Guild-level microbiome signature associated with COVID-19 severity and prognosis

COVID-19 severity has been associated with alterations of the gut microbiota. However, the relationship between gut microbiome alterations and COVID-19 prognosis remains elusive. Here, we performed a genome-resolved metagenomic analysis on fecal samples collected from 300 in-hospital COVID-19 patients at time of admission. Among the 2,568 high quality metagenome-assembled genomes (HQMAGs), Redundancy Analysis identified 33 HQMAGs which showed differential distribution among mild, moderate, and severe/critical severity groups. Random Forest model based on these 33 HQMAGs classified patients from different severity groups (average AUC = 0.79). Co-abundance network analysis found that the 33 HQMAGs were organized as two competing guilds. Guild 1 harbored more genes for short-chain fatty acid biosynthesis, and fewer genes for virulence and antibiotic resistance, compared with Guild 2. Random Forest regression showed that these 33 HQMAGs at admission had the capacity to predict 8 clinical parameters, which are predictors for COVID-19 prognosis, at Day 7 in hospital. Moreover, the dominance of Guild 1 over Guild 2 at admission predicted the death/discharge outcome of the critical patients (AUC = 0.92). Random Forest models based on these 33 HQMAGs classified patients with different COVID-19 symptom severity, and differentiated COVID-19 patients from healthy subjects, non-COVID-19, and pneumonia controls in three independent datasets. Thus, this genome-based guild-level signature may facilitate early identification of hospitalized COVID-19 patients with high risk of more severe outcomes at time of admission.

Comprehensive analyses reveal the impacts of vaccination status and physiological variables in early infection on viral persistence in COVID-19 patients: a retrospective single-center cohort study

BACKGROUNDViral persistence is a crucial factor that influences the communicability of SARS-CoV-2 infection. However, the impacts of vaccination status and physiological variables on viral RNA shedding have not been adequately clarified. METHODSIn this study, we retrospectively collected the clinical records of 377 hospitalized COVID-19 patients, which contained unvaccinated patients and patients received two doses of an inactivated vaccine or an mRNA vaccine. Firstly, we analyzed the impacts of vaccination on disease severity and viral RNA persistence. Next, to clarify the impacts of physiological variables on viral RNA shedding in COVID-19 patients, we retrieved 49 laboratory variables and analyzed their correlations with the duration of viral RNA shedding. Finally, we established a multivariate regression model to predict the duration of viral RNA shedding. RESULTSOur results showed that both inactivated and mRNA vaccines significantly reduced the rate of moderate cases, while the vaccine related shortening of viral RNA shedding were only observed in moderate patients. Correlation analysis showed that 10 significant laboratory variables were shared by the unvaccinated mild patients and mild patients inoculated with an inactivated vaccine, but not by the mild patients inoculated with an mRNA vaccine. Moreover, we demonstrated that a multivariate regression model established based on the variables correlating with viral persistence in unvaccinated mild patients could predict the duration of viral shedding for all groups of patients. CONCLUSIONSVaccination contributed limitedly to the clearance viral RNA in COVID-19 patients. While, laboratory variables in early infection could predict the persistence of viral RNA.

Pre-existing antibodies targeting a dominant linear antibody epitope on SARS-CoV-2 S2 cross-reacted with commensal gut bacteria and shaped immune responses elicited by a candidate vaccine

The origins of pre-existing SARS-CoV-2 cross-reactive antibodies and their potential impacts on vaccine efficacy have not been fully clarified. In this study, we demonstrated that S2 was the prevailing target of the pre-existing S protein cross-reactive antibodies in both healthy human and SPF mice. A dominant antibody epitope was identified on the connector domain of S2 (1147-SFKEELDKYFKNHT-1160, P144), which could be recognized by pre-existing antibodies in both human and mouse. Through metagenomic sequencing and fecal bacteria transplant, we proved that the generation of S2 cross-reactive antibodies was associated with commensal gut bacteria. Furthermore, six P144 specific monoclonal antibodies were isolated from naive SPF mice and proved to cross-react with commensal gut bacteria collected from both human and mouse. Mice with high levels of pre-existing S2 cross-reactive antibodies mounted higher S protein specific binding antibodies, especially against S2, after being immunized with a SARS-CoV-2 S DNA vaccine. Similarly, we found that levels of pre-existing S2 and P144 reactive antibodies correlated positively with RBD specific binding antibody titers after two doses of inactivated SARS-CoV-2 vaccination in human. Finally, we provided data demonstrating that immunization of a SARS-CoV-2 S DNA vaccine could alter the gut microbiota compositions of mice.

