BackgroundComparative studies of the bile microbiota in different biliary obstructive infections remain limited. This study aims to characterize bile microbiota and investigate differences in microbial profiles across various biliary obstructive diseases.MethodsThis study included patients with biliary obstructive diseases admitted to Jinling Hospital and Suqian First Hospital. The cohort consisted of individuals with benign biliary disorders, malignant biliary obstruction, and biliary obstruction secondary to severe acute pancreatitis (SAP) or intestinal fistulas. A total of 133 bile samples were collected from 118 patients and analyzed using next-generation sequencing (NGS) targeting the bacterial 16S rRNA gene and the fungal internal transcribed spacer (ITS) gene. Clinical data, including routine culture results, were extracted from electronic medical records.ResultsNGS targeting the 16S rRNA and ITS revealed a positive rate of 68.42% for bile samples, which was higher than the culture positivity rate of 60.15%, indicating a significant difference (Chi-square test, p < 0.05). The predominant bacteria identified in the bile samples through NGS were Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli. Bacterial species varied among benign biliary diseases, malignant obstructive diseases, and biliary obstruction caused by SAP or intestinal fistulas. Fungi were detected in 7.52% (10/133) of the samples, with 4 samples obtained from patients with biliary obstructive diseases due to SAP. Microbial diversity and clustering analysis showed no significant differences among various biliary disorders. Based on the culture results, the sensitivity and specificity of NGS were 81.82% and 69.64%, respectively.ConclusionThe composition of bile microbes may be related to the etiology of biliary obstruction. Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli are the predominant bacteria found in bile. NGS can be effectively applied for the identification and characterization of bile microbes associated with various biliary obstruction diseases.

Objective:This study investigated the distribution and changes in pancreatic infections among patients with acute pancreatitis (AP) from 2019 to 2023, while exploring the impact of multidrug-resistant bacterial infections on the prognosis of patients with poor outcomes. Methods:This study included patients diagnosed with SAP between 2019 and 2023 and collected the demographic and clinical characteristics of all participants. Based on routine clinical microbiological culture results, the distribution and drug resistance of pathogens associated with pancreatic infections were analyzed. Multivariable logistic regression was used to evaluate the association between multidrug-resistant organism (MDRO) infection and poor prognosis. Results:A total of 1586 pancreatic fluid specimens were analyzed and collected from 843 patients diagnosed with AP. The positive rate of the culture results was 81% (1280/1586), with the predominant pathogens identified as Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterococcus faecium, and Acinetobacter baumannii complex. Of the 843 patients, 756 met the criteria, and the proportion of MDROs in pancreatic infections was 87.57% (662/756). Multivariate logistic regression analysis revealed that septic shock, acute kidney injury, and tracheostomy were associated with a poor prognosis, whereas ICU length of stay, infected pancreatic necrosis, and tracheostomy were associated with multidrug-resistant bacterial infections in patients with severe or critical AP. Conclusion:The proportion of MDRO infections in patients with severe or critical AP was notably high, primarily involving multidrug-resistant Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Septic shock, acute kidney injury, and tracheostomy have been identified as independent risk factors of poor prognosis in patients with severe or critical AP.

This study aims to evaluate and compare the effectiveness of metagenomic next-generation sequencing (mNGS) in identifying pathogens from clinical body fluid samples, with a specific focus on the application of microbial cell-free DNA (cfDNA) mNGS. A total of 125 clinical body fluid samples were collected. All samples underwent mNGS targeting whole-cell DNA (wcDNA), with 30 samples also analyzed for cfDNA mNGS and 41 subjected to 16S rRNA NGS for comparative analysis. Patient clinical data, including culture results, were obtained from electronic medical records. In comparison to cfDNA mNGS, the mean proportion of host DNA in wcDNA mNGS was 84

