Jue Pan

Aspergillus section Nigri is distributed ubiquitously in nature and is reported to be the third most clinically significant species of the Aspergillus genus. In this study, we surveyed Aspergillus section Nigri isolates from Zhongshan Hospital, Fudan University, Shanghai, China, from 2019 to 2023. We determined the species distribution of section Nigri isolates by partial β-tubulin gene sequencing. We characterized the antifungal susceptibility profiles of these isolates to medical azoles (itraconazole, voriconazole, posaconazole, and isavuconazole) using the Sensititre^TM custom-designed broth microdilution system. The cyp51A sequences were compared between azole-resistant and azole-susceptible strains in order to determine the potential antifungal resistance mechanism. A total of 54 Aspergillus section Nigri isolates were obtained. A. tubingensis (50.0%) and A. niger (46.3%) were the most prevalent species. Two isolates of A. welwitschiae were identified. Resistance to Itraconazole, voriconazole, and isavuconazole was found in 26%, 33.3%, and 33.3% of A. tubingensis isolates, respectively. All A. niger and A. welwitschiae isolates were sensitive to these azoles. Three amino acid mutations were found in azole-resistant A. tubingensis isolates, namely Y119F, Y119H, and T321A. Results from this study provide us with an understanding of species distribution and antifungal susceptibility profiles of clinical Aspergillus section Nigri isolates in Eastern China. It highlights the importance of accurate species identification and antifungal susceptibility testing. Our results also suggest that the novel Y119F substitution is potentially a key player in azole resistance.

Despite the recommendation of purified water, dental unit waterlines (DUWLs) readily form biofilm and suffer persistent microbial contamination, threatening both patients and dental staff. This study aimed to evaluate the microbial contamination and practical effectiveness of chemical disinfection in reverse osmosis (RO) water-supplied DUWLs. A single-center, sequential longitudinal study involving 15 dental chairs and 60 terminal outlets was conducted. Two disinfection strategies were sequentially evaluated: shock disinfection with a chlorine-based agent and continuous disinfection using slightly acidic electrolyzed water (SAEW). Heterotrophic plate counts (HPCs) were quantified via R2A culture, and microbial communities were characterized by metagenomic next-generation sequencing (mNGS) on 12 water samples (four terminal outlets and two source-water points, both pre- and post-disinfection). Water quality assessment revealed severe microbial contamination at the terminal outlets, with 73.33% of samples exceeding the threshold (500 CFU/mL) and a median HPC level of 805 CFU/mL. Notably, mNGS identified nucleic acid sequences of Legionella pneumophila, Pseudomonas aeruginosa, and Acanthamoeba in four pre-disinfection terminal-outlet samples. Chlorine-based shock disinfection achieved 100% compliance immediately after treatment; however, by week 5, the percentage above the threshold value had risen to 73.33%, with a median HPC level of 600 CFU/mL. The continuous SAEW disinfection protocol sustained effective microbial control over 55 weeks, with an overall percentage above threshold value of only 3.33%. mNGS analysis further confirmed a reduction in microbial relative abundance following one year of continuous SAEW disinfection. In conclusion, purified RO water alone could not guarantee DUWL microbiological safety, and this study provided practical evidence to support decision-making for DUWL maintenance.

Limited data exist regarding lysogenic phages carried by M. abscessus, as well as regarding their roles played in diseases. Strains identified as M. abscessus from patients were collected. Prophages, virulence factors, and antibiotic resistance genes present in genomes were predicted, and correlations between prophages, virulence factors, antibiotic resistance genes, and clinical patient prognoses were analyzed. A total of 145 prophage sequences were detected in 56 M. abscessus strains. Prophages contained more virulence factors and antibiotic resistance genes, compared to known mycobacteriophages. The average sequence similarity among prophage sequences from a single patient was significantly higher than that among prophages from different patients or between prophages and known phages. The study showed that M. abscessus commonly carries prophages, which are enriched in virulence factors and antibiotic resistance genes relative to known phages, but their relationship to clinical prognoses requires further study. Prophages present in strains from different patients were highly diverse and exhibited low similarity with known mycobacterial phages.

