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Chen L, Zhao Y, Wei J, Huang W, Ma Y, Yang X, Liu Y, Wang J, Xia H, Lou Z. Metagenomic Next-Generation Sequencing for the Diagnosis of Neonatal Infectious Diseases. Microbiol Spectr 2022; 10:e0119522. [PMID: 36409152 PMCID: PMC9769891 DOI: 10.1128/spectrum.01195-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 10/28/2022] [Indexed: 11/23/2022] Open
Abstract
Infectious diseases pose a fatal risk to neonates. Timely and accurate pathogen detection is crucial for proper clinical diagnosis and therapeutic strategies. Limited sample volumes from neonatal patients seriously hindered the accurate detection of pathogens. Here, we unravel that metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) and RNA can achieve unbiased detection of trace pathogens from different kinds of body fluid samples and blood samples. We enrolled 168 neonatal patients with suspected infections from whom blood samples (n = 153), cerebrospinal fluid samples (n = 127), and respiratory tract samples (RTSs) (including bronchoalveolar lavage fluids, sputa, and respiratory secretions) (n = 51) were collected and analyzed using mNGS. High rates of positivity (70.2%; 118/168) of mNGS were observed, and the coincidence rate against the final clinical diagnosis in positive mNGS cases reached 68.6% (81/118). The most common causative pathogens were Klebsiella pneumoniae (n = 12), Escherichia coli (n = 12), and Streptococcus pneumoniae (n = 8). mNGS using cfDNA and RNA can identify microbes that cannot be detected by conventional methods in different body fluid and blood samples, and more than 50% of these microbes were identified as causative pathogens. Further local polynomial regression fitting analysis revealed that the best timing for mNGS detection ranged from 1 to 3 days after the start of continuous antimicrobial therapy. Diagnosed and guided by mNGS results, the therapeutic regimens for 86 out of 117 neonatal patients were changed, most of whom (80/86) completely recovered and were discharged, while 44 out of 86 patients completely or partially stopped unnecessary medication. Our findings highlight the importance of mNGS in detecting causative DNA and RNA pathogens in infected neonatal patients. IMPORTANCE To the best of our knowledge, this is the first report on evaluating the performance of mNGS using cfDNA and RNA from body fluid and blood samples for diagnosing neonatal infections. mNGS of RNA and cfDNA can achieve the unbiased detection and identification of trace pathogens from different kinds of neonatal body fluid and blood samples with a high total coincidence rate (226/331; 68.3%) against final clinical diagnoses by sample. The best timing for mNGS detection in neonatal infections ranged from 1 to 3 days, rather than 0 days, after the start of continuous antimicrobial therapy. Our findings highlight the importance of mNGS in detecting causative DNA and RNA pathogens, and the extensive application of mNGS for the diagnosis of neonatal infections can be expected.
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Affiliation(s)
- Lu Chen
- Xi’an Children’s Hospital, Xi’an, China
| | | | | | | | - Ying Ma
- Xi’an Children’s Hospital, Xi’an, China
| | - Xuefeng Yang
- Neonatal Intensive Care Department, Xi’an Children’s Hospital, Xi’an, China
| | - Yang Liu
- Xi’an Children’s Hospital, Xi’an, China
| | - Jing Wang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Zheng Lou
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
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Toan ND, Darton TC, Huong NHT, Nhat LTH, Nguyen TNT, Tuyen HT, Thinh LQ, Mau NK, Tam PTT, Phuong CN, Nhan LNT, Minh NNQ, Xuan NM, Thuong TC, Hung NT, Boinett C, Reece S, Karkey A, Day JN, Baker S. Clinical and laboratory factors associated with neonatal sepsis mortality at a major Vietnamese children's hospital. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000875. [PMID: 36962870 PMCID: PMC10021837 DOI: 10.1371/journal.pgph.0000875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 07/13/2022] [Indexed: 06/18/2023]
Abstract
