Integrated analysis of gut microbiome and host immune responses in COVID-19 / 医学前沿

Emerging evidence indicates that the gut microbiome contributes to the host immune response to infectious diseases. Here, to explore the role of the gut microbiome in the host immune responses in COVID-19, we conducted shotgun metagenomic sequencing and immune profiling of 14 severe/critical and 24 mild/moderate COVID-19 cases as well as 31 healthy control samples. We found that the diversity of the gut microbiome was reduced in severe/critical COVID-19 cases compared to mild/moderate ones. We identified the abundance of some gut microbes altered post-SARS-CoV-2 infection and related to disease severity, such as Enterococcus faecium, Coprococcus comes, Roseburia intestinalis, Akkermansia muciniphila, Bacteroides cellulosilyticus and Blautia obeum. We further analyzed the correlation between the abundance of gut microbes and host responses, and obtained a correlation map between clinical features of COVID-19 and 16 severity-related gut microbe, including Coprococcus comes that was positively correlated with CD3+/CD4+/CD8+ lymphocyte counts. In addition, an integrative analysis of gut microbiome and the transcriptome of peripheral blood mononuclear cells (PBMCs) showed that genes related to viral transcription and apoptosis were up-regulated in Coprococcus comes low samples. Moreover, a number of metabolic pathways in gut microbes were also found to be differentially enriched in severe/critical or mild/moderate COVID-19 cases, including the superpathways of polyamine biosynthesis II and sulfur oxidation that were suppressed in severe/critical COVID-19. Together, our study highlighted a potential regulatory role of severity related gut microbes in the immune response of host.

Evaluation of the capability of three phenotypic tests used alone or in combination for identification of Staphylococcus aureus / 中华微生物学和免疫学杂志

Objective To evaluate the capability of three tests used alone or in combination for identification of Staphylococcus aureus.Methods Identification of Staphylococcus aureus by the detection of spa gene with PCR and the Vitek-2 system were selected as the reference methods.Comparison of three phenotypic tests including DNase,mannitol fermentation and tube coagulase test was carried out to analyze the sensitivity,specificity,positive/negative predictive value,positive/negative likelihood ratio and Youden index.The consistency,cost and related indexes of the assays were analyzed between the combined phenotypic tests and the reference methods.Results In the present study,324 isolates of Staphylococci,including 293 Staphylococcus aureus and 31 non-Staphylococcus aureus,were collected.Single biochemical test could not identify Staphylococcus aureus efficiently.Comparison between the reference methods and the combined three biochemical tests by Kappa statistic analysis indicated that an overall Kappa value was 0.9441,and the algorithm of combined test was less costly.The sensitivity and specificity of this algorithm were 100％ and 90.3％,respectively.Conclusion The cost-effective algorithm of combined DNase,mannitol fermentation and tube coagulase test could efficiently distinguish Staphylococcus aureus from other Staphylococcus species.

Evaluation on the capability of CHROMagar orientation medium combined with simple biochemical tests for identificaction of common oxidase-negtive gram-negative bacilli / 中华微生物学和免疫学杂志

Objective To evaluate the practicability of CHROMagar orientation medium combined with simple biochemical tests for identification of common oxidase-negtive gram-negative bacilli.Methods The CHROMagar orientation medium was used together with biochemical tests including indole test , ornithine decarboxylase test and lysine decarboxylase test for identification of common oxidase -negtive gram-negative bacilli.The sensitivity, specificity, likelihood ratio, Youden index and Kappa value of the diagnostic assays were evaluated .McNemar test was performed to evaluate facticity, accuracy and cost of the method in com-parison with the Vitek-2 system as reference method .Results The identification of oxidase-negtive gram-negative bacilli from 318 bacterial strains showed that the sensitivities and specificities of CHROMagar orien-tation mediumm in combination with simple biochemical tests to Serratia marcescens, Stenotrophomonas mal-tophilia and Acinetobacter baumannii reached 100%, and for Escherichia coli, Enterobacter aerogenes and Klebsiella pneumoiae were above 90%.The specificities for identification of Enterobacter cloacae, Klebsiella oxytoca, Citrobacter freundii and Proteus mirabilis were all above 90%, but the sensitivities were around 75%-90%.Kappa values of the assays were above 0.85, howerer, which was only 0.5947 for Citrobacter freundii.McNemar test showed that all P values were above 0.05, and cost of the assays was reduced by 90%.Conclusion CHROMagar orientation medium in combination with simple biochemical tests is a cost-effective assay for identification of common oxidase-negtive gram-negative bacilli .