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Reinicke M, Braun SD, Diezel C, Lemuth O, Engelmann I, Liebe T, Ehricht R. From Shadows to Spotlight: Enhancing Bacterial DNA Detection in Blood Samples through Cutting-Edge Molecular Pre-Amplification. Antibiotics (Basel) 2024; 13:161. [PMID: 38391548 PMCID: PMC10886392 DOI: 10.3390/antibiotics13020161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
One of the greatest challenges to the use of molecular methods for diagnostic purposes is the detection of target DNA that is present only in low concentrations. One major factor that negatively impacts accuracy, diagnostic sensitivity, and specificity is the sample matrix, which hinders the attainment of the required detection limit due to the presence of residual background DNA. To address this issue, various methods have been developed to enhance sensitivity through targeted pre-amplification of marker sequences. Diagnostic sensitivity to the single molecular level is critical, particularly when identifying bloodstream infections. In cases of clinically manifest sepsis, the concentration of bacteria in the blood may reach as low as one bacterial cell/CFU per mL of blood. Therefore, it is crucial to achieve the highest level of sensitivity for accurate detection. In the present study, we have established a method that fills the analytical gap between low concentrations of molecular markers and the minimum requirements for molecular testing. For this purpose, a sample preparation of whole blood samples with a directly downstream pre-amplification was developed, which amplifies specific species and resistance markers in a multiplex procedure. When applying pre-amplification techniques, the sensitivity of the pathogen detection in whole blood samples was up to 100 times higher than in non-pre-amplified samples. The method was tested with blood samples that were spiked with several Gram-positive and Gram-negative bacterial pathogens. By applying this method to artificial spiked blood samples, it was possible to demonstrate a sensitivity of 1 colony-forming unit (CFU) per millilitre of blood for S. aureus and E. faecium. A detection limit of 28 and 383 CFU per ml of blood was achieved for E. coli and K. pneumoniae, respectively. If the sensitivity is also confirmed for real clinical blood samples from septic patients, the novel technique can be used for pathogen detection without cultivation, which might help to accelerate diagnostics and, thus, to decrease sepsis mortality rates.
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Affiliation(s)
- Martin Reinicke
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Sascha Daniel Braun
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Celia Diezel
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Oliver Lemuth
- InfectoGnostics Research Campus, 07743 Jena, Germany
- BLINK AG, 07747 Jena, Germany
| | - Ines Engelmann
- InfectoGnostics Research Campus, 07743 Jena, Germany
- BLINK AG, 07747 Jena, Germany
| | - Theresa Liebe
- InfectoGnostics Research Campus, 07743 Jena, Germany
- BLINK AG, 07747 Jena, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich-Schiller University, 07743 Jena, Germany
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Ge H, Liang X, Lu Q, He A, Zhong P, Liu J, Yu Y, Song H. Case report: Intraabdominal infection of Mycobacterium syngnathidarum in an immunocompetent patient confirmed by whole-genome sequencing. Front Med (Lausanne) 2023; 10:1265594. [PMID: 37869158 PMCID: PMC10588666 DOI: 10.3389/fmed.2023.1265594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/15/2023] [Indexed: 10/24/2023] Open
Abstract
Background The taxonomic group of non-tuberculous mycobacteria (NTM) encompasses more than 190 species and subspecies, some of which can cause pulmonary and extrapulmonary diseases across various age groups in humans. However, different subspecies exhibit differential drug sensitivities, and traditional detection techniques struggle to accurately classify NTM. Therefore, clinicians need more effective detection methods to identify NTM subtypes, thus providing personalized medication for patients. Case presentation We present the case of a 47-year-old female patient diagnosed with an intraabdominal infection caused by Mycobacterium syngnathidarum. Despite computed tomography of the chest suggesting potential tuberculosis, tuberculosis infection was ruled out due to negative TB-DNA results for ascites fluid and sputum and limited improvement of lung lesions after treatment. Additionally, acid-fast staining and Lowenstein-Jensen culture results revealed the presence of mycobacterium in ascites fluid. Subsequent whole-genome sequencing (WGS) confirmed the DNA sequences of Mycobacterium syngnathidarum in colonies isolated from the ascites fluid, which was further corroborated by polymerase chain reaction and Sanger sequencing. Ultimately, the patient achieved a complete recovery following the treatment regimen targeting Mycobacterium syngnathidarum, which involved clarithromycin, ethambutol hydrochloride, pyrazinamide, rifampicin, and isoniazid. Conclusion This is the first reported case of Mycobacterium syngnathidarum infection in humans. Mycobacterium syngnathidarum was detected by WGS in this case, suggesting that WGS may serve as a high-resolution assay for the diagnosis of different subtypes of mycobacterium infection.
