Genomic epidemiology reveals early transmission of SARS-CoV-2 and mutational dynamics in Nanning, China.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are a fatal pathogen resulting in substantial morbidity and mortality, and posing a great threat to human health with epidemics and pandemics. METHODS: Next-generation sequencing (NGS) was performed to investigate the SARS-CoV-2 genomic characterization. Phylogenetic analysis of SARS-CoV-2 genomes was used to probe the evolutionary. Homology protein structure modelling was done to explore potential effect of the mutations. RESULTS: The eighty genome sequences of SARS-CoV-2 obtained from the thirty-nine patients with COVID-19. A novel variant with mutation H625R concomitant with S50L in spike glycoprotein had been identified. Phylogenetic analysis revealed that SARS-CoV-2 variants belong to several distinct lineages. Homology modelling indicated that variant with mutation H625R and S50L increases flexibility of S1 subunit. CONCLUSIONS: SARS-CoV-2 genomes are constantly evolving by accumulation of point mutations. The amino acid H625R in combination with S50L may have a significant impact on the interaction between spike glycoprotein and ACE2.

Clinical utilization of multiple antibodies of Mycobacterium tuberculosis for serodiagnosis evaluation of tuberculosis: a retrospective observational cohort study.

OBJECTIVES: We aimed to investigate clinical uncertainties by characterizing the accuracy and utility of commercially available antibodies of Mycobacterium tuberculosis in the diagnostic assessment of suspected tuberculosis in high-burden countries. METHODS: We conducted a retrospective, descriptive, cohort study among participants aged ≥ 18 years with suspected tuberculosis in Nanning, Guangxi, and China. Participants were tested for M. tuberculosis infection using commercially available antibodies against Mycobacterum tuberculosis. Specificity, sensitivity, negative and positive predictive values, and negative and positive likelihood ratios of the tests were determined. Sputum specimens and bronchoalveolar lavage fluid were sent for mycobacterial culture, Xpert MTB/RIF assay, and cell-free M. tuberculosis DNA or RNA assay. Blood samples were used for IGRAs, T-cell counts (CD3 + CD4+ and CD3 + CD8+), and antibodies to tuberculosis test. RESULTS: Of the 1857 participants enrolled in this study, 1772 were included in the analyses, among which, 1311 were diagnosed with active tuberculosis. The specificity of antibody against 16kD for active tuberculosis was 92.7% (95% confidence interval [CI]: 89.3-95.4) with a positive likelihood ratio for active tuberculosis cases of 3.1 (95% CI: 2.1-4.7), which was higher than that of antibody to Rv1636 (90.5% [95% CI: 86.6-93.5]), antibody to 38kD (89.5% [95% CI: 85.5-92.7]), antibody against CFP-10 (82.6% [95% CI: 77.9-86.7]), and antibody against LAM (79.3% [95% CI: 74.3-83.7]). Sensitivity ranged from 15.8% (95% CI: 13.9-17.9) for antibody against Rv1636 to 32.9% (95% CI: 30.4-35.6) for antibody to LAM. CONCLUSIONS: Commercially available antibodies against to Mycobacterium tuberculosis do not have sufficient sensitivity for the diagnostic evaluation of active tuberculosis. However, antibody against Rv1636 and 16kD may have sufficiently high specificities, high positive likelihood ratios, and correspondingly high positive predictive values to facilitate the rule-in of active tuberculosis.

Existing M. tuberculosis antigens do achieve a limited sensitivity and negative predictive value to rule out a diagnosis of tuberculosis.M. tuberculosis antigens may help to rule in a diagnosis of active or latent tuberculosis in clinical setting among the high burden tuberculosis countries.This study is the largest retrospective, descriptive, cohort study to evaluate the clinical utilization of existing M. tuberculosis antigens integrating M. tuberculosis immunogens in patients with suspected active tuberculosis in high-burden country.

Clinical characteristics of platelet-mediated killing circulating parasite of major human malaria.

