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Yin S, Liu Y, Yang X, Lubanga N, Tai P, Xiong M, Fan B, Yang X, Nie Z, Zhang Q, He B. Rapid visual detection of Helicobacter pylori and vacA subtypes by Dual-Target RAA-LFD assay. Clin Chim Acta 2025; 564:119927. [PMID: 39153656 DOI: 10.1016/j.cca.2024.119927] [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: 05/28/2024] [Revised: 07/27/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
BACKGROUND Helicobacter pylori (H. pylori) infects over 50% of the global population and is a significant risk factor for gastric cancer. The pathogenicity of H. pylori is primarily attributed to virulence factors such as vacA. Timely and accurate identification, along with genotyping of H. pylori virulence genes, are essential for effective clinical management and controlling its prevalence. METHODS In this study, we developed a dual-target RAA-LFD assay for the rapid, visual detection of H. pylori genes (16s rRNA, ureA, vacA m1/m2), using recombinase aided amplification (RAA) combined with lateral flow dipstick (LFD) methods. Both 16s rRNA and ureA were selected as identification genes to ensure reliable detection accuracy. RESULTS A RAA-LFD assay was developed to achieve dual-target amplification at a stable 37 °C within 20 min, followed by visualization using the lateral flow dipstick (LFD). The whole process, from amplification to results, took less than 30 min. The 95 % limit of detection (LOD) for 16 s rRNA and ureA, vacA m1, vacA m2 were determined as 3.8 × 10-2 ng/μL, 5.8 × 10-2 ng/μL and 1.4 × 10-2 ng/μL, respectively. No cross-reaction was observed in the detection of common pathogens including Escherichia coli, Klebsiella pneumoniae, Enterococcus faecalis, Staphylococcus aureus, Pseudomonas aeruginosa, and Bacillus subtilis, showing the assay's high specificity. In the evaluation of the clinical performance of the RAA-LFD assay. A total of 44 gastric juice samples were analyzed, immunofluorescence staining (IFS) and quantitative polymerase chain reaction (qPCR) were used as reference methods. The RAA-LFD results for the 16s rRNA and ureA genes showed complete agreement with qPCR findings, accurately identifying H. pylori infection as confirmed by IFS in 10 out of the 44 patients. Furthermore, the assay successfully genotyped vacA m1/m2 among the positive samples, showing complete agreement with qPCR results and achieving a kappa (κ) value of 1.00. CONCLUSION The dual-target RAA-LFD assay developed in this study provides a rapid and reliable method for detecting and genotyping H. pylori within 30 min, minimizing dependency on sophisticated laboratory equipment and specialized personnel. Clinical validation confirms its efficacy as a promising tool for effectively control of its prevalence and aiding in the precise treatment of H. pylori-associated diseases.
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Affiliation(s)
- Sijie Yin
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, China; Department of Laboratory Medicine, Yangzhou HongquanHospital, Yangzhou, China
| | - Yanghe Liu
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, China; Department of Laboratory Medicine, Nanjing Jiangning Hospital of Chinese Medicine, Nanjing, China
| | - Xinyi Yang
- Nanjing Jinling High School Hexi Campus, Nanjing, China
| | - Nasifu Lubanga
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, China
| | - Ping Tai
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, China
| | - Mengqiu Xiong
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, China
| | - Boyue Fan
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, China
| | - Xincheng Yang
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, China
| | - Zhenlin Nie
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, China.
| | - Qingsong Zhang
- Department of Clinical Laboratory, Xuancheng Central Hospital, Xuancheng, China.
| | - Bangshun He
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, China; H. pylori Research Key Laboratory, Nanjing Medical University, Nanjing, China.
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Zhang W, Liu F, Liang E, Zhang L. Evolution of Treatment Modalities for Disseminated HAdV Infection in Neonates. Pediatrics 2024; 154:e2024066677. [PMID: 39238444 DOI: 10.1542/peds.2024-066677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/24/2024] [Accepted: 07/24/2024] [Indexed: 09/07/2024] Open
Abstract
Human adenovirus (HAdV) infection in newborns is a rare condition that typically affects multiple organ systems and has a high mortality rate. We report a case of neonatal HAdV-D37 infection that presented with fever and respiratory distress that was confirmed by metagenomic next-generation sequencing using blood and bronchoalveolar lavage fluid. We treated the patient with intravenous immunoglobulin, methylprednisolone, and anticoagulants, and the patient recovered. Our review of 41 cases of HAdV found that treatment with intravenous immunoglobin might have improved the outcome of HAdV-D infection. We further suggest that glucocorticoid therapy may have additional therapeutic validity in the setting of severe or disseminated disease and that monitoring coagulation function and timely anticoagulation treatment should be considered to prevent complications associated with disseminated intravascular coagulation.
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Affiliation(s)
- Wenjing Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Fang Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Enlin Liang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Li Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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3
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Buddle S, Forrest L, Akinsuyi N, Martin Bernal LM, Brooks T, Venturini C, Miller C, Brown JR, Storey N, Atkinson L, Best T, Roy S, Goldsworthy S, Castellano S, Simmonds P, Harvala H, Golubchik T, Williams R, Breuer J, Morfopoulou S, Torres Montaguth OE. Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses. Genome Med 2024; 16:111. [PMID: 39252069 PMCID: PMC11382446 DOI: 10.1186/s13073-024-01380-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: 04/16/2024] [Accepted: 08/30/2024] [Indexed: 09/11/2024] Open
Abstract
BACKGROUND Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, high sequencing depth requirements, long turnaround times, and limited sensitivity hinder broader adoption. We investigated whether we could overcome these limitations using protocols based on untargeted sequencing with Oxford Nanopore Technologies (ONT), which offers real-time data acquisition and analysis, or a targeted panel approach, which allows the selective sequencing of known pathogens and could improve sensitivity. METHODS We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Bioscience Comprehensive Viral Research Panel (CVRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers. RESULTS Capture with the Twist CVRP increased sensitivity by at least 10-100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT had good sensitivity at high viral loads (60,000 gc/ml), at lower viral loads (600-6000 gc/ml), longer and more costly sequencing runs would be required to achieve sensitivities comparable to the untargeted Illumina protocol. Untargeted ONT provided better specificity than untargeted Illumina sequencing. However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the CVRP and ONT. CONCLUSIONS Metagenomics has the potential to become standard-of-care in diagnostics and is a powerful tool for the discovery of emerging pathogens. Untargeted Illumina and ONT metagenomics and capture with the Twist CVRP have different advantages with respect to sensitivity, specificity, turnaround time and cost, and the optimal method will depend on the clinical context.
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Affiliation(s)
- Sarah Buddle
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Leysa Forrest
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Naomi Akinsuyi
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Luz Marina Martin Bernal
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Tony Brooks
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Cristina Venturini
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Charles Miller
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Julianne R Brown
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Nathaniel Storey
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Laura Atkinson
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Timothy Best
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sunando Roy
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sian Goldsworthy
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sergi Castellano
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heli Harvala
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Division of Infection and Immunity, University College London, London, UK
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
| | - Tanya Golubchik
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Sydney Infectious Diseases Institute, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Rachel Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Judith Breuer
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Sofia Morfopoulou
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK.
| | - Oscar Enrique Torres Montaguth
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
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Qin Y, Zou X, Jin Y, Li J, Cai Q. Cryptococcus Neoformans Osteomyelitis of the Right Ankle Diagnosed by Metagenomic Next-Generation Sequencing in a HIV-Negative Patient with Tuberculous Lymphadenitis and Pulmonary Tuberculosis: A Case Report and Recent Literature Review. Infect Drug Resist 2024; 17:3805-3812. [PMID: 39253606 PMCID: PMC11381933 DOI: 10.2147/idr.s476270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/09/2024] [Indexed: 09/11/2024] Open
Abstract
Aim Cryptococcus neoformans osteomyelitis coupled with tuberculosis and tuberculous lymphadenitis, is a rare occurrence in clinical. Diagnostic challenges arise due to the clinical radiological similarity of this condition to other lung infections and the limited and sensitive nature of traditional approaches. Here, we present a case of co-infection diagnosed using Metagenomic Next-Generation Sequencing, highlighting the effectiveness of advanced genomic techniques in such complex scenarios. Case Presentation We present a case of a 67-year-old female infected with cryptococcal osteomyelitis and presented with swelling and pain in the right ankle. Following a biopsy of the right ankle joint, Metagenomic Next-Generation Sequencing (mNGS) of the biopsy tissue revealed Cryptococcus neoformans infection. Positive results for Cryptococcus capsular antigen and pathological findings confirmed the presence of Cryptococcus neoformans. The patient underwent surgical debridement, coupled with oral fluconazole treatment (300mg/day), leading to the resolution of symptoms. Conclusion Cryptococcus neoformans is an uncommon cause of ankle infection. Metagenomic Next-Generation Sequencing (mNGS) serves as a valuable diagnostic tool, aiding clinicians in differentiating cryptococcal osteomyelitis from other atypical infections.