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Affiliation(s)
- Hu Ge
- Changsha KingMed Center for Clinical Laboratory, Changsha, Hunan, China
| | - Xiongwei Liang
- Changsha KingMed Center for Clinical Laboratory, Changsha, Hunan, China
| | - Qiuran Lu
- Changsha KingMed Center for Clinical Laboratory, Changsha, Hunan, China
| | - Aixiang He
- Rucheng County People's Hospital, Rucheng, Hunan, China
| | - Peiwen Zhong
- Guangzhou KingCreate Biotechnology Company Limited, Guangzhou, Guangdong, China
| | - Jun Liu
- Guangzhou KingCreate Biotechnology Company Limited, Guangzhou, Guangdong, China
| | - Yan Yu
- Changsha KingMed Center for Clinical Laboratory, Changsha, Hunan, China
| | - Honglian Song
- Rucheng County People's Hospital, Rucheng, Hunan, China
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Xu Y, Jiang Y, Wang Y, Meng F, Qin W, Lin Y. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid assists in the diagnosis of pathogens associated with lower respiratory tract infections in children. Front Cell Infect Microbiol 2023; 13:1220943. [PMID: 37822360 PMCID: PMC10562542 DOI: 10.3389/fcimb.2023.1220943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/04/2023] [Indexed: 10/13/2023] Open
Abstract
Worldwide, lower respiratory tract infections (LRTI) are an important cause of hospitalization in children. Due to the relative limitations of traditional pathogen detection methods, new detection methods are needed. The purpose of this study was to evaluate the value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) samples for diagnosing children with LRTI based on the interpretation of sequencing results. A total of 211 children with LRTI admitted to the First Affiliated Hospital of Guangzhou Medical University from May 2019 to December 2020 were enrolled. The diagnostic performance of mNGS versus traditional methods for detecting pathogens was compared. The positive rate for the BALF mNGS analysis reached 95.48% (95% confidence interval [CI] 92.39% to 98.57%), which was superior to the culture method (44.07%, 95% CI 36.68% to 51.45%). For the detection of specific pathogens, mNGS showed similar diagnostic performance to PCR and antigen detection, except for Streptococcus pneumoniae, for which mNGS performed better than antigen detection. S. pneumoniae, cytomegalovirus and Candida albicans were the most common bacterial, viral and fungal pathogens. Common infections in children with LRTI were bacterial, viral and mixed bacterial-viral infections. Immunocompromised children with LRTI were highly susceptible to mixed and fungal infections. The initial diagnosis was modified based on mNGS in 29.6% (37/125) of patients. Receiver operating characteristic (ROC) curve analysis was performed to predict the relationship between inflammation indicators and the type of pathogen infection. BALF mNGS improves the sensitivity of pathogen detection and provides guidance in clinical practice for diagnosing LRTI in children.
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Affiliation(s)
- Yunjian Xu
- Department of Clinical Laboratory, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Yueting Jiang
- Department of Clinical Laboratory, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Yan Wang
- CapitalBio Technology Inc., Beijing, China
| | | | - Wenyan Qin
- CapitalBio Technology Inc., Beijing, China
| | - Yongping Lin
- Department of Clinical Laboratory, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou, China
- Department of Laboratory Medicine, Cancer Hospital Chinese Academy of Medical Sciences, Shenzhen Center, Shenzhen, China
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Wu Z, Yu L, Shi W, Ma J. Argonaute protein-based nucleic acid detection technology. Front Microbiol 2023; 14:1255716. [PMID: 37744931 PMCID: PMC10515653 DOI: 10.3389/fmicb.2023.1255716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023] Open
Abstract
It is vital to diagnose pathogens quickly and effectively in the research and treatment of disease. Argonaute (Ago) proteins are recently discovered nucleases with nucleic acid shearing activity that exhibit specific recognition properties beyond CRISPR-Cas nucleases, which are highly researched but restricted PAM sequence recognition. Therefore, research on Ago protein-mediated nucleic acid detection technology has attracted significant attention from researchers in recent years. Using Ago proteins in developing nucleic acid detection platforms can enable efficient, convenient, and rapid nucleic acid detection and pathogen diagnosis, which is of great importance for human life and health and technological development. In this article, we introduce the structure and function of Argonaute proteins and discuss the latest advances in their use in nucleic acid detection.
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Affiliation(s)
- Zhiyun Wu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Li Yu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Institute of Stem Cell, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Weifeng Shi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Jinhong Ma
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
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Tanny T, Sallam M, Soda N, Nguyen NT, Alam M, Shiddiky MJA. CRISPR/Cas-Based Diagnostics in Agricultural Applications. J Agric Food Chem 2023; 71:11765-11788. [PMID: 37506507 DOI: 10.1021/acs.jafc.3c00913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Pests and disease-causing pathogens frequently impede agricultural production. An early and efficient diagnostic tool is crucial for effective disease management. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein (Cas) have recently been harnessed to develop diagnostic tools. The CRISPR/Cas system, composed of the Cas endonuclease and guide RNA, enables precise identification and cleavage of the target nucleic acids. The inherent sensitivity, high specificity, and rapid assay time of the CRISPR/Cas system make it an effective alternative for diagnosing plant pathogens and identifying genetically modified crops. Furthermore, its potential for multiplexing and suitability for point-of-care testing at the field level provide advantages over traditional diagnostic systems such as RT-PCR, LAMP, and NGS. In this review, we discuss the recent developments in CRISPR/Cas based diagnostics and their implications in various agricultural applications. We have also emphasized the major challenges with possible solutions and provided insights into future perspectives and potential applications of the CRISPR/Cas system in agriculture.
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Affiliation(s)
- Tanzena Tanny
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Mohamed Sallam
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Narshone Soda
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, Mayers Road, Nambour, QLD 4560, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
- Rural Health Research Institute, Charles Sturt University, Orange, NSW 2800, Australia
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He S, Wei J, Feng J, Liu D, Wang N, Chen L, Xiong Y. The application of metagenomic next-generation sequencing in pathogen diagnosis: a bibliometric analysis based on Web of Science. Front Cell Infect Microbiol 2023; 13:1112229. [PMID: 37600953 PMCID: PMC10434771 DOI: 10.3389/fcimb.2023.1112229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Background Infectious disease is a large burden on public health globally. Metagenomic next-generation sequencing (mNGS) has become popular as a new tool for pathogen diagnosis with numerous advantages compared to conventional methods. Recently, research on mNGS increases yearly. However, no bibliometric analysis has systematically presented the full spectrum of this research field. Therefore, we reviewed all the publications associated with this topic and performed this study to analyze the comprehensive status and future hotspots of mNGS for infectious disease diagnosis. Methods The literature was searched in the Web of Science Core Collection and screened without year or language restrictions, and the characteristics of the studies were also identified. The outcomes included publication years, study types, journals, countries, authorship, institutions, frontiers, and hotspots with trends. Statistical analysis and visualization were conducted using VOSviewer (version 1.6.16) and CiteSpace (version 6.1. R3). Results In total, 325 studies were included in the analysis after screening. Studies were published between 2009 and 2022 with a significantly increasing number from 1 to 118. Most of the studies were original articles and case reports. Frontiers in Cellular and Infection Microbiology and Clinical Infectious Disease were the most commonly cited and co-cited journals. Institutions and researchers from China contributed the most to this field, followed by those from the USA. The hotspots and frontiers of these studies are pneumonia, tuberculosis, and central nervous system infections. Conclusion This study determined that mNGS is a hot topic in the diagnosis of infectious diseases with development trends and provides insights into researchers, institutions, hotspots and frontiers in mNGS, which can offer references to related researchers and future research.