Urinary extracellular vesicles (uEVs) are regarded as highly promising liquid-biopsy biomarkers for the early diagnosis and prognosis of bladder cancer (BC). However, detection of uEVs remains technically challenging owing to their huge heterogeneity and ultralow abundance in real samples. We herein present a choline phosphate-grafted platinum nanozyme (Pt@CP) that acts as a universal EV probe for the construction of a high-throughput and high-sensitivity immunoassay, which allowed multiplex profiling of uEV protein markers for BC detection. With the Pt@CP-based immunoassays, three uEV protein markers (MUC-1, CCDC25, and GLUT1) were identified for BC, by which the BC cases (n = 48), cystitis patients (n = 27), and healthy donors (n = 24) were discriminated with high clinical sensitivity and specificity (area under curve = 98.3%). For the BC cases (n = 9) after surgery, the Pt@CP-based immunoassay could report the postoperative residual tumor that cannot be observed by cystoscopy, which is clinically significant for assessing BC recurrence. This work provides generally high sensitivity for EV detection, facilitating the discovery and clinical use of EV-based biomarkers.

ObjectivesThis study aimed to evaluate the clinical performance of plasma cell-free DNA (cfDNA) next-generation sequencing (NGS) for pathogen detection in patients with sepsis.MethodsA total of 43 pairs of blood and plasma samples form 33 blood culture-positive patients were used as testing samples in metagenomic NGS (mNGS) and NGS of 16S ribosomal RNA gene amplicons (16S rRNA NGS). The results of routine tests, including microbial culture, complete blood count, and biochemical tests, were collected from electronic medical records.ResultsUsing blood as an mNGS testing sample, the proportion of host DNA was 99.9%, with only three bacteria and no fungi detected. When using plasma in mNGS, the proportion of host DNA was approximately 97%, with 84 bacteria and two fungi detected. Notably, 16S rRNA NGS detected 15 and 16 bacteria in 43 pairs of blood and plasma samples, respectively. Blood culture detected 49 bacteria (23 gram-negative bacilli and 26 gram-positive cocci) and four fungi, with 14 bacteria considered contaminants by clinical microbiologists. For all blood cultures, plasma cfDNA mNGS detected 78.26% (19/23) gram-negative rods, 17% (2/12) gram-positive cocci, and no fungi. Compared to blood cultures, the sensitivity and specificity of plasma cfDNA mNGS for detecting bacteria and fungi were 62.07% and 57.14%, respectively.ConclusionCompared to blood, plasma is more suitable for the detection of bloodstream infections using mNGS and is less affected by host DNA. The positive detection rate of plasma cfDNA mNGS for bloodstream infections caused by gram-negative bacteria was higher than that caused by gram-positive cocci.

[This corrects the article DOI: 10.2147/IJN.S394666.].

ObjectivesThis study aimed to identify the bacterial composition in the pancreatic fluid of severe and critical acute pancreatitis (SAP and CAP) patients. MethodsA total of 78 pancreatic fluid samples were collected from 56 SAP and CAP patients and analyze using aerobic culture and 16S rRNA gene next-generation sequencing. The clinical data of the patients were obtained from the electronic medical records. ResultsAmong the total 78 samples, 16S rRNA gene NGS identified a total of 660 bacterial taxa, belonging to 216 species in 123 genera. The dominant aerobic bacteria included Klebsiella pneumoniae, Acinetobacter baumannii, and Enterococcus faecium, while the dominant anaerobic bacteria included Bacteroides, Dialister invisus, and Olsenella uli. As compared to aerobic culturing, 95.96% (95/99) of the aerobic cultured bacteria were detected using the 16S rRNA gene NGS. ConclusionThe pancreatic infections in SAP and CAP patients might originate not only from the gut but also from the oral cavity and airways as well as related environments. Dynamic analysis of bacterial profile and abundance showed that some bacteria with low abundance might become the main pathogenic bacteria. There were no significant differences in the bacterial diversity between SAP and CAP.

