Xiaoqin Wang

This study aimed to compare the analytical characteristics and diagnostic performance of short-read next-generation sequencing (NGS) and long-read third-generation sequencing (TGS) for metagenomic pathogen detection, using defined mock communities and clinical bronchoalveolar lavage fluid (BALF) samples. Mock evaluations included microbe-host gradient mixtures (D1/D2) and six complex microbial panels (M1–M6). Sequencing was performed on Illumina, MGI, and Oxford Nanopore Technologies (ONT) platforms. Clinical validation was conducted on 62 BALF samples. Diagnostic performance was assessed against culture, clinical microbiological tests (CMT), and a composite reference standard (CRS). Turnaround times for Illumina and MGI were approximately 18–20 h and 14–19 h, respectively, whereas the ONT workflow was completed within 4–6 h. The microbe-to-host DNA ratio significantly influenced sequencing performance. Depletion of host DNA notably enhanced ONT detection, reducing the false-negative rate for low-abundance microorganisms from 43.3% to 6.7%. For all mock samples, both the Illumina and MGI platforms demonstrated 100% sensitivity and showed highly concordant detection profiles. In clinical specimens, when evaluated against the composite reference standard, the positive percent agreement (PPA) values of NGS and TGS were 93.3% and 90.7%, respectively, with corresponding negative percent agreements (NPAs) of 77.6% and 83.3%. Both platforms identified numerous pathogens that were missed by culture, especially in polymicrobial infections. Among 22 CRS-defined polymicrobial samples, culture identified all pathogens in only 2 cases, whereas NGS and TGS achieved full pathogen recovery in 18 and 17 cases, respectively. Within the evaluated workflows, short-read sequencing showed slightly higher sensitivity and overall stability, whereas host-depleted ONT offered a substantial turnaround-time advantage and may serve as a useful complementary approach in complex or time-sensitive clinical scenarios. IMPORTANCE: Rapid and accurate identification of the microbes causing pneumonia is essential for choosing effective treatment, yet current diagnostic tests are slow and often miss important pathogens. We systematically compared two major DNA sequencing strategies—established short-read platforms and newer long-read nanopore sequencing—using both carefully designed mock communities and real bronchoalveolar lavage samples from patients. We show when removal of human DNA is essential, how mixed infections are best captured, and what trade-offs exist between speed and sensitivity. Our results provide practical guidance on how hospitals can implement sequencing-based diagnostics, when rapid nanopore testing can complement conventional short-read workflows, and how to interpret sequencing read counts in day-to-day clinical decision-making.

FMS-like tyrosine kinase 3 internal tandem duplication (FLT3-ITD) mutations, found in 25%–30% of Acute myeloid leukemia (AML) patients, cause poor prognosis and resistance to FLT3 tyrosine kinase inhibitors (TKIs). We show that APG-115 selectively kills FLT3-ITD cells by activating p53. This critically upregulates TRIM22 (Tripartite motif-containing protein 22), an essential E3 ubiquitin ligase that directly binds FLT3-ITD, promotes its polyubiquitination, and induces its proteasomal degradation. This TRIM22-mediated mechanism offers a novel strategy to overcome intrinsic and acquired TKI resistance. Unlike inhibitors such as AC220, which suppress FLT3 signaling but downregulate p53, APG-115 restores p53 function and induces TRIM22, enabling potent synergy with FLT3 inhibitors. TRIM22 is essential for APG-115’s suppression of leukemia stem cells (LSCs), inducing cell cycle arrest, myeloid differentiation, and reduced clonogenic potential. The combination of APG-115 and AC220 significantly enhances apoptosis in FLT3-ITD AML models and primary cells, while sparing normal cells. It shows robust efficacy in preclinical xenograft models, reducing tumor burden and extending survival. This work establishes targeting the p53/TRIM22 axis, reliant on TRIM22’s unique activity against FLT3-ITD, as a highly promising therapeutic approach for FLT3-ITD AML, including resistant disease.