OBJECTIVE: Microscopy was used to characterize platelet-Plasmodium-infected erythrocyte interactions in patients infected with Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale or Plasmodium malariae, and to investigate the relationship between platelet-associated parasite killing and parasite clearance. METHODS: Data from 244 malaria patients admitted to the Fourth People's Hospital of Nanning between 1 January 2011 and 30 September 2022, and 45 healthy controls, were collected prospectively and assessed retrospectively. Characteristics of platelet-erythrocyte interactions were visualized by microscopy, and blood cell count and clinical profiles of these participants were obtained from the electronic medical records. ANOVA, contingency tables and Cox proportional hazards regression models were used to do statistical analysis on the subgroups. RESULTS: Platelet enlargement and minor pseudopodia development were observed. Platelets were found directly attaching to parasitized erythrocytes by all Plasmodium species studied, especially mature stages, and lysis of parasitized erythrocytes was connected to platelet-mediated cytolysis. Platelet counts were correlated inversely with parasitaemia and duration of parasite clearance. Artemisinin combination therapy was more effective than artemisinin alone in clearing Plasmodium in patients with thrombocytopenia. CONCLUSIONS: Platelet-parasitized erythrocytes cell-to-cell contacts initiated platelet-associated parasite killing and helped to limit Plasmodium infection in cases of human malaria. The weakening platelet-associated parasite killing effects could be counteracted by artemisinin combination therapy in patients with thrombocytopenia.

HighlightsPlatelets directly attaching to parasitized erythrocytes.Platelets correlated inversely with parasitaemia and duration of parasite clearance.Artemisinin combination therapy was more effective than artemisinin alone.Weakening killing effects may counteract by artemisinin combination therapy.

Biochemical characteristics of patients with imported malaria.

Objectives: This study aimed to investigate the clinical and biochemical profiles of patients with imported malaria infection between 1 January 2011 and 30 April 2022 and admitted to the Fourth People's Hospital of Nanning. Methods: This cohort study enrolled 170 patients with conformed imported malaria infection. The clinical and biochemical profiles of these participants were analyzed with malaria parasite clearance, and signs and symptoms related to malaria disappearance were defined as the primary outcome. A multivariable logistic regression model was used to evaluate the odds ratios (ORs) with 95% confidence intervals (CIs) for cerebral malaria. The Cox model was used to estimate the hazard ratios (HRs) with 95% CIs for parasite clearance. Results: Adenosine deaminase and parasitemia were found to be independent risk factors for severe malaria in patients with imported malaria (OR = 1.0088, 95% CI: 1.0010-1.0167, p = 0.0272 and OR = 2.0700, 95% CI: 1.2584-3.4050, p = 0.0042, respectively). A 0.5-standard deviation (SD) increase of variation for urea (HR = 0.6714, 95% CI: 0.4911-0.9180), a 0.5-SD increase of variation for creatinine (HR = 0.4566, 95% CI: 0.2762-0.7548), a 0.25-SD increase of variation for albumin (HR = 0.4947, 95% CI: 0.3197-0.7653), a 0.25-SD increase of variation for hydroxybutyrate dehydrogenase (HR = 0.6129, 95% CI: 0.3995-0.9402), and a 1.0-SD increase of variation for ferritin (HR = 0.5887, 95% CI: 0.3799-0.9125) were associated with a higher risk for increased parasite clearance duration than a low-level change. Conclusions: Aspartate aminotransferase, urea, creatinine, albumin, hydroxybutyrate dehydrogenase, and ferritin are useful biochemical indicators in routine clinical practice to evaluate prognosis for imported malaria.

Viral Dynamic Surveillance in COVID-19 Patients: A Cohort Study.

