identify all associates that cause the infectious process, but also to determine their sensitivity to antibacterial and antifungal drugs in order to select an adequate treatment regimen for a patient. The aim of the study was to investigate the species composition of fungal associates in corona positive and corona negative patients with community-acquired pneumonia (CAP), as well as to determine the spectrum of sensitivity/resistance of yeasts and yeast-like fungi to antimycotic drugs. Material and methods. The species composition of the fungal microflora in sputum samples from 723 patients with CAP, sent from a health care facility in Rostov-on-Don, was investigated. The isolated cultures were identified using bacteriological and mass spectrometric methods. The sensitivity of yeasts to antimycotic drugs was determined by disk-diffusion method. Results. It has been established that yeast and yeast-like fungi were present in sputum samples in 31-32% of patients with CAP in etiologically significant quantities. 10 different types of yeast and yeast-like fungi were identified. Candida albicans was the predominant species in terms of the number of isolated cultures (83%). A re-examination of corona positive patients after their hospital stay revealed a tendency towards an increase in the number and intensity of manifestation of candidal lesions. Moreover, a change in Candida species has been registered, which entails a change in their sensitivity to antifungal drugs. A high percentage of strains resistant to fluconazole was identified after determining the sensitivity of fungi to antimycotics. Conclusion. The data obtained demonstrate that yeast and yeast-like fungi are the dominant associates in complicated forms of CAP. In this regard, it seems appropriate to provide individual microbiological support to patients during their treatment with the identification of all pathogens.
ABSTRACT
This study was undertaken to identify herbal remedies that may be involved in the symptomatic management of COVID-19 disease. From a list of 247 medicinal plants, a bibliographic study was carried out with the richness, the floristic composition, the methods of preparation and use and the active principles of the plants as a variable. The importance value of these plants was also calculated. A Principal Component Analysis showed the links between the parts of plants used, the methods of preparation, the symptoms of COVID-19 disease that can be treated and the active ingredients. The results show that 226 medicinal plants divided into 190 genera and 79 families can be used to treat the symptoms of COVID- 19 disease namely otolaryngologic signs, pulmonary signs and general signs. Of these, twenty-eight (28) can relieve the majority of symptoms of COVID-19 disease. These symptoms are rhinorrhea, cough, fever, headache, vomiting, diarrhea, and muscle aches. These plants are mainly prepared in the form of a decoction and administered mainly orally. They mainly contain flavonoids, coumarins, alkaloids, tannins, steroids, terpenoids, saponosides, essential oils, mucilages, quinones, coumarins. The importance value of these plants is between 85.71 and 57.14%. The results also showed that eight (8) groups of medicinal plants can be distinguished according to the organs used, the methods of preparation, the symptoms of the COVID-19 disease treated and the active ingredients. The results of this study could serve as a database for the formulation of improved traditional drugs in the management of symptoms of COVID-19 disease in Cote d'Ivoire.
ABSTRACT
Background. The COVID-19 pandemic has brought awareness to the dangers of emerging pathogens to global human health and welfare. Sensitivity and flexibility are important features for methods used to detect emerging pathogens. While PCR testing is rapid and sensitive, a significant advantage next generation sequencing (NGS) approaches have over PCR-based analyses is the ability to detect previously undiscovered pathogens while also providing genomic information that can detect SARS-CoV-2 genome sequence, identify source of co-infection, and the host transcriptional response in a single workflow. The critical component enabling this approach is Jumpcode CRISPRclean technology which removes abundant human and bacterial ribosomal RNA sequences from NGS libraries. CRISPRclean workflow easily integrates into next generation sequencing projects Schematic of the Jumpcode CRISPRclean protocol Methods. CRISPRclean was applied to contrived infected tissue samples including human lung RNA spiked with serially diluted amounts of SARS-CoV-2 RNA and bacterial RNA. NEB RNA libraries were prepared and treated with CRISPRclean protocol, then sequenced on Illumina instruments. Data analysis was performed using Jumpcode proprietary software to measure alignment and depletion rates, the Silva database for rRNA read alignment, and Kraken2 and CosmosID pipelines for k-mer based metagenomic investigation. Fold enrichment of SARS-CoV-2 reads after CRISPRclean depletion of libraries prepared from contrived samples. CRISPRclean treatment of the fully contrived samples increases the fraction of reads that map to the SARS-CoV-2 genome by an average of ~10-fold Results. CRISPRclean treatment of the contrived samples increases ~10 fold of reads that map to the SARS-CoV-2 genome. For the 60 viral copies of SARS-CoV-2 sample, the number of reads mapping to the SARSCoV-2 genome increases from ~10,000 reads to ~70,000 reads. A similar increase in reads occurs for S. aureus. The percentage of SARSCoV-2 genome covered at 1X and 10X also increases. Similar results were achieved even after downsampling the datasets to 5M reads. There is a ~4-fold increase in bacterial species detection in these stool samples after CRISPRclean treatment. Percentage of SARSCoV-2 genome covered at 1X and 10X increases as a result of rRNA depletion. Coverage of the SARS-CoV-2 genome at 50 million reads. Number of reads aligning to the S. aureus and SARS-CoV-2 genomes increases after CRISPRclean depletion. For the sample containing 0.0001% SARS-CoV-2, (60 viral copies), the number of reads mapping to the SARS-CoV-2 genome increases from ~10,000 reads to ~70,000 reads. CosmosID Shotgun Metagenomics Analysis heat map showing read alignments to viral genomes. The yellow color indicates high read counts. The CosmosID shotgun metagenomic analysis software was used to analyze the sequencing data, classify the sequences and generate the heat map. Conclusion. Metatranscriptomics powered by CRISPR-mediated rRNA depletion offers a robust methodology to acquire viral genomic data, microbiome composition, co-infection information, and the transcriptional status of the host immune response in a single workflow. This sequencing-based approach can be available on the first day of the next viral outbreak and should be considered as a first-line test for novel zoonotic virus detection. Bacterial species composition of patient stool samples before and after CRISPRclean depletion. ~4-fold increase in bacterial species detection in these stool samples after CRISPRclean treatment. Sequencing data downsampled to 20 million reads.
ABSTRACT
High nitrogen (N) fertilizer inputs accelerate soil acidification and degradation in tea plantations, thus posing a threat to soil microbial diversity, species composition, and ecosystem service functions. The effects of organic fertilizer and biochar applications on improving soil fertility have been extensively studied on cropland;however, little is known about their effectiveness in promoting soil multifunctionality on rapidly expanding acidic soils in tea plantations. In this study, we conducted a two‐year field experiment in a subtropical tea plantation to investigate the effects of organic fertilizer substitution and biochar amendment on soil microbial communities and multifunctionality. The results showed that soil multifunctionality was enhanced in plots amended with organic fertilizer and biochar. Soil multifunctionality was significantly and positively correlated with alpha‐diversity of bacteria but not fungi. We also found that organic fertilizer substitution and biochar amendment improved soil multifunctionality by altering the abundance of keystone species. The abundance of keystone species classified as module hubs in the bacterial co‐occurrence network contributed significantly and positively to soil multifunctionality. In contrast, the keystone species categorized as module hubs in the fungal co‐occurrence network negatively affected soil multifunctionality. Soil pH was a key driver of soil microbial community composition, indicating that the increase in soil pH under organic fertilizer and biochar amendment had a crucial role in biological processes. These results suggest that organic substitution and biochar amendment are beneficial in preventing soil degradation and maintaining soil multifunctionality in subtropical tea plantations.