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Affiliation(s)
- Sike He
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwen Wei
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Dan Liu
- Department of Periodical Press, West China Hospital, Sichuan University, Chengdu, China
| | - Neng Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Liyu Chen
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Xiong
- Department of Periodical Press, West China Hospital, Sichuan University, Chengdu, China
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Luo W, He Y, Xu J, Zhang S, Li C, Lv J, Shen Y, Ou Z, Dong H. Comparison of Third-Generation Sequencing Technology and Traditional Microbiological Detection in Pathogen Diagnosis of Lower Respiratory Tract Infection. Discov Med 2023; 35:332-342. [PMID: 37272100 DOI: 10.24976/discov.med.202335176.34] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
BACKGROUND It is common to obtain a low detection rate and unsatisfactory detection results in complex infection or rare pathogen detection. This retrospective study aimed to illustrate the application value and prospect of the third-generation sequencing technology in lower respiratory tract infection disease. METHODS This study recruited 70 patients with lower respiratory tract infection (LRTI). Pathogen detection of bronchoalveolar lavage fluid (BALF) from all patients was performed using nanopore metagenomic sequencing technology and traditional culture. BALF culture combined with quantitiative PCR (qPCR) was used as a reference standard to analyze the sensitivity and specificity of nanopore sequencing technology. The current study also collected the examination results of enrolled samples using technical methods sputum culture, tuberculosis DNA (TB-DNA), and Xpert MTB/RIF and analyzed the detection efficiency of nanopore sequencing for Mycobacterium tuberculosis. RESULTS The positive rates of pathogens in 70 BALF samples detected by conventional culture and nanopore sequencing were 25.71% and 84.29%, respectively. Among the 59 positive BALF cases using nanopore sequencing, a total of 31 pathogens were identified, of which the proportions of bacteria, fungi, viruses, and other pathogens were 50%, 17%, 32%, and 1%, respectively. Using the results combined with culture and qPCR detection methods as the standard, the pathogen detection of BALF using nanopore sequencing had a sensitivity of 70% and a specificity of 91.7%. Additionally, the positive rate of the detection of M. tuberculosis using nanopore sequencing was 33.3% (6/18). The clinical medication plans of 74.3% (52/70) of the patients were referred to the nanopore sequencing results, of which 31 cases changed their treatment strategy, 21 supported the previous treatment plans, and 90% (47/52) of the patients finally had clinical improvement. CONCLUSIONS BALF detection using nanopore sequencing technology improves the process of detecting pathogens in patients with LRTI, especially for M. tuberculosis, fungi, and viruses, by reducing the report time from three days to six hours. The clinical application prospect of nanopore sequencing technology is promising in the pathogen diagnosis of LRTI.
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Affiliation(s)
- Wang Luo
- Department of Respiratory Medicine, The Zengcheng Branch of Nanfang Hospital, Southern Medical University, 511300 Guangzhou, Guangdong, China
| | - Yanbin He
- Dian Diagnostics Group Co., Ltd., 310000 Hangzhou, Zhejiang, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, 310030 Hangzhou, Zhejiang, China
| | - Jianhui Xu
- Department of Respiratory Medicine, The Zengcheng Branch of Nanfang Hospital, Southern Medical University, 511300 Guangzhou, Guangdong, China
| | - Shuhua Zhang
- Department of Respiratory Medicine, The Zengcheng Branch of Nanfang Hospital, Southern Medical University, 511300 Guangzhou, Guangdong, China
| | - Chunxi Li
- Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, 511300 Guangzhou, Guangdong, China
| | - Jiangfeng Lv
- Dian Diagnostics Group Co., Ltd., 310000 Hangzhou, Zhejiang, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, 310030 Hangzhou, Zhejiang, China
| | - Youfeng Shen
- Chongqing Precision Medical Industry Technology Research Institute, 400000 Chongqing, China
| | - Zhao Ou
- Dian Diagnostics Group Co., Ltd., 310000 Hangzhou, Zhejiang, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, 310030 Hangzhou, Zhejiang, China
| | - Hangming Dong
- Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, 511300 Guangzhou, Guangdong, China
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Ma J, Sabino-Santos G. Editorial: Interactions between pathogens and host immune system in patients with immunodeficiency: estimation from high-throughput sequencing. Front Cell Infect Microbiol 2023; 13:1200638. [PMID: 37260704 PMCID: PMC10228383 DOI: 10.3389/fcimb.2023.1200638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023] Open
Affiliation(s)
| | - Gilberto Sabino-Santos
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA, United States
- Center for Virology Research, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
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Yang P, Zhao L, Gao YG, Xia Y. Detection, Diagnosis, and Preventive Management of the Bacterial Plant Pathogen Pseudomonas syringae. Plants (Basel) 2023; 12:plants12091765. [PMID: 37176823 PMCID: PMC10181079 DOI: 10.3390/plants12091765] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/01/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023]
Abstract
Plant diseases caused by the pathogen Pseudomonas syringae are serious problems for various plant species worldwide. Accurate detection and diagnosis of P. syringae infections are critical for the effective management of these plant diseases. In this review, we summarize the current methods for the detection and diagnosis of P. syringae, including traditional techniques such as culture isolation and microscopy, and relatively newer techniques such as PCR and ELISA. It should be noted that each method has its advantages and disadvantages, and the choice of each method depends on the specific requirements, resources of each laboratory, and field settings. We also discuss the future trends in this field, such as the need for more sensitive and specific methods to detect the pathogens at low concentrations and the methods that can be used to diagnose P. syringae infections that are co-existing with other pathogens. Modern technologies such as genomics and proteomics could lead to the development of new methods of highly accurate detection and diagnosis based on the analysis of genetic and protein markers of the pathogens. Furthermore, using machine learning algorithms to analyze large data sets could yield new insights into the biology of P. syringae and novel diagnostic strategies. This review could enhance our understanding of P. syringae and help foster the development of more effective management techniques of the diseases caused by related pathogens.