Background: Coronavirus disease 2019 (COVID-19) is a potentially fatal pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially those of novel SARS-CoV-2 variants and infection has affected over 700 million people globally. Methods: This retrospective, descriptive study included 118 patients admitted with SARS-CoV-2 infection as confirmed by real-time reverse transcription polymerase chain reaction. Results: The median duration of detectable SARS-CoV-2 infection in patients with high ALT, AST, and PLT/LYMPH, or low CD4+, CD8+, and PLT/MONO was considerably longer. In the risk factor model, multivariate analysis was performed for the estimation of ALT (HR, 0.54; 95% CI, 0.36-0.81), AST (HR, 0.56; 95% CI, 0.34-0.93), CD4+ (HR,0.77; 95% CI, 0.48-1.24), CD8+ (HR,0.64; 95% CI, 0.37-1.11), PLT/LYMPH (HR, 1.16; 95% CI, 0.76-1.77), and PLT/MONO (HR, 0.64; 95% CI, 0.43-0.94). Conclusions: The longer viral RNA duration was associated with a higher International Prognostic Index score (p = 0.0013), demonstrating for the first time that multivariate features of the bioindicators closely associated with SARS-CoV-2-infected patients clear the virus.

Nontuberculous mycobacterial pulmonary disease and associated risk factors in China: A prospective surveillance study.

BACKGROUND: We aimed to address the knowledge gap that exists regarding the epidemiological, demographic, and clinical characteristics of nontuberculous mycobacterial pulmonary diseases (NTM-PDs) among smear-positive patients with symptoms suggestive of pulmonary tuberculosis (PTB) in China. METHODS: Prospective and national surveillance of NTM-PD was performed from 17 hospitals within the China Nontuberculous Mycobacteria Surveillance Study (CNTMS). Patients were eligible for inclusion if they had positive smears during hospitalization. Sputum specimens were collected for molecular species identification. RESULTS: 6,766 patients with valid results were included, consisting of 6,236 (92.2%) with PTB, 458 (6.8%) with NTM-PD, and 72 (1.0%) with colonization. The proportion of NTM-PD in PTB patients exhibited significant geographic diversity, ranging from 3.2% in the northwest to 9.2% in the south. The most prevalent species was Mycobacterium intracellulare, followed by Mycobacterium abscessus complex. Females, elderly people, and patients with bronchiectasis or COPD are at high risk for developing NTM-PD, while patients with diabetes have a lower risk of NTM-PD when compared with non-diabetic patients. Regarding clinical symptoms, lower rates of persistent cough and weight loss were noted in NTM-PD patients than in PTB patients. CONCLUSIONS: Approximately one-fifteenth of PTB patients are afflicted with nontuberculous mycobacterial infections in China. The prevalence of NTM shows geographic diversity across the country, and it showed a gradual increase from north to south and from west to east. NTM-PD patients are prone to exhibit less severe clinical symptoms than PTB patients, highlighting the importance of raising awareness of NTM diseases to improve decision making on how to best screen, diagnose, and treat NTM in TB-endemic settings.

Correlations of disease severity and age with hematology parameter variations in patients with COVID-19 pre- and post-treatment.

BACKGROUND: For better understanding of the pathological changes of COVID-19, benefiting clinical management of the disease and the preparation for future waves of similar pandemics. METHODS: Hematology parameters from a total of 52 cases of COVID-19 admitted for treatment in a designated hospital were retrospectively analyzed. Data were analyzed by SPSS statistical software. RESULTS: Pre-treatment T-cell subsets, total lymphocytes, red blood cell distribution width (RDW), eosinophils, and basophils were significantly lower than that of post-treatment, while the inflammatory indexes neutrophils, neutrophil to lymphocyte ratio (NLR), and C-reactive protein (CRP) levels, as well as red blood cell (RBC) and hemoglobin, were significantly reduced after treatment. The T-cell subsets, total lymphocytes, and basophils in severely and critically ill patients were significantly lower than those in moderately ill patients. Neutrophils, NLR, eosinophils, procalcitonin (PCT), and CRP was significantly higher in severely and critically ill patients than in moderately ill patients. CD3+, CD8+, total lymphocytes, platelets, and basophils in patients older than 50 were lower than that of those younger than 50, while neutrophils, NLR, CRP, and RDW in patients older than 50 were higher than that of younger than 50. There was a positive correlation among prothrombin time (PT), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) in severely and critically ill patients. CONCLUSIONS: T-cell subsets, lymphocyte count, RDW, neutrophils, eosinophils, NLR, CRP, PT, ALT, and AST are important indicators in the management especially for severely and critically ill patients with COVID-19.

