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.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.
3.Application of self-monitoring of blood glucose information management platform based on medical consortium in community patients with type 2 diabetes
Quanying WU ; Lixin GUO ; Chao SUN ; Qi PAN ; Qi ZHOU ; Shuyi YU
Chinese Journal of Nursing 2023;58(24):2949-2956
Objective To study the effect of self-monitoring of blood glucose information management platform based on the medical consortium on the level of blood glucose control by improving the implementation rate of self-monitoring of blood glucose prescriptions for type 2 diabetes patients in the community.Methods A convenient sampling method was used to select 121 patients with type 2 diabetes from April 2021 to April 2023 who were enrolled in a community of a tertiary hospital medical consortium in Beijing.They were randomly divided into 61 patients in an experimental group and 60 patients in a control group.The control group received routine blood glucose monitoring and guidance education,while the experimental group was managed by a self-monitoring of blood glucose information management platform based on the medical consortium with nurses as the main body.Glycated hemoglobin,glucose test,fasting blood sugar,blood glucose 2 hours after meal,and the completion of self blood glucose monitoring prescriptions were evaluated and analyzed in the first week and the twelfth week of the 2 groups.Results 61 cases in the experimental group and 58 cases in the control group completed the follow-up,and the patients who completed the follow-up were analyzed.There was no statistically significant difference in glycated hemoglobin between the 2 groups at baseline(P=0.117).After 12 weeks,the reduction standard-reaching rate in glycated hemoglobin in the experimental group was significantly different from that in the control group(P=0.014).The number of self-monitoring of fasting blood glucose and the total number of other time periods in experimental group were significantly higher than those in the control group(P<0.001);the implementation rate of self-monitoring prescription in the experimental group was better than that in the control group(P<0.001).Conclusion A self blood glucose monitoring information platform was built to manage community type 2 diabetes patients,so that patients can master and implement the personalized blood glucose monitoring prescription formulated by the medical union team with nurses as the main body,and it is conducive to improving the frequency of blood glucose monitoring and the level of blood glucose control of diabetes patients.
4.Feasibility analysis of free disinfection of central venous catheter infusion connector after using disposable disinfection caps
Quanying WU ; Chao SUN ; Lei WANG ; Xia WANG ; Qi ZHOU ; Shuyi YU ; Bo HUANG
Chinese Journal of Modern Nursing 2021;27(33):4551-4555
Objective:To analyze the feasibility of free disinfection of central venous catheter infusion connector after using disposable disinfection caps.Methods:Using the convenient sampling method, a total of 132 patients who were hospitalized in the Department of Hematology of a Class Ⅲ Grade A hospital in Beijing from January to August of 2020 were selected as the research objects. According to the order of hospitalization, they were divided into the experimental group (group A) and the control group (group B) . Group A used disposable disinfection caps to connect the infusion connector, while group B repeatedly wiped the infusion connector for 15 s with 70%-80% alcohol cotton before infusion. According to infusion interval of 8 and 12 h and sampling timing, group A was divided into group A1-8 h and group A2-12 h, while group B was divided into group B1-8 h and group B1-12 h, with 33 cases in each group. Samples from infusion connectors of the 4 groups were collected for bacterial culture and bacterial inhibition on the surface of infusion connectors was compared.Results:There were 2 cases of detachment in A1-8 h group, 3 cases in A2-12 h group and 1 case in B2-12 h group. A total of 126 patients completed the study. A total of 18 patients in group A had bacteria at the infusion connector, which was more than 0 patients in group B, and the difference was statistically significant ( P<0.01) . In A1-8 h group, there was statistically significant difference in the presence of bacteria before and after using disinfection caps ( P<0.01) . There was no statistically significant difference in the presence or absence of bacteria in the infusion connector before and after the use of the infusion caps in the A2-12 h group ( P>0.05) . Conclusions:The disinfection effect of the disposable infusion connector disinfection cap is not the same as that of the disposable alcohol cotton pad disinfection method, but it can inhibit the growth of bacteria on the infusion connector surface within 8 h.
