1.Development of features analysis workflow for Klebsiella pneumoniae based on clinical metagenomics next generation sequencing data
Shuyi WANG ; Qi WANG ; Yuyao YIN ; Yifan GUO ; Shuai MA ; Guankun YIN ; Hui WANG
Chinese Journal of Laboratory Medicine 2025;48(9):1149-1157
Objective:To identify strain-specific features of Klebsiella pneumoniae by analyzing metagenomics next generation sequencing (mNGS) data, thereby expanding the downstream applications of mNGS. Methods:The sequences of K.pneumoniae strains were organized from both the self-built database of the long-term multi-center research cohort in China established by the Peking University People′s Hospital from 2009 to 2020 (with 2 345 sequences) and the public databases (with 19 648 sequences). The existing large-scale databases were compressed, and a set of strains representative of clonal groups were screened. A strain genome information library was constructed based on k-mer features, and the most matching representative sequences in the database were searched for the raw mNGS data. The search results of the self-built library and public library were merged and optimized to update the prediction of antimicrobial-resistance characteristics and avoid the impact of uneven data distribution on the results. A total of 314 clinical samples from patients with K.pneumoniae detected by mNGS in the Clinical Microbiology Laboratory of Peking University People′s Hospital from 2022 to 2024 were retrospectively collected, and 101 samples with positive clinical culture results were selected to validate the prediction results. The antimicrobial-resistance phenotypes were verified by clinical antimicrobial susceptibility test results. Whole-genome sequencing was performed on the culture strains of 14 samples randomly selected using random numbers to verify the genotypes. Single nucleotide polymorphism distance analysis was used to verify the occurrence of outbreak events. The χ2 test and Mann-Whitney U test were used for statistical analysis. Results:A representative strain sequence k-mer feature library containing self-built and public sub-libraries was constructed. The library construction required only about 1 hour with <3 GB storage, with a high compression ratio and low update cost. Using k-mer-based analysis, mNGS data achieved precise strain characterization within 4 minutes and and <5 GB memory occupation. There was a significant difference in the antimicrobial-resistance rates to more than half of the antibiotics between the self-built database (90.8%, 2 130/2 345) and the public database (22.7%, 4 457/19 648) ( χ2=4 634.1, P<0.001). After optimizing the search results, the mean category agreement, sensitivity, and specificity of the prediction for eight antibiotics reached 84.8% (323/381), 78.9% (131/166), and 91.2% (196/215), respectively. The target genotypes were successfully detected in 10 out of 12 samples, and two outbreak events (2 samples per event) were successfully identified. Conclusions:An independent analysis process adapted to the needs of identifying the features of K. pneumoniae strains in mNGS data was developed. This process requires minimal computational resources and processing time and can directly achieve the simultaneous analysis of the antimicrobial-resistance phenotypes of K. pneumoniae at the strain level and their corresponding genomic characteristic profiles based on the raw mNGS reads.
