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Xu X, Zheng Y, Zhang X, Zhang C, Gai W, Yang Z. Utility of Metagenomic Next-Generation Sequencing for Diagnosis of Infectious Diseases in Critically Ill Immunocompromised Pediatric Patients. Infect Drug Resist 2024; 17:3579-3591. [PMID: 39165848 PMCID: PMC11334925 DOI: 10.2147/idr.s472129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 08/09/2024] [Indexed: 08/22/2024] Open
Abstract
Purpose Infections cause high rates of illness and death in children worldwide. However, studies on the clinical value of metagenomic next-generation sequencing (mNGS) for immunocompromised children are still limited. Patients and Methods From June 2021 to December 2023, 119 samples were collected at Pediatric Intensive Care Unit (PICU) of a single-center pediatric hospital and classified into two groups based on their immune states. We compared the diagnostic performance of mNGS and conventional microbiological test (CMT) for pathogen identification, and assessed the clinical impacts of mNGS. Results Among the 119 samples, 48 (40.34%) belonged to the immunocompromised children. mNGS had a higher positivity rate than CMT (76.47% vs 55.46%, P = 0.0006). The positive percent agreement (PPA) of mNGS for immunocompromised children was higher compared to immunocompetent children (95.24% vs 77.78%). The most common pathogens for immunocompromised patients were gram-negative bacteria and herpesvirus. However, immunocompetent children showed a higher detection rate for gram-positive bacteria and respiratory viruses. Furthermore, the proportions of the positive impact of mNGS results were significantly higher in immunocompromised patients compared to immunocompetent patients for both diagnosis (91.67% vs 57.75%) and treatment (95.83% vs 64.79%) (P < 0.0001). Immunocompromised state, length of hospital stays, times stay in ICU, Pediatric Risk of Mortality (PRISM) score, neutrophil percentage (NEUT%) and the ratio of arterial oxygen partial pressure to fractional inspired oxygen (PaO2/FiO2) were considered independent factors for poor prognosis in critically ill pediatric patients. Conclusion In patients from PICU, mNGS had a greater clinical significance in immunocompromised children compared to immunocompetent children. mNGS technology is an important auxiliary method for achieving accurate diagnosis and treatment of critically ill pediatric patients.
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Affiliation(s)
- Xiangzhi Xu
- Department of Pediatric Intensive Care Unit, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yafeng Zheng
- WillingMed Technology (Beijing) Co., Ltd, Beijing, People’s Republic of China
| | - Xiaojing Zhang
- WillingMed Technology (Beijing) Co., Ltd, Beijing, People’s Republic of China
| | - Chenmei Zhang
- Department of Pediatric Intensive Care Unit, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Wei Gai
- WillingMed Technology (Beijing) Co., Ltd, Beijing, People’s Republic of China
| | - Zihao Yang
- Department of Pediatric Intensive Care Unit, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
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Shi P, Liu J, Liang A, Zhu W, Fu J, Wu X, Peng Y, Yuan S, Wu X. Application of metagenomic next-generation sequencing in optimizing the diagnosis of ascitic infection in patients with liver cirrhosis. BMC Infect Dis 2024; 24:503. [PMID: 38769522 PMCID: PMC11107059 DOI: 10.1186/s12879-024-09396-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/09/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is an emerging technique for the clinical diagnosis of infectious disease that has rarely been used for the diagnosis of ascites infection in patients with cirrhosis. This study compared mNGS detection with conventional culture methods for the on etiological diagnosis of cirrhotic ascites and evaluated the clinical effect of mNGS. METHODS A total of 109 patients with ascites due to cirrhosis were included in the study. We compared mNGS with conventional culture detection by analyzing the diagnostic results, pathogen species and clinical effects. The influence of mNGS on the diagnosis and management of ascites infection in patients with cirrhosis was also evaluated. RESULTS Ascites cases were classified into three types: spontaneous bacterial peritonitis (SBP) (16/109, 14.7%), bacterascites (21/109, 19.3%) and sterile ascites (72/109, 66.1%). In addition, 109 patients were assigned to the ascites mNGS-positive group (80/109, 73.4%) or ascites mNGS-negative group (29/109, 26.6%). The percentage of positive mNGS results was significantly greater than that of traditional methods (73.4% vs. 28.4%, P < 0.001). mNGS detected 43 strains of bacteria, 9 strains of fungi and 8 strains of viruses. Fourteen bacterial strains and 3 fungal strains were detected via culture methods. Mycobacteria, viruses, and pneumocystis