Almost all pathogens have DNA or RNA genomes.Theoretically, genomes of pathogens can be effectively detected by sequencing technology , it would be of value for etiological diagnosis of infectious diseases.The next generation sequencing ( NGS) emerged in 2005, the advantages of low cost , high efficiency and high accuracy make it a favorable technical platform for clinical identification of microorganisms.As a new sequencing technique , metagenomic next generation sequencing ( mNGS) has great potential in improving the accuracy and efficiency of pathogenic diagnosis , especially in the areas where conventional diagnostic methods have limitations.This article introduces the common platforms and principle of the high throughput sequencing , reviews the clinical applications and the advantages of mNGS in identification of different pathogenic microorganisms , and reflects on its limitations and seeks possible solutions.

Objective To investigate the clinical features of malignant tumor-related pyogenic liver abscess (PLA), and to provide a basis for early judgment of disease progression and timely and effective treatment. Methods A retrospective analysis was performed for the clinical data of 371 patients with PLA who were admitted to the Second Affiliated of Air Force Medical University, from March 2005 to July 2018, among whom 34 patients with malignant tumor-related PLA were enrolled as tumor group, and after matching for time and at a ratio of 1∶2, 70 patients without malignant tumor-related PLA were enrolled as non-tumor group. Clinical features were compared between the two groups. The group t -test was used for comparison of normally distributed continuous data between groups, and the Mann-Whitney U test was used for comparison of non-normally distributed continuous data between groups; the chi-square test or the Fisher's exact test was used for comparison of categorical data between groups. Results In the tumor group, there were 22 patients with hepatobiliary tumor (64.7%), 7 patients with gastrointestinal tumor (20.6%), and 5 patients with non-gastrointestinal tumor (14.7%). Compared with the non-tumor group, the tumor group had a significantly higher proportion of patients with a history of abdominal surgery (44.1% vs 7.1%, χ 2 =20.142, P < 0.05), liver cirrhosis (26.5% vs 7.1%, χ 2 =7.338, P < 0.05), or an Acute Physiology and Chronic Health Evaluation Ⅱ score of > 16 (44.1% vs 15.7%, χ 2 =9.846, P =0.002). Compared with the non-tumor group in terms of laboratory examination, the tumor group had a significantly lower level of albumin [(27.2±5.2) g/L vs (30.8±2.6) g/L, t =-3.131, P =0.002] and a significantly higher level of total bilirubin [54(13~313) μmol/L vs 33(7~96) μmol/L, U =1 816.0, P < 0.001]. Escherichia coli was the main pathogen in the tumor group (23.5%), while Klebsiella pneumonia was the main pathogen in the non-tumor group (23.5%), and compared with the non-tumor group, the tumor group had a significantly higher proportion of patients infected with more than two types of bacteria (11.8% vs 2.8%). Radiological examination showed that the tumor group had a significantly higher proportion of patients with multiple abscesses than the non-tumor group (47.1% vs 24.3%, χ 2 =5.479, P =0.019). Compared with the non-tumor group, the tumor group had a significantly longer mean length of hospital stay ( U =1 728.5, P < 0.001) and a significantly higher treatment failure rate ( P =0.005). Conclusion Patients with malignant tumor-related PLA often have hepatobiliary tumor, with Escherichia coli as the main pathogen. Abscesses at multiple sites are common, and patients tend to have a poor prognosis. Appropriate antibiotics combined with percutaneous drainage should be used in clinical practice, and for the high-risk population, the threshold for surgical intervention can be lowered to reduce mortality.

Objective To investigate the efficacy of switching to co-formulated elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide (E/c/F/TAF) combined with sofosbuvir/velpatasvir (SOF/VEL) in the treatment of previously untreated chronic hepatitis C patients with HIV/HCV co-infection and the changes in blood lipid levels. Methods This prospective cohort study was conducted among 10 previously untreated chronic hepatitis C patients with HIV/HCV co-infection who attended Department of Infectious Diseases in Tangdu Hospital from July 2019 to May 2021 and achieved continuous HIV suppression after antiretroviral treatment (ART). As for anti-HIV therapy, the ART regimen was switched to the E/c/F/TAF regimen for 32 weeks, and for anti-HCV therapy, the SOF/VEL regimen was started since week 4 after switching and lasted for 12 weeks. Related indices were monitored before and after switching to E/c/F/TAF for anti-HCV therapy and SOF/VEL for anti-HCV therapy, including body weight, body mass index, HCV genotype, alpha-fetoprotein, liver stiffness measurement, CD4 + T cell count, CD4 + T/CD8 + T ratio, hepatic and renal function parameters, blood lipids, HIV RNA, HCV RNA, SVR12, SVR24, and adverse reactions. The Mann-Whitney U test was used for comparison of continuous data between two groups, and a Spearman correlation analysis was performed. Results After 4 weeks of treatment with E/c/F/TAF, 10 patients (HCV genotypes 2a and 1b) had HIV RNA below the lower limit of detection (20 IU/ml) and a significant reduction in albumin ( Z =-2.801, P =0.003 7), with the other indices remaining stable, and the patients reported significant improvements in the adverse events of anti-HIV therapy with the former ART regimen. After 4 weeks of E/c/F/TAF combined with SOF/VEL, the patients had HCV RNA below the lower limit of detection (15 IU/ml), and both SVR12 and SVR24 reached 100%; after 12 weeks of anti-HCV therapy, there were significant reductions in alanine aminotransferase ( Z =-2.732, P =0.004 8) and aspartate aminotransferase ( Z =-2.501, P =0.010 7) and significant increases in total cholesterol (TC) ( Z =-2.797, P =0.003 9) and low-density lipoprotein cholesterol (LDL-C) ( Z =-2.343, P =0.018 5), with a significantly positive correlation between them ( r =0.87, P < 0.001), and all the other indices were normal. Conclusion For previously untreated chronic hepatitis C patients with HIV/HCV co-infection, switching to E/c/F/TAF combined with SOF/VEL has good efficacy, tolerability, and safety, and the combination of the two regimens can avoid drug interaction, achieve a high HCV cure rate, and maintain HIV suppression. Transient increases in TC and LDL-C are observed during combination treatment, which suggests dyslipidemia caused by HCV infection and the pharmacological action of this regimen.