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COVID-19 is a serious infectious disease that has recently swept the world, and research on its causative virus, SARS-CoV-2, remains insufficient. Therefore, this study uses bioinformatics analysis techniques to explore the human digestive tract diseases that may be caused by SARS-CoV-2 infection. The gene expression profile data set, numbered GSE149312, is from the Gene Expression Omnibus (GEO) database and is divided into a 24-h group and a 60-h group. R software is used to analyze and screen out differentially expressed genes (DEGs) and then gene ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses are performed. In KEGG, the pathway of non-alcoholic fatty liver disease exists in both the 24-h group and 60-h group. STRING is used to establish a protein–protein interaction (PPI) network, and Cytoscape is then used to visualize the PPI and define the top 12 genes of the node as the hub genes. Through verification, nine statistically significant hub genes are identified: AKT1, TIMP1, NOTCH, CCNA2, RRM2, TTK, BUB1B, KIF20A, and PLK1. In conclusion, the results of this study can provide a certain direction and basis for follow-up studies of SARS-CoV-2 infection of the human digestive tract and provide new insights for the prevention and treatment of diseases caused by SARS-CoV-2. Supplementary Information The online version contains supplementary material available at 10.1007/s10528-021-10144-w.

Introduction. High mortality associated with carbapenemase-producing Gram-negative bacteria (CP-GNB) has evolved into a global health threat. Rapid and accurate detection as well as prompt treatment are of great significance in this case. Xpert Carba-R, a multiple qualitative analysis designed to detect five clinically relevant carbapenem-resistant gene families within one hour, is regarded as reliable, accurate, and easy-to-operate. This study is to present a systematic evaluation of the performance of Xpert Carba-R in detecting carbapenemase genes in GNB suspected for carbapenemase production. Methods. We searched and screened the literature on “Xpert Carba-R” in the database of PubMed, Web of Science, Embase, and Cochrane Library, employing two independent evaluators to collect data, respectively. Then, statistical analysis of the data obtained was performed by the Stata 12.0 software to measure the accuracy of Xpert Carba-R assay in detecting the carbapenemase genes in GNB. Results. We screened a total of 1767 Gram-negative bacillus isolates documented in 9 articles. The precision of the detection of OXA-48 carbapenemase genes was 100%; that of NDM = 100 %; that of VIM = 100 %. When it came to KPC, the precision rate was 100%; that of IMP = 99 %. The overall accuracy of the detection of carbapenemase genes was 100%. Conclusions. Xpert Carba-R assay demonstrates a 100% precision in identifying carbapenemase genes in GNB. It can be seen that Xpert Carba-R method is an effective tool for early clinical detection, which is suitable for the detection of carbapenase gene in GNB.

Background In the novel coronavirus pandemic, the high infection rate and high mortality have seriously affected people’s health and social order. To better explore the infection mechanism and treatment, the three-dimensional structure of human bronchus has been employed in a better in-depth study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Methods We downloaded a separate microarray from the Integrated Gene Expression System (GEO) on a human bronchial organoids sample to identify differentially expressed genes (DEGS) and analyzed it with R software. After processing with R software, Gene Ontology (GO) and Kyoto PBMCs of Genes and Genomes (KEGG) were analyzed, while a protein–protein interaction (PPI) network was constructed to show the interactions and influence relationships between these differential genes. Finally, the selected highly connected genes, which are called hub genes, were verified in CytoHubba plug-in. Results In this study, a total of 966 differentially expressed genes, including 490 upregulated genes and 476 downregulated genes were used. Analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways related to immune response and cytokines. We construct protein-protein interaction network and identify 10 hub genes, including IL6, MMP9, IL1B, CXCL8, ICAM1, FGF2, EGF, CXCL10, CCL2, CCL5, CXCL1, and FN1. Finally, with the help of GSE150728, we verified that CXCl1, CXCL8, CXCL10, CCL5, EGF differently expressed before and after SARS-CoV-2 infection in clinical patients. Conclusions In this study, we used mRNA expression data from GSE150819 to preliminarily confirm the feasibility of hBO as an in vitro model to further study the pathogenesis and potential treatment of COVID-19. Moreover, based on the mRNA differentiated expression of this model, we found that CXCL8, CXCL10, and EGF are hub genes in the process of SARS-COV-2 infection, and we emphasized their key roles in SARS-CoV-2 infection. And we also suggested that further study of these hub genes may be beneficial to treatment, prognostic prediction of COVID-19.