Development of an Innovative Process for High-Temperature Fruit Juice Extraction Using a Novel Thermophilic Endo-Polygalacturonase From Penicillium oxalicum.

Efficient and cost-effective production of thermophilic endo-polygalacturonase is desirable for industrial fruit juice production, because its application could shorten the processing time and lower the production cost, by eliminating the separate step of pectin degradation. However, no endo-polygalacturonase that both functions well at sufficiently high temperature and can be manufactured economically, has been reported previously. In this study, the cDNA encoding a thermophilic endo-polygalacturonase from Penicillium oxalicum CZ1028, was cloned and over-expressed in Pichia pastoris GS115 and Escherichia coli BL21(DE3). The recombinant proteins PoxaEnPG28B-Pp (from P. pastoris) and PoxaEnPG28B-Ec (from E. coli) were isolated and purified. PoxaEnPG28B-Pp was sufficiently thermostable for potential industrial use, but PoxaEnPG28B-Ec was not. The optimal pH and temperature of PoxaEnPG28B-Pp were pH 5.0 and 65°C, respectively. The enzyme had a low K m of 1.82 g/L and a high V max of 77882.2 U/mg, with polygalacturonic acid (PGA) as substrate. The performance of PoxaEnPG28B-Pp in depectinization of papaya, plantain and banana juices at 65°C for 15 min was superior to that of a reported mesophilic endo-polygalacturonase. PoxaEnPG28B-Pp is the first endo-polygalacturonase reported to show excellent performance at high temperature. An innovative process, including a step of simultaneous heat-treatment and depectinization of fruit pulps with PoxaEnPG28B-Pp, is reported for the first time.

Tolerance against butanol stress by disrupting succinylglutamate desuccinylase in Escherichia coli.

Background: The four-carbon alcohol, butanol, is emerging as a promising biofuel and efforts have been undertaken to improve several microbial hosts for its production. However, most organisms have very low tolerance to n-butanol (up to 2% (v/v)), limiting the economic viability of butanol production. Although genomic tools (transcriptomics, proteomics, and metabolomics) have been widely used to investigate the cellular response to butanol stress, the existing knowledge of the molecular mechanisms involved in butanol tolerance is limited, and strain improvement is difficult due to the complexity of the regulatory network. Results: In this study, a butanol-tolerant Escherichia coli was constructed by disrupting gene astE (encoding succinylglutamate desuccinylase) to obtain higher butanol tolerance (increased by 34.6%). To clarify the tolerance mechanism, a metabolome analysis was also performed. As a result, a total of 73 metabolites (11 elevated and 62 decreased) were significantly changed. Most of the downregulated metabolites were mainly involved in the l-arginine degradation pathway, sulfate metabolic pathway, and 2-methylcitrate metabolic pathway. To further analyze the differential gene expression, a transcriptome was created. In total, 311 genes (113 upregulated and 198 downregulated) showed over a twofold difference and were associated with carbohydrate metabolism, energy metabolism, and ABC transporters. The integration of metabolomics and transcriptomics found that acid-activated glutaminase ybaS and the amino acid antiporter gadC were significantly up-regulated, but the levels of l-arginine and glutamate were not significantly increased and decreased. Therefore, the changes of amino acids between strains BW25113 and BW25113-ΔastE were measured by amino acid analysis. The ability of a mutant strain against acid stress was also measured by the growth experiment under various pH conditions in the absence of butanol. Conclusions: Based on the above experiments, it could be concluded that mutant BW25113-ΔastE mainly regulated intracellular pH-homeostasis to adapt to butanol stress, indicating the non-negligible impact of pH on microbial butanol tolerance, broadening our understanding of microbial butanol tolerance and providing a novel strategy for the rational engineering of a more robust butanol-producing host.