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Affiliation(s)
- Yao Qin
- Department of Tuberculosis, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
| | - Xingwu Zou
- Department of Tuberculosis, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
| | - Yanghui Jin
- Department of Orthopaedic, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
| | - Jinmeng Li
- Department of Pharmacy, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
| | - Qingshan Cai
- Department of Tuberculosis, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
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5
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Hu W, Li X, Guo W, Shangguan Y, Xia J, Feng X, Sheng C, Ji Z, Ding C, Xu K. The Utility of Real-Time PCR, Metagenomic Next-Generation Sequencing, and Culture in Bronchoalveolar Lavage Fluid for Diagnosis of Pulmonary Aspergillosis. J Mol Diagn 2024; 26:832-842. [PMID: 38972592 DOI: 10.1016/j.jmoldx.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/31/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024] Open
Abstract
Timely detection of Aspergillus infection is crucial given the high mortality rate of pulmonary aspergillosis (PA). Here, the diagnostic performances for PA of mycological culture, Aspergillus real-time PCR, and metagenomic next-generation sequencing (mNGS) assay from bronchoalveolar lavage fluid, were evaluated. In total, 139 patients with suspected fungal pneumonia were enrolled between December 2021 and July 2023, collecting 139 bronchoalveolar lavage fluid samples for real-time PCR and culture, with 87 undergoing mNGS assay. The sensitivity, specificity, positive predictive value, negative predictive value, and area under the curve with 95% CIs of these assays for PA were as follows: 35.3% (14.2%-61.7%), 100.0% (94.0%-100.0%), 100.0% (54.1%-100.0%), 84.5% (79.3%-88.6%), and 0.676 (0.560-0.779), respectively, for culture; 82.4% (56.6%-96.2%), 98.3% (91.1%-100.0%), 93.3% (66.4%-99.0%), 95.2% (87.6%-98.2%), and 0.903 (0.815-0.959), respectively, for same diagnostic performance of real-time PCR and mNGS; and 94.1% (71.3%-99.9%), 96.7% (88.5%-99.6%), 88.9% (67.1%-96.9%), 98.3% (89.6%-99.7%), and 0.954 (0.880-0.989), respectively, for real-time PCR combining mNGS; real-time PCR, mNGS, and their combination significantly improved in area under the curve values over culture (P < 0.001), but real-time PCR testing and mNGS had no significant difference with each other and their combination. Overall, the performance of culture was limited by low sensitivity; both real-time PCR and mNGS assays as single diagnostic tests are promising compared with culture and combined tests.
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Affiliation(s)
- Wenjuan Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Xiaomeng Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Wanru Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Yanwan Shangguan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Jiafeng Xia
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Xuewen Feng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Chengmin Sheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Zhongkang Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Cheng Ding
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Kaijin Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China.
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6
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Kim S, Kim N, Park WB, Kang CK, Park JH, Lee ST, Jung KH, Park KI, Lee SK, Moon J, Chu K. Real-time application of ITS and D1-D3 nanopore amplicon metagenomic sequencing in fungal infections: Enhancing fungal infection diagnostics. Int J Med Microbiol 2024; 316:151630. [PMID: 39029415 DOI: 10.1016/j.ijmm.2024.151630] [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: 03/20/2024] [Revised: 05/28/2024] [Accepted: 07/09/2024] [Indexed: 07/21/2024] Open
Abstract
While fungal infections cause considerable morbidity and mortality, the performance of the current diagnostic tests for fungal infection is low. Even though fungal metagenomics or targeted next-generation sequencing have been investigated for various clinical samples, the real-time clinical utility of these methods still needs to be elucidated. In this study, we used internal transcribed spacer (ITS) and D1-D3 ribosomal DNA nanopore amplicon metagenomic sequencing to assess its utility in patients with fungal infections. Eighty-four samples from seventy-three patients were included and categorized into 'Fungal infection,' 'Fungal colonization,' and 'Fungal contamination' groups based on the judgement of infectious disease specialists. In the 'Fungal infection' group, forty-seven initial samples were obtained from forty-seven patients. Three fungal cases detected not by the sequencing but by conventional fungal assays were excluded from the analysis. In the remaining cases, the conventional fungal assay-negative/sequencing-positive group (n=11) and conventional fungal assay-positive/sequencing-positive group (n=33) were compared. Non-Candida and non-Aspergillus fungi infections were more frequent in the conventional-negative/sequencing-positive group (p-value = 0.031). We demonstrated the presence of rare human pathogens, such as Trichosporon asahii and Phycomyces blakesleeanus. In the 'Fungal infection' group and 'Fungal colonization' group, sequencing was faster than culturing (mean difference = 4.92 days, p-value < 0.001/ mean difference = 4.67, p-value <0.001). Compared to the conventional diagnostic methods including culture, nanopore amplicon sequencing showed a shorter turnaround time and a higher detection rate for uncommon fungal pathogens.
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Affiliation(s)
- Seondeuk Kim
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Narae Kim
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Soon-Tae Lee
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Keun-Hwa Jung
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung-Il Park
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Neurology, Seoul National University Hospital Healthcare System Gangnam Center, 152, Teheran-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Sang Kun Lee
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jangsup Moon
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Kon Chu
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
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7
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Su LD, Chiu CY, Gaston D, Hogan CA, Miller S, Simon DW, Thakur KT, Yang S, Piantadosi A. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Central Nervous System Infections: Advances and Challenges. Mol Diagn Ther 2024; 28:513-523. [PMID: 38992308 DOI: 10.1007/s40291-024-00727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 07/13/2024]
Abstract
Central nervous system (CNS) infections carry a substantial burden of morbidity and mortality worldwide, and accurate and timely diagnosis is required to optimize management. Metagenomic next-generation sequencing (mNGS) has proven to be a valuable tool in detecting pathogens in patients with suspected CNS infection. By sequencing microbial nucleic acids present in a patient's cerebrospinal fluid, brain tissue, or samples collected outside of the CNS, such as plasma, mNGS can detect a wide range of pathogens, including rare, unexpected, and/or fastidious organisms. Furthermore, its target-agnostic approach allows for the identification of both known and novel pathogens. This is particularly useful in cases where conventional diagnostic methods fail to provide an answer. In addition, mNGS can detect multiple microorganisms simultaneously, which is crucial in cases of mixed infections without a clear predominant pathogen. Overall, clinical mNGS testing can help expedite the diagnostic process for CNS infections, guide appropriate management decisions, and ultimately improve clinical outcomes. However, there are key challenges surrounding its use that need to be considered to fully leverage its clinical impact. For example, only a few specialized laboratories offer clinical mNGS due to the complexity of both the laboratory methods and analysis pipelines. Clinicians interpreting mNGS results must be aware of both false negatives-as mNGS is a direct detection modality and requires a sufficient amount of microbial nucleic acid to be present in the sample tested-and false positives-as mNGS detects environmental microbes and their nucleic acids, despite best practices to minimize contamination. Additionally, current costs and turnaround times limit broader implementation of clinical mNGS. Finally, there is uncertainty regarding the best practices for clinical utilization of mNGS, and further work is needed to define the optimal patient population(s), syndrome(s), and time of testing to implement clinical mNGS.
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Affiliation(s)
- LingHui David Su
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
| | - Charles Y Chiu
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Laboratory Medicine and Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - David Gaston
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Catherine A Hogan
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steve Miller
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Delve Bio, Inc., San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Dennis W Simon
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pediatric Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kiran T Thakur
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Neurology, Columbia University Irving Medical Center-New York Presbyterian Hospital, New York, NY, USA
| | - Shangxin Yang
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anne Piantadosi
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA.
- Department of Pathology and Laboratory Medicine, and Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 101 Woodruff Circle, Atlanta, GA, USA.
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8
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Yin Y, Zhu P, Guo Y, Li Y, Chen H, Liu J, Sun L, Ma S, Hu C, Wang H. Enhancing lower respiratory tract infection diagnosis: implementation and clinical assessment of multiplex PCR-based and hybrid capture-based targeted next-generation sequencing. EBioMedicine 2024; 107:105307. [PMID: 39226681 PMCID: PMC11403251 DOI: 10.1016/j.ebiom.2024.105307] [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: 04/13/2024] [Revised: 08/09/2024] [Accepted: 08/11/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Shotgun metagenomic next-generation sequencing (mNGS) is widely used to detect pathogens in bronchoalveolar lavage fluid (BALF). However, mNGS is complex and expensive. This study explored the feasibility of targeted next-generation sequencing (tNGS) in distinguishing lower respiratory tract infections in clinical practice. METHODS We used 229 retrospective BALF samples to establish thresholds and diagnostic values in a prospective cohort of 251 patients. After target pathogen selection, primer and probe design, optimization experiments, and bioinformatics analysis, multiplex PCR-based tNGS (mp-tNGS) and hybrid capture-based tNGS (hc-tNGS), targeting 198 and 3060 pathogens (DNA and RNA co-detection workflow) were established and performed. FINDINGS mp-tNGS and hc-tNGS took 10.3 and 16 h, respectively, with low sequencing data sizes of 0.1 M and 1 M reads, and test costs reduced to a quarter and half of mNGS. The LoDs of mp-tNGS and hc-tNGS were 50-450 CFU/mL. mp-tNGS and hc-tNGS were highly accurate, with 86.5% and 87.3% (vs. 85.5% for mNGS) sensitivities and 90.0% and 88.0% (vs. 92.1% for mNGS) specificities. tNGS detection rates for casual pathogens were 84.3% and 89.5% (vs. 88.5% for mNGS), significantly higher than conventional microbiological tests (P < 0.001). In seven samples, tNGS detected Pneumocystis jirovecii, a fungus not detected by mNGS. Whereas mNGS detected six samples with filamentous fungi (Rhizopus oryzae, Aureobasidium pullulans, Aspergillus niger complex, etc.) which missed by tNGS. The anaerobic bacteria as pathogen in eight samples was failed to detect by mp-tNGS. INTERPRETATION tNGS may offer a new, broad-spectrum, rapid, accurate and cost-effective approach to diagnosing respiratory infections. FUNDING National Natural Science Foundation of China (81625014 and 82202535).
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Affiliation(s)
- Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Pengyuan Zhu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, China
| | - Yifan Guo
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yingzhen Li
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Jun Liu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, China
| | - Lingxiao Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shuai Ma
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Chaohui Hu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, China.
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.
