Identification of an IGHV3-53-Encoded RBD-Targeting Cross-Neutralizing Antibody from an Early COVID-19 Convalescent.

Since November 2021, Omicron has emerged as the dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, and its sublineages continue to appear one after another, significantly reducing the effectiveness of existing therapeutic neutralizing antibodies (NAbs). It is urgent to develop effective NAbs against circulating Omicron variants. Here, we isolated receptor binding domain (RBD)-specific single memory B cells via flow cytometry from a COVID-19 convalescent. The antibody variable region genes of the heavy chain (VHs) and light chain (VLs) were amplified and cloned into expression vectors. After antibody expression, ELISA screening and neutralizing activity detection, we obtained an IGHV3-53-encoded RBD-targeting cross-neutralizing antibody D6, whose VL originated from the IGKV1-9*01 germlines. D6 could potently neutralize circulating Omicron variants (BA.1, BA.2, BA.4/5 and BF.7), with IC50 values of less than 0.04 µg/mL, and the neutralizing ability against XBB was reduced but still effective. The KD values of D6 binding with RBD of the prototype and BA.1 were both less than 1.0 × 10-12 M. The protein structure of the D6-RBD model indicates that D6 interacts with the RBD external subdomain and belongs to the RBD-1 community. The sufficient contact and deep interaction of D6 HCDR3 and LCDR3 with RBD may be the crucial reason for its cross-neutralizing activity. The sorting and analysis of mAb D6 will provide important information for the development of anti-COVID-19 reagents.

Phytoplankton species composition as bioindicator in the largest fragmented channel of the Pearl River, China.

To test the serial discontinuity concept (SDC) predictions in a regulated river ecosystem, environmental parameters and phytoplankton community structure were determined in a subtropical river (China) which was regulated by 11 cascade dams. Our results showed that total phosphorus (TP) and silicate during the wet period in several dams supported the SDC predictions. Variations of phytoplankton species composition in several cascade dams, such as Datengxia (DTX) and Changzhou (CZ), also supported the SDC predictions. Moreover, the stations near the dams showed the maximum or minimum values of total species numbers in each cascade segment. Predictive model indicated that the types of phytoplankton decreased in the middle reaches, conforming to SDC predictions. In the whole system of cascading dams, an increase in silicate concentration and phytoplankton communities in the downstream was also consistent with SDC predictions. Therefore, these findings aligned with the SDC predictions in the aspects of both single dam and whole cascade dam system to some extent. In future research, our aim is to further investigate the effects of cascade damming on additional phytoplankton-related indices in this aquatic ecosystem. We hope to gather more comprehensive data to fully validate the SDC predictions.

Function rather than structure of phytoplankton community reveals changes of water quality in an ecological restored lake.

Although phytoplankton is well known as robust bioindicators to aquatic environments, their indicating functions based on different community parameters remain to be understood. In order to filter effective bioindicators in aquatic ecosystems, four phytoplankton community parameters including species richness (SR), total biomass (SBP), functional groups (FGBP), and size-fractionated chlorophyll-a (SC) were demonstrated in a subtropical artificial lake with ecological restoration in South China. Our results indicated that all the above four parameters exhibited high sensitivity to environmental variations and illustrated distinct aspects of indicating functions to aquatic environments due to their individual biological characteristics. Based on FGBP, both spatial and temporal differences in phytoplankton community could be identified. SR and SBP only classified the spatial and temporal distributions, respectively, while SC could distinguish the sewage outfalls from other sites. In terms of ecological management, two parameters (SR and FGBP) could distinguish the restored waters from untreated environments as non-point source pollution, and another parameter SC could indicate the sewage outfalls as point source pollution. Therefore, the combination of the above two categories of phytoplankton community parameters could make the strongest indicating functions. Our study provided greater insight into indicating functions of phytoplankton community parameters in an ecological restored lake and enabled better managements in such artificial lakes.

Immunity Induced by Inactivated SARS-CoV-2 Vaccine: Breadth, Durability, Potency, and Specificity in a Healthcare Worker Cohort.