2.Effect of salidroside on the immune function of BCG-infected macrophages
Shuyi NI ; Zhao JIANG ; Zhongtao WANG ; Shumei HE
Journal of Shanghai Jiaotong University(Medical Science) 2025;45(4):426-433
Objective·To Investigate the effects of salidroside(SAL)on the immune response of macrophages infected with BCG.Methods·RAW264.7 mouse macrophages were infected with BCG,and the experiments were divided into blank control(BCG),salidroside(SAL+BCG),isoniazid(INH+BCG),and salidroside+isoniazid(SAL+INH+BCG)groups.The effects of SAL and INH on the proliferation of RAW264.7 cells were detected by MTT colorimetric assay,and the experimental concentrations of SAL and INH were screened.After the establishment of the BCG-infected macrophage model,intracellular bacterial survival was detected by bacterial plate count and flow cytometry following salidroside pretreatment.The levels of tumor necrosis factor-α(TNF-α),interferon-γ(IFN-γ),interleukin-6(IL-6),and interleukin-10(IL-10)in the culture supernatants were measured by enzyme-linked immunosorbent assay,and apoptosis levels were assessed by flow cytometry.Results·SAL at a concentration of 800 μmol/L and INH at 10 μmol/L were selected for subsequent experiments.Compared with the BCG group,SAL pretreatment for 36 h had the best effect,and the growth of BCG in macrophages in the administered group was inhibited.The inhibitory effect of the combined application of SAL and INH was obvious and statistically significant.Compared with the BCG group,SAL alone led to decreased secretion of TNF-α,IFN-γ,IL-6,and IL-10,although the differences were not statistically significant.However,the combination of SAL and INH caused a significant decrease in the levels of TNF-α,IL-6 and IL-10 in the supernatants of the cells(all P<0.05).Compared with the BCG group,in the early stage of the infection,SAL and INH were able to significantly reduce the apoptotic levels of BCG-infected RAW264.7 cells(P=0.008,P=0.032),and the combined application of SAL and INH significantly enhanced the apoptosis levels of BCG-infected RAW264.7 cells in the late stage of infection(P=0.001).Conclusion·In BCG-infected macrophages,SAL can exhibit antimycobacterial effects on the host by enhancing macrophage immune function,suppressing intracellular bacterial survival,and concurrently mitigating the inflammatory response elicited by BCG infection.
3.Effect of salidroside on the immune function of BCG-infected macrophages
Shuyi NI ; Zhao JIANG ; Zhongtao WANG ; Shumei HE
Journal of Shanghai Jiaotong University(Medical Science) 2025;45(4):426-433
Objective·To Investigate the effects of salidroside(SAL)on the immune response of macrophages infected with BCG.Methods·RAW264.7 mouse macrophages were infected with BCG,and the experiments were divided into blank control(BCG),salidroside(SAL+BCG),isoniazid(INH+BCG),and salidroside+isoniazid(SAL+INH+BCG)groups.The effects of SAL and INH on the proliferation of RAW264.7 cells were detected by MTT colorimetric assay,and the experimental concentrations of SAL and INH were screened.After the establishment of the BCG-infected macrophage model,intracellular bacterial survival was detected by bacterial plate count and flow cytometry following salidroside pretreatment.The levels of tumor necrosis factor-α(TNF-α),interferon-γ(IFN-γ),interleukin-6(IL-6),and interleukin-10(IL-10)in the culture supernatants were measured by enzyme-linked immunosorbent assay,and apoptosis levels were assessed by flow cytometry.Results·SAL at a concentration of 800 μmol/L and INH at 10 μmol/L were selected for subsequent experiments.Compared with the BCG group,SAL pretreatment for 36 h had the best effect,and the growth of BCG in macrophages in the administered group was inhibited.The inhibitory effect of the combined application of SAL and INH was obvious and statistically significant.Compared with the BCG group,SAL alone led to decreased secretion of TNF-α,IFN-γ,IL-6,and IL-10,although the differences were not statistically significant.However,the combination of SAL and INH caused a significant decrease in the levels of TNF-α,IL-6 and IL-10 in the supernatants of the cells(all P<0.05).Compared with the BCG group,in the early stage of the infection,SAL and INH were able to significantly reduce the apoptotic levels of BCG-infected RAW264.7 cells(P=0.008,P=0.032),and the combined application of SAL and INH significantly enhanced the apoptosis levels of BCG-infected RAW264.7 cells in the late stage of infection(P=0.001).Conclusion·In BCG-infected macrophages,SAL can exhibit antimycobacterial effects on the host by enhancing macrophage immune function,suppressing intracellular bacterial survival,and concurrently mitigating the inflammatory response elicited by BCG infection.