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Affiliation(s)
- Piao Yang
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Science, The Ohio State University, Columbus, OH 43210, USA
| | - Lijing Zhao
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Science, The Ohio State University, Columbus, OH 43210, USA
| | - Yu Gary Gao
- OSU South Centers, The Ohio State University, 1864 Shyville Road, Piketon, OH 45661, USA
- Department of Extension, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Ye Xia
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Science, The Ohio State University, Columbus, OH 43210, USA
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Chen T, Zhang L, Huang W, Zong H, Li Q, Zheng Y, Lv Q, Kong D, Ren Y, Jiang Y, Li Y, Liu P. Detection of Pathogens and Antimicrobial Resistance Genes in Ventilator-Associated Pneumonia by Metagenomic Next-Generation Sequencing Approach. Infect Drug Resist 2023; 16:923-936. [PMID: 36814827 PMCID: PMC9939671 DOI: 10.2147/idr.s397755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/26/2023] [Indexed: 02/16/2023] Open
Abstract
Background The early identification of pathogens and their antibiotic resistance are essential for the management and treatment of patients affected by ventilator-associated pneumonia (VAP). However, microbiological culture may be time-consuming and has a limited culturability of many potential pathogens. In this study, we developed a rapid nanopore-based metagenomic next-generation sequencing (mNGS) diagnostic assay for detection of VAP pathogens and antimicrobial resistance genes (ARGs). Patients and Methods Endotracheal aspirate (ETA) samples from 63 patients with suspected VAP were collected between November 2021 and July 2022. Receiver operating characteristic (ROC) curves were established to compare the pathogen identification performance of the target pathogen reads, reads percent of microbes (RPM) and relative abundance (RA). The evaluation of the accuracy of mNGS was performed comparing with the gold standard and the composite standard, respectively. Then, the ARGs were analyzed by mNGS. Results ROC curves showed that RA has the highest diagnostic value and the corresponding threshold was 9.93%. The sensitivity and specificity of mNGS test were 91.3% and 78.3%, respectively, based on the gold standard, while the sensitivity and specificity of mNGS test were 97.4% and 100%, respectively, based on the composite standard. A total of 13 patients were virus-positive based on mNGS results, while the coinfection rate increased from 27% to 46% compared to the rate obtained based on clinical findings. The mNGS test also performed well at predicting antimicrobial resistance phenotypes. Patients with a late-onset VAP had a significantly greater proportion of ARGs in their respiratory microbiome compared to those with early-onset VAP (P = 0.041). Moreover, the median turnaround time of mNGS was 4.43 h, while routine culture was 72.00 h. Conclusion In this study, we developed a workflow that can accurately detect VAP pathogens and enable prediction of antimicrobial resistance phenotypes within 5 h of sample receipt by mNGS.
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Affiliation(s)
- Ting Chen
- The PLA 307 Clinical College of Anhui Medical University, The Fifth Clinical Medical College of Anhui Medical University, Hefei, People’s Republic of China,Department of Critical Care Medicine, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100071, People’s Republic of China
| | - Lei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Huijun Zong
- The PLA 307 Clinical College of Anhui Medical University, The Fifth Clinical Medical College of Anhui Medical University, Hefei, People’s Republic of China,Department of Critical Care Medicine, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100071, People’s Republic of China
| | - Qian Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Yuhao Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Yan Li
- The PLA 307 Clinical College of Anhui Medical University, The Fifth Clinical Medical College of Anhui Medical University, Hefei, People’s Republic of China,Department of Critical Care Medicine, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100071, People’s Republic of China,Correspondence: Yan Li, The PLA 307 Clinical College of Anhui Medical University, The Fifth Clinical Medical College of Anhui Medical University, Hefei, 230032, People’s Republic of China, Email
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China,Peng Liu, Beijing Institute of Microbiology and Epidemiology, Dongdajie Road 20, Beijing, 100071, People’s Republic of China, Tel +86-010-66948487, Email
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Niu S, Zhao L. Metagenomic next-generation sequencing clinches the diagnosis of Legionella pneumonia in a patient with acute myeloid leukemia: A case report and literature review. Front Cell Infect Microbiol 2022; 12:924597. [PMID: 36478673 PMCID: PMC9720252 DOI: 10.3389/fcimb.2022.924597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/06/2022] [Indexed: 11/22/2022] Open
Abstract
Legionella pneumonia caused by Legionella pneumophila is a multi-system disease that is a life-threatening, acute, and severe form of pneumonia. L. pneumophila is widespread and the clinical manifestations of Legionella pneumonia are similar to those of typical and atypical pneumonia. Current diagnostic scores and radiologic evidence have limited diagnostic value. Thus, it is likely that many cases of Legionella pneumonia remain unreported. We describe a woman with a medical history of acute myeloid leukemia who suffered from repeated fever, and no relief following initial empirical antibiotic treatment. Ultimately, she was diagnosed with Legionella pneumonia based on metagenomic next-generation sequencing (mNGS). We also performed a systematic review of the literature and identified 5 other patients who were diagnosed with Legionella pneumonia using mNGS, and reviewed their clinical characteristics, biological characteristics, epidemiological features, laboratory results, clinical findings, and treatments. This literature review showed that accurate etiological diagnosis is becoming increasingly essential for a definitive diagnosis and treatment strategies. The clinical manifestations of Legionella pneumonia are non-specific, and many routine laboratory diagnostic tests cannot identify Legionella. mNGS, an indispensable approach for identifying microorganisms, can provide a promising tool for the rapid and accurate etiological diagnosis methods contributing to early diagnosis, early treatment, and improved prognosis, especially for uncommon species such as L. pneumophila.