Vaccination has proven to be highly effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but the long-term immunogenicity and the functional preserved immune responses of vaccines are needed to inform evolving evidence-based guidelines for boosting schedules. We enrolled 205 healthcare workers into a cohort study; all had received three doses of BBIBP-CorV (China Sinopharm Bio-Beijing Company, Beijing, China) inactivated vaccine. We assessed SARS-CoV-2 specific binding antibodies, neutralizing antibodies, and peripheral T and B cell responses. We demonstrated that more robust antibody responses to SARS-CoV-2 were elicited by booster immunization compared with primary vaccination. Neutralizing antibody titers to SARS-CoV-2 Omicron BA.1 were also efficiently elevated post-homologous vaccine booster despite being in a lower titer compared with the prototype stain. In addition to S-specific humoral and cellular immunity, BBIBP-CorV also induced N-specific antibody and effector T cell responses. The third-dose vaccination led to further expansion of critical polyfunctional T cell responses, likely an essential element for vaccine protection. In particular, a functional role for Tfh cell subsets in immunity was suggested by the correlation between both CD4+ Tfh and CD8+ Tfh with total antibody, IgG, B cell responses, and neutralizing antibodies. Our study details the humoral and cellular responses generated by the BBIBP-CorV booster vaccination in a seven-month follow-up study. There is a clear immunologic boosting value of homologous inactivated SARS-CoV-2 vaccine boosters, a consideration for future vaccine strategies.

Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents.

Introduction: The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been posing a severe threat to global public health. Although broadly neutralizing antibodies have been used to prevent or treat corona virus disease 2019 (COVID-19), new emerging variants have been proven resistant to these antibodies. Methods: In this study, we isolated receptor binding domain (RBD)-specific memory B cells using single-cell sorting method from two COVID-19 convalescents and expressed the antibody to test their neutralizing activity against diverse SARS-CoV-2 variants. Then, we resolved antibody-RBD complex structures of potent RBD-specific neutralizing antibodies by X-ray diffraction method. Finally, we analyzed the whole antibody repertoires of the two donors and studied the evolutionary pathway of potent neutralizing antibodies. Results and discussion: We identified three potent RBD-specific neutralizing antibodies (1D7, 3G10 and 3C11) from two COVID-19 convalescents that neutralized authentic SARS-CoV-2 WH-1 and Delta variant, and one of them, 1D7, presented broadly neutralizing activity against WH-1, Beta, Gamma, Delta and Omicron authentic viruses. The resolved antibody-RBD complex structures of two antibodies, 3G10 and 3C11, indicate that both of them interact with the external subdomain of the RBD and that they belong to the RBD-1 and RBD-4 communities, respectively. From the antibody repertoire analysis, we found that the CDR3 frequencies of the light chain, which shared high degrees of amino acid identity with these three antibodies, were higher than those of the heavy chain. This research will contribute to the development of RBD-specific antibody-based drugs and immunogens against multiple variants.

Epstein-Barr virus variation in people living with human immunodeficiency virus in southeastern China.

BACKGROUND: Patients infected with HIV are at high risk of developing Epstein-Barr Virus (EBV)-related diseases. The genotype and viral biological behavior of EBV infection in patients with human immunodeficiency virus-1 (HIV) in China remain unclear. This study analyzed the characteristics of EBV in patients infected with HIV in southeastern China. METHODS: A total of 162 HIV-infected patients and 52 patients without HIV were enrolled in this study. EBV viral load in blood was determined by fluorescence quantitative PCR. EBV typing was performed using saliva according to polymorphisms in the EBNA3C region. EBV LMP-1 carboxy terminus (C-ter) was sequenced, and compared with the epidemic strains in the world. RESULTS: Among HIV infected patients, the EBV strain variant was mainly EBV-1, while EBV-2 had a higher viral load than EBV-1 (P = 0.001) and EBV-1/2 (P = 0.002). HIV infected patients had higher active virus replication. The EBV LMP-1 variants were mainly the China1 variant. HIV-infected patients had different nucleic acid positions of 30-bp deletion (del30) and had a higher incidence of high 33-bp tandem repeats (rep33) copies than non-HIV-infected patients. There was a difference in the mutations of EBV LMP-1 C-ter del30 and ins15 between HIV infected patients and the control group (P < 0.001). CONCLUSION: In southeastern China, EBV in HIV-infected patients had higher active virus replication; EBV infection was mainly EBV-1, and EBV-2 infection has higher EBV virus load; hotspot mutations of LMP-1 C-ter were different between HIV-infected patients and non-HIV-infected patients. TRIAL REGISTRATION: This study was approved by the ethics committee of the First Affiliated Hospital of Zhejiang University School of Medicine (Approval No. 2018764), and registered in Chinese Clinical Trial Registry on 3 June 2019 (ChiCTR, ChiCTR1900023600, http://www.chictr.org.cn/usercenter.aspx ).