This study aimed to investigate the molecular epidemiological characteristics of carbapenem-resistant Klebsiella pneumoniae (CRKP), elucidate the mechanisms underlying ceftazidime-avibactam (CZA) resistance and identify the risk factors associated with the emergence of CZA resistance. Clinical and microbiological data from 292 hospitalized patients with CRKP infections were retrospectively collected at the First Affiliated Hospital of Xi'an Jiaotong University from January 2024 to March 2025. Ptients were categorized into CZA-susceptible (n=228) and CZA-resistant (n=64) CRKP groups based on the findings of CZA susceptibility testing. A total of five carbapenemase genes (blaKPC, blaNDM, blaVIM, blaIMP and blaOXA) were identified by the lateral flow assay and their respective subtypes of the genes was identified by PCR amplification followed by sanger sequencing. The relative expression of blaKPC was quantified using real-time quantitative PCR (RT-qPCR). Independent risk factors for CZA-resistant CRKP infections were identified using multivariate logistic regression analysis. Among the 292 CRKP isolates, a total of 64 were CZA-resistant CRKP strains. Among these, isolates co-producing KPC and NDM accounted for 42.18%; those producing NDM alone accounted for 35.94%, those producing KPC alone accounted for 15.63%, isolates co-expressing NDM and IMP accounted for 1.56%, and carbapenemase-negative isolates accounted for 4.69%. Among the 10 KPC-only producing isolates, 8 were KPC mutants, including five harboring blaKPC-33, two harboring blaKPC-90 and one harboring blaKPC-78. Additionally, the relative gene expression levels of two blaKPC-2 isolates increased by 2.80- and 3.07-fold, respectively. This study demonstrates that, alongside MBLs, mutated KPC variants serve as the predominant mechanism underlying high-level CZA resistance. The multivariate logistic regression analysis showed that the patients receiving renal replacement therapy (OR = 2.611, 95 % CI: 1.192 - 5.721) and those with previous exposure to CZA (OR = 2.749, 95 % CI: 1.269 5.953) were independent risk factors for CZA-resistant CRKP infections.

Background: Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related deaths worldwide, with a poor prognosis and high mortality rates. Therapeutic resistance, high recurrence, and limited treatment options contribute to its aggressive nature. The TMF1-regulated nuclear protein 1 (TRNP1) is a highly conserved nuclear protein, recently implicated in tumorigenesis. TRNP1 is upregulated in HCC, but its role in tumorigenesis and immunotherapy resistance remains underexplored. This study investigates the mechanical roles of TRNP1 in HCC progression through the c-Kit/signal transducers and activators of transcription 3 (STAT3) signaling pathway and its impact on immunotherapy efficacy, particularly in the context of programmed cell death protein 1 (PD-1) blockade. Methods: The expression of TRNP1 was analyzed using bioinformatics tools and confirmed through HCC patient tissue samples. Knockdown and overexpression models of TRNP1 were established in HCC cell lines to investigate its effects on cellular behaviors, including proliferation, migration, invasion, and apoptosis. Transcriptomics explored downstream pathways, identifying the c-Kit/STAT3 signaling axis. In vivo experiments assessed the efficacy of combining TRNP1 knockdown with anti-PD-1 therapy in reducing tumor volume. Results: TRNP1 was significantly upregulated in HCC tissues compared to adjacent non-cancerous tissues. High TRNP1 expression correlated with reduced overall survival (OS) and disease-free survival (DFS). TRNP1 knockdown inhibited tumor cell proliferation, colony formation, migration, and invasion while promoting apoptosis. In contrast, TRNP1 overexpression enhanced these malignant phenotypes. Mechanistically, TRNP1 promoted HCC progression by activating the c-Kit/STAT3 signaling pathway. Notably, TRNP1 knockdown, combined with PD-1 blockade, further reduced tumor volume, enhancing the efficacy of immunotherapy. Conclusions: This study establishes TRNP1 as a tumor-promoting factor in HCC, driving cancer progression via the c-Kit/STAT3 pathway. Moreover, TRNP1 knockdown sensitizes tumors to PD-1 blockade, suggesting a novel therapeutic strategy for improving immunotherapy outcomes in HCC patients. TRNP1 could serve as a potential biomarker and therapeutic target in HCC treatment.