4.Measuring distance between the fetal bladder neck and rectal end using prenatal MRI
Yaxian CAO ; Shuyi LIU ; Zhen CHEN ; Rui WANG ; Li HUANG ; Xiaochun ZHANG
Chinese Journal of Perinatal Medicine 2025;28(5):403-407
Objective:To measure the distance between the fetal bladder neck and the rectal end using prenatal MRI and analyze the developmental patterns of this distance and the gender differences in the second and third trimesters of pregnancy.Methods:This retrospective cohort study involved fetuses born at Guangzhou Women and Children's Medical Center, Guangzhou Medical University after regular prenatal examinations from January 2019 to December 2022 and confirmed to have typical anorectal structures after birth. These fetuses had undergone prenatal MRI examinations for reasons other than abdominal issues. The morphology of the fetuses' colons, rectums, and bladders was observed, and the vertical distance between the bladder neck and the rectal end was measured on sagittal T1weighted imaging. Differences in the distance between male and female fetuses were analyzed. The fetuses were divided into five groups based on their gestational age at the time of MRI examination (23-24 weeks, >24-26 weeks, >26-28 weeks, >28- 30 weeks, and >30-32 weeks), and the changes in the distance with gestational age were analyzed. Statistical analysis was performed using t-test, Kruskal-Wallis test, and Spearman correlation analysis. Pairwise comparisons among multiple groups were conducted using the Bonferroni method. Results:(1) A total of 142 fetuses were included in this study, all of which were singletons, with 73 males (51.4%) and 69 females (48.6%). The gestational age at the MRI examination was 28 weeks (26-30 weeks). (2) All fetuses had meconium filling the entire rectum and colon, with the rectal end located 0.570-2.610 cm below the bladder neck. (3) The distance between the bladder neck and the rectal end was shorter in male fetuses than in female fetuses [(1.140±0.261) vs. (1.519±0.405) cm, t=-6.58, P<0.001]. (4) In female fetuses, four pairs of groups showed statistically significant differences in the distance (23-24 weeks group vs. >26-28 weeks, >28- 30 weeks, and >30-32 weeks groups, and >24-26 weeks group vs. >30-32 weeks group). However, only two groups of male fetuses (23-24 weeks group vs. >28-30 weeks group) had statistically significant differences in the distance (all P<0.005). (5) The distance was moderately correlated with gestational age in male fetuses ( r=0.42, P<0.001), but they were strongly correlated in female fetuses ( r=0.66, P<0.001). Conclusions:The distance between the bladder neck and the rectal end in fetuses shows certain developmental patterns and gender differences in pregnancy's second and third trimesters. The correlation between the value and gestational age is stronger in female fetuses.
5.Animal study results of a novel designed transcatheter mitral valve replacement system
Da ZHU ; Shouzheng WANG ; Jianbin GAO ; Zhiling LUO ; Ke YANG ; Chunmei XIE ; Pengxu KONG ; Shuyi FENG ; Hong JIANG ; Xiangbin PAN
Chinese Journal of Cardiology 2025;53(3):287-292
Objective:To preliminarily assess the biocompatibility and durability of the TruDelta TM transcatheter mitral valve replacement (TMVR) system. Method:Six adult sheep were divided into 3 groups based on the duration of follow-up: 30 days ( n=1), 90 days ( n=3) and 180 days ( n=2). The TruDelta TM TMVR system was implanted through a transapical approach under transesophageal echocardiographic guidance. The operability of the TMVR system was evaluated using an instrument performance evaluation scale (consisting of 39 items), with scores ranging from 1 (worst) to 10 (best) assigned by the operator. Echocardiography was conducted preoperatively, immediately after surgery, and at 30, 90, and 180 days post-implantation. At the last follow-up time point, the intervention mitral valve membrane and major organs were dissected for observation. The artificial valves were taken for hematoxylin eosin (HE) staining and observed under a scanning electron microscope. Result:All six procedures were successfully completed using 29S size TruDelta TM TMVR device. At the final follow-up, echocardiogram demonstrated good valve function without obvious paravalvular leakage, with a transvalvular gradient of (7.8±3.2) mmHg (1 mmHg=0.133 kPa) and a mitral valve orifice area of (1.8±0.2) cm 2. Autopsy findings revealed no structural valve failure and almost complete endothelialization (>75%) with 90 to 180 days. Both HE staining and scanning electron microscopy confirmed optimal endothelialization of the valve stent. Conclusion:The preclinical animal study indicates that the TruDelta TM device exhibits favorable biocompatibility and durability.