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Affiliation(s)
- Siqiang Niu
- Zhengzhou University, Zhengzhou, Henan, China,Henan Provincial People’s Hospital, Zhengzhou, Henan, China,Xinxiang City Central Hospital, Xinxiang, Henan, China
| | - Limin Zhao
- Department of Respiratory and Critical Care Medicine, Henan Provincial People’s Hospital, Zhengzhou, Henan, China,People's Hospital of Zhengzhou University, Zhengzhou, Henan, China,People's Hospital of Henan University, Zhengzhou, Henan, China,*Correspondence: Limin Zhao,
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12
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Cheng H, Sun Y, Yang Q, Deng M, Yu Z, Zhu G, Qu J, Liu L, Yang L, Xia Y. A rapid bacterial pathogen and antimicrobial resistance diagnosis workflow using Oxford nanopore adaptive sequencing method. Brief Bioinform 2022; 23:6762743. [PMID: 36259361 DOI: 10.1093/bib/bbac453] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/16/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022] Open
Abstract
Metagenomic sequencing analysis (mNGS) has been implemented as an alternative approach for pathogen diagnosis in recent years, which is independent of cultivation and is able to identify all potential antibiotic resistance genes (ARGs). However, current mNGS methods have to deal with low amounts of prokaryotic deoxyribonucleic acid (DNA) and high amounts of host DNA in clinical samples, which significantly decrease the overall microbial detection resolution. The recently released nanopore adaptive sampling (NAS) technology facilitates immediate mapping of individual nucleotides to a given reference as each molecule is sequenced. User-defined thresholds allow for the retention or rejection of specific molecules, informed by the real-time reference mapping results, as they are physically passing through a given sequencing nanopore. We developed a metagenomics workflow for ultra-sensitive diagnosis of bacterial pathogens and ARGs from clinical samples, which is based on the efficient selective 'human host depletion' NAS sequencing, real-time species identification and species-specific resistance gene prediction. Our method increased the microbial sequence yield at least 8-fold in all 21 sequenced clinical Bronchoalveolar Lavage Fluid (BALF) samples (4.5 h from sample to result) and accurately detected the ARGs at species level. The species-level positive percent agreement between metagenomic sequencing and laboratory culturing was 100% (16/16) and negative percent agreement was 100% (5/5) in our approach. Further work is required for a more robust validation of our approach with large sample size to allow its application to other infection types.
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Affiliation(s)
- Hang Cheng
- School of Medicine, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Yuhong Sun
- School of Environmental Science & Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Qing Yang
- School of Environmental Science & Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Minggui Deng
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518055, China
| | - Zhijian Yu
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518055, China
| | - Gang Zhu
- Third People's Hospital of Shenzhen, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiuxin Qu
- Third People's Hospital of Shenzhen, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518055, China
| | - Lei Liu
- Third People's Hospital of Shenzhen, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518055, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Yu Xia
- School of Environmental Science & Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China
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13
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Yan H, Li Z, Xia H, Li Q, Bai H. A case report on mixed pulmonary infection of Nocardia nova, Mycobacterium tuberculosis, and Aspergillus fumigatus based on metagenomic next-generation sequencing. Front Public Health 2022; 10:927338. [PMID: 36148364 PMCID: PMC9485662 DOI: 10.3389/fpubh.2022.927338] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/29/2022] [Indexed: 01/24/2023] Open
Abstract
Background Pulmonary infection is one of the common complications of long-term use of glucocorticoids. Severe infections not only increase the length of hospital stay and treatment costs but also cause progression or recurrence of the primary disease. Case description Herein, we reported a case of mixed pulmonary infection secondary to glucocorticoid use. Rare pathogens such as Nocardia nova, Mycobacterium tuberculosis, Aspergillus fumigatus, and cytomegalovirus were detected by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and lung puncture tissue. Combining the results of conventional pathogen detection and clinical symptoms, the patient was diagnosed with mixed pulmonary infection by multiple pathogens. After timely targeted medication, the patient was finally discharged with a good prognosis. Conclusion To our knowledge, this is the first case report on mixed pulmonary infection with pathogens including Nocardia nova, Mycobacterium tuberculosis, Aspergillus fumigatus, and human cytomegalovirus. As a new clinical diagnostic method, mNGS has great advantages in diagnosis of diseases such as mixed infections.