Sepsis is a major cause of neonatal mortality and children born in low- and middle-income countries (LMICs) are at greater risk of severe neonatal infections than those in higher-income countries. Despite this disparity, there are limited contemporaneous data linking the clinical features of neonatal sepsis with outcome in LMICs. Here, we aimed to identify factors associated with mortality from neonatal sepsis in Vietnam. We conducted a prospective, observational study to describe the clinical features, laboratory characteristics, and mortality rate of neonatal sepsis at a major children's hospital in Ho Chi Minh City. All in-patient neonates clinically diagnosed with probable or culture-confirmed sepsis meeting inclusion criteria from January 2017 to June 2018 were enrolled. We performed univariable analysis and logistic regression to identify factors independently associated with mortality. 524 neonates were recruited. Most cases were defined as late-onset neonatal sepsis and were hospital-acquired (91.4% and 73.3%, respectively). The median (IQR) duration of hospital stay was 23 (13-41) days, 344/524 (65.6%) had a positive blood culture (of which 393 non-contaminant organisms were isolated), and 69/524 (13.2%) patients died. Coagulase-negative staphylococci (232/405; 57.3%), Klebsiella spp. (28/405; 6.9%), and Escherichia coli (27/405; 6.7%) were the most isolated organisms. Sclerema (OR = 11.4), leukopenia <4,000/mm3 (OR = 7.8), thrombocytopenia <100,000/mm3 (OR = 3.7), base excess < -20 mEq/L (OR = 3.6), serum lactate >4 mmol/L (OR = 3.4), extremely low birth weight (OR = 3.2), and hyperglycaemia >180 mg/dL (OR = 2.6) were all significantly (p<0.05) associated with mortality. The identified risk factors can be adopted as prognostic factors for the diagnosis and treatment of neonatal sepsis and enable early risk stratification and interventions appropriate to reduce neonatal sepsis in LMIC settings.
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Affiliation(s)
- Nguyen Duc Toan
- Clinical Departments, Children’s Hospital 1, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Wellcome Trust Africa and Asia Programmes, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Department of Paediatrics, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Thomas C. Darton
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, United Kingdom
| | - Nguyen Hoang Thien Huong
- Clinical Departments, Children’s Hospital 1, Ho Chi Minh City, Vietnam
- Department of Paediatrics, Vietnam National University School of Medicine, Ho Chi Minh City, Vietnam
| | - Le Thanh Hoang Nhat
- Hospital for Tropical Diseases, Wellcome Trust Africa and Asia Programmes, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - To Nguyen Thi Nguyen
- Hospital for Tropical Diseases, Wellcome Trust Africa and Asia Programmes, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ha Thanh Tuyen
- Hospital for Tropical Diseases, Wellcome Trust Africa and Asia Programmes, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Le Quoc Thinh
- Clinical Departments, Children’s Hospital 1, Ho Chi Minh City, Vietnam
| | - Nguyen Kien Mau
- Clinical Departments, Children’s Hospital 1, Ho Chi Minh City, Vietnam
| | - Pham Thi Thanh Tam
- Hospital for Tropical Diseases, Wellcome Trust Africa and Asia Programmes, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Cam Ngoc Phuong
- Hanh Phuc International Hospital, Binh Duong Province, Vietnam
| | - Le Nguyen Thanh Nhan
- Clinical Departments, Children’s Hospital 1, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Wellcome Trust Africa and Asia Programmes, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Ngo Minh Xuan
- Department of Paediatrics, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Tang Chi Thuong
- Department of Paediatrics, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
- Department of Health, Ho Chi Minh City, Vietnam
| | - Nguyen Thanh Hung
- Clinical Departments, Children’s Hospital 1, Ho Chi Minh City, Vietnam
- Department of Paediatrics, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
- Department of Paediatrics, Vietnam National University School of Medicine, Ho Chi Minh City, Vietnam
| | | | - Stephen Reece
- Kymab, Babraham Research Campus, Cambridge, United Kingdom
| | - Abhilasha Karkey
- Wellcome Trust Africa and Asia Programmes, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Jeremy N. Day
- Hospital for Tropical Diseases, Wellcome Trust Africa and Asia Programmes, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
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