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Lei Y, Guo Q, Liu J, Huang H, Han P. Staphylococcus cohnii infection diagnosed by metagenomic next generation sequencing in a patient on hemodialysis with cirrhotic ascites: a case report. Front Cell Infect Microbiol 2023; 13:1240283. [PMID: 37808911 PMCID: PMC10556727 DOI: 10.3389/fcimb.2023.1240283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Background Patients with spontaneous bacterial peritonitis (SBP) often just receive empirical antibiotic therapy, as pathogens can be identified in only few patients using the techniques of conventional culture. Metagenomic next generation sequencing (mNGS) is a useful tool for diagnosis of infectious diseases. However, clinical application of mNGS in diagnosis of infected ascites of cirrhotic patients is rarely reported. Case presentation A 53-year-old male with cirrhosis on regular hemodialysis presented with continuous abdominal pain. After treatment with empiric antibiotics, his inflammatory parameters decreased without significant relief of abdominal pain. Finally, based on ascites mNGS detection, he was diagnosed as infection of Staphylococcus cohnii (S.cohnii), a gram-positive opportunistic pathogen. With targeted antibiotic treatment, the bacterial peritonitis was greatly improved and the patient's abdominal pain was significantly alleviated. Conclusions When conventional laboratory diagnostic methods and empirical antibiotic therapy fail, proper application of mNGS can help identify pathogens and significantly improve prognosis and patients' symptoms.
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Affiliation(s)
| | | | | | - Huanjun Huang
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ping Han
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Clinical Evaluation of Metagenomic Next-Generation Sequencing Method for the Diagnosis of Suspected Ascitic Infection in Patients with Liver Cirrhosis in a Clinical Laboratory. Microbiol Spectr 2023; 11:e0294622. [PMID: 36625589 PMCID: PMC9927505 DOI: 10.1128/spectrum.02946-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS), mostly carried out in independent clinical laboratories, has been increasingly applied in clinical pathogen diagnosis. We aimed to explore the feasibility of mNGS in clinical laboratories and analyze its potential in the diagnosis of infectious ascites. Two reference panels composed of 12 strains commonly appearing in peritonitis were constructed to evaluate the performance metrics based on in-house mNGS protocols. The mNGS clinical detection value was analyzed in 211 ascitic samples and compared with culture and composite standards. Finally, eight patients with cirrhosis were prospectively enrolled to verify the clinical value of mNGS in peritoneal infection diagnosis. The mNGS analytical performance showed that the assay had great linearity, specificity, stability, interference, and limits of detection of 33 to 828 CFU/mL. The sensitivity and specificity of mNGS for bacterial or fungal detection using culture standards were 84.2% and 82.0%, respectively. After adjustment using digital PCR and clinical judgment, the sensitivity and specificity increased to 87.2% and 90.1%, respectively. Compared with culture, mNGS detected a broad range of pathogens and more polymicrobial infections (49% versus 9%, P < 0.05). The pathogen results were obtained within 24 h using mNGS in eight prospective cases, which effectively guided antibiotics therapy. mNGS testing in clinical laboratories affiliated with a hospital has certain advantages. It has unique superiority in pathogens detection, particularly in patients with polymicrobial infections. However, considering spectrum characteristics and test cost, pertinent pathogen panels should be developed in clinical practice. IMPORTANCE This study established and evaluated a complete metagenomics next-generation sequencing assay to improve the diagnosis of suspected ascitic infection in a clinical laboratory affiliated with a hospital. The assay is superior to traditional culture testing and will aid in the early and accurate identification of pathogens, particularly in patients with polymicrobial infections. This assay is also essential for precision therapy and can reduce the incidence of drug resistance stemming from irrational use of antibiotics.