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Affiliation(s)
- Haiming Yan
- Department of Infectious Diseases, The First People's Hospital of Foshan, Foshan, China
| | - Zhandong Li
- Department of Infectious Diseases, The First People's Hospital of Foshan, Foshan, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Qixin Li
- Department of Laboratory, The First People's Hospital of Foshan, Foshan, China,Qixin Li
| | - Honglian Bai
- Department of Infectious Diseases, The First People's Hospital of Foshan, Foshan, China,*Correspondence: Honglian Bai
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14
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Zhang L, Chen T, Wang Y, Zhang S, Lv Q, Kong D, Jiang H, Zheng Y, Ren Y, Huang W, Liu P, Jiang Y. Comparison Analysis of Different DNA Extraction Methods on Suitability for Long-Read Metagenomic Nanopore Sequencing. Front Cell Infect Microbiol 2022; 12:919903. [PMID: 35837476 PMCID: PMC9273838 DOI: 10.3389/fcimb.2022.919903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is a novel useful strategy that is increasingly used for pathogens detection in clinic. Some emerging mNGS technologies with long-read ability are useful to decrease sequencing time and increase diagnosed accuracy, which is of great significance in rapid pathogen diagnosis. Reliable DNA extraction is considered critical for the success of sequencing; hence, there is thus an urgent need of gentle DNA extraction method to get unbiased and more integrate DNA from all kinds of pathogens. In this study, we systematically compared three DNA extraction methods (enzymatic cell lysis based on MetaPolyzyme, mechanical cell lysis based on bead beating, and the control method without pre-cell lysis, respectively) by assessing DNA yield, integrity, and the microbial diversity based on long-read nanopore sequencing of urine samples with microbial infections. Compared with the control method, the enzymatic-based method increased the average length of microbial reads by a median of 2.1-fold [Inter Quartile Range (IQR), 1.7-2.5; maximum, 4.8) in 18 of the 20 samples and the mapped reads proportion of specific species by a median of 11.8-fold (Inter Quartile Range (IQR), 6.9-32.2; maximum, 79.27]. Moreover, it provided fully (20 of 20) consistent diagnosed results to the clinical culture and more representative microbial profiles (P < 0.05), which all strongly proves the excellent performance of enzymatic-based method in long-read mNGS-based pathogen identification and potential diseases diagnosis of microbiome related.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ting Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
- The Fifth Medical Center of PLA General Hospital, The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Ye Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Shengwei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
- Department of Clinical Laboratory, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuhao Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
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15
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Du Y, Zhang Z, Chen C, Xia H, Zhang H, Guo Z, Wang Y. Case Report: Report of Infective Endocarditis Caused by Abiotrophia defectiva and Literature Review. Front Pediatr 2022; 10:894049. [PMID: 35874573 PMCID: PMC9299070 DOI: 10.3389/fped.2022.894049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE To report the clinical features of the first child with infective endocarditis (IE) caused by Abiotrophia defectiva in mainland China and to raise awareness of the disease. METHODS The clinical data of a child with IE caused by A. defectiva admitted to Xi'an Children's Hospital in July 2021 were collected, and the relevant literature was reviewed. RESULTS The child was a female, 8 years old, admitted with fever for 4 days and right-sided limb weakness for 3 days. The illness started with suppurative tonsillitis, followed by headache, fatigue, right-sided mouth, slurred speech, right limb weakness, and unstable holding. Transthoracic echocardiography showed that the mitral valve vegetation was formed and vegetation could also be seen at the entrance of the pulmonary vein at the posterior wall of the left atrium. Cranial contrast-enhanced MRI + magnetic resonance angiography showed multiple intracranial pseudoaneurysm formation and pontine infarction. After A. defectiva was detected by metagenomic next-generation sequencing (mNGS) in cerebrospinal fluid and blood detected, the infection was controlled by anti-infective treatment with meropenem and vancomycin. On the 36th day after admission, due to severe headache and slurred speech, the head CT showed hemorrhage of right parietal pseudoaneurysm and cerebral sickle hernia, and right temporo-occipital hematoma evacuation, cerebrovascular malformation resection, and cranial decompression were performed immediately. After the surgery, her speech ability gradually recovered, the muscle strength of her left upper limb was about grade III, while the muscle strength of the rest of the limbs was normal. After a total of 60 days of hospitalization, her family requested to be discharged. CONCLUSION This pediatric patient is the first case of childhood IE caused by A. defectiva in mainland China, and the first time in the world that A. defectiva was detected by mNGS in patients with IE.
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Affiliation(s)
- Yanqiang Du
- Department of Pediatric Intensive Care Unit of Xi'an Children's Hospital, National Children's Regional Medical Center (Northwest), Children's Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Zhan Zhang
- Department of Ultrasound of Xi'an Children's Hospital, National Children's Regional Medical Center (Northwest), Children's Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Chao Chen
- Imaging Department of Xi'an Children's Hospital, National Children's Regional Medical Center (Northwest), Children's Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Han Xia
- Hugobiotech Co., Ltd., Beijing, China
| | - Hua Zhang
- Department of Pediatric Intensive Care Unit of Xi'an Children's Hospital, National Children's Regional Medical Center (Northwest), Children's Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Zhangyan Guo
- Department of Pediatric Intensive Care Unit of Xi'an Children's Hospital, National Children's Regional Medical Center (Northwest), Children's Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yi Wang
- Department of Pediatric Intensive Care Unit of Xi'an Children's Hospital, National Children's Regional Medical Center (Northwest), Children's Hospital, Xi'an Jiaotong University, Xi'an, China
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16
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Kiguli S, Olopot-Olupot P, Alaroker F, Engoru C, Opoka RO, Tagoola A, Hamaluba M, Mnjalla H, Mpoya A, Mogaka C, Nalwanga D, Nabawanuka E, Nokes J, Nyaigoti C, Briend A, van Woensel JBM, Grieve R, Sadique Z, Williams TN, Thomas K, Harrison DA, Rowan K, Maitland K. Children's Oxygen Administration Strategies And Nutrition Trial (COAST-Nutrition): a protocol for a phase II randomised controlled trial. Wellcome Open Res 2021; 6:221. [PMID: 34734123 PMCID: PMC8529399 DOI: 10.12688/wellcomeopenres.17123.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
Background: To prevent poor long-term outcomes (deaths and readmissions) the integrated global action plan for pneumonia and diarrhoea recommends under the 'Treat' element of Protect, Prevent and Treat interventions the importance of continued feeding but gives no specific recommendations for nutritional support. Early nutritional support has been practiced in a wide variety of critically ill patients to provide vital cell substrates, antioxidants, vitamins, and minerals essential for normal cell function and decreasing hypermetabolism. We hypothesise that the excess post-discharge mortality associated with pneumonia may relate to the catabolic response and muscle wasting induced by severe infection and inadequacy of the diet to aid recovery. We suggest that providing additional energy-rich, protein, fat and micronutrient ready-to-use therapeutic feeds (RUTF) to help meet additional nutritional requirements may improve outcome. Methods: COAST-Nutrition is an open, multicentre, Phase II randomised controlled trial in children aged 6 months to 12 years hospitalised with suspected severe pneumonia (and hypoxaemia, SpO 2 <92%) to establish whether supplementary feeds with RUTF given in addition to usual diet for 56-days (experimental) improves outcomes at 90-days compared to usual diet alone (control). Primary endpoint is change in mid-upper arm circumference (MUAC) at 90 days and/or as a composite with 90-day mortality. Secondary outcomes include anthropometric status, mortality, readmission at days 28 and 180. The trial will be conducted in four sites in two countries (Uganda and Kenya) enrolling 840 children followed up to 180 days. Ancillary studies include cost-economic analysis, molecular characterisation of bacterial and viral pathogens, evaluation of putative biomarkers of pneumonia, assessment of muscle and fat mass and host genetic studies. Discussion: This study is the first step in providing an option for nutritional support following severe pneumonia and will help in the design of a large Phase III trial. Registration: ISRCTN10829073 (6 th June 2018) PACTR202106635355751 (2 nd June 2021).
