A Method of Evaluating Safe Operating Space: Focus on Geographic Regions, Income Levels and Developing Pathway.

Safe and Just Space (SJS) is a framework for determining the range where the use of natural resources within the Earth's carrying capacity can maintain human well-being. However, there has been no systematic monitoring and evaluation of their sustainability across time and space. Here we developed and applied a model and a sustainable development human safe operation space (SDHSOS) index to assess the sustainability capacity and development path of 149 countries from 2000 to 2018. The results demonstrate that (1) The overall sustainable development capacity of all countries is at the middle or lower level and that it has increased over time. (2) The sustainability of natural and socio-economic dimensions and their degree of change show obvious geographic differences and income differences. (3) The national development path divided by income is characterized by a decline in natural environment dimensions and an increase in socio-economic dimensions, which mainly reflects a traditional development path model that promotes social welfare at the expense of the natural environment. This study suggests that nations can accurately identify development characteristics, expand their comparative advantages is the key to improving sustainable development capabilities.

Peripheral immune phenotypes and T cell receptor repertoire in pneumocystis pneumonia in HIV-1 infected patients.

BACKGROUND: The host immune response to pneumocystis pneumonia (PCP) involves interactions among immune cell subsets and cytokines. However, the definite pathogenesis and immunological influences of P. jirovecii have not been fully elucidated. METHODS: Mass cytometry and high-throughput sequencing of the T cell receptor (TCR) were used to profile the host immune response to human immunodeficiency virus-1 (HIV-1) and P. jirovecii infection. RESULTS: Our findings demonstrated that patients with PCP showed different immune cell proportions when compared to healthy controls. Changes in cytokines were found after anti-PCP treatment, suggested that cytokines may play an important role in controlling the pathogen. Furthermore, PCP patients showed marked reduction of TCR repertoire diversity. The diversity of TCR repertoire was restored by the anti-PCP treatment. CONCLUSION: In summary, we profiled the composition and characteristics of immune environment in response to HIV-1 and P. jirovecii infection, which may contribute to elucidating host immunity.

Exploring complex water stress-gross primary production relationships: Impact of climatic drivers, main effects, and interactive effects.

The dominance of vapor pressure deficit (VPD) and soil water content (SWC) for plant water stress is still under debate. These two variables are strongly coupled and influenced by climatic drivers. The impacts of climatic drivers on the relationships between gross primary production (GPP) and water stress from VPD/SWC and the interaction between VPD and SWC are not fully understood. Here, applying statistical methods and extreme gradient boosting models-Shapley additive explanations framework to eddy-covariance observations from the global FLUXNET2015 data set, we found that the VPD-GPP relationship was strongly influenced by climatic interactions and that VPD was more important for plant water stress than SWC across most plant functional types when we removed the effect of main climatic drivers, e.g. air temperature, incoming shortwave radiation and wind speed. However, we found no evidence for a significant influence of elevated CO2 on stress alleviation, possibly because of the short duration of the records (approximately one decade). Additionally, the interactive effect between VPD and SWC differed from their individual effect. When SWC was high, the SHAP interaction value of SWC and VPD on GPP was decreased with increasing VPD, but when SWC was low, the trend was the opposite. Additionally, we revealed a threshold effect for VPD stress on GPP loss; above the threshold value, the stress on GPP was flattened off. Our results have important implications for independently identifying VPD and SWC limitations on plant productivity, which is meaningful for capturing the magnitude of ecosystem responses to water stress in dynamic global vegetation models.

Salivary microbial diversity at different stages of human immunodeficiency virus infection.