Purpose: To analyze the changing distribution and drug resistance of pathogenic bacteria in patients with bloodstream infections (BSIs), thereby providing reference for hospital anti-infection treatment. Methods: The clinical data, distribution of pathogenic bacteria and antimicrobial susceptibility profiles of patients with positive blood cultures at the First Affiliated Hospital of Xi’an Jiaotong University from January 1, 2015 to December 31, 2024 were collected retrospectively. WHONET 5.6 software was used for data analysis. The χ² test and Fisher exact test were used for statistical analysis. Results: A total of 9372 bacterial strains were isolated from blood cultures. Gram-negative bacterial predominated (66.8%), markedly surpassing Gram-positive bacterial (33.2%). The top five pathogens were Escherichia coli (30.1%), Klebsiella pneumoniae (15.8%), Enterococcus faecium (6.9%), coagulase-negative Staphylococci (6.3%) and Staphylococcus aureus (6.1%). The detection rate of methicillin-resistant Staphylococcus aureus ranged from 25.8% to 38.4%, and it remained susceptible to vancomycin, linezolid, and teicoplanin. The detection rate of methicillin-resistant coagulase-negative Staphylococci peaked at 77.7% to 82.4%. Enterococcus faecium showed resistance to ampicillin exceeding 75%, with resistance rates to vancomycin and linezolid increasing from 0% to 5.8% and 1.2%, respectively. Escherichia coli demonstrated high susceptibility to Carbapenems, with imipenem resistance remaining low (1.6– 2.2%). The resistance rates of Klebsiella pneumoniae to imipenem rose from 3.2% to 25.6%.The resistance rate of carbapenem-resistant Pseudomonas aeruginosa decreased from 36.4% in 2015– 2016 to 16.5% in 2023– 2024. However, the resistance rate of carbapenem-resistant Acinetobacter baumannii significantly increased from 47.2% to 75.7% during the same period. Conclusion: The pathogenic bacteria in blood cultures isolates at this hospital are predominantly Gram-negative, with Escherichia coli and Klebsiella pneumoniae being the most common pathogens. The increasing trends of carbapenem-resistant Klebsiella pneumoniae, Acinetobacter baumannii and methicillin-resistant coagulase-negative Staphylococci underscore the urgent need for enhanced surveillance of pathogen distribution and antimicrobial resistance in bloodstream infections to guide rational antimicrobial use.

Leishmaniasis is a neglected tropical disease with significant global public health implications, leading to diverse clinical manifestations. It disproport

Background: This study aimed to explore the causal relationships between 1,400 plasma metabolites and various chronic liver conditions, including liver fibrosis or cirrhosis, liver carcinoma, hepatic failure, and metabolic liver disorders. Methods: This study used a two-sample Mendelian randomization (MR) method. Forward analysis focused on associations with four liver disease categories, whereas reverse analysis examined links with specific metabolites or ratios. Five MR methods were applied, primarily the inverse variance weighted (IVW) method. The IVW, Egger, and Weighted Median analyses showed p-values < 0.05 with positive directions, suggesting strong positive effects. The IVW analysis alone indicated a potential positive effect with p-value < 0.05. Sensitivity analyses ensured the results’ robustness and validity. Results: In the forward causal analysis, we identified 252 potential causal associations, 13 of which were notably strong. Specifically, six plasma metabolites and metabolic ratios were found to increase the risk of fibrosis/cirrhosis, while the other three were associated with an increased likelihood of liver cancer. Additionally, three were positively correlated with metabolic liver disease risk and one was inversely related to liver failure risk. In contrast, reverse causal analysis revealed that fibrosis/cirrhosis was linked to ten plasma metabolites and metabolic ratios, whereas liver cancer was associated with three plasma metabolites and metabolic ratios. Conclusion: Our findings underscore the significant association between an elevated glucose-to-mannose ratio and a range of liver conditions, including fibrosis/cirrhosis, metabolic liver disease, and hepatoma, thereby highlighting the crucial role of glucose metabolism in liver disease.