5.Summary of the best evidence for alleviating intraoperative pain in patients undergoing local anesthesia
Linxia YANG ; Chunhua ZHANG ; Shuyi QI ; Shanfei LIN ; Hui WANG
Chinese Journal of Modern Nursing 2021;27(34):4645-4650
Objective:To search, evaluate and integrate the best evidence for alleviating intraoperative pain in patients undergoing local anesthesia, so as to provide a basis for formulating intraoperative pain control plan for patients undergoing local anesthesia.Methods:Evidence-based questions were built based on the PICO model. BMJ Best Practice, UpToDate, US Guidelines, National Institute for Health and Clinical Excellence, Scottish Intercollegiate Guidelines Network, Joanna Briggs Institute Evidence-based Health Care Center, Cochrane Library, MedlinePlus, PubMed, CINAHL, Medlive, CNKI and Wanfang Database were searched for guidelines, expert consensus, evidence summary, systematic review and other evidence on alleviating intraoperative pain in patients undergoing local anesthesia. The search time was from the establishment of the database to March 30, 2020. Two researchers with evidence-based nursing knowledge independently evaluated the quality of the literature and the level of evidence.Results:A total of 7 articles were included, including 1 guideline, 1 clinical decision and 5 systematic reviews. The 16 best evidences were summarized from 5 aspects, such as preoperative evaluation, pain recognition, intraoperative pain intervention measures, surgical pain evaluation and health education.Conclusions:This study summarizes the current best evidence for reducing the pain during local anesthesia in patients undergoing local anesthesia and provides evidence-based evidence for the selection of intraoperative pain control programs for local anesthesia in related departments.
6.Magnetic resonance imaging changes and curative effects of early different pressure hyperbaric oxygen on moderate and severe traumatic brain injury in rats
Ya′nan QI ; Dazhi GUO ; Shuyi PAN
Chinese journal of nautical medicine and hyperbaric medicine 2020;27(1):37-41
Objective:To investigate the characteristics of magnetic resonance imaging changes and the curative effects of early different pressure hyperbaric oxygen (HBO) on moderate and severe traumatic brain injury in rats.Methods:Sixty healthy clean male adult Sprague-Dawle rats were randomly divided into four groups by random number table: traumatic brain injury group (TBI group), sham operation group (sham group. Only opening the skull, but no head strike), 0.15 MPa HBO group (giving 0.15 MPa HBO to TBI rats), and 0.25 MPa HBO group (giving 0.25 MPa HBO to TBI rats). Each group has 15 rats. All rats were subjected to modified neurological severity score (mNSS) evaluation and MRI examination on day 1 (D1), day 3 (D3), and day 7 (D7) respectively. Three regions of interest (ROI) were taken from the high-signal regions of the magnetic resonance DWI image. The apparent diffusion coefficient (ADC) of each region was measured. The ratios of the ADC of the lesion side to the ADC of the normal contralateral side, i. e. the relative ADC (rADC), were compared.Results:(1) On D1, all the rADC values of ROIs in each group were not statistically significant ( P>0.05). On D3, the rADC values of different ROIs in 0.15 MPa HBO and 0.25 MPa HBO groups were all lower than those in TBI group ( P< 0.05), but all higher than sham group ( P<0.05); there was no significant difference between 0.15 MPa HBO and 0.25 MPa HBO groups ( P>0.05). On D7, the rADC values of different ROIs in 0.15 MPa HBO and 0.25 MPa HBO groups were all lower than those of TBI group ( P< 0.05); there was no significant difference when those compared with sham group ( P>0.05), and there was no significant difference between 0.15 MPa HBO and 0.25 MPa HBO groups ( P>0.05). (2) On D1, there was no significant difference in mNSS scores among TBI group, 0.15 MPa HBO group and 0.25 MPa HBO group ( P>0.05), but the mNSS scores of TBI group, 0.15 MPa HBO group and 0.25 MPa HBO group were all significantly higher than that of sham group ( P<0.05). On D3, the mNSS scores of 0.15 MPa HBO and 0.25 MPa HBO groups were all lower than that of TBI group ( P<0.05), but all higher than that of sham group ( P<0.05); there was no significant difference between 0.15 MPa HBO group and 0.25 MPa HBO group ( P>0.05). On D7, the scores of mNSS in 0.15 MPa HBO and 0.25 MPa HBO groups were all lower than that in TBI group ( P<0.05), but all slightly higher than that in sham group ( P>0.05). Conclusion:There is definite curative effect of early HBO on moderate and severe TBI, but the pressure of HBO may not be the key factor in determining prognosis.