Human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) disrupts the host microbial balance. During disease progression, the oral microbial environment is altered in untreated people living with HIV/AIDS (PLWHA); however, no studies have reported changes in salivary microbial diversity during different stages of HIV infection. Therefore, in this study, we aimed to assess the relationships between immune dysfunction and changes in saliva microbiota. To this end, we collected saliva samples from 11 HIV-negative individuals and 44 PLWHA during different stages based on the Centers for Disease Control and Prevention criteria (stage 0, early stage during the first 6 months after infection; stages 1, 2, and 3 associated with CD4+ T-lymphocyte counts of ≥500, 200-499, and ≤200 or opportunistic infection, respectively). We analyzed salivary microbial community diversity using polymerase chain reaction amplification and Illumina MiSeq sequencing. We found that HIV-positive individuals had significantly greater alpha-diversity in the microbial community composition compared with HIV-negative controls (P < 0.05) except for AIDS (stage 3); however, the predominant salivary microbiota in the five groups remained similar. Porphyromonas in the four positive groups was the only genus that was significantly less abundant in the HIV-positive groups than in the control group (P < 0.05). There were some consistencies between the general abundance of salivary microbiota and AIDS disease progression. Lots of bacterial abundances in the saliva increased dramatically during the acute HIV infection (stage 0), and some of the negligible and abnormally proliferating bacteria in the asymptomatic stage showed a downward trend. Additionally, in the AIDS stage, partial inhibition was observed. Notably, Porphyromonas was closely related to the immune activation of HIV, showing a decline in abundance once infected with HIV. Solobacterium, which induces inflammation, was negatively correlated with CD4 counts. Overall, our findings provided important insights into changes in salivary microbial diversity in PLWHA.

Association of the IL-6 Rs1800796 SNP with Concentration/dose Ratios of Tacrolimus and Donor Liver Function after Transplantation.

Interleukin-6 (IL-6) is a proinflammatory cytokine that plays a range of important roles such as in inflammation, immune response, and cell growth regulation. Here, we aimed to assess the potential influence of the IL-6 single nucleotide polymorphism (SNP) rs1800796 on the concentration/dose (C/D) ratios of tacrolimus and donor liver function in Chinese liver transplant patients. A total of 331 liver transplant patients were included in this study. The C/D ratios and the ALT, AST, T-BIL, ALP, and GGT levels were analyzed at different time points in patients with and without the IL-6 rs1800796 SNP. The IL-6 rs1800796 polymorphism in recipients was found to be correlated with the C/D ratios of tacrolimus at months 2 to month 6 after transplantation. Also, the rs1800796 SNP in donors was found to influence liver function (shown in the data of ALT, AST, T-BIL, ALP and GGT) in recipients at the early post-transplant stage after transplantation. In conclusion, the IL-6 rs1800796 polymorphism was associated with the C/D ratios of tacrolimus and post-transplant donor liver function.

Downregulated Gene Expression Spectrum and Immune Responses Changed During the Disease Progression in Patients With COVID-19.

BACKGROUND: The World Health Organization characterizes novel coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a pandemic. Here, we investigated the clinical, cytokine levels; T-cell proportion; and related gene expression occurring in patients with COVID-19 on admission and after initial treatment. METHODS: Eleven patients diagnosed with COVID-19 with similar initial treatment regimens were enrolled in the hospital. Plasma cytokine, peripheral T cell proportions, and microfluidic quantitative polymerase chain reaction analyses for gene expression were conducted. RESULTS: Five patients with mild and 6 with severe disease were included. Cough and fever were the primary symptoms in the 11 COVID-19 cases. Older age, higher neutrophil count, and higher C-reactive protein levels were found in severe cases. IL-10 level significantly varied with disease progression and treatment. Decreased T-cell proportions were observed in patients with COVID-19, especially in severe cases, and all were returned to normal in patients with mild disease after initial treatment, but only CD4+ T cells returned to normal in severe cases. The number of differentially expressed genes (DEGs) increased with the disease progression, and decreased after initial treatment. All downregulated DEGs in severe cases mainly involved Th17-cell differentiation, cytokine-mediated signaling pathways, and T-cell activation. After initial treatment in severe cases, MAP2K7 and SOS1 were upregulated relative to that on admission. CONCLUSIONS: Our findings show that a decreased T-cell proportion with downregulated gene expression related to T-cell activation and differentiation occurred in patients with severe COVID-19, which may help to provide effective treatment strategies for COVID-19.