How do multidimensional traits of dominant diatom Aulacoseira respond to abiotic and biotic factors in a river delta system?

Trait-based approaches are being increasingly applied in ecology, and the influence of individual-level trait variation on communities and species has been demonstrated. However, the responses of individual trait variation to environmental changes remain to be explored. To examine the indicating functions of multidimensional traits, individual-level measurements of the dominant diatom genus Aulacoseira Thwaites in the Pearl River Delta were performed, and corresponding responses of three trait indices (trait richness, trait evenness, and trait dispersion) to abiotic and biotic factors were examined. Our results indicated that the three individual trait diversity indices were regulated by different factors. Trait richness was only significantly affected by abiotic factors (temperature), while trait evenness and trait dispersion were regulated by both abiotic and biotic factors. In addition, the direct influence of abiotic factors was more significant than that of biotic factors, implying that the multidimensional trait variation of Aulacoseira was more responsive to environmental changes than to interspecific interactions. Therefore, the multidimensional trait variation of Aulacoseira could be used as an effective indicator to track environmental changes. Our study elucidated the mechanisms relating individual-level trait variation to phytoplankton community dynamics; this could improve our ability to forecast changes in ecosystem properties across environmental gradients.

Construction of SARS-CoV-2 receptor binding domain molecular probe and its application in the isolation of neutralizing antibodies / 中国热带医学

@#Abstract: Objective　To construct SARS-CoV-2 receptor binding domain molecular probe for monoclonal memory B cell sorting and obtain RBD specific neutralizing antibodies from peripheral blood mononuclear cells (PBMCs) of COVID-19 convalescents by single-cell sorting. Methods　The SARS-CoV-2 RBD sequence was downloaded from GenBank, and the Avi tag and 6-histidine tags were added at the C-terminal. After codon optimization, it was chemically synthesized, cloned into the pDRVI1.0 vector, expressed after transfection of 293F cells, and biotinylated consequently. RBD-specific B cells were sorted out with this probe1 from the PBMCs of convalescents recovered from COVID-19. After B cells were lysed, the variable regions of heavy chain and light chain were amplified, cloned into the antibody expression vector, and transfected into 293F cells to express the antibody. Then the antibody was purified from the supernatant using protein A column and SARS-CoV-2 pseudovirus was used to test their neutralizing activity. Results　RBD-Avi probe was produced and successfully biotinylated sequentially with an efficiency of 30%-50%. Western blot analysis revealed that the biotinylated probe was recognized by the antibodies purified from COVID-19 convalescent plasma. Using this probe, 7 and 16 RBD-specific memory B cells were successfully isolated from the PBMCs of two convalescent individuals, accounting for 0.24% and 0.17% of the total cell population, respectively. After amplifying the variable regions of antibody heavy and light chains from the lysed B cells, 7 and 12 pairs of antibody heavy-light chains were obtained. A total of 16 antibodies were expressed in the convalescent individuals, and most of the purified antibodies showed neutralizing activity against the pseudovirus, with IC50 values of 6 antibodies below 1 μg/mL. The IC50 values of XJ-A9 and SCF-F1 against the wild-type pseudovirus were 0.07 μg/mL and 0.35 μg/mL, respectively. Conclusion　The SARS-CoV-2 RBD molecular probe constructed in this study has good antigenicity, and the isolated antibodies present neutralizing activity against wild-type SARS-CoV-2 pseudovirus.

Pre-existing anti-HCoV-OC43 immunity influences the durability and cross-reactivity of humoral response to SARS-CoV-2 vaccination.