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Li B, Hong C, Fan Z, Cai S, He Q, Lan X, Lai Q, Ji Y, Luo W, Li J, Cheng X, Liu M, Gu Y, Lu G, Li S, Wang Y, Weng X, Niu X, Liu Q, Jalan R, Chen J. Prognostic and therapeutic significance of microbial cell-free DNA in plasma of people with acute decompensation of cirrhosis. J Hepatol 2023; 78:322-332. [PMID: 36309130 DOI: 10.1016/j.jhep.2022.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 09/13/2022] [Accepted: 10/11/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND & AIMS Although the effect of bacterial infection on cirrhosis has been well-described, the effect of non-hepatotropic virus (NHV) infection is unknown. This study evaluated the genome fragments of circulating microorganisms using metagenomic next-generation sequencing (mNGS) in individuals with acute decompensation (AD) of cirrhosis, focusing on NHVs, and related the findings to clinical outcomes. METHODS Plasma mNGS was performed in 129 individuals with AD of cirrhosis in the study cohort. Ten healthy volunteers and 20, 39, and 81 individuals with stable cirrhosis, severe sepsis and hematological malignancies, respectively, were enrolled as controls. Validation assays for human cytomegalovirus (CMV) reactivation were performed in a validation cohort (n = 58) and exploratory treatment was instituted. RESULTS In the study cohort, 188 microorganisms were detected in 74.4% (96/129) of patients, including viruses (58.0%), bacteria (34.1%), fungi (7.4%) and chlamydia (0.5%). A NHV signature was identified in individuals with AD, and CMV was the most frequent NHV, which correlated with the clinical effect of empirical antibiotic treatment, progression to acute-on-chronic liver failure, and 90-day mortality. The NHV signature in individuals with acute-on-chronic liver failure was similar to that in those with sepsis and hematological malignancies. CMV was detected in 24.1% (14/58) of patients in the validation cohort. Of the 14 cases with detectable CMV by mNGS, nine were further validated by real-time PCR or pp65 antigenemia testing. Three patients with CMV reactivation received ganciclovir therapy in an exploratory manner and experienced clinical resolutions. CONCLUSIONS The results of this study suggest that NHVs may play a pathogenic role in complicating the course of AD. Further validation is needed to define whether this should be incorporated into the routine management of individuals with AD of cirrhosis. IMPACT AND IMPLICATIONS A non-hepatotropic virus (NHV) signature, which was similar to that in individuals with sepsis and hematological malignancies, was identified in individuals with acute decompensation of cirrhosis. The detected viral signature had clinical correlates, including clinical efficacy of empirical antibiotic treatment, progression to acute-on-chronic liver failure and short-term mortality. Cytomegalovirus reactivation, which is treatable, may adversely affect clinical outcomes in some individuals with decompensated cirrhosis. Routine screening for NHVs, especially cytomegalovirus, may be useful for the management of individuals with acute decompensation of cirrhosis.
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Affiliation(s)
- Beiling Li
- Hepatology Unit, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Changze Hong
- Hepatology Unit, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhiping Fan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shumin Cai
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qinjun He
- Hepatology Unit, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoqin Lan
- Hepatology Unit, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qintao Lai
- Hepatology Unit, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yali Ji
- Hepatology Unit, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wenfan Luo
- Hepatology Unit, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Junying Li
- Hepatology Unit, Zengcheng Branch, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiao Cheng
- Hepatology Unit, Zengcheng Branch, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Miaoxia Liu
- Hepatology Unit, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yixiu Gu
- Hepatology Unit, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guanting Lu
- Hepatology Unit, Zengcheng Branch, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shaochuan Li
- Realmeta Technology Co.,Ltd, Guangzhou, China; Goodwill Clinical Laboratories Co.,Ltd, Guangzhou, China
| | - Yali Wang
- BGI Infection Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Xing Weng
- BGI Infection Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Xiaoyun Niu
- Realmeta Technology Co.,Ltd, Guangzhou, China; Goodwill Clinical Laboratories Co.,Ltd, Guangzhou, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rajiv Jalan
- Hepatology Unit, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China; Liver Failure Group, Institute for Liver and Digestive Health, UCL Medical School, London, UK; European Foundation for the Study of Chronic Liver Failure, Barcelona, Spain.
| | - Jinjun Chen
- Hepatology Unit, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China; Hepatology Unit, Zengcheng Branch, Nanfang Hospital, Southern Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Viral Hepatitis Research, China.
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