Mitochondrial DNA mutations accumulated in HIV-1-infected children who have an excellent virological response when exposed to long-term antiretroviral therapy.

Objectives: There is growing concern about mitochondrial DNA (mtDNA) mutations with long-term NRTI exposure in HIV-1 infected children. Methods: Twenty-four HIV-1 infected children who started ART more than 2 years earlier who had an excellent virological response and had not changed their regimen were enrolled retrospectively. Their corresponding PBMCs in 2009 (T1), 2010 (T2) and 2013 (T3) were included. Sequencing of the entire mtDNA using next-generation sequencing revealed the spectrum of mtDNA variants. Results: The trend showed that the number of mtDNA mutations during ART occurred as T1 < T2 < T3 (P = 0.086). Interestingly, the numbers of whole mtDNA mutations at T3 (median 41, range 24-62) were significantly greater than at T1 (34, 25-46, P = 0.029). A positive correlation was found between total mtDNA mutations and treatment time (r = 0.352, P = 0.002). During the observation period, mtDNA mutations more frequently occurred in the D-loop, cytochrome b (CYTB) and 12S rRNA regions. The heteroplasmic ratio of T3 was higher than that of T1 in CYTB and 12S rRNA (P = 0.034 and P = 0.042, respectively). High heteroplasmic population levels were found at nt 263 (A263G, D-loop) and nt 8860 (A8860G, ATPase6). A significant difference in heteroplasmy between T1, T2 and T3 occurred at nt 14783 (T14783C, CYTB, P = 0.048, T3 > T2 > T1). Conclusions: Our findings reveal the spectrum of mtDNA variants in HIV-1-infected children who had an excellent virological response. mtDNA mutations accumulated during ART may play an important role in facilitating the occurrence of mitochondrial dysfunction.

Discordant patterns of tissue-specific genetic characteristics in the HIV-1 env gene from HIV-associated neurocognitive disorder (HAND) and non-HAND patients.

The genetic evolution of HIV-1 in the central nervous system (CNS) is different from that in peripheral tissues. We analyzed 121 clonal sequences of the V3-V5 regions of the env gene generated from paired cerebrospinal fluid (CSF) and plasma samples from nine chronically infected patients (four with HIV-associated neurocognitive disorder (HAND) and five without HAND). The sequence analysis indicated the significant differences between CSF and plasma was only observed in the C4 region (P = 0.043) in HAND patients. Significant increases in synonymous substitutions (dS) within the V4 region (P = 0.020) and in nonsynonymous substitutions (dN) within the C4 region (P = 0.029) were observed in the CSF-derived sequences. By contrast, CSF-derived sequences from non-HAND patients showed similar levels of diversity; dS and dN as the plasma-derived sequences. Signature differences between the CSF- and plasma-derived sequences were found at 12 amino acid positions for HAND patients and nine positions for non-HAND patients. Interestingly, five sites (positions 388, 396, 397, 404, and 406) that all belong to signature patterns exhibited positive selection pressure in CSF samples, but only site 406 was positively selected in the plasma samples from the HAND patients. Conversely, in the non-HAND patients, there were four sites (positions 397, 404, 432, and 446) showed positive selection pressure in the plasma samples, but only site 446 in the CSF samples. These results suggest that discordant patterns of genetic evolution occur between the tissue-specific HIV-1 quasispecies in the HAND and non-HAND patients. Viral molecular heterogeneity between specific tissues is greater in patients with HAND compared to non-HAND patients.

The effects of Qingchang Ligan formula on hepatic encephalopathy in mouse model: results from gut microbiome-metabolomics analysis.