Purpose: This study was conducted in order to properly understand whether prior seasonal human coronavirus (HCoV) immunity could impact the potential cross-reactivity of humoral responses induced by SARS-CoV-2 vaccine, thereby devising universal coronavirus vaccines for future outbreaks. Methods: We performed enzyme-linked immunosorbent assay (ELISA) to quantify the immunoglobulin G (IgG) antibody levels to spike (S) protein and S1 subunit of HCoVs (HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E), and ELISA [anti-RBD and anti-nucleoprotein (N)], chemiluminescence immunoassay assays (anti-RBD), pseudovirus neutralization test, and authentic viral neutralization test to detect the binding and neutralizing antibodies to SARS-CoV-2 in the vaccinees. Results: We found that the antibody of seasonal HCoVs did exist before vaccination and could be boosted by SARS-CoV-2 vaccine. A further analysis demonstrated that the prior S and S1 IgG antibodies of HCoV-OC43 were positively correlated with anti-RBD and neutralization antibodies to SARS-CoV-2 at 12 and 24 weeks after the second vaccination, and the correlation is more statistically significant at 24 weeks. The persistent antibody levels of SARS-CoV-2 were observed in vaccinees with higher pre-existing HCoV-OC43 antibodies. Conclusion: Our data indicate that inactivated SARS-CoV-2 vaccination may confer cross-protection against seasonal coronaviruses in most individuals, and more importantly, the pre-existing HCoV-OC43 antibody was associated with protective immunity to SARS-CoV-2, supporting the development of a pan-coronavirus vaccine.

Exploring Rapid and Effective Screening Methods for Anti-SARS-CoV-2 Neutralizing Antibodies in COVID-19 Convalescent Patients and Longitudinal Vaccinated Populations.

Assessing the duration of neutralizing antibodies (nAbs) following SARS-CoV-2 infection or vaccination is critical to evaluate the protective immunity and formulate public health strategies. In this study, SARS-CoV-2 Ab ELISA (enzyme-linked immunosorbent assay), chemiluminescent microparticle immunoassay (CMIA), as well as pseudovirus neutralization test (PVNT) were performed in two cohorts, convalescent patients (CP) from coronavirus disease 2019 (COVID-19) and BBIBP-CorV vaccinated population. It was found that nAbs and binding antibodies emerged at 14 days post the 1st dose of vaccination, reached peaks at 28 days after 2nd dose vaccination and then gradually declined over time. CP-6M (convalescent patients up to 6 months) from COVID-19 presented stronger nAbs or binding antibodies responses than vaccinees 90 days or 180 days after 2nd dose vaccination. CMIA or SARS-CoV-2 Ab ELISA correlated well with PVNT with high consistency in the two cohorts. It shown that nAbs and binding antibodies can keep 6 months both in CP and vaccinees. Most importantly, our data show the application of using CMIA and SARS-CoV-2 Ab ELISA as rapid screening tests for nAb titer and could be used as alternative strategies for quickly evaluating SARS-CoV-2 nAbs responses in vaccine research.

Oral Microbiota Is Associated With Immune Recovery in Human Immunodeficiency Virus-Infected Individuals.

The role of the oral microbiota in HIV-infected individuals deserves attention as either HIV infection or antiretroviral therapy (ART) may have effect on the diversity and the composition of the oral microbiome. However, few studies have addressed the oral microbiota and its interplay with different immune responses to ART in HIV-infected individuals. Salivary microbiota and immune activation were studied in 30 HIV-infected immunological responders (IR) and 34 immunological non-responders (INR) (≥500 and < 200 CD4 + T-cell counts/µl after 2 years of HIV-1 viral suppression, respectively) with no comorbidities. Metagenome sequencing revealed that the IR and the INR group presented similar salivary bacterial richness and diversity. The INR group presented a significantly higher abundance of genus Selenomonas_4, while the IR group manifested higher abundances of Candidatus_Saccharimonas and norank_p_Saccharimonas. Candidatus_Saccharimonas and norank_p_Saccharimonas were positively correlated with the current CD4 + T-cells. Candidatus_Saccharimonas was positively correlated with the markers of adaptive immunity CD4 + CD57 + T-cells, while negative correlation was found between norank _p_Saccharimonas and the CD8 + CD38 + T-cells as well as the CD4/CD8 + HLADR + CD38 + T-cells. The conclusions are that the overall salivary microbiota structure was similar in the immunological responders and immunological non-responders, while there were some taxonomic differences in the salivary bacterial composition. Selenomona_4, Candidatus_Saccharimonas, and norank _p_Saccharimonas might act as important factors of the immune recovery in the immunodeficiency patients, and Candidatus_Saccharimonas could be considered in the future as screening biomarkers for the immune responses in the HIV-infected individuals.