were detected only by the mNGS method. The mNGS assay produced a greater polymicrobial infection rate than the culture method (55% vs. 16%). Considering the polymorphonuclear neutrophil (PMN) counts, the overall percentage of pathogens detected by the two methods was comparable, with 87.5% (14/16) in the PMN ≥ 250/mm3 group and 72.0% (67/93) in the PMN < 250/mm3 group (P > 0.05). Based on the ascites PMN counts combined with the mNGS assay, 72 patients (66.1%) were diagnosed with ascitic fluid infection (AFI) (including SBP and bacterascites), whereas based on the ascites PMN counts combined with the culture assay, 37 patients (33.9%) were diagnosed with AFI (P < 0.05). In 60 (55.0%) patients, the mNGS assay produced positive clinical effects; 40 (85.7%) patients had their treatment regimen adjusted, and 48 patients were improved. The coincidence rate of the mNGS results and clinical findings was 75.0% (60/80). CONCLUSIONS Compared with conventional culture methods, mNGS can improve the detection rate of ascites pathogens, including bacteria, viruses, and fungi, and has significant advantages in the diagnosis of rare pathogens and pathogens that are difficult to culture; moreover, mNGS may be an effective method for improving the diagnosis of ascites infection in patients with cirrhosis, guiding early antibiotic therapy, and for reducing complications related to abdominal infection. In addition, explaining mNGS results will be challenging, especially for guiding the treatment of infectious diseases.
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Affiliation(s)
- Pei Shi
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - Juan Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - An Liang
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - Wentao Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - Jiwei Fu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - Xincheng Wu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - Yuchen Peng
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - Songsong Yuan
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China.
| | - Xiaoping Wu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China.
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Zhang H, Liang R, Zhu Y, Hu L, Xia H, Li J, Ye Y. Metagenomic next-generation sequencing of plasma cell-free DNA improves the early diagnosis of suspected infections. BMC Infect Dis 2024; 24:187. [PMID: 38347444 PMCID: PMC10863141 DOI: 10.1186/s12879-024-09043-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) could improve the diagnosed efficiency of pathogens in bloodstream infections or sepsis. Little is known about the clinical impact of mNGS test when used for the early diagnosis of suspected infections. Herein, our main objective was to assess the clinical efficacy of utilizing blood samples to perform mNGS for early diagnosis of suspected infections, as well as to evaluate its potential in guiding antimicrobial therapy decisions. METHODS In this study, 212 adult hospitalized patients who underwent blood mNGS test in the early stage of suspected infections were enrolled. Diagnostic efficacy of mNGS test and blood culture was compared, and the clinical impact of mNGS on clinical care was analyzed. RESULTS In our study, the total detection rate of blood mNGS was significantly higher than that of culture method (74.4% vs. 12.1%, P < 0.001) in the paired mNGS test and blood culture. Blood stream infection (107, 67.3%) comprised the largest component of all the diseases in our patients, and the detection rate of single blood sample subgroup was similar with that of multiple type of samples subgroup. Among the 187 patients complained with fever, there was no difference in the diagnostic efficacy of mNGS when blood specimens or additional other specimens were used in cases presenting only with fever. While, when patients had other symptoms except fever, the performance of mNGS was superior in cases with specimens of suspected infected sites and blood collected at the same time. Guided by mNGS results, therapeutic regimens for 70.3% cases (149/212) were changed, and the average hospitalized days were significantly shortened in cases with the earlier sampling time of admission. CONCLUSION In this study, we emphasized the importance of blood mNGS in early infectious patients with mild and non-specific symptoms. Blood mNGS can be used as a supplement to conventional laboratory examination, and should be performed as soon as possible to guide clinicians to perform appropriate anti-infection treatment timely and effectively. Additionally, combining the contemporaneous samples from suspected infection sites could improve disease diagnosis and prognoses. Further research needs to be better validated in large-scale clinical trials to optimize diagnostic protocol, and the cost-utility analysis should be performed.