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Affiliation(s)
- Sarah Kiguli
- Paediatrics, Makerere University, Kampala, Uganda
| | | | | | - Charles Engoru
- Paediatrics, Soroti Regional Referral Hospital, Soroti, Uganda
| | | | - Abner Tagoola
- Paediatrics, Jinja Regional Referral Hospital, Jinja, Uganda
| | - Mainga Hamaluba
- Paediatrics, Kilifi County Hospital, Kilifi, Kilifi, POBox230, Kenya
| | - Hellen Mnjalla
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
| | - Ayub Mpoya
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
| | - Christabel Mogaka
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
| | | | | | - James Nokes
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
| | - Charles Nyaigoti
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
| | - André Briend
- School of Medicine, University of Tampere, Tampere, Finland
| | - Job B. M. van Woensel
- Paediatric Intensive Care Unit, Emma Children’s Hospital and Academic Medical Center, Amsterdam, The Netherlands
| | - Richard Grieve
- Centre for Statistical Methodology, London School of Hygiene & Tropical Medicine, London, UK
| | - Zia Sadique
- Centre for Statistical Methodology, London School of Hygiene & Tropical Medicine, London, UK
| | - Thomas N. Williams
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
- Department of Infectious Disease and Institute of Global Health and Innovation, Imperial College London, London, UK
| | - Karen Thomas
- Intensive Care National Audit, London, WC1V 6AZ, UK
| | | | | | - Kathryn Maitland
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
- Department of Infectious Disease and Institute of Global Health and Innovation, Imperial College London, London, UK
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17
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Kiguli S, Olopot-Olupot P, Alaroker F, Engoru C, Opoka RO, Tagoola A, Hamaluba M, Mnjalla H, Mpoya A, Mogaka C, Nalwanga D, Nabawanuka E, Nokes J, Nyaigoti C, Briend A, van Woensel JBM, Grieve R, Sadique Z, Williams TN, Thomas K, Harrison DA, Rowan K, Maitland K. Children's Oxygen Administration Strategies And Nutrition Trial (COAST-Nutrition): a protocol for a phase II randomised controlled trial. Wellcome Open Res 2021; 6:221. [PMID: 34734123 PMCID: PMC8529399 DOI: 10.12688/wellcomeopenres.17123.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2021] [Indexed: 09/22/2023] Open
Abstract
Background: To prevent poor long-term outcomes (deaths and readmissions) the integrated global action plan for pneumonia and diarrhoea recommends under the 'Treat' element of Protect, Prevent and Treat interventions the importance of continued feeding but gives no specific recommendations for nutritional support. Early nutritional support has been practiced in a wide variety of critically ill patients to provide vital cell substrates, antioxidants, vitamins, and minerals essential for normal cell function and decreasing hypermetabolism. We hypothesise that the excess post-discharge mortality associated with pneumonia may relate to the catabolic response and muscle wasting induced by severe infection and inadequacy of the diet to aid recovery. We suggest that providing additional energy-rich, protein, fat and micronutrient ready-to-use therapeutic feeds (RUTF) to help meet additional nutritional requirements may improve outcome. Methods: COAST-Nutrition is an open, multicentre, Phase II randomised controlled trial in children aged 6 months to 12 years hospitalised with suspected severe pneumonia (and hypoxaemia, SpO 2 <92%) to establish whether supplementary feeds with RUTF given in addition to usual diet for 56-days (experimental) improves outcomes at 90-days compared to usual diet alone (control). Primary endpoint is change in mid-upper arm circumference (MUAC) at 90 days and/or as a composite with 90-day mortality. Secondary outcomes include anthropometric status, mortality, readmission at days 28 and 180. The trial will be conducted in four sites in two countries (Uganda and Kenya) enrolling 840 children followed up to 180 days. Ancillary studies include cost-economic analysis, molecular characterisation of bacterial and viral pathogens, evaluation of putative biomarkers of pneumonia, assessment of muscle and fat mass and host genetic studies. Discussion: This study is the first step in providing an option for nutritional support following severe pneumonia and will help in the design of a large Phase III trial. Registration: ISRCTN10829073 (6 th June 2018) PACTR202106635355751 (2 nd June 2021).