Cryptococcosis in patients with liver cirrhosis: Death risk factors and predictive value of prognostic models.

BACKGROUND: Liver cirrhosis is associated with immune deficiency, which causes these patients to be susceptible to various infections, including cryptococcus infection. Mortality in cirrhotic patients with cryptococcosis has increased. The present study was to explore the risk factors of mortality and the predictive ability of different prognostic models. METHODS: Forty-seven cirrhotic patients with cryptococcosis at a tertiary care hospital were included in this retrospective study. Data on demographics, clinical parameters, laboratory exams, diagnostic methods, medication during hospitalization, severity scores and prognosis were collected and analyzed. Student's t test and Mann-Whitney test were used to compare characteristics of survivors and non-survivors at a 90-day follow-up and cerebrospinal fluid (CSF) manifestations of cryptococcal meningitis. Multivariate Cox regression analysis was used to identify the independent risk factors for mortality. Kaplan-Meier curves were used to analyze patient survival. Receiver operating characteristic (ROC) curves were used to evaluate the different prognostic factors. RESULTS: The 30- and 90-day survival rates were 93.6% and 80.9%, respectively, in cirrhotic patients with cryptococcosis. Cryptogenic liver diseases [hazard ratio (HR) = 7.567, 95% confidence interval (CI): 1.616-35.428, P = 0.010], activated partial thromboplastin time (APTT) (HR = 1.117, 95% CI: 1.016-1.229, P = 0.022) and Child-Pugh score (HR = 2.146, 95% CI: 1.314-3.504, P = 0.002) were risk factors for 90-day mortality in cirrhotic patients with cryptococcosis. Platelet count (HR = 0.965, 95% CI: 0.940-0.991, P = 0.008) was a protective factor. APTT (HR = 1.120, 95% CI: 1.044-1.202, P = 0.002) and Child-Pugh score (HR = 1.637, 95% CI: 1.086-2.469, P = 0.019) were risk factors for 90-day mortality in cirrhotic patients with cryptococcal meningitis. There was significant difference in the percentage of lymphocytes in CSF between survivors and non-survivors [60.0 (35.0-75.0) vs. 95.0 (83.8-97.2), P < 0.001]. The model of end-stage liver disease-sodium (MELD-Na) score was more accurate for predicting 30-day mortality both in patients with cryptococcosis [area under curve (AUC): 0.826, 95% CI: 0.618-1.000] and those with cryptococcal meningitis (AUC: 0.742, 95% CI: 0.560-0.924); Child-Pugh score was more useful for predicting 90-day mortality in patients with cryptococcosis (AUC: 0.823, 95% CI: 0.646-1.000) and those with cryptococcal meningitis (AUC: 0.815, 95% CI: 0.670-0.960). CONCLUSIONS: These results showed that cryptogenic liver diseases, APTT and Child-Pugh score were associated with mortality in cirrhotic patients with cryptococcosis and cryptococcal meningitis. MELD-Na score was important for predicting 30-day mortality, and Child-Pugh score was critical for predicting 90-day mortality.

Environmental regulations on bacterial abundance in the South China Sea inferred from regression models.