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Huang Z, Hu B, Li J, Feng M, Wang Z, Huang F, Xu H, Liu L, Shang W. Metagenomic versus targeted next-generation sequencing for detection of microorganisms in bronchoalveolar lavage fluid among renal transplantation recipients. Front Immunol 2024; 15:1443057. [PMID: 39253087 PMCID: PMC11381253 DOI: 10.3389/fimmu.2024.1443057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 08/01/2024] [Indexed: 09/11/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS), which provides untargeted and unbiased pathogens detection, has been extensively applied to improve diagnosis of pulmonary infection. This study aimed to compare the clinical performance between mNGS and targeted NGS (tNGS) for microbial detection and identification in bronchoalveolar lavage fluid (BALF) from kidney transplantation recipients (KTRs). Methods BALF samples with microbiological results from mNGS and conventional microbiological test (CMT) were included. For tNGS, samples were extracted, amplified by polymerase chain reaction with pathogen-specific primers, and sequenced on an Illumina Nextseq. Results A total of 99 BALF from 99 KTRs, among which 93 were diagnosed as pulmonary infection, were analyzed. Compared with CMT, both mNGS and tNGS showed higher positive rate and sensitivity (p<0.001) for overall, bacterial and fungal detection. Although the positive rate for mNGS and tNGS was comparable, mNGS significantly outperformed tNGS in sensitivity (100% vs. 93.55%, p<0.05), particularly for bacteria and virus (p<0.001). Moreover, the true positive rate for detected microbes of mNGS was superior over that of tNGS (73.97% vs. 63.15%, p<0.05), and the difference was also significant when specific for bacteria (94.59% vs. 64.81%, p<0.001) and fungi (93.85% vs. 72.58%, p<0.01). Additionally, we found that, unlike most microbes such as SARS-CoV-2, Aspergillus, and EBV, which were predominantly detected from recipients who underwent surgery over 3 years, Torque teno virus (TTV) were principally detected from recipients within 1-year post-transplant, and as post-transplantation time increased, the percentage of TTV positivity declined. Conclusion Although tNGS was inferior to mNGS owing to lower sensitivity and true positive rate in identifying respiratory pathogens among KTRs, both considerably outperformed CMT.
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Affiliation(s)
- Zhaoru Huang
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bingxue Hu
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, China
| | - Jinfeng Li
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Min Feng
- Surgical Intensive Care Unit, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Wang
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fengxiang Huang
- Respiratory Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huan Xu
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, China
| | - Lei Liu
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenjun Shang
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Zhang X, Ye J, Wang L, Zhang L, Wang L, Jin H. Nanopore Sequencing Technology: A Reliable Method for Pathogen Diagnosis in Elderly Patients with Community-Acquired Pneumonia. Infect Drug Resist 2024; 17:3659-3667. [PMID: 39205800 PMCID: PMC11352510 DOI: 10.2147/idr.s475861] [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: 04/27/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
Purpose Next-generation sequencing of the metagenome (mNGS) is gaining traction as a valuable tool for diagnosing infectious diseases. Compared to mNGS, pathogen detection based on Oxford Nanopore Technology further shortens the detection time. This study seeks to assess the efficacy of Nanopore sequencing in identifying pathogens associated with community-acquired pneumonia (CAP) among elderly individuals in China. Patients and Methods From January 2023 to June 2023, elderly patients with CAP were prospectively recruited from Hangzhou First People's Hospital. A comprehensive set of clinical data was gathered, and bronchoalveolar lavage (BAL) fluid samples were collected. Concurrently, pathogen identification was performed using conventional microbiological diagnostic methods, Illumina sequencing, and Nanopore sequencing, and the diagnostic efficacy of pathogen detection was compared. Results The study included a total of 29 patients. The diagnostic positivity rates of traditional microbiological detection, Illumina sequencing, and Nanopore sequencing were 24.1%, 51.7%, and 48.3%, respectively. Their diagnostic specificities were 91.7%, 50%, and 75%, respectively. Compared to traditional microbiological detection, both Nanopore and Illumina sequencing showed significantly increased sensitivity. However, Nanopore sequencing exhibited relatively better consistency with the final clinical comprehensive diagnosis, with a Kappa value of 0.574. This outperformed traditional microbiological detection and Illumina sequencing, which had a Kappa value of 0.296 and 0.402, respectively. In addition, Nanopore sequencing required the shortest turnaround time. Conclusion Nanopore sequencing technology demonstrates as a reliable and rapid method for detecting pathogens in elderly patients with CAP.
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Affiliation(s)
- Xiyue Zhang
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
| | - Jian Ye
- Department of Respiratory Medicine, Zhejiang Hospital, Hangzhou, People’s Republic of China
| | - Limin Wang
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
| | - Liuhai Zhang
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
| | - Liusheng Wang
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
| | - Hualiang Jin
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
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Wang S, Sun S, Wang Q, Chen H, Guo Y, Cai M, Yin Y, Ma S, Wang H. PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak alerting. Commun Biol 2024; 7:1038. [PMID: 39179660 PMCID: PMC11344050 DOI: 10.1038/s42003-024-06720-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024] Open
Abstract
Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain feature identification in CMg samples and CRKP traceability. A database targeting high-prevalence horizontal gene transfer in CRKP strains and a ST11-only database for distinguishing two sub-lineages in China were created. To make the database user-friendly, facilitate immediate downstream strain feature identification from raw Nanopore metagenomic data, and avoid the need for phylogenetic analysis from scratch, we developed data analysis methods. The methods included pre-performed phylogenetic analysis, gene-isolate-cluster index and multilevel pan-genome database and reduced storage space by 10-fold and random-access memory by 52-fold compared with normal methods. PathoTracker can provide accurate and fast strain-level analysis for CMg data after 1 h Nanopore sequencing, allowing early warning of outbreaks. A user-friendly page ( http://PathoTracker.pku.edu.cn/ ) was developed to facilitate online analysis, including strain-level feature, species identifications and phylogenetic analyses. PathoTracker proposed in this study will aid in the downstream analysis of CMg.
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Affiliation(s)
- Shuyi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Shijun Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Qi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yifan Guo
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Meng Cai
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shuai Ma
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China.
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12
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Yuan J, Wang L, Zhang W, Deng C, Li Q, Meng Y, Chen Y. Performance of metagenomic Next-Generation Sequencing and metagenomic Nanopore Sequencing for the diagnosis of tuberculosis in HIV-positive patients. Front Cell Infect Microbiol 2024; 14:1423541. [PMID: 39233907 PMCID: PMC11371759 DOI: 10.3389/fcimb.2024.1423541] [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: 04/26/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024] Open
Abstract
Background Patients who were infected by the Human Immunodeficiency Virus (HIV) could have weakened immunity that is complicated by opportunistic infections, especially for Mycobacterium tuberculosis (MTB). Notably, the HIV-MTB co-infection will accelerate the course of disease progress and greatly increase the mortality of patients. Since the traditional diagnostic methods are time-consuming and have low sensitivity, we aim to investigate the performance of mNGS (metagenomic Next-Generation Sequencing) and mNPS (metagenomic NanoPore Sequencing) for the rapid diagnosis of tuberculosis in HIV-infected patients. Methods The 122 HIV-infected patients were enrolled for the retrospective analysis. All of the patients underwent traditional microbiological tests, mNGS, and (or) mNPS tests. The clinical comprehensive diagnosis was used as the reference standard to compare the diagnostic performance of culture, mNGS, and mNPS on tuberculosis. We also investigate the diagnostic value of mNGS and mNPS on mixed-infection. Furthermore, the treatment adjustment directed by mNGS and mNPS was analyzed. Results Compared with the composite reference standard, the culture showed 42.6% clinical sensitivity and 100% specificity, and the OMT(other microbiological testing) had 38.9% sensitivity and 100% specificity. The mNGS had 58.6% clinical sensitivity and 96.8% specificity, and the mNPS had 68.0% clinical sensitivity and 100% specificity. The proportion of mixed-infection cases (88.9%) in the TB group was higher than those in the non-TB group (54.8%) and the mNGS and mNPS are more competitive on mixed-infection diagnosis compared with the traditional methods. Furthermore, there are 63 patients (69.2%) and 36 patients (63.2%) achieved effective treatment after receiving the detection of mNPS and mNGS, respectively. Conclusion Our study indicated that mNPS and mNGS have high sensitivity and specificity for TB diagnosis compared with the traditional methods, and mNPS seems to have better diagnostic performance than mNGS. Moreover, mNGS and mNPS showed apparent advantages in detecting mixed infection. The mNPS and mNGS-directed medication adjustment have effective treatment outcomes for HIV-infected patients who have lower immunity.
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Affiliation(s)
- Jing Yuan
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Lanchun Wang
- Medical Center, Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Hangzhou, China
| | - Wei Zhang
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Changgang Deng
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Qisui Li
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Yamin Meng
- Medical Center, Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Hangzhou, China
| | - Yaokai Chen
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
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Chen J, Qin Z, Jia Z. The application status of sequencing technology in global respiratory infectious disease diagnosis. Infection 2024:10.1007/s15010-024-02360-4. [PMID: 39152290 DOI: 10.1007/s15010-024-02360-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Next-generation sequencing (NGS) has revolutionized clinical microbiology, particularly in diagnosing respiratory infectious diseases and conducting epidemiological investigations. This narrative review summarizes conventional methods for routine respiratory infection diagnosis, including culture, smear microscopy, immunological assays, image techniques as well as polymerase chain reaction(PCR). In contrast to conventional methods, there is a new detection technology, sequencing technology, and here we mainly focus on the next-generation sequencing NGS, especially metagenomic NGS(mNGS). NGS offers significant advantages over traditional methods. Firstly, mNGS eliminates assumptions about pathogens, leading to faster and more accurate results, thus reducing diagnostic time. Secondly, it allows unbiased identification of known and novel pathogens, offering broad-spectrum coverage. Thirdly, mNGS not only identifies pathogens but also characterizes microbiomes, analyzes human host responses, and detects resistance genes and virulence factors. It can complement targeted sequencing for bacterial and fungal classification. Unlike traditional methods affected by antibiotics, mNGS is less influenced due to the extended survival of pathogen DNA in plasma, broadening its applicability. However, barriers to full integration into clinical practice persist, primarily due to cost constraints and limitations in sensitivity and turnaround time. Despite these challenges, ongoing advancements aim to improve cost-effectiveness and efficiency, making NGS a cornerstone technology for global respiratory infection diagnosis.