6.Meta-analysis of the efficacy and safety of negative-pressure wound therapy in the treatment of infected wounds in orthopedic trauma patients
Shuyi YUAN ; Lulu TANG ; Ansu WANG ; Jiayi FENG ; Xiaotong LIU ; Tongxia XIA
Chinese Journal of Trauma 2025;41(1):82-89
Objective:To explore the efficacy and safety of negative-pressure wound therapy (NPWT) in treating infected wounds in orthopedic trauma patients.Methods:China National Knowledge Infrastructure, China Biomedical Literature Database, Wanfang Data Knowledge Service Platform, PubMed, Web of Science, Cochrane Library, and CINAHL were searched for randomized controlled trials (RCT) and cohort studies examining the impact of NPWT on wound healing in orthopedic trauma infections. The retrieval time was from the establishment of the databases to October 2024. RevMan 5.4 software was used for Meta-analysis. The patients were divided into two groups according to different treatment methods: the intervention group, treated with NPWT, and the control group, treated with conventional treatment. The observed indicators included clinical efficacy, wound healing quality, length of hospital stay, wound healing time, incidence of complications, secondary surgery rate, and duration of antibiotic use. Publication bias analysis was performed on the observed indicators through Begg and Egger tests.Results:A total of 13 studies were included, comprising 11 RCT and 2 cohort studies, involving a total of 3 538 patients, with 1 762 in the intervention group and 1 776 in the control group. The meta-analysis results indicated that the intervention group had better clinical efficacy ( OR=7.08, 95% CI 5.31, 9.45, P<0.01), higher wound healing quality ( MD=4.15, 95% CI 3.99, 4.32, P<0.01), shorter length of hospital stay ( MD=-13.38, 95% CI -14.39, -12.38, P<0.01), shorter wound healing time ( MD=-8.11, 95% CI -10.22, -6.00, P<0.01), lower incidence of complications, lower secondary surgery rate ( OR=0.22, 95% CI 0.09, 0.57, P<0.01), and shorter duration of antibiotic use ( MD=-7.61, 95% CI -8.06, -7.16, P<0.01) when compared with the control group. No significant publication bias was observed in the aforementioned indicators ( P>0.05). Conclusion:Compared with the conventional treatment, NPWT can enhance the clinical efficacy and wound healing quality of infected wounds in orthopedic trauma patients, shorten length of hospital stay and wound healing time, reduce the incidence of complications and secondary surgery rates, and shorten the duration of antibiotic use.
7.Immersive virtual reality-guided core stability training can improve the balance of ischemic stroke survivors
Jianhua LI ; Shiyuan WANG ; Shuyi RUANWEI ; Min YAN ; Ting GAO ; Tiangao LIN ; Yang LIU ; Fangchao WU ; Zhiping LIAO ; Jian WANG
Chinese Journal of Physical Medicine and Rehabilitation 2025;47(7):601-607
Objective:To explore the effectiveness of immersive virtual reality (VR)-guided core stability-assisted training in improving the balance of ischemic stroke survivors.Methods:Sixty-six hemiplegic ischemic stroke survivors were randomly divided into a conventional rehabilitation training group (CON) of 32 and an immersive VR-guided core stability-assisted training group (VR-TOT) of 34. In addition to basic internal medical treatment, the CON group underwent conventional rehabilitation therapy, while the VR-TOT group received VR-guided core stability-assisted training. Before and after 4 weeks of the treatments, the subjects′ balance was evaluated using the Fugl-Meyer balance scale. A three-dimensional force platform was used to collect the sway amplitude, sway speed, peripheral area and total trajectory length of the center of pressure COP of the bilateral plantar in the left-right and anterior-posterior directions while the subjects stood with the eyes open and closed.Results:After the treatments, the average Fugl-Meyer balance scores of both groups had improved significantly. In the eyes-open condition, after the treatment, there was a significant decrease in the average COP sway