Background: Nontuberculous mycobacterial pulmonary disease (NTM-PD) is an increasingly prevalent chronic infection, where the host immune status plays a crucial role in disease susceptibility and progression. The complex pulmonary microenvironment, characterized by diverse microbial communities and host immune interactions, exhibits distinct features that may be fundamentally altered by the patient’s underlying immune state. Methods: A total of 111 sputum specimens and 64 bronchoalveolar lavage fluid (BALF) specimens were collected from 143 patients diagnosed with NTM-PD under different immune states. Metagenomic sequencing was performed on these specimens to characterize and compare the pulmonary microenvironmental features among NTM-PD patients with a distinct immune status through comprehensive bioinformatic analyses. Results: The immunosuppressed group exhibited a lower α-diversity in sputum specimens (p < 0.05). Principal Coordinates Analysis (PCoA) of β-diversity for sputum and BALF specimens revealed significant differences between the groups (p < 0.05). Linear discriminant analysis Effect Size (LEfSe) analysis identified species enriched in the immunosuppressed group. A co-occurrence network analysis indicated that the immunosuppressed group had more structured and actively connected networks compared to the control group. The Mantel test confirmed that the abundance of these species enriched was associated with clinical immune–inflammation-related indicators in patients. Conclusions: Our study reveals the pulmonary microenvironment in immunosuppressed patients with NTM-PD. Further work is required to explore the two-way relationship between micro-organisms and immune and inflammatory responses, with the influence on patient outcomes.

Objectives: To investigate the associations between the overall burden of comorbidity, inflammatory indicators in plasma and Ct values among the elderly with COVID-19.Methods: We conducted a retrospective observational study. The results of each nucleic acid test of during hospitalization were obtained. Linear regression models assessed the associations between the overall burden of comorbidity, inflammatory indicators in plasma and Ct values among the elderly. A causal mediation analysis was performed to assess the mediation effects of inflammatory indicators on the association between the overall burden of comorbidity and Ct values.Results: A total of 767 COVID-19 patients aged ≥ 60 years were included between April 2022 and May 2022. Patients with a high burden of comorbidity had significantly lower Ct values of the ORF gene than subjects with a low burden of comorbidity (median, 24.81 VS 26.58, P < 0.05). Linear regression models showed that a high burden of comorbidity was significantly associated with higher inflammatory responses, including white blood cell count, neutrophil count and C-reactive protein. Also, white blood cell count, neutrophil count, C-reactive protein and the overall burden of comorbidity assessed by age-adjusted Charlson comorbidity index were independent risk factors for the Ct values. A mediation analysis detected the mediation effect of white blood cells on the association between the burden of comorbidity and Ct values, with the indirect effect estimates of 0.381 (95% CI: 0.166, 0.632, P < 0.001). Similarly, the indirect effect of C-reactive protein was -0.307 (95% CI: -0.645, -0.064, P = 0.034). White blood cells and C-reactive protein significantly mediated the relationship between the burden of comorbidity and Ct values by 29.56% and 18.13% of the total effect size, respectively.Conclusions: Inflammation mediated the association between the overall burden of comorbidity and Ct values among elderly with COVID-19, which suggests that combined immunomodulatory therapies could reduce the Ct values for such patients with a high burden of comorbidity.