7.Magnetic resonance imaging changes and curative effects of early different pressure hyperbaric oxygen on moderate and severe traumatic brain injury in rats
Ya′nan QI ; Dazhi GUO ; Shuyi PAN
Chinese journal of nautical medicine and hyperbaric medicine 2020;27(1):37-41
Objective:To investigate the characteristics of magnetic resonance imaging changes and the curative effects of early different pressure hyperbaric oxygen (HBO) on moderate and severe traumatic brain injury in rats.Methods:Sixty healthy clean male adult Sprague-Dawle rats were randomly divided into four groups by random number table: traumatic brain injury group (TBI group), sham operation group (sham group. Only opening the skull, but no head strike), 0.15 MPa HBO group (giving 0.15 MPa HBO to TBI rats), and 0.25 MPa HBO group (giving 0.25 MPa HBO to TBI rats). Each group has 15 rats. All rats were subjected to modified neurological severity score (mNSS) evaluation and MRI examination on day 1 (D1), day 3 (D3), and day 7 (D7) respectively. Three regions of interest (ROI) were taken from the high-signal regions of the magnetic resonance DWI image. The apparent diffusion coefficient (ADC) of each region was measured. The ratios of the ADC of the lesion side to the ADC of the normal contralateral side, i. e. the relative ADC (rADC), were compared.Results:(1) On D1, all the rADC values of ROIs in each group were not statistically significant ( P>0.05). On D3, the rADC values of different ROIs in 0.15 MPa HBO and 0.25 MPa HBO groups were all lower than those in TBI group ( P< 0.05), but all higher than sham group ( P<0.05); there was no significant difference between 0.15 MPa HBO and 0.25 MPa HBO groups ( P>0.05). On D7, the rADC values of different ROIs in 0.15 MPa HBO and 0.25 MPa HBO groups were all lower than those of TBI group ( P< 0.05); there was no significant difference when those compared with sham group ( P>0.05), and there was no significant difference between 0.15 MPa HBO and 0.25 MPa HBO groups ( P>0.05). (2) On D1, there was no significant difference in mNSS scores among TBI group, 0.15 MPa HBO group and 0.25 MPa HBO group ( P>0.05), but the mNSS scores of TBI group, 0.15 MPa HBO group and 0.25 MPa HBO group were all significantly higher than that of sham group ( P<0.05). On D3, the mNSS scores of 0.15 MPa HBO and 0.25 MPa HBO groups were all lower than that of TBI group ( P<0.05), but all higher than that of sham group ( P<0.05); there was no significant difference between 0.15 MPa HBO group and 0.25 MPa HBO group ( P>0.05). On D7, the scores of mNSS in 0.15 MPa HBO and 0.25 MPa HBO groups were all lower than that in TBI group ( P<0.05), but all slightly higher than that in sham group ( P>0.05). Conclusion:There is definite curative effect of early HBO on moderate and severe TBI, but the pressure of HBO may not be the key factor in determining prognosis.
8.Gene detection and multilocus sequence typing of carbapenem resistant Klebsiella pneumonia
Liang JIN ; Qi WANG ; Shuyi WANG
The Journal of Practical Medicine 2017;33(24):4156-4160
Objective To investigate the cause of high isolation rate of carbapenem resistant Klebsiella pneumoniae(CRKP)in the first half of 2016 and the mechanism of its resistance and homology,in order to pro-vide basis for the control of nosocomial infection.Methods We collected CRKP from January to June 2016 to con-firm carbapenemase phenotype by modified Hodge test. Carbapenemase genes were amplified by using PCR meth-od,and the PCR product was sequencing to determine the genotypes by multilocus sequence analysis(MLST)to analyze the homology.Results From January 2016 to June,89 non redundant KPN89 strains were isolated, with 41 strains of CRKP and the isolation rate was 46.07%.CRKP was mainly isolated from Department of Critical Care Medicine,Department of Neurosurgery,Department of Respiration and so on. The specimens were sputum, blood,urine,cerebrospinal fluid specimens. Forty-one strains of CRKP were 100% sensitive to polymyxin, 95.12% sensitive to complement and 4.88% sensitive to minocycline,and were resistant to the other 23 antimicrobi-al agents. Hodge test of 41 strains of CRKP was positive and sequencing confirmed that all carried KPC-2 type of carbapenems.MLST classification results belonged to type ST11. Conclusions CRKP outbroken in our hospital is MLST typing of type sT11. With serious drug resistance,it may be the same strain spread among different pa-tients in different wards and the main drug resistance mechanism is producing type KPC-2 carbapenems. All rele-vant departments should carry out epidemiological investigations timely for the prevention and control.
9.A survey on medical students about the awareness of medical laws and communication between medical students and old patients
Jing ZHU ; Huiqi GAO ; Feng YIN ; Shuyi QI ; Hui HAN
Chinese Journal of Medical Education Research 2011;10(7):861-863
A total of 120 medical students were surveyed to investigate the current status of communication between medical students and old patients and the awareness of medical laws. The questionnaire shows many students don't have enough knowledge of communication skills and medical laws. Furthermore, the most important reason of the medical disputes is the lack of communication between doctors and patients so the cultivation of communication skills and legal knowledge should be strengthened.