Virus-host interactome and proteomic survey of PMBCs from COVID-19 patients reveal potential virulence factors influencing SARS-CoV-2 pathogenesis

The ongoing coronavirus disease (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a global public health concern due to relatively easy person-to-person transmission and the current lack of effective antiviral therapy. However, the exact molecular mechanisms of SARS-CoV-2 pathogenesis remain largely unknown. We exploited an integrated proteomics approach to systematically investigate intra-viral and virus-host interactomes for the identification of unrealized SARS-CoV-2 host targets and participation of cellular proteins in the response to viral infection using peripheral blood mononuclear cells (PBMCs) isolated from COVID-19 patients. Using this approach, we elucidated 251 host proteins targeted by SARS-CoV-2 and more than 200 host proteins that are significantly perturbed in COVID-19 derived PBMCs. From the interactome, we further identified that non-structural protein nsp9 and nsp10 interact with NKRF, a NF-[Kcy]B repressor, and may precipitate the strong IL-8/IL-6 mediated chemotaxis of neutrophils and overexuberant host inflammatory response observed in COVID-19 patients. Our integrative study not only presents a systematic examination of SARS-CoV-2-induced perturbation of host targets and cellular networks to reflect disease etiology, but also reveals insights into the mechanisms by which SARS-CoV-2 triggers cytokine storms and represents a powerful resource in the quest for therapeutic intervention.

Durability of neutralizing antibodies and T-cell response post SARS-CoV-2 infection / 医学前沿

The ongoing pandemic of Coronavirus disease 19 (COVID-19) is caused by a newly discovered β Coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). How long the adaptive immunity triggered by SARS-CoV-2 can last is of critical clinical relevance in assessing the probability of second infection and efficacy of vaccination. Here we examined, using ELISA, the IgG antibodies in serum specimens collected from 17 COVID-19 patients at 6-7 months after diagnosis and the results were compared to those from cases investigated 2 weeks to 2 months post-infection. All samples were positive for IgGs against the S- and N-proteins of SARS-CoV-2. Notably, 14 samples available at 6-7 months post-infection all showed significant neutralizing activities in a pseudovirus assay, with no difference in blocking the cell-entry of the 614D and 614G variants of SARS-CoV-2. Furthermore, in 10 blood samples from cases at 6-7 months post-infection used for memory T-cell tests, we found that interferon γ-producing CD4

Species distribution characteristics of nontuberculous mycobacteria isolated from patients with acquired immunodeficiency syndrome in Shanghai / 中华传染病杂志

Objective To investigate the species distribution characteristics of nontuberculous mycobacteria(NTM)in acquired immunodeficiency syndrome(AIDS)patients in Shanghai,and to provide evidences for clinical treatment.Methods A total of 775 Mycobacteria strains were isolated from patients(including 129 isolates from AIDS patients and 646 isolates from HIV-negative patients)admitted to Shanghai Public Health Clinical Center during 2015.All the species were identified by the sequence analysis of 16S rRNA gene and hsp65 gene.Differences in the species distribution were compared between patients with and without HIV infection.CD4+T lymphocyte count was detected by flow cytometry and its relation with mycobacteria infection was also analyzed.Chi-square test was used for comparison between groups.Results The ratio of NTM isolation from HIV-negative patients was 15.79%(102/646),while that was 46.51% in AIDS patients(60/129),and the difference was statistically significant(x2=61.38,P <0.01).Among the 60 NTM strains isolated from AIDS patients,mycobacterium avium-intracelluare complex(MAC)and Mycobacterium gordonae were the predominant species(43.33% and 20.00%,respectively).Moreover,five Mycobacterium colombiense strains,which were relatively rare,were also obtained.A total of 102 NTM were identified from HIV-negative patients,of which Mycobacterium gordonae(32 isolates,31.37%)and MAC(30 isolates,29.41%)were the most frequently isolated.In addition,the positive rates of NTM and MAC were significantly higher in patients with CD4+T lymphocyte counts ≤50 cells/μL(58.33% and 76.92%,respectively)than those with CD4+T lymphocyte counts>50 cells/μL(20.00% and 15.38%,respectively)(x2=4.048 and 6.524,respectively,both P<0.05).Four out of five Mycobacterium colombiense infected patients died of disseminated infections,except the remaining one whose CD4+T lymphocyte counts>50 cells/μL.Conclusions The prevalence of NTM isolation is significant higher in AIDS patients than HIV-negative patients in Shanghai,and the most prevalent NTM species is MAC.The NTM infection in AIDS patients is related with low CD4+T lymphocyte counts.