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Affiliation(s)
- Jingyuan Chen
- Department of Global Health, School of Public Health, Peking University, Beijing, China
| | - Zhen Qin
- School of Public Health, Peking University, Beijing, China
| | - Zhongwei Jia
- Department of Global Health, School of Public Health, Peking University, Beijing, China.
- Center for Intelligent Public Health, Institute for Artificial Intelligence, Peking University, Beijing, China.
- Center for Drug Abuse Control and Prevention, National Institute of Health Data Science, Peking University, Beijing, China.
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Saxena J, Das S, Kumar A, Sharma A, Sharma L, Kaushik S, Kumar Srivastava V, Jamal Siddiqui A, Jyoti A. Biomarkers in sepsis. Clin Chim Acta 2024; 562:119891. [PMID: 39067500 DOI: 10.1016/j.cca.2024.119891] [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: 06/06/2024] [Revised: 07/20/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Sepsis is a life-threatening condition characterized by dysregulated host response to infection leading to organ dysfunction. Despite advances in understanding its pathology, sepsis remains a global health concern and remains a major contributor to mortality. Timely identification is crucial for improving clinical outcomes, as delayed treatment significantly impacts survival. Accordingly, biomarkers play a pivotal role in diagnosis, risk stratification, and management. This review comprehensively discusses various biomarkers in sepsis and their potential application in antimicrobial stewardship and risk assessment. Biomarkers such as white blood cell count, neutrophil to lymphocyte ratio, erythrocyte sedimentation rate, C-reactive protein, interleukin-6, presepsin, and procalcitonin have been extensively studied for their diagnostic and prognostic value as well as in guiding antimicrobial therapy. Furthermore, this review explores the role of biomarkers in risk stratification, emphasizing the importance of identifying high-risk patients who may benefit from specific therapeutic interventions. Moreover, the review discusses the emerging field of transcriptional diagnostics and metagenomic sequencing. Advances in sequencing have enabled the identification of host response signatures and microbial genomes, offering insight into disease pathology and aiding species identification. In conclusion, this review provides a comprehensive overview of the current understanding and future directions of biomarker-based approaches in sepsis diagnosis, management, and personalized therapy.
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Affiliation(s)
- Juhi Saxena
- Department of Biotechnology, Parul Institute of Technology, Parul University, Vadodara, Gujarat, India
| | - Sarvjeet Das
- Department of Life Science, Parul Institute of Applied Science, Parul University, Vadodara, Gujarat, India
| | - Anshu Kumar
- Department of Life Science, Parul Institute of Applied Science, Parul University, Vadodara, Gujarat, India
| | - Aditi Sharma
- Department of Pharmacology, School of Pharmaceutical Sciences, Shoolini University of Biotechnology,and Management Sciences, Solan 173229, Himachal Pradesh, India
| | - Lalit Sharma
- Department of Pharmacology, School of Pharmaceutical Sciences, Shoolini University of Biotechnology,and Management Sciences, Solan 173229, Himachal Pradesh, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | | | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha'il, P.O. Box 2440, Ha'il, Saudi Arabia
| | - Anupam Jyoti
- Department of Life Science, Parul Institute of Applied Science, Parul University, Vadodara, Gujarat, India.
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Oki H, Niwa R, Pranee S, Motooka D, Onda Y, Nakata J, Nakajima H, Oka Y, Sugiyama H, Yoshii Y, Anzai N, Nakamura S, Iida T. Identification of causative fungus from sterile abscess using metagenomics followed by in situ hybridization. Access Microbiol 2024; 6:000779.v3. [PMID: 39148686 PMCID: PMC11325578 DOI: 10.1099/acmi.0.000779.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/24/2024] [Indexed: 08/17/2024] Open
Abstract
Introduction. Invasive fungal infections require early diagnosis for treatment. Microscopic observation of biopsy and blood culture is the gold standard for the identification of the causative fungus, but it is difficult to identify the causative pathogen by a sterile abscess biopsy. Case Presentation. We present a case report of breakthrough invasive trichosporonosis in a 65-year-old Japanese male with acute myeloid leukaemia receiving antifungal prophylaxis. Blood cultures showed no fungal growth, and a liver biopsy and a removed spleen with abscess showed fragmented fungi, but no fungal identification was possible. This report demonstrates that retrospective analyses were able to identify the causative fungus. Conclusion. We narrowed down the candidate fungi by deep sequencing of the ITS1 region of fungal genome and confirmed that the fungus observed in the specimen was Trichosporon asahii by in situ hybridization using a DNA probe targeting 26S rRNA.
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Affiliation(s)
- Hiroya Oki
- Department of Infection Metagenomics, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- NGS Core Facility, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
| | - Ryotaro Niwa
- Department of Hematology and Oncology, Takatsuki Red Cross Hospital, Osaka, Japan
- Department of Hematology, Yodogawa Christian Hospital, Osaka, Japan
| | - Somboonthum Pranee
- Department of Bacterial Infections, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- NGS Core Facility, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Integrated Frontier Research for Medical Science Division (iFremed), Osaka University, Osaka, Japan
| | - Yoshiyuki Onda
- Department of Hematology and Oncology, Takatsuki Red Cross Hospital, Osaka, Japan
- Department of Hematology and Oncology, Osaka Red Cross Hospital, Osaka, Japan
| | - Jun Nakata
- Department of Clinical Laboratory and Biomedical Sciences, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hiroko Nakajima
- Department of Cancer Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yoshihiro Oka
- Department of Cancer Stem Cell Biology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Immunopathology, Immunology Frontier Research Center (World Premier International Research Center), Osaka University, Osaka, Japan
| | - Haruo Sugiyama
- Department of Cancer Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuka Yoshii
- NGS Core Facility, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
| | - Naoyuki Anzai
- Department of Hematology and Oncology, Takatsuki Red Cross Hospital, Osaka, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- NGS Core Facility, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Integrated Frontier Research for Medical Science Division (iFremed), Osaka University, Osaka, Japan
| | - Tetsuya Iida
- Department of Infection Metagenomics, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- Department of Bacterial Infections, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
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Zhang H, Lu M, Guo C, Wang L, Ye K, Zhao Q, Yang J, Yang L, Li T. Clinical impact of metagenomic next-generation sequencing of bronchoalveolar lavage fluids for the diagnosis of pulmonary infections in respiratory intensive care unit. Heliyon 2024; 10:e35287. [PMID: 39170112 PMCID: PMC11336462 DOI: 10.1016/j.heliyon.2024.e35287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024] Open
Abstract
Background The real-world clinical impact of mNGS on BALF in the respiratory intensive care unit (RICU) is not yet fully understood. Methods We investigated the clinical impact of mNGS on BALF samples obtained from 92 patients admitted to the RICU over a 2-year period. We utilized both mNGS and culture methods to evaluate the effectiveness of mNGS in diagnosing pulmonary infections. The clinical impact of mNGS were evaluated by the clinician committees. Results Among the 92 diagnosed patients, 78 cases (84.7 %) were determined to have infectious diseases caused by pathogenic microorganisms, and the bacterial infections constituted the most prevalent diagnostic category. For mixed infection, the most common type was the Pneumocystis jironecii and cytomegalovirus co-infection. The mNGS results had a positive impact on the clinical management of 43 cases (46.7 %). Moreover, 19 cases (44.2 %) of positive clinical impacts were solely based on new diagnoses made possible by mNGS results. These new diagnoses were particularly helpful for identifying rare pathogens, which could not be detected by conventional diagnostic methods. Conclusions The BALF mNGS has a positive real-world impact in RICU. Clinician committee play a critical role in ensuring the appropriate use of mNGS.
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Affiliation(s)
- Heng Zhang
- Department of Emergency, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, 100853, China
| | - Ming Lu
- Laboratory Medicine Department, Tangshan Nanhu Hospital, Hebei, 063000, China
| | - Chaomin Guo
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Lifeng Wang
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Kun Ye
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qiang Zhao
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jiyong Yang
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Liuyang Yang
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Tanshi Li
- Department of Emergency, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, 100853, China
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Deng QM, Zhang J, Zhang YY, Jia M, Ding DS, Fang YQ, Wang HZ, Gu HC. Diagnosis and treatment of refractory infectious diseases using nanopore sequencing technology: Three case reports. World J Clin Cases 2024; 12:5208-5216. [DOI: 10.12998/wjcc.v12.i22.5208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/29/2024] [Accepted: 06/17/2024] [Indexed: 06/30/2024] Open
Abstract
BACKGROUND Infectious diseases are still one of the greatest threats to human health, and the etiology of 20% of cases of clinical fever is unknown; therefore, rapid identification of pathogens is highly important. Traditional culture methods are only able to detect a limited number of pathogens and are time-consuming; serologic detection has window periods, false-positive and false-negative problems; and nucleic acid molecular detection methods can detect several known pathogens only once. Three-generation nanopore sequencing technology provides new options for identifying pathogens.
CASE SUMMARY Case 1: The patient was admitted to the hospital with abdominal pain for three days and cessation of defecation for five days, accompanied by cough and sputum. Nanopore sequencing of the drainage fluid revealed the presence of oral-like bacteria, leading to a clinical diagnosis of bronchopleural fistula. Cefoperazone sodium sulbactam treatment was effective. Case 2: The patient was admitted to the hospital with fever and headache, and CT revealed lung inflammation. Antibiotic treatment for Streptococcus pneumoniae, identified through nanopore sequencing of cerebrospinal fluid, was effective. Case 3: The patient was admitted to our hospital with intermittent fever and an enlarged neck mass that had persisted for more than six months. Despite antibacterial treatment, her symptoms worsened. The nanopore sequencing results indicate that voriconazole treatment is effective for Aspergillus brookii. The patient was diagnosed with mixed cell type classical Hodgkin's lymphoma with infection.