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Affiliation(s)
- Hui Zhang
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ruobing Liang
- Department of Scientific Affaires, Hugobiotech Co., Ltd, Beijing, China
| | - Yunzhu Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lifen Hu
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Han Xia
- Department of Scientific Affaires, Hugobiotech Co., Ltd, Beijing, China.
| | - Jiabin Li
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
- Institute of Bacterial Resistance, Anhui Medical University, Hefei, China.
- Anhui Center for Surveillance of Bacterial Resistance, Hefei, China.
| | - Ying Ye
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
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Chen Y, Wang J, Niu T. Clinical and diagnostic values of metagenomic next-generation sequencing for infection in hematology patients: a systematic review and meta-analysis. BMC Infect Dis 2024; 24:167. [PMID: 38326763 PMCID: PMC10848439 DOI: 10.1186/s12879-024-09073-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/29/2024] [Indexed: 02/09/2024] Open
Abstract
OBJECTIVES This meta-analysis focused on systematically assessing the clinical value of mNGS for infection in hematology patients. METHODS We searched for studies that assessed the clinical value of mNGS for infection in hematology patients published in Embase, PubMed, Cochrane Library, Web of Science, and CNKI from inception to August 30, 2023. We compared the detection positive rate of pathogen for mNGS and conventional microbiological tests (CMTs). The diagnostic metrics, antibiotic adjustment rate and treatment effective rate were combined. RESULTS Twenty-two studies with 2325 patients were included. The positive rate of mNGS was higher than that of CMT (blood: 71.64% vs. 24.82%, P < 0.001; BALF: 89.86% vs. 20.78%, P < 0.001; mixed specimens: 82.02% vs. 28.12%, P < 0.001). The pooled sensitivity and specificity were 87% (95%CI: 81-91%) and 59% (95%CI: 43-72%), respectively. The reference standard/neutropenia and research type/reference standard may be sources of heterogeneity in sensitivity and specificity, respectively. The pooled antibiotic adjustment rate according to mNGS was 49.6% (95% CI: 41.8-57.4%), and the pooled effective rate was 80.9% (95% CI: 62.4-99.3%). CONCLUSION mNGS has high positive detection rates in hematology patients. mNGS can guide clinical antibiotic adjustments and improve prognosis, especially in China.
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Affiliation(s)
- Yuhui Chen
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinjin Wang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Ting Niu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China.