amplitude in the anteroposterior direction on the hemiplegic side among the CON group, as well as in both the mediolateral and anteroposterior directions on both sides in the VR-TOT group. The sway velocity in the anteroposterior direction on the hemiplegic side had decreased significantly in both groups, and the sway velocity in both the mediolateral and anteroposterior directions on the non-hemiplegic side had also decreased significantly. In the CON group the peripheral area on the non-hemiplegic side had decreased and the total trajectory length had shortened significantly. In the VR-TOT group there were significant decreases in the peripheral area on both sides and in the total trajectory length on both sides. Comparing the two groups after treatment, the peripheral area on the hemiplegic side in the VR-TOT group was significantly smaller. In the eyes-closed condition, the sway amplitude of the COP on the hemiplegic side in the anteroposterior direction and on the non-hemiplegic side in both the mediolateral and anteroposterior directions had decreased significantly in the VR-TOT group after the treatment. The average sway velocity had decreased significantly in the anteroposterior direction on the non-hemiplegic side in the CON group. In the VR-TOT group this was observed in the anteroposterior direction on the hemiplegic side and in both the mediolateral and anteroposterior directions on the healthy side. In the CON group the average peripheral area of the COP on the hemiplegic side had decreased, and the total trajectory length had shortened, both significantly. In the VR-TOT group, the peripheral area on the non-hemiplegic side had decreased significantly as well.Conclusions:Core stability-assisted training based on immersive virtual reality can effectively improve the balance of ischemic stroke survivors. It shows promise for clinical application.
8.Latent profile analysis of ego depletion in patients with heart failure and its influence on self-management behavior
Xiu TAO ; Min GAO ; Fan WU ; Shuyi SUN ; Jing LU ; Gaoqin WEN ; Qin WANG ; Guozhen SUN
Chinese Journal of Nursing 2025;60(16):1933-1940
Objective To explore the characteristics of latent profiles of ego depletion in patients with heart failure,and analyze the impacts of these profiles on patients' self-management behavior.Methods 280 heart failure patients who were hospitalized in a tertiary grade A hospital were conveniently selected in Nanjing from April to October 2024 as study subjects.The investigation utilized a general information questionnaire,the Ego-Depletion Scale for Heart Failure Patients,the Self-Management Scale of Heart Failure Patients,and the Chronic Disease Self-Efficacy Scale.The latent profile categories of ego depletion was explored in heart failure patients.Univariate analysis and multiple Logistic regression analysis were used to investigate the influencing factors of different latent profile categories and the impact of each category on patients' self-management levels.Results The ego depletion of 255 heart failure patients could be classified into 3 latent profiles:self-adaptive low depletion group(35.29%),symptom distressed moderate depletion group(43.53%),and social life change high depletion group(21.18%).Multiple Logistic regression analysis showed that residence,primary caregiver,education level,New York Heart Association cardiac function grade,and self-efficacy score were factors influencing the potential profile of ego depletion in heart failure patients(P<0.05).The comparison of self-management scores among patients in different latent profiles of ego depletion showed statistically significant differences(P<0.05).Conclusion The level of ego depletion in patients with heart failure is high with significant heterogeneity.Medical staff should pay attention to the heterogeneity and influencing factors of ego depletion in patients with heart failure in time,and develop personalized comprehensive intervention strategies to alleviate ego depletion and improve their self-management levels.