Bacteria play a critical role in carbon cycling and nutrient remineralization. To reveal potential mechanisms controlling bacterial abundance in the upper 200 m of the South China Sea (SCS), the generalized linear model (GLM), generalized additive model (GAM) and generalized boosted model (GBM) were constructed to address the relationship between bacterial abundance and environmental factors, including geographical variables, biotic variables and water chemistry. GAM and GBM were found suitable for modeling bacterial abundance in the SCS. The predictive performance of GBM was superior to GLM and GAM for bacterial distribution. In addition, bacterial abundance predicted by GBM from environmental parameters was highly consistent with the observations, indicating that GBM was robust to predict bacterial abundance from environmental parameters. Furthermore, the key environmental factors modulating the horizontal and vertical distribution of bacteria were determined based on models. Horizontally, surface bacterial abundance decreased from onshore to offshore, which was primarily regulated by salinity and chlorophyll-a. Vertically, bacterial abundance decreased with depth. Chlorophyll-a was primarily responsible for vertical variability in bacterial abundance in the upper 100 m, where temperature was higher than the optimum temperature (21 °C) for bacterial growth. In contrast, temperature was a dominant factor regulating bacterial abundance below 100 m, where temperature was below 21 °C and positively correlated with BA. Viruses and nutrients played less important roles in regulating bacterial abundance than chlorophyll-a and temperature in the SCS. Our models elucidated environmental regulations on bacterial abundance, which was helpful for us to understand bacterial carbon cycling in the SCS.

Effect of Ocean Acidification on Bacterial Metabolic Activity and Community Composition in Oligotrophic Oceans, Inferred From Short-Term Bioassays.

Increasing anthropogenic CO2 emissions in recent decades cause ocean acidification (OA), affecting carbon cycling in oceans by regulating eco-physiological processes of plankton. Heterotrophic bacteria play an important role in carbon cycling in oceans. However, the effect of OA on bacteria in oceans, especially in oligotrophic regions, was not well understood. In our study, the response of bacterial metabolic activity and community composition to OA was assessed by determining bacterial production, respiration, and community composition at the low-pCO2 (400 ppm) and high-pCO2 (800 ppm) treatments over the short term at two oligotrophic stations in the northern South China Sea. Bacterial production decreased significantly by 17.1-37.1 % in response to OA, since bacteria with high nucleic acid content preferentially were repressed by OA, which was less abundant under high-pCO2 treatment. Correspondingly, shifts in bacterial community composition occurred in response to OA, with a high fraction of the small-sized bacteria and high bacterial species diversity in a high-pCO2 scenario at K11. Bacterial respiration responded to OA differently at both stations, most likely attributed to different physiological responses of the bacterial community to OA. OA mitigated bacterial growth efficiency, and consequently, a larger fraction of DOC entering microbial loops was transferred to CO2.

Clinical features and Outcomes of Cryptococcemia patients with and without HIV infection.

BACKGROUND: The effects of cryptococcemia on patient outcomes in those with or without HIV remain unclear. METHODS: One hundred and seventy-nine cryptococcemia patients were enrolled in this retrospective study. Demographic characteristics, blood test results and outcome were compared between the two groups. RESULTS: The diagnosis time of Cryptococcus infection was 2.0(0-6.0) days for HIV-infected patients, 5.0 (1.5-8.0) days for HIV-uninfected patients (p = .008), 2.0 (1.0-6.0) days for cryptococcal meningitis (CM) patients and 6.0 (5.0-8.0) days for non-CM patients (p < .001). HIV infection [adjusted odds ratio (AOR) (95% confidence interval): 6.0(2.3-15.9)], CRP < 15 mg/L [AOR:3.7(1.7-8.1)) and haemoglobin > 110 g/L [AOR:2.5(1.2-5.4)] were risk factors for CM development. Forty-six (25.7%) patients died within 90 days. ICU stay [AOR:2.8(1.1-7.1)], hypoalbuminemia [AOR:2.7(1.4-5.3)], no anti-cryptococcal treatment [AOR:4.7(1.9-11.7)] and altered consciousness [AOR:2.4(1.0-5.5)] were independent risk factors for 90-day mortality in all patients. HIV infection did not increase the 90-day mortality of cryptococcemia patients when anti-Cryptococcus treatment was available. Non-Amphotericin B treatment [AOR:3.4(1.0-11.2)] was associated with 90-day mortality in HIV-infected patients, but age ≥ 50.0 years old [AOR:2.7(1.0-2.9)], predisposing disease [AOR:4.1(1.2-14.2)] and altered consciousness [AOR:3.7(1.1-12.9)] were associated with 90-day mortality in HIV-uninfected patients who accepted anti-Cryptococcus treatment. CONCLUSION: HIV infection increased the incidence of CM rather than mortality in cryptococcemia patients. The predictive model was completely divergent in HIV-infected and HIV-uninfected patients, suggesting that novel strategies for diagnosis and treatment algorithms are urgently needed.

Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals.

BACKGROUND: Although gut microbiota dysbiosis has been reported in HIV infected individuals recently, the relationship between the gut microbiota and immune activation in patients with different immune responses to highly active antiretroviral therapy (HAART) is still not well understood. Gut microbiota and immune activation were studied in 36 non-HIV-infected subjects (healthy controls) and 58 HIV-infected individuals, including 28 immunological responders (IR) and 30 immunological non-responders (INR) (≥500 and < 200 CD4+ T-cell counts/µl after 2 years of HIV-1 viral suppression respectively) without comorbidities. RESULTS: Metagenome sequencing revealed that HIV-infected immunological responders and immunological non-responders could not recover completely from the gut microbiota dysbiosis. At a 97% similarity level, the relative abundances of Fusobacterium, Ruminococcus gnavus and Megamonas were greater, whereas Faecalibacterium, Alistipes, Bifidobacterium, Eubacterium rectale and Roseburia were more depleted in the IR and INR groups than those in the healthy controls. Ruminococcaceae and Alistipes were positively correlated with nadir and current CD4+ T-cell counts, but negatively correlated with CD8 + CD57+ T-cell counts. Inflammation markers and translocation biomarkers (LPS) levels were positively correlated with the abundances of genera Ruminococcus and Fusobacterium but were negatively correlated with the genus Faecalibacterium. The relative abundances of Escherichia-Shigella and Blautia were significantly higher in the IR than those in the INR group. Escherichia-Shigella were negatively correlated with the CD4/CD8 ratio but positively correlated with the amount of CD8 + CD57+ T-cells. Roseburia and Blautia were negatively associated with nadir CD4+ T-cell and positively associated with CD8 + CD57+ T-cell counts. CONCLUSIONS: Gut microbiota dysbiosis may be one of the factors contributing to different immune responses and treatment outcomes to HAART.

A Pilot Study of Echinocandin Combination with Trimethoprim/Sulfamethoxazole and Clindamycin for the Treatment of AIDS Patients with Pneumocystis Pneumonia.

BACKGROUND AND OBJECTIVES: Pneumocystis pneumonia (PCP) is a common opportunistic infection in acquired immune deficiency syndrome (AIDS) patients that continues to result in a high mortality rate. To develop a better treatment strategy and improve PCP prognosis, a cohort study was conducted to evaluate the therapeutic potential of echinocandin treatment for AIDS patients with PCP (AIDS-PCP). METHODS: The AIDS-PCP patients were analyzed in our retrospective cohort study that were hospitalized in The First Affiliated Hospital of Zhejiang University during 2013-2018. The antifungal effects of echinocandins were evaluated in two subgroups that were classified by oxygenation as a proxy for the disease state: PaO2/FiO2 > 200 mmHg and PaO2/FiO2 ≤ 200 mmHg. Intergroup comparisons and survival curves were used to evaluate the effectiveness of the two AIDS-PCP treatment regimens. RESULTS: During the follow-up, 182 AIDS-PCP patients were diagnosed and analyzed in the study. After excluding 55 patients with other superinfections and five patients that were treated with HAART, the remaining 122 patients were enrolled in the study. The group treated with echinocandins combined with trimethoprim-sulfamethoxazole (TMP-SMZ) and clindamycin exhibited a lower mortality rate (9.62%, 5/52) than did the group with TMP-SMZ and clindamycin treatment (20%, 14/70). For AIDS-PCP patients in the PaO2/FiO2 > 200 mmHg subgroup, treatment with echinocandins combined with TMP-SMZ and clindamycin significantly reduced their mortality rate (4.44% (2/45) vs. 18.18% (10/55), P = 0.035). CONCLUSION: The results of this study indicate that treatment with echinocandins in combination with the standard TMP-SMZ and clindamycin regimen can improve the prognosis and reduce the mortality rate in patients with mild to moderate AIDS-PCP disease.