Investigation of drug resistance and multilocus sequence typing for differentiation of strains of Candida tropicalis of Shanghai / 中华预防医学杂志

Objective@#To analyze the drug resistance of clinical isolates of Candida tropicalis in patients with infectious diseases, and preliminarily study their molecular characteristics.@*Methods@#95 strains of Candida tropicalis were isolated from the fungal culture specimens of 87 patients with infectious diseases in Shanghai Public Health Clinical Center from 2012 to 2015. Meanwhile, basic clinical data of patients were collected. The drug resistance of the strains to fungal drugs was analyzed by ATB FUNGUS 3 drug sensitivity test strips. All strains were classified by Multilocus sequence typing(MLST). Then, homology analysis was conducted by MEGA 5.2 software, and the evolutionary tree was mapped by using UPGMA method.@*Results@#Patients distribution of strains was rendered as following: 31 strains from TB patients, 21 strains from HIV/AIDS patients, 19 strains from patients with liver disease, and 24 strains from rare cause infection or fever patients. The drug resistance rate to five antifungal drugs commonly used in clinical (amphotericin B, 5-fluorine cytosine, fluconazole, itraconazole, voriconazole) were 2.11% (2 strains), 0, 26.32% (25 strains), 26.32% (25 strains), and 26.32% (25 strains) respectively. Among the 25 azole-resistant strains: 14 strains were from rare cause infection or fever patients, 8 strains were from HIV/AIDS patients, and 3 strains were from tuberculosis patients. In MLST, 72 sequence types (ST types) were produced, 70 of which were new types. Evolutionary tree analysis showed that 95 strains of clinical strains distribute as three large clusters. 24 azole resistant strains (96.0%) were located in CLUSER Ⅰ.@*Conclusion@#The isolated Candida tropicalis were mainly resistant to azole drugs. MLST typing indicates that they was closely related to their genetic background.

Influences of hypoxia inducible factor-1α on the expression of inflammatory cytokines in mice with influenza A (H1N1) virus infection / 中华微生物学和免疫学杂志

Objective@#To analyze the changes in the expression of hypoxia inducible factor-1α (HIF-1α) and inflammatory cytokines and to investigate the role of HIF-1α in regulating the production of inflammatory cytokines during influenza A (H1N1) virus infection.@*Methods@#BALB/c mice were injected with H1N1 virus to establish the mouse model of H1N1 virus infection. Fifteen BALB/c mice were randomly divided into three groups: control group, H1N1 virus group and H1N1 virus+ HIF-1α inhibitor group. Inflammatory cytokines (IL-6, TNF-α, IL-1β and IL-10) in samples of serum and lung tissues were detected by Luminex and ELISA. Levels of HIF-1α in serum and lung tissue samples were detected by Western blot and ELISA, respectively.@*Results@#Compared with the control group, the levels of inflammatory cytokines in serum (IL-6, TNF-α, IL-1β and IL-10) and lung tissues (IL-6 and TNF-α) and the expression of HIF-1α in serum and lung tissues in the H1N1 virus group were significantly increased. The levels of HIF-1α, IL-6, TNF-α IL-1β and IL-10 in lung tissues in H1N1 virus+ HIF-1α inhibitor group were significantly lower than those of the H1N1 virus group.@*Conclusion@#During H1N1 virus infection, the levels of inflammatory cytokines and HIF-1α were significantly increased. The production of inflammatory cytokines was significantly reduced after inhibiting HIF-1α expression, suggesting that HIF-1α might promote the production of inflammatory cytokines.