Background: Hepatic encephalopathy (HE) is a neurological disorder resulting from advanced liver injury. HE has a high mortality rate and poor prognosis. The pathogenesis of HE is still unclear, which has led to the lack of a satisfactory specific treatment method. There is increasing evidence that the intestinal flora affects the communication between the gut and the brain in the pathogenesis of HE. Adjusting the intestinal flora has had a beneficial effect on HE in recent studies, and the Qingchang Ligan formula (QCLG) has been shown in previous studies to regulate intestinal flora and metabolites. In this study, we established a thioacetamide-induced HE mouse model to evaluate the protective effect of QCLG on HE and explore its potential mechanism, which also demonstrated that intestinal flora dysbiosis is involved in the pathogenesis of HE. Methods: Mice were intraperitoneally injected with thioacetamide (TAA, 150 mg/kg) to induce HE. Additionally, they were orally administered Qingchang Ligan Formula (QCLG) at a dose of 6.725 g/kg·d for seven days, while control mice received an equal volume of saline via gavage. Subsequently, samples were subjected to 16S ribosomal ribonucleic acid (rRNA) gene sequencing, high-performance liquid chromatography-mass spectrometry (LC-MS), and RNA-sequencing (RNA-seq) analysis. Result: QCLG improved weight loss, cognitive impairment, neurological function scores, blood ammonia, and brain gene expression of interleukin-6 (TNF-α), Interleukin-1ß (IL-1ß), and interleukin-6 (IL-6) induced by HE. Moreover, QCLG increased the levels of liver function indicators, including alanine aminotransferase (ALT), aspartate aminotransferase (AST), and serum TNF-α, IL-1ß, and IL-6. 16S RNA sequencing revealed increased Oscillibacter, Colidextribacter, and Helicobacter in TAA-induced mouse fecal samples. Also, the abundance of Bifidobacterium decreases TAA-induced mouse fecal samples. In contrast, QCLG treatment significantly restored the gut microbial community. Metabolomics indicated significant differences in some metabolites among the normal control, treatment, and model groups, including 5-methoxytryptophan, Daidzein, Stercobilin, and Plumieride (PLU). Conclusion: QCLG can alleviate neuroinflammation and prevent HE caused by liver injury by regulating intestinal flora in mouse models.

Integrated analysis of microbiome and host transcriptome unveils correlations between lung microbiota and host immunity in bronchoalveolar lavage fluid of pneumocystis pneumonia patients.

OBJECTIVE: The lung microbiota of patients with pulmonary diseases is disrupted and impacts the immunity. The microbiological and immune landscape of the lungs in patients with pneumocystis pneumonia (PCP) remains poorly understood. METHODS: Multi-omics analysis and machine learning were performed on bronchoalveolar lavage fluid to explore interaction between the lung microbiota and host immunity in PCP. Then we constructed a diagnostic model using differential genes with LASSO regression and validated by qPCR. The immune infiltration analysis was performed to explore the landscape of lung immunity in patients with PCP. RESULTS: Patients with PCP showed a low alpha diversity of lung microbiota, accompanied by the elevated abundance of Firmicutes, and the differential expressed genes (DEGs) analysis displayed a downregulation of MAPK signaling. The MAPK10, TGFB1, and EFNA3 indicated a potential to predict PCP (AUC = 0.86). The lung immune landscape in PCP showed the lower levels of naïve CD4+ T cells and activated dendritic cells. The correlation analysis of the MAPK signaling pathway-related DEGs and the differential microorganisms at the level of phylum showed that the Firmicutes was negatively correlated with these DEGs. CONCLUSION: We profiled the characteristics of lung microbiota and immune landscape in PCP, which may contribute to elucidating the mechanism of PCP.

Clinical evaluation of droplet digital pcr for suspected ascites infection in patients with liver cirrhosis.