CONCLUSION Three-generation nanopore sequencing technology allows for rapid and accurate detection of pathogens in human infectious diseases.
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Affiliation(s)
- Qing-Mei Deng
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei 230031, Anhui Province, China
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Jian Zhang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Yi-Yong Zhang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Min Jia
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Du-Shan Ding
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Yu-Qin Fang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Hong-Zhi Wang
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei 230031, Anhui Province, China
| | - Hong-Cang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
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Hu X, Jiang L, Liu X, Chang H, Dong H, Yan J, Zhou X, Kong M. The diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in critically ill patients with respiratory tract infections. Microbiol Spectr 2024; 12:e0045824. [PMID: 38916357 PMCID: PMC11302328 DOI: 10.1128/spectrum.00458-24] [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: 03/09/2024] [Accepted: 05/18/2024] [Indexed: 06/26/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is an unbiased and rapid method for detecting pathogens. This study enrolled 145 suspected severe pneumonia patients who were admitted to the Affiliated Hospital of Jining Medical University. This study primarily aimed to determine the diagnostic performance of mNGS and conventional microbiological tests (CMTs) using bronchoalveolar lavage fluid samples for detecting pathogens. Our findings indicated that mNGS performed significantly higher sensitivity (97.54% vs 28.68%, P < 0.001), coincidence (90.34% vs 35.17%, P < 0.001), and negative predictive value (80.00% vs 13.21%, P < 0.001) but performed lower specificity than CMTs (52.17% vs 87.5%, P < 0.001). Streptococcus pneumoniae as the most common bacterial pathogen had the largest proportion (22.90%, 30/131) in this study. In addition to bacteria, fungi, and virus, mNGS can detect a variety of atypical pathogens such as Mycobacterium tuberculosis and non-tuberculous. Mixed infections were common in patients with severe pneumonia, and bacterial-fungal-viral-atypical pathogens were the most complicated infection. After adjustments of antibiotics based on mNGS and CMTs, the clinical manifestation improved in 139 (95.86%, 139/145) patients. Our data demonstrated that mNGS had significant advantage in diagnosing respiratory tract infections, especially atypical pathogens and fungal infections. Pathogens were detected timely and comprehensively, contributing to the adjustments of antibiotic treatments timely and accurately, improving patient prognosis and decreasing mortality potentially.IMPORTANCEMetagenomic next-generation sequencing using bronchoalveolar lavage fluid can provide more comprehensive and accurate pathogens for respiratory tract infections, especially when considering the previous usage of empirical antibiotics before admission or complicated clinical presentation. This technology is expected to play an important role in the precise application of antimicrobial drugs in the future.
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Affiliation(s)
- Xiaohang Hu
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Liqing Jiang
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Xiaowei Liu
- Department of Intensive Care Unit, Affiliated Hospital of Jining Medical University,Jining Medical University, Shandong Jining, China
| | - Hong Chang
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Haixin Dong
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Jinyan Yan
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Xiaoya Zhou
- Medical Laboratory of Jining Medical University, Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Min Kong
- Medical Laboratory of Jining Medical University, Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical University, Jining Medical University, Shandong Jining, China
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Yin Y, Shen J, Du Z, Wang B, Wang G, Chen H, Wang J, An Y, Liu C, Wang H. Clinical and cost analysis of an ultra-rapid metagenomic sequencing test for pathogen detection in adult patients with sepsis. Chin Med J (Engl) 2024; 137:1882-1884. [PMID: 38879803 DOI: 10.1097/cm9.0000000000003175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Indexed: 08/06/2024] Open
Affiliation(s)
- Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Jiawei Shen
- Department of Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Zhenshan Du
- Medical Department, Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, Zhejiang 310030, China
| | - Bin Wang
- Department of Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Guangjie Wang
- Department of Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Jun Wang
- Medical Department, Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, Zhejiang 310030, China
| | - Youzhong An
- Department of Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Chao Liu
- Medical Department, Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, Zhejiang 310030, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
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Wu X, Qin N, Peng X, Wang L. Exploring odontogenic brain abscesses: a comprehensive review. Acta Neurol Belg 2024; 124:1155-1165. [PMID: 38722527 DOI: 10.1007/s13760-024-02569-y] [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: 02/04/2024] [Accepted: 04/29/2024] [Indexed: 07/25/2024]
Abstract
INTRODUCTION Whether in neurology or dentistry, odontogenic brain abscess stands as an ailment demanding undivided attention. The onset of this disease is insidious, with a relatively low incidence rate but a markedly high fatality rate. Moreover, its symptoms lack specificity, easily leading to misdiagnosis, oversight, and treatment delays. Hence, clinicians should maintain heightened vigilance when faced with pathogenic bacteria of dental origin in patients. AREAS COVERED This paper encapsulates the latest research findings on the clinical manifestations and essential treatment points of odontogenic brain abscess. It may offer a crucial reference for prompt diagnosis and improved therapeutic approaches. EXPERT OPINIONS Odontogenic brain abscess, an infection of the cerebral parenchyma, usually appears in immunocompromised patients with dental ailments or postdental surgeries. The main pathogenic microorganisms include Streptococcus intermedius, Fusobacterium nucleatum, Streptococcus anginosus, and Millerella. Given the undetectable and nonspecific symptoms in patients, the diagnostic process relies on microbiological methods. Therefore, clinicians should actively investigate and identify the pathogenic microorganisms of odontogenic brain abscess for early detection and selection of appropriate treatment regimens to avoid disease management delays.
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Affiliation(s)
- Xingguo Wu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ningxiang Qin
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xi Peng
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Liang Wang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Zhang F, Wang Z, Men S, Zhang J, Wang L. Two novel compound heterozygous loss-of-function mutations cause fetal IRAK-4 deficiency presenting with Pseudomonas Aeruginosa sepsis. Clin Immunol 2024; 265:110268. [PMID: 38838930 DOI: 10.1016/j.clim.2024.110268] [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: 11/26/2023] [Revised: 03/29/2024] [Accepted: 06/02/2024] [Indexed: 06/07/2024]
Abstract
PURPOSE To report a case of a five-month-old Chinese infant who died of interleukin-1 receptor-associated kinase-4 (IRAK-4) deficiency presenting with rapid and progressive Pseudomonas aeruginosa sepsis. METHODS The genetic etiology of IRAK-4 deficiency was confirmed through trio-whole exome sequencing and Sanger sequencing. Functional consequences were invested using an in vitro minigene splicing assay. RESULTS Trio-whole exome sequencing of genomic DNA identified two novel compound heterozygous mutations, IRAK-4 (NM_016123.3): c.942-1G > A and c.644_651+ 6delTTGCAGCAGTAAGT in the proband, which originated from his symptom-free parents. These mutations were predicted to cause frameshifts and generate three truncated proteins without enzyme activity. CONCLUSIONS Our findings expand the range of IRAK-4 mutations and provide functional support for the pathogenic effects of splice-site mutations. Additionally, this case highlights the importance of considering the underlying genetic defects of immunity when dealing with unusually overwhelming infections in previously healthy children and emphasizes the necessity for timely treatment with wide-spectrum antimicrobials.
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Affiliation(s)
- Fang Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Zhiwei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Shuai Men
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Jinglu Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Leilei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China.
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Han J, Wei FL, Wu HX, Guo LY, Guo S, Han Y, Sun YN, Hou W, Hu ZJ. Clinical evaluation of droplet digital pcr for suspected ascites infection in patients with liver cirrhosis. Hepatol Int 2024; 18:1249-1260. [PMID: 38683274 DOI: 10.1007/s12072-024-10669-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/01/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND Droplet digital PCR (ddPCR) is increasingly used in diagnosing clinical pathogens, but its effectiveness in cirrhosis patients with suspected ascites infection remains uncertain. METHODS The diagnostic performance of ddPCR was assessed in 305 ascites samples, utilizing culture and clinical composite standards. The quantitative value and potential clinical impact of ddPCR were further analyzed in patients with spontaneous bacterial peritonitis. RESULTS With culture standards, ddPCR demonstrated a sensitivity of 86.5% and specificity of 83.2% for bacterial or fungal detection. After adjustment of clinical composite criteria, specificity increased to 96.4%. Better diagnostic performance for all types of targeted pathogens, particularly fungi, was observed with ddPCR compared to culture, and more polymicrobial infections were detected (30.4% versus 5.7%, p < 0.001). Pathogen loads detected by ddPCR correlated with white blood cell count in ascites and blood, as well as polymorphonuclear cell (PMN) count in ascites, reflecting infection status rapidly. A positive clinical impact of 55.8% (43/77) was observed for ddPCR, which was more significant among patients with PMN count ≤ 250/mm3 in terms of medication adjustment and new diagnosis. ddPCR results for fungal detection were confirmed by clinical symptoms and other microbiological tests, which could guide antifungal therapy and reduce the risk of short-term mortality. CONCLUSIONS ddPCR, with appropriate panel design, has advantages in pathogen detection and clinical management of ascites infection, especially for patients with fungal and polymicrobial infections. Patients with atypical spontaneous bacterial peritonitis benefited more from ddPCR.