Comparison of three mouse models infected with influenza virus by aerosol / 中国实验动物学报

Objective To compare and analyze the differences and characteristics of three strain mouse models in-fected by influenza virus aerosol inhalation, and provide the reference for choosing the appropriate infection model in the re-search of pathogenesis of influenza and the development of vaccines and drugs.Method C57BL/6, BALB/c and ICR mice were infected with A/Puerto Rico/8/34 (H1N1) virus strain by aerosol inhalation.The symptoms and body weight of mice were observed every day.At 3, 7, 14 days after infection, the mice were sacrificed.The lungs of mice were weighed, then virus assay and pathological observation were carried out.Results The three strains of mice were infected.The sur-vival rate in the C57BL/6 mice was lower than those in the BALB/c and ICR mice.The lung index and viral load of C57BL/6 mice were significantly higher than those of ICR mice ( P<0.05) at 3 days after infection.The pathological changes of C57BL/6 mice were also more obvious than other two strains.Compared with other two mouse strains, the weight recovery of BALB/c mice was the slowest.The survival rate in BALB/c mice was higher than that of C57BL/6 mice and lower than that of ICR mice.The lung index and viral load were not significantly different among the three strains of in-fected mice.The pathological changes among the three strains of infected mice were similar, but the degrees of pathological changes in the BALB/c mice were milder than in the C57BL/6 mice and worse than in the ICR mice.Compared with other two mouse strains, the process of disease is similar, but the body weight, mortality, lung index, viral load, and the micro-scopic pathological changes were lighter in the ICR mice than in the other two strain mice.Conclusions The three strain mouse models can be established by influenza virus aerosol inhalation, but showing different characteristics.Appropriate strain mice can be chosen to build model according to different research purpose in the experiment.

Analysis of twin-arginine translocation system gene homology and transcription in Vibrio species / 中华预防医学杂志

<p><b>OBJECTIVE</b>To determine the function of twin-arginine translocation system (Tat) and gene cluster in Vibrio strains and to analyze the homology of tat gene cluster among different Vibrio spp. strains based on N16961 and tatABC mutant strains N169-dtat.</p><p><b>METHODS</b>Different serotypes of biotype strains of Vibrio spp. were selected to detect the transcription of 4 genes of Tat transport system and upstream ubi aarF gene and downstream cyt551 gene by the total RNA reverse transcription and homologicity of the gene cluster by sequencing analysis.</p><p><b>RESULTS</b>Our results showed that the 4 genes of tat cluster (tatA, tatB, tatC, and tatE) were intragenic and co-transcribed. We found that ubi aarF gene could be co-transcribed with tatA, tatB, but not with tatC. The electron transport chain and energy metabolism-related genes, cytochrome C551 peroxidase gene, and 4 genes located at upstream of tatABC operon were not transcribed with tatABC. Although the co-transcription between ubi aarF and tatAB was blocked in N169-dtat strain, they were still transcribed separately. Homologous analysis of genes of tat cluster in different types of Vibrio cholerae showed that tat gene cluster was a very conservative.</p><p><b>CONCLUSION</b>The ubi and aarF gene might be co-transcribed with genes of tat cluster in Vibrio cholerae, which and the close relationship showed that they might play a key function in Vibrio cholerae.</p>

The infection and molecular characteristics of Vibrio parahaemolyticus isolated from intestinal outpatient in two sentinel hospitals in Shanghai, 2010-2012 / 中华预防医学杂志