BACKGROUND: Droplet digital PCR (ddPCR) is increasingly used in diagnosing clinical pathogens, but its effectiveness in cirrhosis patients with suspected ascites infection remains uncertain. METHODS: The diagnostic performance of ddPCR was assessed in 305 ascites samples, utilizing culture and clinical composite standards. The quantitative value and potential clinical impact of ddPCR were further analyzed in patients with spontaneous bacterial peritonitis. RESULTS: With culture standards, ddPCR demonstrated a sensitivity of 86.5% and specificity of 83.2% for bacterial or fungal detection. After adjustment of clinical composite criteria, specificity increased to 96.4%. Better diagnostic performance for all types of targeted pathogens, particularly fungi, was observed with ddPCR compared to culture, and more polymicrobial infections were detected (30.4% versus 5.7%, p < 0.001). Pathogen loads detected by ddPCR correlated with white blood cell count in ascites and blood, as well as polymorphonuclear cell (PMN) count in ascites, reflecting infection status rapidly. A positive clinical impact of 55.8% (43/77) was observed for ddPCR, which was more significant among patients with PMN count ≤ 250/mm3 in terms of medication adjustment and new diagnosis. ddPCR results for fungal detection were confirmed by clinical symptoms and other microbiological tests, which could guide antifungal therapy and reduce the risk of short-term mortality. CONCLUSIONS: ddPCR, with appropriate panel design, has advantages in pathogen detection and clinical management of ascites infection, especially for patients with fungal and polymicrobial infections. Patients with atypical spontaneous bacterial peritonitis benefited more from ddPCR.

Development of a droplet digital polymerase chain reaction assay for the sensitive detection of total and integrated HIV-1 DNA.

BACKGROUND: Total human immunodeficiency virus (HIV) DNA and integrated HIV DNA are widely used markers of HIV persistence. Droplet digital polymerase chain reaction (ddPCR) can be used for absolute quantification without needing a standard curve. Here, we developed duplex ddPCR assays to detect and quantify total HIV DNA and integrated HIV DNA. METHODS: The limit of detection, dynamic ranges, sensitivity, and reproducibility were evaluated by plasmid constructs containing both the HIV long terminal repeat (LTR) and human CD3 gene (for total HIV DNA) and ACH-2 cells (for integrated HIV DNA). Forty-two cases on stable suppressive antiretroviral therapy (ART) were assayed in total HIV DNA and integrated HIV DNA. Correlation coefficient analysis was performed on the data related to DNA copies and cluster of differentiation 4 positive (CD4 + ) T-cell counts, CD8 + T-cell counts and CD4/CD8 T-cell ratio, respectively. The assay linear dynamic range and lower limit of detection (LLOD) were also assessed. RESULTS: The assay could detect the presence of HIV-1 copies 100% at concentrations of 6.3 copies/reaction, and the estimated LLOD of the ddPCR assay was 4.4 HIV DNA copies/reaction (95% confidence intervals [CI]: 3.6-6.5 copies/reaction) with linearity over a 5-log 10 -unit range in total HIV DNA assay. For the integrated HIV DNA assay, the LLOD was 8.0 copies/reaction (95% CI: 5.8-16.6 copies/reaction) with linearity over a 3-log 10 -unit range. Total HIV DNA in CD4 + T cells was positively associated with integrated HIV DNA ( r = 0.76, P <0.0001). Meanwhile, both total HIV DNA and integrated HIV DNA in CD4 + T cells were inversely correlated with the ratio of CD4/CD8 but positively correlated with the CD8 + T-cell counts. CONCLUSIONS: This ddPCR assay can quantify total HIV DNA and integrated HIV DNA efficiently with robustness and sensitivity. It can be readily adapted for measuring HIV DNA with non-B clades, and it could be beneficial for testing in clinical trials.

Crosstalk between human immunodeficiency virus infection and salivary bacterial function in men who have sex with men.

