Objective To investigate the clinical application value of GeneXpert Mycobacterium tuberculosis (MTB)/ rifampin (RIF) in urine samples for tuberculosis diagnosis. Methods The patients with clinically highly suspected tuberculosis admitted to West China Hospital of Sichuan University between January 1, 2018 and June 1, 2023 were selected retrospectively. The diagnostic efficacy of urine GeneXpert MTB/RIF detection, such as sensitivity, specificity, positive predictive value, and negative predictive value, were retrospectively analyzed to evaluate its clinical value in the diagnosis of tuberculosis. Correlation analysis was further conducted to explore the correlation between positive levels of GeneXpert MTB/RIF in urine samples and laboratory test indicators. Results A total of 400 patients were included. Among them, 163 cases were in the clinical tuberculosis group and 237 cases were in the clinical non tuberculosis group. In the clinical tuberculosis group, 112 cases were urogenital tuberculosis patients and 51 cases were non-urogenital tuberculosis patients. The sensitivity, specificity, positive predictive value, and negative predictive value of urine GeneXpert MTB/RIF in the diagnosis of tuberculosis were 55.2%, 97.5%, 93.8% and 76.0%, respectively. The sensitivity, specificity, positive predictive value, and negative predictive value of urine GeneXpert MTB/RIF in the diagnosis of urogenital tuberculosis were 65.2%, 92.0%, 76.0% and 87.2%, respectively, and the diagnostic sensitivity was further improved. Correlation analysis showed that the positive degree of urine GeneXpert MTB/RIF was correlated with the levels of hemoglobin, serum total protein, blood serum albumin, and other indicators. Conclusions Urine GeneXpert MTB/RIF detection offers high sensitivity and specificity in the diagnosis of tuberculosis, especially in urogenital tuberculosis, which is helpful for the early and rapid diagnosis of tuberculosis patients. The positive degree reported by the GeneXpert MTB/RIF in urine may indicate disease severity.
ObjectiveTo explore the pathogenesis of tuberculosis and provide new ideas for its early diagnosis and treatment.MethodsGSE54992 gene expression profile was obtained from the gene expression database. Differentially expressed genes (DEGs) were screened using National Center forBiotechnology Information platform, and GO enrichment analysis, pathway analysis, pathway network analysis, gene network analysis, and co-expression analysis were performed to analyze the DEGs.ResultsCompared with the control group, a total of 3 492 genes were differentially expressed in tuberculosis. Among them, 1 686 genes were up-regulated and 1 806 genes were down-regulated. DEGs mainly involved small molecule metabolic processes, signal transduction, immune response, inflammatory response, and innate immune response. Pathway analysis revealed chemokine signaling pathway, tuberculosis, NF-Kappa B signaling pathway, cytokine-cytokine receptor interaction, and so on; gene signal network analysis found that the core genes were AKT3, PLCB1, MAPK8, and NFKB1; co-expression network analysis speculated that the core genes were PYCARD, TNFSF13, PHPT1, COMT, and GSTK1.ConclusionsAKT3, PYCARD, IRG1, CD36 and other genes and their related biological processes may be important participants in the occurrence and development of tuberculosis. Bioinformatics can help us to comprehensively study the mechanism of disease occurrence, which can provide potential targets for the diagnosis and treatment of tuberculosis.
ObjectiveTo investigate the associations of signal transducers and activators of transcription 6 (STAT6) gene polymorphisms with susceptibility to tuberculosis in western Chinese Han population.MethodsA total of 900 tuberculosis patients and 1 534 healthy controls of West China Hospital of Sichuan University were enrolled from January 2014 to February 2016. Improved multiplex ligation detection reaction method was used to detect four polymorphisms (rs1059513, rs73118432, rs841718, and rs10783813) of STAT6 gene. The allelic frequencies, genetic types, and different genetic models were analyzed using the chi-square test and unconditional logistic regression models to evaluate the associations of STAT6 gene with tuberculosis risk.ResultsEventually, a total of 856 cases and 1 511 health controls were recruited in our study. No significant differences were observed in allele frequencies, genotype distributions, or genetic models (additive model, dominant model and recessive model) at rs1059513, rs73118432, rs841718, and rs10783813 in STAT6 gene (P>0.05). We found a strong linkage disequilibrium among rs73118432, rs841718, and rs10783813, but there was no statistical difference in haplotype frequencies between the two groups (P>0.05).ConclusionsSTAT6 gene rs73118432, rs841718, rs10783813, and rs1059513 polymorphisms might have no associations with tuberculosis susceptibility in western Chinese Han population. Further studies with larger sample sizes are needed to comfirm these results.