<p><b>OBJECTIVE</b>To analyze virulence genes and molecular characteristics of Vibrio parahaemolyticus isolated from sporadic cases with diarrhea in tow sentinel hospitals of Shanghai, 2010-2012.</p><p><b>METHODS</b>A total of 2 729 stool samples were collected from two surveillance sentinel hospitals in Shanghai 2010-2012. Vibrio parahaemolyticus strains were isolated and identified from diarrhea out patients using TCBS agar plates and biochemical reactions. Thermostable direct hemolysingene (tdh), thermostable-related hemolysin gene (trh), hemolysin gene (tlh) were detected by multiplex PCR method. Isolates were analyzed by PFGE and MLST. The PFGE profiles were analyzed using BioNumerics software.</p><p><b>RESULTS</b>A total of 30 clinical Vibrio parahaemolyticus strains isolated from 2 729 stool samples. The anually Vibrio parahaemolyticus isolation rate during 2010 to 2012 were 1.1%(11/973), 1.0%(11/1 120) and 1.3%(8/636) respectively. The PCR positive rates of virulence genes tlh, tdh and trh were 100%, 97% and 0 respectively. The Vibrio parahaemolyticus strains were divided into 13 PFGE types (P1-P13)and 3 ST types (ST-189, ST-799, ST-3). Among 13 PFGE types, P4 was the main PFGE type, accounting for 30%(9/30). P9, P10 were accounting for 12% (4/30) respectively, P1, P2, P12, P13 were accounting for 7%(2/30) respectively, the others types were 3%(1/30) respectively. MLST analysis results showed there are three ST types, ST3 was 84%(25/30), ST189 and ST799 were accounting for 13% (4/30) and 3% (1/30) respectively.</p><p><b>CONCLUSION</b>The infection rate of Vibrio parahaemolyticus was not very high from 2010-2012 in Shanghai, all strains were positive for tlh and negative for trh. ST3 was the major type of Vibrio parahaemolyticus.</p>

Enzyme-linked immunospot assay combined with serum latex agglutination test for diagnosis of pulmonary tuberculosis and concomitant pulmonary cryptococcosis / 中国感染与化疗杂志

Objective To evaluate the value of enzyme-linked immunospot assay (TB ELISPOT) combined with serum latex agglutination test (LA) for diagnosis of pulmonary tuberculosis plus pulmonary cryptococcosis.Methods Serum and biopsy specimens of 76 patients, who were suspected of pulmonary tuberculosis and/or pulmonary cryptococcosis based on clinical and imaging features, were collected from March 2006 to September 2008 in Shanghai Public Health Clinical Center. TB ELISPOT assay, LA and histopathological examination were performed in all the patients. Results Histopathological and pathogenic examination confirmed pulmonary cryptococcosis in 15 cases and pulmonary tuberculosis in 22 cases, pulmonary tuberculosis plus pulmonary cryptococcosis in 8 cases. The sensitivity and specificity of TB ELISPOT were 91% and 94.4%. The sensitivity and specificity of LA were both 100%. TB ELISPOT assay and LA test were both positive in the 8 cases of pulmonary tuberculosis plus pulmonary cryptococcosis.Conclusions The value of enzyme-linked immunospot assay combined with serum latex agglutination test is high for diagnosis of pulmonary tuberculosis plus pulmonary cryptococcosis.

Development of mycobacterial inducible expression system and application for immunological diagnostics on tuberculosis / 中华微生物学和免疫学杂志

Objective To develop mycobacterial inducible expression vectors which permit to overexpress Mycobacterium tuberculosis (Mtb) immunodominant antigen, and to analyze its immunogenicity after purification by affinity chromatography. Methods The regulatory region of M. smegmatis (Ms) acet-amidase(pACE) was obtained by PCR amplification, and was used as promoter to construct the mycobacteri-al inducible expression vectors, pMF series. The coding gene of Mtb chimeric antigen Ag856A2 which is a recombinant Ag85A with 2 copies of ESAT-6 inserted in its Acc Ⅰ site and showed excellent immunogenicity in the animal experiments we described previously, was cloned into the pMF vector series, and was induced to express by the addition of acetamide. The recombinant protein expressed in the Ms was purified by the Ni~(2+)-NTA affinity chromatography, the resulted homologous recombinant antigen was added into the spleen cells separated from BCG vaccinated mice, and the immunogenicity was analyzed by the IFN-γ ELISPOT as-say. Results The mycobacterial inducible expression vectors, pMF series was constructed successfully, target antigen could be. induced to express in the Ms by the addition of 0.02% acetamide, and could be puri-fied by the Ni~(2+) -NTA affinity chromatography due to the addition of 6×His tag in the vector pMF406. Fur-thermore, the mycobactefial homologous antigen could induce more IFN-γ secretion than the heterogonous one. Conclusion The mycobacterial inducible expression system based on the regulatory region of Ms acet-amidase as promoter could permit the Mtb target antigen of interest overexpression and purification, and the immunogenicity of the homologous antigen from Ms is better than that of be expressed from E. coli, which may be more potential for immunological detection of tuberculosis.