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Chen Y, Wang J, Gan X, Li M, Liao Y, Zhou Y, Niu T. Application of plasma metagenomic next-generation sequencing improves prognosis in hematology patients with neutropenia or hematopoietic stem cell transplantation for infection. Front Cell Infect Microbiol 2024; 14:1338307. [PMID: 38371300 PMCID: PMC10869557 DOI: 10.3389/fcimb.2024.1338307] [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: 11/14/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024] Open
Abstract
Introduction Metagenomic next-generation sequencing (mNGS) is a novel technique for detecting pathogens. This retrospective study evaluated the diagnostic value of mNGS using plasma for infections in hematology patients and its impact on clinical treatment and prognosis in different subgroups of hematology patients. Methods A total of 153 hematology patients with suspected infection who underwent mNGS using plasma were enrolled in the study. Their clinical histories, conventional microbiological test (CMT) results, mNGS results, treatment and prognosis were retrospectively analyzed. Results In 153 plasma samples, mNGS yielded a higher positivity rate than CMT (total: 88.24% vs. 40.52%, P<0.001; bacteria: 35.95% vs. 21.57%, P < 0.01; virus: 69.93% vs. 21.57%, P<0.001; fungi: 20.26% vs. 7.84%, P<0.01). mNGS had a higher positivity rate for bacteria and fungi in the neutropenia group than in the non-neutropenia group (bacteria: 48.61% vs. 24.69%, P<0.01; fungi: 27.78% vs. 13.58%, P<0.05). mNGS demonstrated a greater advantage in the group of patients with hematopoietic stem cell transplantation (HSCT). Both the 3-day and 7-day efficacy rates in the HSCT group were higher than those in the non-HSCT group (3-day: 82.22% vs. 58.65%, P < 0.01; 7-day: 88.89% vs. 67.31%, P < 0.01), and the 28-day mortality rate was lower in the HSCT group than in the non-HSCT group (6.67% vs. 38.89%, P < 0.000). The neutropenia group achieved similar efficacy and mortality rates to the non-neutropenia group (7-day efficiency rate: 76.39% vs. 71.43%, P > 0.05; mortality rate: 29.17% vs. 29.63%, P > 0.05) with more aggressive antibiotic adjustments (45.83% vs. 22.22%, P < 0.01). Conclusion mNGS can detect more microorganisms with higher positive rates, especially in patients with neutropenia. mNGS had better clinical value in patients with hematopoietic stem cell transplantation (HSCT) or neutropenia, which had a positive effect on treatment and prognosis.
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Affiliation(s)
- Yuhui Chen
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinjin Wang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Xinai Gan
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Meng Li
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Liao
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Yongzhao Zhou
- Integrated Care Management Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ting Niu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
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Xie Y, Qiu X, Gong J, Yuan Y, Xie D, Li S. Clinical application of whole exome sequencing technology in small-for-gestational-age children. Am J Transl Res 2023; 15:6813-6822. [PMID: 38186994 PMCID: PMC10767522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/25/2023] [Indexed: 01/09/2024]
Abstract
AIM To apply whole exome sequencing (WES) for molecular diagnosis of small-for-gestational-age (SGA) children. METHODS We retrospectively analyzed the data of 60 SGA children in our hospital, and performed developmental assessment, laboratory tests, imaging tests, and whole exome sequencing (WES), which were combined with clinical phenotypes to clarify the pathogenicity of the variant genes in the children. RESULTS Sixty SGA children were tested, and pathogenic SGA was detected at relatively high frequencies on chromosomes 7, 8, and 22. Of these, karyotype analysis clearly suggested developmental disorders in 4 patients. Also, a case of Wiedemann-Steiner syndrome due to a de novo nonsense variant in the KMT2A gene was detected. CONCLUSIONS The use of WES testing technology to increase the diagnosis rate of children with special SGA is conducive to the correct diagnosis and treatment of such children.
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Affiliation(s)
- Yunyun Xie
- Department of Children Health, Jiangxi Provincial Children's Hospital Nanchang 330006, Jiangxi, China
| | - Xiaolu Qiu
- Department of Children Health, Jiangxi Provincial Children's Hospital Nanchang 330006, Jiangxi, China
| | - Jun Gong
- Department of Children Health, Jiangxi Provincial Children's Hospital Nanchang 330006, Jiangxi, China
| | - Yufeng Yuan
- Department of Children Health, Jiangxi Provincial Children's Hospital Nanchang 330006, Jiangxi, China
| | - Dan Xie
- Department of Children Health, Jiangxi Provincial Children's Hospital Nanchang 330006, Jiangxi, China
| | - Shouming Li
- Department of Children Health, Jiangxi Provincial Children's Hospital Nanchang 330006, Jiangxi, China
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