Objective Using molecular biology method to detect and genotype human papilloma virus (HPV) in women taking physical examination in West China Hospital, Sichuan University, to explore the infection status and genotype distribution of HPV in normal women in Chengdu area, and to provide basis for early effective prevention and control of cervical cancer and domestic research and development of HPV vaccine. Methods Flow fluorescent hybridization technique was used to detect and genotype HPV-DNA in 25 148 healthy women taking physical examination in West China Hospital, Sichuan University between May 1st, 2018 and May 31st, 2019. The overall positive HPV infection rate, HPV genotype distribution, and characteristics of HPV infections were analyzed and calculated, and the HPV infection rates of different age groups were calculated and compared by chi-square test using SPSS 17.0 software. Results The overall positive rate of HPV infection was 12.19% (3 066/25 148). The high-risk HPV genotypes infection rate was 8.69% (2 186/25 148), and the top five subtypes with the highest infection rates were HPV52, HPV53, HPV58, HPV16, and HPV39. The low-risk HPV genotypes infection rate was 4.66% (1 171/25 148), and the top five subtypes with the highest infection rates were HPV61, HPV81, HPV43, HPV44, and HPV6. Single subtype infections were the main infections with a proportion of 81.74% (2 506/3 066), and the most common multiple infections were double infections which accounted for 13.96% (428/3 066). In different age groups, the HPV infection rate of group 60-69 was the highest (12.87%), while that of group 70-89 was the lowest (10.88%), but the difference among different age groups was not statistically significant (χ2=4.035, P=0.544). Conclusion According to the results of this study in women taking physical examination in West China Hospital, Sichuan University, we suggest adding HPV52, HPV53, and HPV58 which have the highest infection rate in high-risk HPV subtypes to the evaluation of domestic HPV vaccine screening and the cervical cancer prevention and control system.
ObjectiveTo analyze hepatitis B virus (HBV) genotype distribution and drug-resistant mutations in West China Hospital of Sichuan University, providing basis for hepatitis B individualized treatment.MethodsA total of 786 chronic hepatitis B patients admitted to West China Hospital of Sichuan University from January 2016 to December 2018 were enrolled in the study. Genotype and drug-resistant mutations were analyzed by Sanger sequencing, and statistical analysis was conducted by χ2 test.ResultsThree genotypes (B, C and D) were identified in 786 samples, 489 (62.2%) in genotype B, 291 (37.0%) in genotype C , and 6 (0.8%) in genotype D. The distribution differences of B and C genotypes in age and ethnic groups were statistically significant (P<0.05). Among them, 627 cases had drug-resistant mutations, with a drug-resistant mutation rate of 79.8%. A total of 262 cases (33.3%) were resistant to lamivudine and tibivudine, 102 cases (13.0%) were resistant to lamivudine, tibivudine and entecavir; 83 cases (10.6%) were resistant to adefovir dipivoxil. No tenofovir resistant strains were detected in 786 samples. There were statistically significant differences in drug resistance between B and C genotypes (χ2=14.356, P<0.01). The most common single mutation was M204I [179 cases (22.8%)], followed by 46 cases (5.9%) of A181V/T associated with adefovir dipivoxil resistance. The most common mixed mutation was L180M+M204V/I in 83 cases (10.6%), and another 102 cases (13.0%) showed M250V and/or V173L and/or T184A/G/S/I and/or S202G/I with L180M+M204V/I.ConclusionsHBV genotypes in West China Hospital of Sichuan University are mainly B and C, and the situation of drug resistance is severe and the mutation pattern is complex. Therefore, detecting HBV genotype and drug resistance mutation is necessary, which may develop better clinical treatments.
Objective To analyze the human leukocyte antigen (HLA) gene polymorphism and haplotype frequency and distribution in Han patients with end stage renal disease (ESRD) in Sichuan province, and explore the correlation of HLA gene polymorphism and haplotype with the susceptibility to ESRD in Sichuan Han patients. Methods Polymerase chain reaction-sequence specific oligonucleotide probe hybridization typing technique was used to detect the HLA-A, -B, -DRB1, and -DQB1 genotypes of Han patients with ESRD and healthy participants. The allele and haplotype frequencies in the ESRD group and the control group were analyzed using SPSS 25.0 and Arlequin 3.5.2.2 softwares. Results A total of 756 ESRD patients and 1118 healthy participants were enrolled. In the four loci of HLA-A, -B, -DRB1, and -DQB1, the frequency of HLA-B*39 allele in the ESRD group was higher than that in the control group [3.37% vs. 2.19%; χ2=4.850, P=0.028, odds ratio (OR)=1.558, 95% confidence interval (CI) (1.047, 2.319)], the frequency of HLA-DQB1*06 allele in the ESRD group was lower than that in the control group [17.39% vs. 21.20%; χ2=8.264, P=0.004, OR=0.783, 95%CI (0.662, 0.925)], and the frequency of HLA-DQB1*04 allele in the ESRD group was higher than that in the control group [7.41% vs. 5.46%; χ2=5.867, P=0.015, OR=1.386, 95%CI (1.063, 1.807)]. The frequencies of 10 haplotypes, including HLA-A*11-B*39, HLA-DRB1*15-DQB1*06, and HLA-DRB1*04-DQB1*04, were significantly different between the ESRD group and the control group (P<0.05), among which 9 haplotypes were possibly susceptible to ESRD and 1 haplotype was possibly protective. Conclusions HLA gene polymorphism is closely related to the susceptibility to ESRD. HLA-B*39 and HLA-DQB1*04 may be susceptible genes for ESRD in Sichuan Han patients, while HLA-DQB1*06 may be a protective gene. In addition, 10 HLA haplotypes are possibly associated with the susceptibility to ESRD in Sichuan Han patients.