10.Effects of drug serum in broken bushen yizhi formulas on cell model of Alzheimer disease
Yunbo CHEN ; Shilong LAI ; Jingqing HU ; Qi WANG ; Shuyi CHENG
Chinese Journal of Tissue Engineering Research 2005;9(32):250-253
BACKGROUND:Chinese herb, bushen yizhi formula protects at certain extent learning and memory in rat model of Alzheimer disease. The drug serum in this formula can alleviate neurotoxic reaction of nerve tumor cell NG 108-15 to beta-amyloid protein. In order to understand further the mechanism and compatibility of the formula, it is necessary to carry on the study on the broken formulas.OBJECTIVE:To study the effect of drug serum in subgroups of broken bushen yizhi formulas on growth and differentiation of cell model of Alzheimer disease and probe into the compatibility rule of bushen yizhi formula in view of serum pharmacology.DESIGN: Randomized controlled experiment.SETTING: DME Center of Clinical Pharmacological Institute Affiliated to Guangzhou University of Traditional Chinese Medicine.PARTICIPANTS:The experiment was performed in DME Center of Clinical Pharmacological Institute Affiliated to Guangzhou University of Traditional Chinese Medicine from January to August 2003, in which, 40 healthy male SD rats of 3 months old were employed and NG108-15 cell line was frozen-preserved.into the control, original formula group (No. 1 group) [shechuanzi (Cnidium monnieri (L.) Cuss), gouqizi (Lycium barbarum L.), renshen (Panax ginseng C.A.Mey.), heshouwu (Polygonum multiflorum Thunb.), danpi (Paeonia Suffruticisa Andr.) and bingpian (Borneolum)], kidney replenishment group (No.2 group) [shechuanzi (Cnidium monnieri (L.) Cuss), gouqizi (Lycium barbarum L.), etc.], group for benefiting qi and nourishing blood (No.3 group)[renshen (Panaz ginseng C.A.Mey), zhishouwu (Polygonum multiflorum Thunb.), etc.] and group with bingpian (Borneolum) removed (No.4 group)[Panax ginseng C.A.Mey.], heshouwu (Polygonum multiflorum Thunb.) and danpi (Paeonia Suffruticisa Andr.)], 8 rats in each group. The concentrated Chinese herbal solutions of every group were applied at 10 μL/g (equal to 6 g/kg of raw herbs) for gastric infusion successively,continuously for 1 month. In the control, the physical saline solution of equal dosage was used for infusion. Two hours after the last gastric infusion in rats of each group,the blood was collected from heart after anesthesia and the serum was sepaNG108-15 cell cultured in vitro was divided into 6 groups. In the control and model group, normal rat serum was contained in proliferated culture solution. In the rest 4 groups, the drug serum of No. 1 group and 3 sub-groups was contained.Simultaneously, beta-amyloid protein 25-35 in each hole was prepared to the terminal concentration 5 μmol/L (except in the control) and the culture went on for 48 hours.MAIN OUTCOME MEASURES:MTT method was used to determine proliferated number and survival rate of cells. Simultaneously, the ratio of neurite cells to total cell count and average length of neurit were determined.icantly than the control (0.520±0.022, 0.665±0.037, P < 0.01), and that in every drug serum group was higher than model group, of which, the result vival rate of differentiated cells: That in model group was lower significantly than the control (58.4%, 100%) and that in every drug serum group was higher than model group, of which, the result in No.4 group was the most tal cell count: That in model group was lower significantly than the control [(42.95±11.42)%, (58.75±12.84)%, P < 0.01] and that in every drug serum group was higher than model group, of which, the result in No.4 group was rite: That in model group was shorter significantly than the control [(356.0 ±109.0), (493.8±133.0) μm, P < 0.01] and that in every drug serum group was longer than model group, of which, the result in No.4 group was the most significant [(486.8±79.2) μm, P < 0.01].CONCLUSION: The drug serum in all of bushen yizhi formula and every subgroup inhibits at certain extent the injury of beta-amyloid protein 25-35 to NG108-15 cell, but the results of each group are various. The protection of drug serum to the cell in every group is in the sequence from strong to weak as group with bingpian removed > original formula group > kidney replenishment group > group for benefiting qi and nourishing blood. It is to expect a further study on the efficacy of group with bingpian removed.

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