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Affiliation(s)
- Sarah Kiguli
- Paediatrics, Makerere University, Kampala, Uganda
| | | | | | - Charles Engoru
- Paediatrics, Soroti Regional Referral Hospital, Soroti, Uganda
| | | | - Abner Tagoola
- Paediatrics, Jinja Regional Referral Hospital, Jinja, Uganda
| | - Mainga Hamaluba
- Paediatrics, Kilifi County Hospital, Kilifi, Kilifi, POBox230, Kenya
| | - Hellen Mnjalla
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
| | - Ayub Mpoya
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
| | - Christabel Mogaka
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
| | | | | | - James Nokes
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
| | - Charles Nyaigoti
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
| | - André Briend
- School of Medicine, University of Tampere, Tampere, Finland
| | - Job B. M. van Woensel
- Paediatric Intensive Care Unit, Emma Children’s Hospital and Academic Medical Center, Amsterdam, The Netherlands
| | - Richard Grieve
- Centre for Statistical Methodology, London School of Hygiene & Tropical Medicine, London, UK
| | - Zia Sadique
- Centre for Statistical Methodology, London School of Hygiene & Tropical Medicine, London, UK
| | - Thomas N. Williams
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
- Department of Infectious Disease and Institute of Global Health and Innovation, Imperial College London, London, UK
| | - Karen Thomas
- Intensive Care National Audit, London, WC1V 6AZ, UK
| | | | | | - Kathryn Maitland
- KEMRI Wellcome TRust Research Programme, Kilifi, Kilifi, POBox230, Kenya
- Department of Infectious Disease and Institute of Global Health and Innovation, Imperial College London, London, UK
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18
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He R, Wang Q, Wang J, Tang J, Shen H, Zhang X. Better choice of the type of specimen used for untargeted metagenomic sequencing in the diagnosis of periprosthetic joint infections. Bone Joint J 2021; 103-B:923-930. [PMID: 33934659 DOI: 10.1302/0301-620x.103b5.bjj-2020-0745.r1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AIMS As a proven and comprehensive molecular technique, metagenomic next-generation sequencing (mNGS) has shown its potential in the diagnosis of pathogens in patients with periprosthetic joint infection (PJI), using a single type of specimen. However, the optimal use of mNGS in the management of PJI has not been explored. In this study, we evaluated the diagnostic value of mNGS using three types of specimen with the aim of achieving a better choice of specimen for mNGS in these patients. METHODS In this prospective study, 177 specimens were collected from 59 revision arthroplasties, including periprosthetic tissues, synovial fluid, and prosthetic sonicate fluid. Each specimen was divided into two, one for mNGS and one for culture. The criteria of the Musculoskeletal Infection Society were used to define PJI (40 cases) and aseptic failure (19 cases). RESULTS The sensitivity and specificity of mNGS in the diagnosis of PJI were 95% and 94.7%, respectively, for all types of specimen. The sensitivity and specificity were 65% and 100%, respectively, for periprosthetic tissues, 87.5% and 94.7%, respectively, for synovial fluid, and 92.5% and 94.7%, respectively, for prosthetic sonicate fluid. The mNGS of prosthetic sonicate fluid outperformed that for other types of specimen in the rates of detection of pathogens (84.6%), sequencing reads (> ten-fold) and the rate of genome coverage (> five-fold). CONCLUSION mNGS could serve as an accurate diagnostic tool in the detection of pathogens in patients with a PJI using three types of specimen. Due to its superior perfomance in identifying a pathogen, mNGS of prosthetic sonicate fluid provides the most value and may partly replace traditional tests such as bacteriological culture in these patients. Cite this article: Bone Joint J 2021;103-B(5):923-930.
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Affiliation(s)
- Renke He
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qiaojie Wang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Wang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Tang
- Clinical Laboratory, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Hao Shen
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xianlong Zhang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
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Zhou Y, Chen E, Wu X, Hu Y, Ge H, Xu P, Zou Y, Jin J, Wang P, Ying K. Rational lung tissue and animal models for rapid breath tests to determine pneumonia and pathogens. Am J Transl Res 2017; 9:5116-5126. [PMID: 29218109 PMCID: PMC5714795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 10/16/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVE This study works to develop novel models that may be adopted for earlier non-invasive breathomics tests to determine pneumonia pathogens. METHODS Two types of pneumonia models were created, both in vitro and in vivo. Paraneoplasm lung tissue and specific pathogen-free (SPF) rabbits were adopted and separately challenged with sterile saline solution control or three pathogens: Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. After inoculation, headspace air or exhaled air were absorbed by solid phase micro-extraction (SPME) fibers and subsequently analyzed with gas chromatograph Mass Spectrometer (GCMS). RESULTS Pneumonia and pathogen-specific discriminating VOC patterns (1H-Pyrrole-3-carbonitrile, Diethyl phthalate, Cedrol, Decanoic acid, Cyclohexane, Diisooctyl phthalate) were determined. CONCLUSION Our study successfully generated nosocomial pneumonia models for pneumonia diagnosis and pathogen-discriminating breath tests. The tests may allow for earlier pneumonia and pathogen diagnoses, and may transfer empirical therapy to targeted therapy earlier, thus improving clinical outcomes.
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Affiliation(s)
- Yong Zhou
- Respiratory Department, Sir Run Run Shaw Hospital, Medical School, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Enguo Chen
- Respiratory Department, Sir Run Run Shaw Hospital, Medical School, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Xiaohong Wu
- Respiratory Department, Sir Run Run Shaw Hospital, Medical School, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Yanjie Hu
- Respiratory Department, Sir Run Run Shaw Hospital, Medical School, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Huiqing Ge
- Respiratory Therapy Department, Sir Run Run Shaw Hospital, Medical School, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Peifeng Xu
- Respiratory Therapy Department, Sir Run Run Shaw Hospital, Medical School, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Yingchang Zou
- Biosensor National Special Lab, Key Lab for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Joy Jin
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California San FranciscoUSA
| | - Ping Wang
- Biosensor National Special Lab, Key Lab for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Kejing Ying
- Respiratory Department, Sir Run Run Shaw Hospital, Medical School, Zhejiang UniversityHangzhou, Zhejiang, China
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