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Affiliation(s)
- Jie Han
- Beijing You'An Hospital, Capital Medical University, No. 8 You An Men Wai Street, Fengtai District, Beijing, 100069, China
- Beijing Precision Medicine and Transformation Engineering Technology Research Center of Hepatitis and Liver Cancer, Beijing Institute of Hepatology, Beijing You'An Hospital, Capital Medical University, No. 8 You An Men Wai Street, Fengtai District, Beijing, 100069, China
| | - Fei-Li Wei
- Beijing Precision Medicine and Transformation Engineering Technology Research Center of Hepatitis and Liver Cancer, Beijing Institute of Hepatology, Beijing You'An Hospital, Capital Medical University, No. 8 You An Men Wai Street, Fengtai District, Beijing, 100069, China
| | - Hao-Xin Wu
- Beijing You'An Hospital, Capital Medical University, No. 8 You An Men Wai Street, Fengtai District, Beijing, 100069, China
| | - Lu-Yao Guo
- Beijing You'An Hospital, Capital Medical University, No. 8 You An Men Wai Street, Fengtai District, Beijing, 100069, China
| | - Shan Guo
- Beijing Precision Medicine and Transformation Engineering Technology Research Center of Hepatitis and Liver Cancer, Beijing Institute of Hepatology, Beijing You'An Hospital, Capital Medical University, No. 8 You An Men Wai Street, Fengtai District, Beijing, 100069, China
| | - Ying Han
- Beijing You'An Hospital, Capital Medical University, No. 8 You An Men Wai Street, Fengtai District, Beijing, 100069, China
| | - Ya-Nan Sun
- Beijing You'An Hospital, Capital Medical University, No. 8 You An Men Wai Street, Fengtai District, Beijing, 100069, China
| | - Wei Hou
- Beijing You'An Hospital, Capital Medical University, No. 8 You An Men Wai Street, Fengtai District, Beijing, 100069, China.
| | - Zhong-Jie Hu
- Beijing You'An Hospital, Capital Medical University, No. 8 You An Men Wai Street, Fengtai District, Beijing, 100069, China.
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Cai X, Sun C, Zhong H, Cai Y, Cao M, Wang L, Sun W, Tao Y, Ma G, Huang B, Yan S, Zhong J, Wang J, Lu Y, Guan Y, Song M, Wang Y, Li Y, Su X. The value of metagenomic next-generation sequencing with different nucleic acid extracting methods of cell-free DNA or whole-cell DNA in the diagnosis of non-neutropenic pulmonary aspergillosis. Front Cell Infect Microbiol 2024; 14:1398190. [PMID: 39135636 PMCID: PMC11317373 DOI: 10.3389/fcimb.2024.1398190] [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: 03/09/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024] Open
Abstract
Purpose Metagenomic next-generation sequencing(mNGS) is a novel molecular diagnostic technique. For nucleic acid extraction methods, both whole-cell DNA (wcDNA) and cell-free DNA (cfDNA) are widely applied with the sample of bronchoalveolar lavage fluid (BALF). We aim to evaluate the clinical value of mNGS with cfDNA and mNGS with wcDNA for the detection of BALF pathogens in non-neutropenic pulmonary aspergillosis. Methods mNGS with BALF-cfDNA, BALF-wcDNA and conventional microbiological tests (CMTs) were performed in suspected non-neutropenic pulmonary aspergillosis. The diagnostic value of different assays for pulmonary aspergillosis was compared. Results BALF-mNGS (cfDNA, wcDNA) outperformed CMTs in terms of microorganisms detection. Receiver operating characteristic (ROC) analysis indicated BALF-mNGS (cfDNA, wcDNA) was superior to culture and BALF-GM. Combination diagnosis of either positive for BALF-mNGS (cfDNA, wcDNA) or CMTs is more sensitive than CMTs alone in the diagnosis of pulmonary aspergillosis (BALF-cfDNA+CMTs/BALF-wcDNA+CMTs vs. CMTs: ROC analysis: 0.813 vs.0.66, P=0.0142/0.796 vs.0.66, P=0.0244; Sensitivity: 89.47% vs. 47.37%, P=0.008/84.21% vs. 47.37%, P=0.016). BALF-cfDNA showed a significantly greater reads per million (RPM) than BALF-wcDNA. The area under the ROC curve (AUC) for RPM of Aspergillus detected by BALF-cfDNA, used to predict "True positive" pulmonary aspergillosis patients, was 0.779, with a cut-off value greater than 4.5. Conclusion We propose that the incorporation of BALF-mNGS (cfDNA, wcDNA) with CMTs improves diagnostic precision in the identification of non-neutropenic pulmonary aspergillosis when compared to CMTs alone. BALF-cfDNA outperforms BALF-wcDNA in clinical value.
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Affiliation(s)
- Xiaomin Cai
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Chao Sun
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Huanhuan Zhong
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Suzhou University, Suzhou, China
| | - Yuchen Cai
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Min Cao
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Li Wang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenkui Sun
- Department of Respiratory and Critical Care Medicine, Jiangsu Province Hospital, The First Affiliated of Nanjing Medical University, Nanjing, China
| | - Yujian Tao
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Guoer Ma
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Baoju Huang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Shengmei Yan
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jinjin Zhong
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jiamei Wang
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Yajie Lu
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yuanlin Guan
- Department of Research and Development, Hugobiotech Co., Ltd., Beijing, China
| | - Mengyue Song
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Suzhou University, Suzhou, China
| | - Yujie Wang
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yuanyuan Li
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xin Su
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
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Wu J, Zhang Y, Duan J, Wei Y, Miao Y. A metagenomic next-generation sequencing (mNGS)-based analysis of bronchoalveolar lavage samples in patients with an acute exacerbation of chronic obstructive pulmonary disease. J Mol Histol 2024:10.1007/s10735-024-10225-1. [PMID: 39060894 DOI: 10.1007/s10735-024-10225-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
The role of the bronchoalveolar lavage fluid (BALF) microbiome in acute exacerbations of chronic obstructive pulmonary disease (AECOPD) remains unclear. The advent of the metagenomic next-generation sequencing (mNGS) has made it possible to reveal the complex microbiome composition of the respiratory tract. This study aimed to explore whether there are differences in the BALF microbiome of AECOPD patients with different lung functions. We enrolled 55 AECOPD patients and divided them into a mild group (n = 31) and a severe group (n = 24) according to their lung function. We collected BALF and submitted it to mNGS and bioinformatics analysis. At the species level, mNGS identified 264 bacteria, 13 fungi and 12 viruses in the mild group, and 174 bacteria, 6 fungi and 6 viruses in the severe group. Mixed bacterial and viral infection occurred in both groups. At the genus level, Rothia and Veillonella were more abundant in the mild group, while Pseudomonas and Staphylococcus were more abundant in the severe group. At the species level, compared with the mild group, the relative abundance of Haemophilus influenzae and Pseudomonas aeruginosa was increased in the severe group. Besides, the BALF microbiome composition was similar between the two groups, and there was no significant difference in α and β diversity. Forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) (%) showed no significant correlation with the Shannon or Simpson index. The microbiome abundance was different between the mild and severe groups; however, microbiome diversity was similar between the two groups. Based on our findings, Haemophilus influenzae and Pseudomonas aeruginosa may be the pathogenic bacteria that cause the difference in lung function in patients with AECOPD.
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Affiliation(s)
- Junfang Wu
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China
| | - Yongqing Zhang
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China
| | - Jinjin Duan
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China
| | - Yiqun Wei
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China
| | - Yi Miao
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China.
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Chai K, Wang H, Guan Y, Shi R, Stalin A, Zhai Y, Zhou J, Qiao C, Yang S, Li J, Zhang X, Wu J. Effectiveness of Bairui granules in the treatment of respiratory tract infections: A systematic review and meta-analysis. Medicine (Baltimore) 2024; 103:e38904. [PMID: 39029033 PMCID: PMC11398807 DOI: 10.1097/md.0000000000038904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Respiratory tract infections (RTIs) are characterized by a high mortality rate and clinical incidence. Bairui granules (BG), which employ a method of heat elimination and detoxification, have demonstrated benefits in the treatment of infectious respiratory diseases. METHODS A computerized search of 6 databases was conducted to identify randomized controlled trials (RCTs) relevant to the treatment of RTIs with BG up to November 30, 2023. Two researchers independently conducted data extraction, risk of bias assessment, and grading analysis. To evaluate the stability of the results, trial sequential analysis was employed. RESULTS This meta-analysis included 31 RCTs with a total of 4073 patients and demonstrated that the use of BG in the treatment of RTIs was associated with enhanced treatment efficacy (relative risk = 1.19, 95% credible interval: 1.16-1.22, P < .001). It also indicated a faster resolution of symptoms including pulmonary rales, cough, and fever, as well as a reduction in serological index factors, compared to the use of Western medicine treatment (WT) alone. Additionally, the duration of hospitalization for patients was significantly reduced (relative risk = -1.36, 95% credible interval: -1.55 to -1.17, P < .001). Trial sequential analysis confirmed the stability and conclusive evidence of the study results. The efficacy of treating RTIs with BG, either alone or in combination with WT, was found to be superior to WT alone. However, further high-quality RCTs are necessary to validate these outcomes. CONCLUSION The effectiveness of treating RTIs using BG alone or in combination with WT was determined to be superior to using WT alone, with no serious adverse effects observed. However, additional RCTs are essential to further confirm the findings of this study.
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Affiliation(s)
- Keyan Chai
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Haojia Wang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Yueqin Guan
- Jiuhua Huayuan Pharmaceutical Co., Ltd, Anhui, Chuzhou, China
| | - Rui Shi
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Antony Stalin
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Yiyan Zhai
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jiying Zhou
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Chuanqi Qiao
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Siyun Yang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jiaqi Li
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaomeng Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jiarui Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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Hu Y, Zhao Y, Zhang Y, Chen W, Zhang H, Jin X. Cell-free DNA: a promising biomarker in infectious diseases. Trends Microbiol 2024:S0966-842X(24)00168-9. [PMID: 38997867 DOI: 10.1016/j.tim.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 06/08/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024]
Abstract
Infectious diseases pose serious threats to public health worldwide. Conventional diagnostic methods for infectious diseases often exhibit low sensitivity, invasiveness, and long turnaround times. User-friendly point-of-care tests are urgently needed for early diagnosis, treatment monitoring, and prognostic prediction of infectious diseases. Cell-free DNA (cfDNA), a promising non-invasive biomarker widely used in oncology and pregnancy, has shown great potential in clinical applications for diagnosing infectious diseases. Here, we discuss the most recent cfDNA research on infectious diseases from both the pathogen and host perspectives. We also discuss the technical challenges in this field and propose solutions to overcome them. Additionally, we provide an outlook on the potential of cfDNA as a diagnostic, treatment, and prognostic marker for infectious diseases.