Introduction: The increasing use of gold nanoparticles (Au NPs) in the medical field has raised concerns about the potential adverse effect of Au NPs exposure. However, it is difficult to assess the health risks of Au NPs exposure at the individual organ level using current measurement techniques.Methods: The physical and chemical properties of Au NPs were characterized by transmission electron microscope (TEM), Fourier transform infrared (FTIR), and zeta sizer. The RNA-seq data of Au NPs-exposed worms were analyzed. The food intake was measured by liquid culture and Pharyngeal pumping rate. The function of the smell and taste neurons was evaluated by the chemotaxis and avoidance assay. The activation of ASE neurons was analyzed by calcium imaging. The gene expression of ins-22 and egl-19 was obtained from the C. elegans single cell RNA-seq databases.Results: Our data analysis indicated that 62.8% of the significantly altered genes were functional in the nervous system. Notably, developmental stage analysis demonstrated that exposure to Au NPs interfered with animal development by regulating foraging behavior. Also, our chemotaxis results showed that exposure to Au NPs reduced the sensation of C. elegans to NaCl, which was consistent with the decrease in calcium transit of ASEL. Further studies confirmed that the reduced calcium transit was dependent on voltage-gated calcium channel EGL-19. The neuropeptide INS-22 was partially involved in Au NPs-induced NaCl sensation defect. Therefore, we proposed that Au NPs reduced the calcium transit in the ASEL neuron through egl-19-dependent calcium channels. It was partially regulated by the DAF-16 targeting neuropeptide INS-22.Discussion: Our results demonstrate that Au NPs affect food sensation by reducing the calcium transit in ASEL neurons, which further leads to reduced pharynx pumping and feeding defects. The toxicology studies of Au NPs from worms have great potential to guide the usage of Au NPs in the medical field such as targeted drug delivery.

A high glucose diet (HGD) is associated with many metabolic diseases including type 2 diabetes, and cardiovascular diseases. Additionally, a HGD increases the oxidative stress resistance of young animals but shortens their lifespan. To investigate the role of HGD feeding on the aging of aged animals, we tested for oxidative stress resistance and changes in lifespan using C. elegans. We showed that a HGD extends the lifespan of aged worms that are dependent on oxidative stress resistance. Furthermore, we measured the lifespan of oxidative stress responding genes of HGD-fed worms. We found that gpdh-1 and col-92 are highly expressed in HGD and paraquat (PQ) treated worms. Further experiments indicated that intestinal gpdh-1 is essential for the HGD induced lifespan extension of aged worms. Our studies provide new insights into understanding the correlation between glucose metabolism, oxidative stress resistance, and aging.

Urinary monitoring of diseases has gained considerable attention due to its simple and non-invasive sampling. However, urinalysis remains limited by the dearth of reliable urinary biomarkers and the intrinsically enormous heterogeneity of urine samples. Herein, we report, to our knowledge, the first renal-clearable Raman probe encoded by an internal standard (IS)-conjugated reporter that acts as a quantifiable urinary biomarker for reliable monitoring of cancer development, simultaneously eliminating the impact of sample heterogeneity. Upon delivery of the probes into tumor microenvironments, the endogenously overexpressed β-glucuronidase (GUSB) can cleave the target-responsive residues of the probes to produce IS-retained gold nanoclusters, which were excreted into host urine and analyzed by Au growth-based surface-enhanced Raman spectroscopy. As a result, the in vivo GUSB activity was transformed into in vitro quantitative urinary signals. Based on this IS-encoded synthetic biomarker, both the cancer progression and therapy efficacy were quantitatively monitored, potentiating clinical implications.