Background: The Corona Virus Disease 2019 (COVID-19) pandemic poses a serious public health threat to the survival and health of people all over the world. We analyzed related mRNA data and gene expression profiles of human cell lines infected with SARS-CoV-2 obtained from GEO (GSE148729), using bioinformatics tools. Differentially expressed genes (DEGs) of human cells infected with SARS-CoV-2 were identified.Method: The GSE148729 datasets were downloaded from the Gene Expression Omnibus (GEO) database. To explore the Biological significance of DEGs, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of the DEGs was performed. Protein-protein interaction (PPI) networks of the DEGs were constructed by using the STRING database. The hub genes were selected using the Cytoscape Software, and a t-test was performed to validate the hub genes.Result: A total of 1241 DEGs were screened, including 1049 up-regulated genes and 192 down-regulated genes. Besides, 10 hub genes were obtained from the PPI network, among which the expression level of CXCL2, Etv7, and HIST1H2BG was found to be statistically significant.Conclusion: In conclusion, bioinformatics analysis reveals genes and cellular pathways that are significantly altered in SARS-CoV-2 infected cells. This is conducive to further guide the clinical study of SARS-CoV-2 and provides new perspectives for vaccine development.

Mounting evidence suggests that probiotics can be used to treat allergic asthma by modulating the gut microbiota, and that the effects of probiotics may be influenced by environmental factors such as diet. We conducted a rat model with allergic asthma (AA) modulated byLactobacillus paracasei, feeding up with high-fat or high-fiber diets based on collecting data from 85 questionnaires. The systemic proinflammatory cytokines were detected by ELISA and the overall structure of fecal microbiota was analyzedvia16S rRNA gene sequencing. The results showed consumption of a high-fiber diet alleviated the allergic symptoms and airway inflammation, and led to improving the imbalance of T-helper type 1 (Th1)/Th2 cells with increased expression of interferon-γ and decreased expression of interleukin-4. Whereas, the high-fat diet had deteriorating implications and skewed the inflammatory perturbation. Furthermore, abundances of phylum Bacteroidetes, families Muribaculaceae, Tannerellaceae, Prevotellaceae, Enterococcaceae, genera Allobaculum, Parabacteroides, and Enterococcus were enriched inL.paracasei-modulating rats fed with high-fiber diet. Firmicutes and Proteobacteria, families Lachnospiraceae, Ruminococcaceae and Desulfovibrionaceae, genera Blautia, unidentified_Ruminococcaceae, unidentified_Clostridiales and Oscillibacter were in relatively high abundance in the rats administered high-fat diet. Association between changed microbiota and inflammatory cytokines was also conferred. These data indicated that the efficacy ofL.paracaseiin allergic asthma was influenced by different dietary patterns. Hence, diet is important for probiotic therapy when managing allergic asthma.

BackgroundStaphylococcus aureus-induced bacteremia has an impact on human health due to its high mortality rate of 20–30%. To better study the invasion process of staphylococcus aureus, we conducted a study in human endothelial cells to try to find a link between the infection process and bacteremia at the molecular level.MethodsIn this study, the datasets GSE13736, GSE82036 were analyzed using R software to identify differentially expressed genes. Only the infection samples of four different strains had differential gene expression compared to the control samples. Then the GO analysis and KEGG analysis were conducted to construct a protein-protein interaction (PPI) network which shows the interaction and influence relationship between these differential genes. Finally, the central gene of the selected CytoHubba plug-in was verified using GraphPad Prism 8.ResultsThere were 421 differential genes in the Strain 6850, including 64 up-regulated and 357 down-regulated; There were 319 differential genes in the Strain 8325-4, including 14 up-regulated and 305 down-regulated. There were 90 differential genes in the Strain K70058396, including 12 up-regulated and 78 down-regulated. There were 876 differential genes in the Strain K1801/10, accompanied by 261 up-regulated and 615 down-regulated. An analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways associated with immune response and cytokines; Verification of the hub gene can provide a molecular basis for studying the relationship between invasive endothelial infection and bacteremia.ConclusionsWe found specific gene expression patterns in endothelial cells in response to infection with Strain K70058396, and these central genes and their expression products (RSAD2, DDX58, IFITT3, and IFIH1) play a key role in this process of infection.