Background: Engaging in anal sexual intercourse markedly increases the risk of developing HIV among men who have sex with men (MSM); oral sexual activities tend to uniquely introduce gut-derived microbes to salivary microbiota, which, combined with an individual's positive HIV status, may greatly perturb oral microecology. However, till date, only a few published studies have addressed this aspect. Methods: Based on 16S rRNA sequencing data of bacterial taxa, MicroPITA picks representative samples for metagenomic analysis, effectively revealing how the development and progression of the HIV disease influences oral microbiota in MSM. Therefore, we collected samples from 11 HIV-negative and 44 HIV-positive MSM subjects (stage 0 was defined by HIV RNA positivity, but negative or indeterminate antibody status; stages 1, 2, and 3 were defined by CD4+ T lymphocyte counts ≥ 500, 200-499, and ≤ 200 or opportunistic infection) and selected 25 representative saliva samples (5 cases/stage) using MicroPITA. Metagenomic sequencing analysis were performed to explore whether positive HIV status changes salivary bacterial KEGG function and metabolic pathway in MSM. Results: The core functions of oral microbiota were maintained across each of the five groups, including metabolism, genetic and environmental information processing. All HIV-positive groups displayed KEGG functions of abnormal proliferation, most prominently at stage 0, and others related to metabolism. Clustering relationship analysis tentatively identified functional relationships between groups, with bacterial function being more similar between stage 0-control groups and stage 1-2 groups, whereas the stage 3 group exhibited large functional changes. Although we identified most metabolic pathways as being common to all five groups, several unique pathways formed clusters for certain groups; the stage 0 group had several, while the stage 2 and 3 groups had few, such clusters. The abundance of K03046 was positively correlated with CD4 counts. Conclusion: As HIV progresses, salivary bacterial function and metabolic pathways in MSM progressively changes, which may be related to HIV promoting abnormal energy metabolism and exacerbate pathogen virulence. Further, infection and drug resistance of acute stage and immune cell destruction of AIDS stage were abnormally increased, predicting an increased risk for MSM individuals to develop systemic and oral diseases.

Discordant genotypic resistance and HIV-1 genetic diversity from paired plasma and cerebrospinal fluid samples in Chinese settings.

In the highly active antiretroviral therapy era, the incidence of human immunodeficiency virus (HIV)-associated neurocognitive disorder remains high with the improved survival. The prevalence of resistance differs across geographical areas and HIV subtypes. Currently, little information on the resistance patterns in the central nervous system (CNS) is available in Chinese settings. In this study, we sequenced and analyzed the pol gene from paired cerebrospinal fluid and plasma samples of 34 Chinese HIV-infected patients. We found that eight subjects harbored mutations that confer drug resistance, and of these, six subjects exhibited discordant resistance patterns between the CNS and the blood. The levels of viral diversity in the CNS were significantly higher than those in the blood (p < 0.0001). Our results contribute to improving our understanding of HIV neuropathogenesis and help to optimize neuro-acquired immunodeficiency syndrome treatment.

High levels of divergent HIV-1 quasispecies in patients with neurological opportunistic infections in China.

Despite the fact that the survival of people infected with human immunodeficiency virus (HIV) has improved worldwide because of the increasingly powerful and highly active antiretroviral therapy, opportunistic infections (OIs) of the central nervous system (CNS) remain a serious burden. HIV-1 is capable of entering the CNS through infected peripheral monocytes, but its effect on OIs of CNS remains unclear. In this study, we investigated the characteristics of HIV-1 in acquired immunodeficiency syndrome (AIDS) patients with CNS OIs. A total of 24 patients with CNS OIs and 16 non-CNS OIs (control) cases were selected. These AIDS patients were infected with HIV-1 by paid blood donors in China. HIV-1 loads in plasma and cerebrospinal fluid (CSF) were detected using RT-PCR, and the C2-V5 region of HIV-1 envelope gene was amplified from viral quasispecies isolated from CSF using nested PCR. The CSF HIV-1 load of CNS OIs was higher than that of non-CNS OIs, but plasma HIV-1 load of CNS OIs was not higher than that of non-CNS OIs. The nucleotide sequence of C2-V5 region of the HIV-1 quasispecies isolated from the CSF of CNS OIs had a high diversity, and the HIV-1 quasispecies isolated from the CSF of CNS OIs revealed R5 tropism as 11/25 charge rule. These results suggest that high levels of divergent HIV-1 quasispecies in the CNS probably contribute to opportunistic infections.