In December 2019, a severe acute respiratory syndrome caused by SARS-CoV-2 spread rapidly worldwide. Portable nucleic acid tests of SARS-CoV-2 are critically important for diagnostics. In this study, we used an isothermal amplification method—Multienzyme Isothermal Rapid Amplification (MIRA)—for rapid detection of SARS-CoV-2. We designed the primers and probes in ORF1ab and N gene of SARS-CoV-2. The amplicons could be monitored by lateral flow dipsticks (LFDs). The reaction temperature, time, concentrations of primers and probes, and working volume were optimized. Four commercial swab collection buffers were used to test the amplification efficacy of our assay without RNA extraction. Our assay was able to amplify duplex targets of SARS-CoV-2 in one single reaction using one-step RT-MIRA. The assay worked well in a low volume of 10 μl at 38°C for 20 min. Using three collection buffers without guanidinium, our assay was able to amplify efficaciously without RNA extraction. The 95% limit of detection (LoD) of the RT-MIRA assay was 49.5 (95% CI, 46.8–52.7) copies/ml for ORF1ab gene and 48.8 (95% CI, 46.5–52.6) copies/ml for N gene. There is no cross-reaction with other human respiratory pathogens, such as SARS-CoV, MERS-CoV, influenza A virus, influenza B virus, human adenovirus, respiratory syncytial virus, human parainfluenza virus, and coronavirus 229E in our assay. The precision evaluation revealed that the C50 − 20% to C50+20% range bounds the C5–C95 interval. This assay also showed high anti-interference ability. The extraction-free RT-MIRA and qPCR detection results of 243 nucleic acid specimens from suspected patients or national references showed a 100.0% (95% confidence interval, 94.2%–100.0%) positive predictive value and a 100.0% (95% confidence interval, 92.7%–100.0%) negative predictive value. Compared with qPCR, the kappa value of the two assays was 1.00 ( P < 0.0001). In conclusion, we provide a portable and visualized method for detection of SARS-CoV-2 without RNA extraction, allowing its application in SARS-CoV-2 on-site detection.

The increasing use of gold nanoparticles (NPs) raises concerns about the potential effect of gold NPs exposure on human health. Therefore, gold NPs exposure is hard to evaluate at the organ level with current measurement technology. The bio-distribution assay showed that intestine was the organ with most gold NPs accumulated in C. elegans . However, our data indicated that 62.8% of the significant altered genes were function in the nervous system using tissue enrichment analysis. Notably, developmental stage analysis has demonstrated that NP exposure interfered with the development of animals. Furthermore, the transcription factors DAF-16 was regulating the oxidative stress genes induced by gold NPs. Therefore, we proposed the localization of the oxidative stress genes in the neuron cells and how their expression affect neuron communication. Our results demonstrate that the gold NPs-induced oxidative stress affects the nervous system via physical damage to the neurons and disruption of cell-to-cell communication. Future toxicology research on gold NPs should focus on neurons. ![Figure][1] Graphical abstract [1]: pending:yes

We present a detailed study on visual detection of influenza viruses by duplex recombinase polymerase amplification (RPA) with lateral flow dipsticks (LFDs). The LFD consisted of two test lines and a control line, on which anti-fluorescein isothiocyanate antibodies, anti-digoxigenin antibodies, and biotinylated bovine serum albumin were immobilized, respectively. The performance of the LFD was evaluated with dual-labeled DNA amplicons. The results indicate that the detection of DNA amplicons by LFDs is specific and sensitive, with detection limits of 5.80 fmol for fluorescein isothiocyanate-labeled amplicons and 8.39 fmol for digoxigenin-labeled amplicons. We next developed a duplex RPA–LFD assay for simultaneous detection of influenza A virus and influenza B virus, and then optimized the parameters, including the reaction temperature, reaction time, and concentrations of primers and probes. Assessment of the specificity and sensitivity indicated that this assay is sensitive and specific for simultaneous detection of influenza viruses, with detection limits of 50 copies per reaction for influenza B virus and 500 copies per reaction for influenza A virus, without cross-reactivity with other pathogens. Compared with real-time PCR as a reference method to detect influenza viruses in clinical samples, the clinical sensitivity of the duplex RPA–LFD assay was 78.57% for influenza A virus and 87.50% for influenza B virus, with 100% specificity. In conclusion, the duplex RPA–LFD assay is a rapid, cost-effective, and sensitive method for the identification of influenza viruses.