Background: At present, the infection and prevalence rates of tuberculosis (TB) are still high in worldwide. The Xpert MTB/RIF technology has improved the diagnosis speed of Mycobacterium tuberculosis (MTB) and facilitated the rapid treatment of TB patients. Methods: We searched experimental data derived from Xpert MTB/RIF for detecting MTB in gastric aspirates in PubMed, Embase, Web Of Science, and the Cochrane Library databases between January 2012 to April 2019. A summary receiver operating characteristic curve (SROC curve) was used to analyze the pooled sensitivity, pooled specificity, PLR, NLR, and DOR for determining the accuracy of the test. Results: Our database search resulted in 10 relevant articles. The pooled sensitivity of Xpert MTB/RIF for detecting TB in GA was 86% (95% CI, 83–89%), and I2 = 93.4%. The pooled specificity was 92% (95% CI, 90–93%) and I2 = 97.8%. In addition, the positive LR was 12.12 (95% CI, 5.60–26.21), negative LR was 0.20 (95% CI, 0.11–0.36), and the diagnostic odds ratio (DOR) was 147.04 (95% CI, 37.20–581.19). Using the SROC curve, the AUC was 0.9730 and Q* was 0.9248 (SE = 0.0261). The publication bias was P=0.517 (P>0.05). Conclusions: The Xpert MTB/RIF for detecting MTB in gastric aspirates was highly accurate. In addition, we observed that the publication bias in the present study was low. Hence, the Xpert MTB/RIF technology is highly accurate and has the advantage of rapid testing for MTB in clinical samples.

OBJECTIVES/HYPOTHESIS Eosinophilic and noneosinophilic chronic rhinosinusitis with nasal polyps (ECRSwNP and NECRSwNP) show distinguished clinical pathology, but their underlying mechanism remains unclear. We aimed to investigate the clinical, hematological, and histopathological changes in chronic rhinosinusitis with nasal polyps (CRSwNP) endotypes and its association with microbiota. STUDY DESIGN A comparative cross-sectional study. METHODS A comparative study of 46 patients with CRSwNP (34.69 ± 16.39 years old) who underwent endoscopic sinus surgery were recruited and subdivided into ECRSwNP and NECRSwNP groups based on eosinophilic tissue inflammation; 12 healthy controls were also included. A structured histopathological analysis was conducted, and complete blood count was determined in patients. Endoscopic-guided middle meatus swabs and fecal samples were collected from the patients and controls and subsequently subjected to 16S rRNA gene sequencing on Illumina MiSeq. RESULTS Compared to NECRSwNP, ECRSwNP showed a statistically significant increase in the computed tomography score, endoscopic score, blood eosinophil percentage, tissue eosinophil count, inflammation degree, subepithelial edema, and eosinophil aggregation. Airway microbiota communities differed among the three groups. The abundance of Moraxella and Parvimonas was significantly higher in the ECRSwNP group. Distinct microbiota dysbiosis in CRSwNP endotypes was found to be correlated with different clinical pathologies. Moreover, the gut microbiota in ECRSwNP and NECRSwNP showed dysbiosis, that is, significant decrease in the abundance of Actinobacteria in the former and significant increase in the abundance of Enterobacterales and several genera in NECRSwNP. CONCLUSIONS Significant clinical pathology and microbiota changes were evident in patients with ECRSwNP and NECRSwNP. Distinct microbiota dysbiosis was correlated with different clinical pathologies. Understanding these differences may improve the prognosis and treatment of chronic rhinosinusitis. LEVEL OF EVIDENCE 4 Laryngoscope, 131:E34-E44, 2021.