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Affiliation(s)
- Yuxuan Hu
- BGI Research, Shenzhen 518083, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | | | - Yan Zhang
- BGI Research, Shenzhen 518083, China
| | - Weijun Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | | | - Xin Jin
- BGI Research, Shenzhen 518083, China; The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou 510006, China; Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China; Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Shenzhen, China.
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Xiao ST, Zhang HQ, Wang YX. Isolated neural arch tuberculosis with tuberculomas: case report. Skeletal Radiol 2024; 53:1417-1421. [PMID: 37712982 DOI: 10.1007/s00256-023-04450-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/12/2023] [Accepted: 08/26/2023] [Indexed: 09/16/2023]
Abstract
We reported a case of atypical spinal tuberculosis on the posterior elements of lumbar spine in a 52-year-old female. It was easy to be misdiagnosed as spinal tumor due to its imaging characteristics. We performed puncture biopsy to initially consider tuberculosis, and then the patient was accepted surgical treatment. The intraoperative removed specimen was sent to pathological examination, microbial culture, Xpert MTB/RIF and metagenomic next-generation sequencing (mNGS) and then the diagnosis of neural arch tuberculosis was confirmed. After operation, the patient obtained stable effect by anti-tuberculosis drug treatment. In a word, the uncommon case had an important reference significance for the diagnosis of atypical spine tuberculosis and differentiation from spinal tumors. It is critical to make right preliminary diagnosis by appropriate examination as it determined the next diagnosis and treatment in special and rare clinical cases.
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Affiliation(s)
- Shun-Tian Xiao
- Department of Spine Surgery and Orthopaedics, Xiangya Spinal Surgery Center, Xiangya Hospital of Central South University, Xiang Ya Road 87, Changsha, 410008, Hunan Province, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital of Central South University, Changsha, 410008, Hunan Province, China
| | - Hong-Qi Zhang
- Department of Spine Surgery and Orthopaedics, Xiangya Spinal Surgery Center, Xiangya Hospital of Central South University, Xiang Ya Road 87, Changsha, 410008, Hunan Province, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital of Central South University, Changsha, 410008, Hunan Province, China
| | - Yu-Xiang Wang
- Department of Spine Surgery and Orthopaedics, Xiangya Spinal Surgery Center, Xiangya Hospital of Central South University, Xiang Ya Road 87, Changsha, 410008, Hunan Province, China.
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital of Central South University, Changsha, 410008, Hunan Province, China.
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Visedthorn S, Klomkliew P, Sawaswong V, Sivapornnukul P, Chanchaem P, Saejew T, Pavatung P, Kanjanabuch T, Payungporn S. Bacterial classification based on metagenomic analysis in peritoneal dialysis effluent of patients with chronic kidney disease. Biomed Rep 2024; 21:102. [PMID: 38800037 PMCID: PMC11117105 DOI: 10.3892/br.2024.1790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
End-stage kidney disease (ESKD) is the final stage of chronic kidney disease (CKD), in which long-term damage has been caused to the kidneys to the extent that they are no longer able to filter the blood of waste and extra fluid. Peritoneal dialysis (PD) is one of the treatments that remove waste products from the blood through the peritoneum which can improve the quality of life for patients with ESKD. However, PD-associated peritonitis is an important complication that contributes to the mortality of patients, and the detection of bacterial pathogens is associated with a high culture-negative rate. The present study aimed to apply a metagenomic approach for the bacterial identification in the PD effluent (PDE) of patients with CKD based on 16S ribosomal DNA sequencing. As a result of this investigation, five major bacteria species, namely Escherichia coli, Phyllobacterium myrsinacearum, Streptococcus gallolyticus, Staphylococcus epidermidis and Shewanella algae, were observed in PDE samples. Taken together, the findings of the present study have suggested that this metagenomic approach could provide a greater potential for bacterial taxonomic identification compared with traditional culture methods, suggesting that this is a practical and culture-independent alternative approach that will offer a novel preventative infectious strategy in patients with CDK.
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Affiliation(s)
- Suthida Visedthorn
- Medical Biochemistry Program, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavit Klomkliew
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorthon Sawaswong
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Pavaret Sivapornnukul
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Prangwalai Chanchaem
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thunvarat Saejew
- Center of Excellence in Kidney Metabolic Disorders, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Preeyarat Pavatung
- Center of Excellence in Kidney Metabolic Disorders, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Talerngsak Kanjanabuch
- Center of Excellence in Kidney Metabolic Disorders, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Division of Nephrology, Department of Internal Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- CAPD Excellence Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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Abstract
This review delves into the rapidly evolving landscape of liquid biopsy technologies based on cell-free DNA (cfDNA) and cell-free RNA (cfRNA) and their increasingly prominent role in precision medicine. With the advent of high-throughput DNA sequencing, the use of cfDNA and cfRNA has revolutionized noninvasive clinical testing. Here, we explore the physical characteristics of cfDNA and cfRNA, present an overview of the essential engineering tools used by the field, and highlight clinical applications, including noninvasive prenatal testing, cancer testing, organ transplantation surveillance, and infectious disease testing. Finally, we discuss emerging technologies and the broadening scope of liquid biopsies to new areas of diagnostic medicine.
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Affiliation(s)
- Conor Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Lauren Ahmann
- Department of Pathology, Stanford University, Stanford, California, USA;
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Wei Gu
- Department of Pathology, Stanford University, Stanford, California, USA;
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30
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Pham D, Sivalingam V, Tang HM, Montgomery JM, Chen SCA, Halliday CL. Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches. J Fungi (Basel) 2024; 10:447. [PMID: 39057332 PMCID: PMC11278267 DOI: 10.3390/jof10070447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Invasive fungal diseases (IFDs) comprise a growing healthcare burden, especially given the expanding population of immunocompromised hosts. Early diagnosis of IFDs is required to optimise therapy with antifungals, especially in the setting of rising rates of antifungal resistance. Molecular techniques including nucleic acid amplification tests and whole genome sequencing have potential to offer utility in overcoming limitations with traditional phenotypic testing. However, standardisation of methodology and interpretations of these assays is an ongoing undertaking. The utility of targeted Aspergillus detection has been well-defined, with progress in investigations into the role of targeted assays for Candida, Pneumocystis, Cryptococcus, the Mucorales and endemic mycoses. Likewise, whilst broad-range polymerase chain reaction assays have been in use for some time, pathology stewardship and optimising diagnostic yield is a continuing exercise. As costs decrease, there is also now increased access and experience with whole genome sequencing, including metagenomic sequencing, which offers unparalleled resolution especially in the investigations of potential outbreaks. However, their role in routine diagnostic use remains uncommon and standardisation of techniques and workflow are required for wider implementation.
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Affiliation(s)
- David Pham
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Varsha Sivalingam
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Helen M. Tang
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - James M. Montgomery
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
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Shi T, Yu Y, Shen Y, Shen M, Du Y, Zhang M, Mei Z, Ding Y, Feng J, Zhu M, Ge F, Zhao Q, Wang R, Jie Z. Serum C-reactive protein to albumin ratio as a potential risk indicator of pneumonia caused by Chlamydia psittaci: a multicenter retrospective study. Front Cell Infect Microbiol 2024; 14:1371625. [PMID: 38988811 PMCID: PMC11233447 DOI: 10.3389/fcimb.2024.1371625] [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: 01/16/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024] Open
Abstract
Introduction The aim of the study was to describe psittacosis pneumonia and to assess the predictive value of the C-reactive protein/albumin ratio in psittacosis pneumonia for severity. Methods Data on psittacosis pneumonia cases diagnosed using metagenomic sequencing were collected from three hospitals in Shanghai, China from Oct. 2019 to Oct. 2022. Serum levels of C-reactive protein and albumin were measured and the C-reactive protein to albumin ratio (CAR) was calculated. Spearman's correlation analysis, ordered logistic regression analysis, and receiver operating characteristic curve analysis were conducted to examine the correlation and predictive ability of the three indicators on the severity of the disease. Results A total of 27 patients with psittacosis pneumonia were enrolled, with an average age of 62 years and 70.4% being male. 44.4% of patients had a clear history of contact with poultry or birds. The predominant symptom was fever (100%). Patients treated in the respiratory intensive care unit (RICU) had a higher likelihood of experiencing wheezing (88.9% versus 33.3%, P=0.013) and chest tightness (88.9% vs. 33.3%, P=0.013) than those in the general ward (Non-RICU). The proportion of patients with pleural effusion was significantly higher in the RICU compared to the Non-RICU (88.9% vs. 38.9%, P=0.019). The RICU group had a significantly higher CAR than the Non-RICU group (9.41 vs. 4.05, P=0.017). This result was accompanied by higher intubation and ventilator support (33.3% vs. 0.0%, P=0.029), higher PCT and CRP levels and lower albumin and PaCO2 levels in the RICU than in the Non-RICU. Logistic regression analysis indicated that CAR (OR 1.49; 95% CI 1.07-2.06, P=0.017) was risk factor for prolonged hospitalization (> 14 days). Discussion Elevated serum CAR levels were found to be associated with a greater risk of severe psittacosis pneumonia. Consequently, it may serve as an uncomplicated and useful diagnostic tool for clinicians to promptly and precisely ascertain the severity of psittacosis pneumonia, ultimately aiding them in devising the most optimal therapeutic plan.