Objective: To compare the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for cryptococcosis in patients with different immune statuses with that of conventional detection.Methods: A total of 1442 specimens including 71 specimens from patients with cryptococcosis were analyzed in the study. The chi square test was used to screen the sensitivity and specificity of different detection methods for different specimen types. One-way ANOVA was used to compare the mNGS results with age, CD4, lymphocytes, IFN, IL-6, IL-2 and serum antigen assay.Results: The sensitivity of mNGS was 44.29% in Cryptococcus infection cases. The positive rate of mNGS results for bronchoalveolar lavage fluid (BALF, 87.50%) from immunocompromised patients was higher than that of BALF from immunocompetent patients (40.00%, p=0.04). The sensitivity of the serum Cryptococcus capsular antigen assay was 80.00% in immunocompetent patients and 96.42% in immunocompromised patients (p = 0.049). A positive rate of detection of Cryptococcus from mNGS was higher when cryptococcal antigen ≥1:160 (p=0.022) in immunocompromised patients. A positive rate of detection of Cryptococcus from mNGS was higher when lymphocyte counts were lower in both immunocompetent patients(p=0.017) and in immunocompromised patients(p=0.029).Conclusions: The sensitivity of mNGS is lower than that of serum cryptococcal antigen assay and histopathology in immunocompetent patients. However, BALF detection is recommend for immunocompromised patients compared with tissue and CSF. The positive mNGS result was correlated with lower lymphocyte counts, higher IL-2 and higher serum antigen assay in immunocompromised patients.

Low CD4 T cell count predicts radiological progression in severe and critically ill COVID-19 patients: a case control study Qingqing Wang, Yumeng Yao, Zheyong Huang, Jiatian Cao, Chouwen Zhu, Kaihuan Yu, Jue Pan, Bijie Hu

Urban particulate matter (PM), a great danger to public health, is associated with increasing risk of pulmonary diseases. However, the involved key genes and signaling pathways mediating the cellular responses to urban PM are largely unknown. In this study, human bronchial epithelial cells BEAS-2B was exposed to Standard reference material (SRM) 1649b, followed by RNA-sequencing (RNA-seq) and a combination of different bioinformatics analysis. A total of 201 genes (111 upregulated and 90 downregulated) were identified as the differentially expressed genes (DEGs). Moreover, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) unveiled several significant genes and pathways involved in PM-induced lung toxicity. Protein-protein interaction (PPI) network was performed with the Search Tool for the Retrieval of Interacting Genes (STRING), and the hub gene modules were recognized by Molecular Complex Detection (MCODE), a plug-in of Cytoscape. Moreover, Connectivity Map (CMap) analysis found six candidate small molecular compounds to reverse PM-altered gene expression, including aminohippuric acid, captopril, cinoxacin, fasudil, pargyline, and altizide. Finally, the expressions of part vital genes related to inflammation (IL-1β, CXCL2, CXCL5, CXCL8), ferroptosis (HMOX1, GCLM), and autophagy (BECN1, MAPK1LC3B) were in accordance with the RNA-seq data, with a concentration-dependent manner. This study may be helpful in revealing the complex molecular mechanisms underlying PM-induced lung toxicity and provide some new therapeutic targets for PM-related pulmonary diseases.

A 50-year-old woman presented with right back pain, low fever, leukocytosis, a high level of C-reactive protein and a high erythrocyte sedimentation rate. Abdominal magnetic resonance imaging (MRI) revealed a hypodense lesion in the right suprarenal region, while PET/CT showed mildly increased metabolic activity. A CT-guided percutaneous puncture was performed, and foul-smelling thick pus was removed, which indicated an anaerobic infection. A smear of the pus showed both gram-positive and gram-negative microorganisms. Traditional culture only detected Escherichia coli, Proteus mirabilis, and Actinomyces turicensis. While surprisingly, metagenomic next-generation sequencing (mNGS) of both the pus and blood showed high reads of multiple pathogens, including anaerobes and the three culture-positive pathogens. Thus, adrenal gland abscess was confirmed, and a combination therapy of catheter drainage and effective antimicrobial treatment was started. Six days later, the patient had clinically improved and mNGS showed dramatically decreased reads of all pathogens. A follow-up lab examination of inflammatory biomarkers was normal, and the adrenal mass was reduced radiographically.