Streptococcus agalactiae is a major pathogenic bacterium causing perinatal infections in humans. In the present study, a novel real-time fluorescence loop-mediated isothermal amplification technology was successfully developed and evaluated for the detection of S. agalactiae in a single reaction. Six specific primers were designed to amplify the corresponding six regions of fbs B gene of S. agalactiae, using Bst DNA polymerase with DNA strand displacement activity at a constant temperature for 60 min. The presence of S. agalactiae was indicated by the fluorescence in real-time. Amplification of the targeted gene fragment was optimized with the primer 1 in the current setup. Positive result was only obtained for Sa by Real-LAMP among 10 tested relevant bacterial strains, with the detection sensitivity of 300 pg/µl. Real-LAMP was demonstrated to be a simple and rapid detection tool for S. agalactiae with high specificity and stability, which ensures its wide application and broad prospective utilization in clinical practice for the rapid detection of S. agalactiae.

Kidney diseases are common and the incidence rate is increasing. Gut microbiota is involved in metabolic and immune regulation of the host. Genetic, alimentary and environmental disease factors may change gut flora and increase opportunistic and pathogenic bacteria, contributing to immune or non-immune mediated kidney diseases including IgA nephropathy and diabetic nephropathy. Additionally, bacterial metabolites may be a source of uremic toxins. Thus, identification of diversity, composition, and metabolic and immunologic features of gut bacteria in chronic kidney diseases may help understand pathogenetic mechanism and develop therapy for diseases.

To investigate the effects of orally administrated Saccharomyces boulardii (S. boulardii) on the progress of carbon tetrachloride (CCl4)-induced liver fibrosis, 34 male Wistar rats were randomly divided into four experimental groups including the control group (n = 8), the cirrhotic group (n = 10), the preventive group (n = 8), and the treatment group (n = 8). Results showed that the liver expression levels of collagen, type I, alpha 1 (Col1A1), alpha smooth muscle actin (αSMA), transforming growth factor beta (TGF-β) and the serum levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), and malondialdehyde (MDA) increased significantly in cirrhotic rats compared with control and decreased by S. boulardii administration. Treatment of S. boulardii also attenuated the increased endotoxin levels and pro-inflammatory cytokines in CCl4-treated rats. And, these were associated with the changes of intestinal permeability and fecal microbial composition. Our study suggested that oral administration of S. boulardii can promote the liver function of CCl4-treated rats, and the preventive treatment of this probiotic yeast may decelerate the progress of liver fibrosis.

Hyperuricemia is well known as the cause of gout. In recent years, it has also been recognized as a risk factor for arteriosclerosis, cerebrovascular and cardiovascular diseases, and nephropathy in diabetic patients. Foods high in purine compounds are more potent in exacerbating hyperuricemia. Therefore, the development of probiotics that efficiently degrade purine compounds is a promising potential therapy for the prevention of hyperuricemia. In this study, fifty-five lactic acid bacteria isolated from Chinese sauerkraut were evaluated for the ability to degrade inosine and guanosine, the two key intermediates in purine metabolism. After a preliminary screening based on HPLC, three candidate strains with the highest nucleoside degrading rates were selected for further characterization. The tested biological characteristics of candidate strains included acid tolerance, bile tolerance, anti-pathogenic bacteria activity, cell adhesion ability, resistance to antibiotics and the ability to produce hydrogen peroxide. Among the selected strains, DM9218 showed the best probiotic potential compared with other strains despite its poor bile resistance. Analysis of 16S rRNA sequences showed that DM9218 has the highest similarity (99%) to Lactobacillus plantarum WCFS1. The acclimated strain DM9218-A showed better resistance to 0.3% bile salt, and its survival in gastrointestinal tract of rats was proven by PCR-DGGE. Furthermore, the effects of DM9218-A in a hyperuricemia rat model were evaluated. The level of serum uric acid in hyperuricemic rat can be efficiently reduced by the intragastric administration of DM9218-A (P

Several characteristics of current infectious diseases show that most patients of infectious disease are immune tolerant hosts. Most infection-induced microorganisms come from patients themselves and people around them with normal indigenous microflora. The effectiveness of antibiotics are weakened with the emergence of multidrug resistant strains. The model of ‘infection→antibiotics→reinfection→reuse of antibiotics’ must not be followed in order to more effectively fight against infection from various critical points such as outbreaks and spreads. Infectious microecology provides theoretical and practical support to avoid and control infections. The introduction of mechanisms and applications of probiotics in prevention and control of infectious diseases will be introduced and discussed below in details.