Cytokines in CSF correlate with HIV-associated neurocognitive disorders in the post-HAART era in China.

In the current era of highly active antiretroviral therapy (HAART), the incidence of HIV dementia has declined, but the prevalence of HIV-associated neurocognitive disorder (HAND) remains high. HIV-induced systemic and localized inflammation is considered to be one of the mechanisms of HAND. Changes in cytokine levels in the cerebrospinal fluid (CSF) during HIV infection might help to identify HAND. To investigate whether the cytokine profile of the CSF during HIV infection could be used as a biomarker of HAND, we compared cytokine levels in the CSF of HIV-infected cases with and without neurocognitive impairment. Cytokine concentrations in the CSF were measured by quantification bioassays (Luminex xMAP). HIV-infected cases with neurocognitive impairment demonstrated higher levels of interleukin (IL)-8, monocyte chemotactic protein (MCP)-1, induced protein (IP)-10, and granulocyte colony-stimulating factor (G-CSF) in the CSF than those without neurocognitive impairment (G-CSF (p = 0.0003), IL-8 (p = 0.0046), IP-10 (p < 0.0001), and MCP-1 (p < 0.0001)). There was no significant impact of HAART on cytokine levels in the CSF, except for IP-10, which was higher in HAART-treated patients with impaired cognition (p = 0.0182). Findings from this preliminary study suggest that elevated levels of the cytokines IL-8, MCP-1, G-CSF, and IP-10 in the CSF are associated with neurocognitive impairment in HIV infection, and these cytokines likely represent a biomarker profile for HAND.

Clinical Evaluation of Metagenomic Next-Generation Sequencing Method for the Diagnosis of Suspected Ascitic Infection in Patients with Liver Cirrhosis in a Clinical Laboratory.

Metagenomic next-generation sequencing (mNGS), mostly carried out in independent clinical laboratories, has been increasingly applied in clinical pathogen diagnosis. We aimed to explore the feasibility of mNGS in clinical laboratories and analyze its potential in the diagnosis of infectious ascites. Two reference panels composed of 12 strains commonly appearing in peritonitis were constructed to evaluate the performance metrics based on in-house mNGS protocols. The mNGS clinical detection value was analyzed in 211 ascitic samples and compared with culture and composite standards. Finally, eight patients with cirrhosis were prospectively enrolled to verify the clinical value of mNGS in peritoneal infection diagnosis. The mNGS analytical performance showed that the assay had great linearity, specificity, stability, interference, and limits of detection of 33 to 828 CFU/mL. The sensitivity and specificity of mNGS for bacterial or fungal detection using culture standards were 84.2% and 82.0%, respectively. After adjustment using digital PCR and clinical judgment, the sensitivity and specificity increased to 87.2% and 90.1%, respectively. Compared with culture, mNGS detected a broad range of pathogens and more polymicrobial infections (49% versus 9%, P < 0.05). The pathogen results were obtained within 24 h using mNGS in eight prospective cases, which effectively guided antibiotics therapy. mNGS testing in clinical laboratories affiliated with a hospital has certain advantages. It has unique superiority in pathogens detection, particularly in patients with polymicrobial infections. However, considering spectrum characteristics and test cost, pertinent pathogen panels should be developed in clinical practice. IMPORTANCE This study established and evaluated a complete metagenomics next-generation sequencing assay to improve the diagnosis of suspected ascitic infection in a clinical laboratory affiliated with a hospital. The assay is superior to traditional culture testing and will aid in the early and accurate identification of pathogens, particularly in patients with polymicrobial infections. This assay is also essential for precision therapy and can reduce the incidence of drug resistance stemming from irrational use of antibiotics.

Regional urbanicity levels modify the association between ambient air pollution and prevalence of obesity: A nationwide cross-sectional survey.