9.Characteristics of clustered cases of severe fever with thrombocytopenia syndrome in Jiangsu province, 2018-2024
Yuhao TAO ; Shuyi LIANG ; Xiaochen WANG ; Zhifeng LI ; Yin WANG ; Changjun BAO
Chinese Journal of Experimental and Clinical Virology 2025;39(3):319-323
Objective:This study analyzed the epidemiological characteristics of the clustered cases of severe fever with thrombocytopenia syndrome (SFTS) in Jiangsu province, so as to provide a scientific basis for prevention and control efforts.Methods:In this study we searched for cases related to clustered outbreaks and conducted epidemiological investigations of the cases, their co-exposed individuals, and close contacts. The basic information of the cases and their disease progression were collected and documented. The source of infection and transmission routes were analyzed. Fisher’s exact probability test and independent samples t-test were used to compare the differences between index and secondary cases. Results:From 2018 and 2024, a total of nine cluster outbreaks were reported in Jiangsu province, involving 32 cases of SFTS with 12 fatalities. Seven clustered outbreaks occurred in rural communities, while two occurred in medical institutions. The primary cause of these outbreaks was direct contact with confirmed cases.Conclusions:In recent years, Jiangsu province has experienced multiple clustered outbreaks of SFTS. Targeted health education should be implemented in high-risk areas to increase awareness of personal protective measures. Medical institutions should standardize the management of confirmed cases, educate patients′ families about prevention and control measures, and strengthen training for healthcare workers to ensure effective infection control within hospitals.
10.Development of features analysis workflow for Klebsiella pneumoniae based on clinical metagenomics next generation sequencing data
Shuyi WANG ; Qi WANG ; Yuyao YIN ; Yifan GUO ; Shuai MA ; Guankun YIN ; Hui WANG
Chinese Journal of Laboratory Medicine 2025;48(9):1149-1157
Objective:To identify strain-specific features of Klebsiella pneumoniae by analyzing metagenomics next generation sequencing (mNGS) data, thereby expanding the downstream applications of mNGS. Methods:The sequences of K.pneumoniae strains were organized from both the self-built database of the long-term multi-center research cohort in China established by the Peking University People′s Hospital from 2009 to 2020 (with 2 345 sequences) and the public databases (with 19 648 sequences). The existing large-scale databases were compressed, and a set of strains representative of clonal groups were screened. A strain genome information library was constructed based on k-mer features, and the most matching representative sequences in the database were searched for the raw mNGS data. The search results of the self-built library and public library were merged and optimized to update the prediction of antimicrobial-resistance characteristics and avoid the impact of uneven data distribution on the results. A total of 314 clinical samples from patients with K.pneumoniae detected by mNGS in the Clinical Microbiology Laboratory of Peking University People′s Hospital from 2022 to 2024 were retrospectively collected, and 101 samples with positive clinical culture results were selected to validate the prediction results. The antimicrobial-resistance phenotypes were verified by clinical antimicrobial susceptibility test results. Whole-genome sequencing was performed on the culture strains of 14 samples randomly selected using random numbers to verify the genotypes. Single nucleotide polymorphism distance analysis was used to verify the occurrence of outbreak events. The χ2 test and Mann-Whitney U test were used for statistical analysis. Results:A representative strain sequence k-mer feature library containing self-built and public sub-libraries was constructed. The library construction required only about 1 hour with <3 GB storage, with a high compression ratio and low update cost. Using k-mer-based analysis, mNGS data achieved precise strain characterization within 4 minutes and and <5 GB memory occupation. There was a significant difference in the antimicrobial-resistance rates to more than half of the antibiotics between the self-built database (90.8%, 2 130/2 345) and the public database (22.7%, 4 457/19 648) ( χ2=4 634.1, P<0.001). After optimizing the search results, the mean category agreement, sensitivity, and specificity of the prediction for eight antibiotics reached 84.8% (323/381), 78.9% (131/166), and 91.2% (196/215), respectively. The target genotypes were successfully detected in 10 out of 12 samples, and two outbreak events (2 samples per event) were successfully identified. Conclusions:An independent analysis process adapted to the needs of identifying the features of K. pneumoniae strains in mNGS data was developed. This process requires minimal computational resources and processing time and can directly achieve the simultaneous analysis of the antimicrobial-resistance phenotypes of K. pneumoniae at the strain level and their corresponding genomic characteristic profiles based on the raw mNGS reads.

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