Background This comprehensive review sought to investigate the correlation between PLR and LMR with overall longevity (OS), recurrence-free interval (DFS), and malignancy-related survival (CSS) among individuals diagnosed with colorectal carcinoma. Methods A comprehensive review of relevant studies was carried out using prominent digital repositories to locate research articles that provided hazard estimates (HRs) for PLR and LMR in individuals diagnosed with colorectal cancer. Potential publication bias was examined through graphical funnel plot assessments, while additional subgroup analyses were conducted based on patient demographics and consideration of C-index. Results Nineteen studies were included for PLR and OS analysis, showing that high PLR was associated with increased mortality risk (HR = 1.23, 95%CI = 1.04–1.44, p = 0.01). For LMR and OS, 14 studies were analyzed, indicating that low LMR was linked to higher mortality risk (HR = 1.63, 95%CI = 1.29–2.06, p < 0.0001). Subgroup analyses showed stronger associations in the western population and studies with C-index adjustments. Regarding DFS, no significant association was found with PLR (HR = 1.14, 95%CI = 0.93–1.40, p = 0.21), while low LMR increased recurrence risk (HR = 1.31, 95%CI = 1.15–1.48, p < 0.0001). High PLR and low LMR were associated with worse CSS, with no significant heterogeneity observed. Conclusion Elevated PLR and reduced LMR are linked to unfavorable survival prospects in individuals with colon malignancy.

Objective This retrospective study explored the clinical impact of hepatitis C virus (HCV) infection in maintenance hemodialysis (MHD) patients through comprehensive analysis of liver/renal function parameters, cellular immunity profiles, and long-term survival outcomes.MethodsThe study enrolled 28 HCV-infected MHD patients (MHD-HCV group), 28 HCV-negative MHD patients (MHD group), and 21 healthy controls (NC group) retrospectively. Liver and renal functions, lymphocyte subset analysis, and interleukin-10 (IL-10) levels were assessed. Overall survival at a median follow-up of 4 years was compared between the MHD-HCV and MHD groups.ResultsBiochemical analysis demonstrated significantly elevated liver enzymes in the MHD-HCV group compared to MHD group, with mean alanine aminotransferase (ALT) levels of 26.6 ± 18.6 vs. 10.1 ± 7.1U/L (P < 0.001) and aspartate aminotransferase (AST) levels of 20.0 ± 9.0 vs. 11.8 ± 5.5U/L (P = 0.001).Furthermore, the MHD-HCV group had elevated total bile acid (7.70 ± 7.17 vs. 3.44 ± 1.75, P = 0.007), total protein (67.9 ± 5.2 vs. 63.9 ± 5.6, P = 0.012), globulin (31.1 ± 5.9 vs. 26.5 ± 3.6, P = 0.003). Immunological profiling revealed significant upregulation of both regulatory T cells (Tregs: 4.48 ± 2.94 vs. 2.48 ± 1.81, P < 0.001) and interleukin-10 (IL-10: 78.7 ± 45.1 vs. 34.2 ± 15.2, P < 0.001).The patients in the MHD-HCV group had higher mortality risk compared with those in the MHD group (χ2=4.383, P = 0.036).Conclusion HCV infection in MHD patients leads to non-negligible liver dysfunction, elevated Tregs and IL-10, as well as higher mortality.