Short-Course Rather Than Low-Dose Amphotericin B May Exert Potential Influence on Mortality in Cryptococcal Meningitis Patients Treated With Amphotericin B Plus Flucytosine Alone or in Combination With Fluconazole.

BACKGROUND: The influence of Amphotericin B (AmB) dose and the addition of fluconazole (Flu) on the AmB + 5-flucytosine (5FC) regimen for cryptococcal meningitis (CM) treatment remain debatable. METHODS: A retrospective study was conducted to compare 44 CM patients treated with AmB + 5FC and 78 CM patients treated with AmB + 5FC + Flu using the propensity score matching method. The effects of AmB dosage, AmB course and Flu addition on the cerebrospinal fluid (CSF) chemical profile recovery, adverse effects, and 90-day mortality were compared between the groups. RESULTS: No differences in adverse effects, the rate of the 14-day CSF chemical profile recovery and 90-day cumulative survival rate (91.2% vs. 87.5%, P = 0.637) were observed between the AmB + 5FC group and the AmB + 5FC + Flu group. However, the incidence rates of hypokalemia (33.9%) and creatinine elevation (7.1%) in patients treated with an AmB dosage of 0.4-0.5 mg/kg/d were less than those (53.0 and 22.7%, respectively) treated with an AmB dosage of 0.6-0.7 mg/kg/d (P = 0.034 and P = 0.018, respectively). The 90-day cumulative survival rate was 70.1% for patients treated with AmB for <14 days and 96.4% for patients treated with AmB for ≥14 days (log-rank P < 0.001). Multivariate Cox proportional hazards models suggested the hazard ratio was 26.8 (95% CI: 3.9-183.2) for patients treated with AmB < 14 days than those treated with AmB ≥ 14 days (P = 0.001). CONCLUSION: Treatment with AmB less than 14 days was associated with a higher 90-day mortality in CM patients. A relative lower dosage but prolonged course of AmB in the +5FC ± Flu regimen led to favorable trends of fewer adverse effects and comparable clinical efficacy.

Polymorphisms involving the Pneumocystis jirovecii-related genes in AIDS patients in eastern China.

OBJECTIVE: To investigate the genetic polymorphisms of mitochondrial large ribosomal subunit (mtLSU)-rRNA, dihydrofolate reductase (DHFR), dihydropteroate synthase (DHPS), cytochrome b (CYB), and superoxide dismutase (SOD) genes and its correlation with clinical outcomes of Pneumocystis jirovecii pneumonia in acquired immune deficiency(AIDS) patients. METHODS: Eighty AIDS patients with P. jirovecii pneumonia that were admitted to our hospital from 2016 to 2018 were included in this study. Their demographic information and clinical data were collected, as well as corresponding saliva specimens for PCR and sequencing of mtLSU-rRNA, DHFR, DHPS, CYB, and SOD genes to analyze genetic polymorphisms, different polymorphic combinations, and clinical outcomes. RESULTS: Of the 80 saliva specimens, mtLSU-rRNA was successfully amplified and sequenced in 30 cases; CYB was successfully amplified and sequenced in 26 cases; and SOD, DHFR, and DHPS were successfully amplified and sequenced in 18 cases. These results indicate that The mtLSU-rRNA, CYB, and SOD genes were highly polymorphic. mt85T and CYB1 were the variants dominantly detected at the mtLSU-rRNA and CYB loci, respectively. The SOD1 and SOD2 variants (each in 50% of the cases) were detected at the SOD locus. Among the 18 cases that were successfully amplified and sequenced for DHFR and DHPS, three DHFR nonsense mutations and no DHPS mutation were observed. The mt85C, CYB1, SOD1, and DHFR312T genes harbored common polymorphisms (n = 4; 22.22%) and the mt85T, CYB1, SOD1, DHFR312T genes were associated with poor clinical outcomes. CONCLUSION: The types of genetic polymorphisms and polymorphic combinations of mtLSU-rRNA, DHFR, DHPS, CYB, and SOD in P. jirovecii were related to the clinical outcomes of patients with P. jirovecii pneumonia in Zhejiang Province, China.