Ambient air pollution exposure may increase the risk of obesity, but the population susceptibility associated with urbanicity has been insufficiently investigated. Based on a nationwide representative cross-sectional survey on 44,544 adults, high-resolution night light satellite remote sensing products, and multi-source ambient air pollution inversion data, the present study evaluated the associations of fine particulate matter (PM2.5) and nitrogen dioxide (NO2) concentrations with the prevalence of obesity and abdominal obesity. We further calculated the associations in regions with different urbanicity levels characterized by both administrative classification of urban/rural regions and night light index (NLI). We found that 10 µg/m3 increments in PM2.5 at 1-year moving average and in NO2 at 5-year moving average were associated with increased prevalence of obesity [odds ratios (OR) = 1.16 (1.14, 1.19); 1.12 (1.09, 1.15), respectively] and abdominal obesity [OR = 1.08 (1.07, 1.10); 1.07 (1.05, 1.09), respectively]. People in rural regions experienced stronger adverse effects than those in urban regions. For instance, a 10 µg/m3 increment in PM2.5 was associated with stronger odds of obesity in rural regions than in urban regions [OR = 1.27 (1.23, 1.31) vs 1.10 (1.05, 1.14), P for interaction <0.001]. In addition, lower NLI values were associated with constantly amplified associations of PM2.5 and NO2 with obesity and abdominal obesity (all P for interaction <0.001). In summary, people in less urbanized regions are more susceptible to the adverse effects of ambient air pollution on obesity, suggesting the significance of collaborative planning of urbanization development and air pollution control, especially in less urbanized regions.

Analysis of Immune and Inflammatory Microenvironment Characteristics of Noncancer End-Stage Liver Disease.

Chronic liver injury eventually progresses to cirrhosis and end-stage liver disease (ESLD), which are the leading causes of death in patients with liver disease worldwide. ESLD has a variety of etiologies and a complex pathogenesis. This study analyzed the characteristics of ESLD by studying the immune microenvironment and inflammatory microenvironment of ESLD caused by 4 noncancer diseases, including HBV-ALF, ALF, AILD, and AH. We collected transcriptome data from noncancer ESLD patients, collected liver tissue samples and blood samples from ESLD liver transplant patients, and analyzed the immune and inflammatory microenvironments in the liver and blood. The results showed that with the exception of HBV-induced ESLD, there were no significant differences in immune microenvironment scores among patients with ESLD caused by other noncancer diseases. Moreover, there were no significant differences in the inflammatory microenvironment in the liver and blood of patients with ESLD caused by the 4 noncancer diseases. Furthermore, we found that the cytokine, IL-15, could predict the prognosis of ESLD patients.

Mutations in the major hydrophilic region (MHR) of hepatitis B virus genotype C in North China.

Hepatitis B virus (HBV) can evolve by mutations in the major hydrophilic region (MHR) of the HBV surface antigen (HBsAg) to permit its escape from neutralization by antibodies such as HBV surface antibody (anti-HBs) and from host immune responses. This study investigated the prevalence and pattern of MHR mutations in North China and the clinical correlations of these mutations. The MHRs of 161 HBsAg-positive patients were amplified using nested PCR, and directly sequenced to identify MHR mutations. It was showed that among the 161 patients infected with HBV genotype C in North China, the overall frequency of MHR mutation was 46.6%. Furthermore, MHR mutations were associated with high white blood cell counts (P = 0.025), high bilirubin levels (P = 0.048), and cirrhosis (P = 0.010). The most frequent mutations in patients with both HBsAg-positive and anti-HBs-positive were located in subregion 1 and 3 of MHR, specifically, residue Q101 (29.9%) and I126 (70.6%), which was different from the mutation pattern found in Western Europe and the United States. Taken together, these data indicated important virological and clinical aspects of HBV evolution in terms of the surface gene of genotype C, which might be important for its response to the currently available HBV vaccine.