Three reverse transcription recombinase polymerase amplification assays with lateral flow dipsticks (RT-RPA-LFD) were developed for identification of the matrix and hemagglutinin (HA) genes to detect influenza A virus and distinguish subtypes H1 and H3. Assessment of the assays' specificity showed that there was no cross-reactivity with other targets. Their limits of detection were 123.6 copies per reaction for the matrix gene, 677.1 copies per reaction for the H1 HA gene, and 112.2 copies/reaction for the H3 HA gene. Of 111 samples tested by RT-RPA-LFD assays, 27 were positive for influenza A virus, 14 were positive for H1, and 10 were positive for H3. Compared to the results obtained from real-time RT-PCR assays, the sensitivity of RT-RPA-LFD assays was 75%, 93.33% and 71.43% for the matrix, H1, and H3, with 100% specificity. The sensitivity of RT-RPA-LFD assays is lower than that of real-time RT-PCR, comparable or better than that of conventional RT-PCR, and much better than that of RIDTs. In conclusion, these assays offer an efficient and reliable tool for identification and subtyping of influenza A virus (subtype H1 and H3) in the resource-limited setting.

通过分析中国棉花的进口行情,回顾国内外棉花市场的变化动态,结合美国农业部(U SDA)对世界棉花行情的展望预测,研究了近几年美国棉制纺织品和服装产品的进出口变化趋势,预测了世界棉花市场行情的发展趋势.研究结果显示:世界棉花生产将继续向丰产区域集中,全球主要国家的棉花贸易量将逐步增长,总体而言,世界棉花行情也将慢慢复苏.

BACKGROUND:Long noncoding RNAs (lncRNAs) have recently received wide attention as key molecules that mediate a variety of physiological and pathological processes by regulating gene expression; however, knowledge of lncRNAs in rheumatoid arthritis (RA) is limited. Thus, we investigated the lncRNA expression profile in fibroblast-like synoviocytes (FLSs) from patients with RA and explored the function of abundantly expressed lncRNAs.METHODS:LncRNA and mRNA microarrays were performed to identify differentially expressed lncRNAs in RA FLSs compared with normal FLSs. Quantitative polymerase chain reaction (qPCR) was used to validate the results, and correlation analysis was used to analyze the relationship between these aberrantly expressed lncRNAs and clinical characteristics. A receiver operating characteristic (ROC) curve was constructed to evaluate the diagnostic value of the lncRNAs identified.RESULTS:According to the gene expression profiles, 135 lncRNAs were differentially expressed between RA and normal FLSs. Furthermore, qPCR data showed that lncRNA ENST00000483588 was up-regulated and that three lncRNAs (ENST00000438399, uc004afb.1, and ENST00000452247) were down-regulated in RA FLSs. The expression level of ENST00000483588 was positively correlated with the level of C-reactive protein and the Simplified Disease Activity Index score. Moreover, the areas under the ROC curve were 0.85, 0.92, 0.97, and 0.92 for ENST00000483588, ENST00000438399, uc004afb.1, and ENST00000452247, respectively.CONCLUSIONS:The results indicate that the dysregulation of ENST00000483588, ENST00000438399, uc004afb.1, and ENST00000452247 may be involved in the pathological processes of RA and that these lncRNAs may have potential value for the diagnosis and assessment of the disease activity of RA.

To determine the efficiency of RNA extraction methods based on magnetic beads, three different bead-based methods (one using silica-coated magnetic beads [SMNP], one using immunomagnetic beads conjugated to a specific antibody [IMB], and one using magnetic beads to nonspecifically adsorb virions [MNP]) were compared with the TRIzol method for the extraction of cucumber green mottle mosaic virus (CGMMV) RNA from cucumber leaves by real-time RT-PCR. The results indicated that the extraction efficiency of the SMNP method was 10 times higher than those of the IMB and MNP methods and 100 times higher than that of the TRIzol method. Therefore, the SMNP method could be considered for use in quarantine measures for the prevention and control of the disease caused by CGMMV.