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Affiliation(s)
- Tianyun Shi
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
- Center of Community-Based Health Research, Fudan University, Shanghai, China
| | - Yunxia Yu
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
- Center of Community-Based Health Research, Fudan University, Shanghai, China
| | - Yao Shen
- Department of Pulmonary and Critical Care Medicine, Shanghai Pudong Hospital, Shanghai, China
| | - Meili Shen
- Medical Department, Nanjing Dinfectome Technology Inc., Nanjing, China
| | - Yong Du
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
- Center of Community-Based Health Research, Fudan University, Shanghai, China
| | - Meng Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
- Center of Community-Based Health Research, Fudan University, Shanghai, China
| | - Zhoufang Mei
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
- Center of Community-Based Health Research, Fudan University, Shanghai, China
| | - Yi Ding
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
- Center of Community-Based Health Research, Fudan University, Shanghai, China
| | - Jingjing Feng
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
- Center of Community-Based Health Research, Fudan University, Shanghai, China
| | - Moran Zhu
- Department of Pulmonary and Critical Care Medicine, Shanghai Pudong Hospital, Shanghai, China
| | - Fangxia Ge
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Qi Zhao
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Ruilan Wang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Zhijun Jie
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
- Center of Community-Based Health Research, Fudan University, Shanghai, China
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Peng G, Lin Y, Zou Q, Peng H, Lei A, Zou X, Xu Z, Sun H, Ning X, Huang M. Malassezia restricta as an unexpected cause of infectious osteomyelitis diagnosed by metagenomic sequencing: a case report and literature review. BMC Infect Dis 2024; 24:643. [PMID: 38926679 PMCID: PMC11210095 DOI: 10.1186/s12879-024-09512-9] [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: 01/18/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Malassezia restricta, a lipophilic and lipodependent yeast belonging to the basidiomycetes group, is an opportunistic fungal pathogen associated with various skin diseases, including seborrheic dermatitis and dandruff. Typically, Malassezia infection in neonates manifests as fungemia or hematogenous dissemination to the bone or lungs. However, vertebral osteomyelitis caused by these fungi is rarely reported owing to non-specific clinical presentations and laboratory/imaging findings. The Pathogen Metagenomics Sequencing (PMseq) technique enables direct high-throughput sequencing of infected specimens, facilitating the rapid and accurate detection of all microorganisms in clinical samples through comprehensive reports. CASE PRESENTATION A 52-year-old male was admitted to our hospital on July 20, 2022 with a 3-month history of ambulatory difficulties and localized low back pain. Magnetic Resonance Imaging (MRI) examination of the spinal column revealed irregular bone destruction affecting the L2, L3, and L5 vertebral bodies. Additionally, low T1 and high T2 intensity lesions were observed at the intervertebral discs between L3 and L5. The presumptive diagnosis of tuberculous spondylitis was made based on the imaging findings, despite negative results in all mycobacterium tests. However, the patient exhibited no improvement after receiving regular anti-tuberculosis treatment for 3 months. Subsequent MRI revealed an expansive abnormal signal within the vertebral body, leading to progressive bone destruction. The absence of spinal tuberculosis or other infective microorganisms was confirmed through culture from blood and pathological tissue from the L4 vertebral body. Subsequently, PMseq was performed on the specimens, revealing M. restricta as the predominant pathogen with the highest relative abundance value. The pathological examination revealed the presence of fungal mycelium in the L4 vertebral body, with positive findings on periodic Schiff-methenamine and periodic acid-Schiff staining. The anti-tuberculosis treatment was discontinued, and an antifungal combination of fluconazole and voriconazole was administered. All symptoms were resolved after 7 consecutive months of treatment, and the patient was able to ambulate autonomously. Vertebral lesions were reduced on MRI during the 13-month follow-up. CONCLUSIONS M. restricta is not a commonly recognized pathogen associated with infectious vertebral osteomyelitis. However, PMseq can aid in diagnosis, timely treatment, and decision making for some non-specific infectious diseases.
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Affiliation(s)
- Guoxuan Peng
- Department of Orthopaedics, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Yuan Lin
- Department of Orthopaedics, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
- School of Clinical Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Qiang Zou
- Department of Orthopaedics, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Hongcheng Peng
- Department of Orthopaedics, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
- School of Clinical Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Anyi Lei
- Department of Orthopaedics, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
- School of Clinical Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Xu Zou
- Department of Orthopaedics, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
- School of Clinical Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Zhe Xu
- School of Clinical Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
- Guihang Guiyang Hospital, Guiyang, 550006, Guizhou, China
| | - Hong Sun
- Department of Orthopaedics, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Xu Ning
- Department of Orthopaedics, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China
| | - Mingzhi Huang
- Department of Orthopaedics, Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, Guizhou, China.
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Chen H, Zhan M, Liu S, Balloux F, Wang H. Unraveling the potential of metagenomic next-generation sequencing in infectious disease diagnosis: Challenges and prospects. Sci Bull (Beijing) 2024; 69:1586-1589. [PMID: 38670851 DOI: 10.1016/j.scib.2024.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/12/2024] [Accepted: 02/22/2024] [Indexed: 04/28/2024]
Affiliation(s)
- Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Minghua Zhan
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Si Liu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Francois Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China.
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Cenzato N, Occhipinti C, D’amici E, Savadori P, Baldini B, Maspero C. Microbiological Analysis of Plaque and Its Composition in Three Patient Groups under Different Orthodontic Treatments. Dent J (Basel) 2024; 12:168. [PMID: 38920869 PMCID: PMC11203159 DOI: 10.3390/dj12060168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/17/2024] [Accepted: 05/31/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND This article analyzes differences in microbiological parameters and periodontal health conditions among three patient groups: those undergoing conventional orthodontic treatment with fixed appliances, patients undergoing orthodontic treatment with clear aligners, and a control group receiving no treatment. MATERIALS AND METHODS In this study, 60 patients were enrolled. The microbiological analysis employed a qualitative and semi-quantitative methodology of bacterial morphotype analysis. RESULTS The analyses revealed a significant difference in favor of clear oral and periodontal health aligners. This could be attributed to better bacterial biofilm removal and reduced mechanical stress on the periodontal ligament, factors facilitated by the ease of clear aligner removal. Significant differences (p-value < 0.05) were observed for the Full-Mouth Plaque Score, Full-Mouth Bleeding Score, Plaque Index, and periodontal health assessment measurements. CONCLUSIONS Although overall hygiene appears to be improved in patients in the aligners group compared to those treated with conventional orthodontic appliances, there are no statistically significant results regarding plaque composition. Microbiological aspects will be further addressed using more specific techniques in the follow-up of this research.
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Affiliation(s)
- Niccolò Cenzato
- Department of Biomedical, Surgical and Dental Sciences, School of Dentistry, University of Milan, 20122 Milan, Italy (C.O.); (E.D.); (C.M.)
- Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Chiara Occhipinti
- Department of Biomedical, Surgical and Dental Sciences, School of Dentistry, University of Milan, 20122 Milan, Italy (C.O.); (E.D.); (C.M.)
- Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Elena D’amici
- Department of Biomedical, Surgical and Dental Sciences, School of Dentistry, University of Milan, 20122 Milan, Italy (C.O.); (E.D.); (C.M.)
- Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Paolo Savadori
- Department of Biomedical, Surgical and Dental Sciences, School of Dentistry, University of Milan, 20122 Milan, Italy (C.O.); (E.D.); (C.M.)
- Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Benedetta Baldini
- Department of Electronics, Information and Bioengineering, Politecnico Di Milano, 20133 Milan, Italy;
| | - Cinzia Maspero
- Department of Biomedical, Surgical and Dental Sciences, School of Dentistry, University of Milan, 20122 Milan, Italy (C.O.); (E.D.); (C.M.)
- Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
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35
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Han D, Yu F, Zhang D, Hu J, Zhang X, Xiang D, Lou B, Chen Y, Zheng S. Molecular rapid diagnostic testing for bloodstream infections: Nanopore targeted sequencing with pathogen-specific primers. J Infect 2024; 88:106166. [PMID: 38670268 DOI: 10.1016/j.jinf.2024.106166] [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: 02/10/2024] [Revised: 04/01/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Nanopore sequencing, known for real-time analysis, shows promise for rapid clinical infection diagnosis but lacks effective assays for bloodstream infections (BSIs). METHODS We prospectively assessed the performance of a novel nanopore targeted sequencing (NTS) assay in identifying pathogens and predicting antibiotic resistance in BSIs, analyzing 387 blood samples from December 2021 to April 2023. RESULTS The positivity rate for NTS (69.5 %, 269/387) nearly matches that of metagenomic next-generation sequencing (mNGS) (74.7 %, 289/387; p = 0.128) and surpasses the positivity rate of conventional blood culture (BC) (33.9 %, 131/387; p < 0.01). Frequent pathogens detected by NTS included Klebsiella pneumoniae (n = 54), Pseudomonas aeruginosa (n = 36), Escherichia coli (n = 36), Enterococcus faecium(n = 30), Acinetobacter baumannii(n = 26), Staphylococcus aureus(n = 23), and Human cytomegalovirus (n = 37). Against a composite BSI diagnostic standard, NTS demonstrated a sensitivity and specificity of 84.0 % (95 % CI 79.5 %-87.7 %) and 90.1 % (95 % CI 81.7 %-88.5 %), respectively. The concordance between NTS and mNGS results (the percentage of total cases where both either detected BSI-related pathogens or were both negative) was 90.2 % (359/387), whereas the consistency between NTS and BC was only 60.2 % (233/387). In 80.6 % (50/62) of the samples with identical pathogens identified by both NTS tests and BCs, the genotypic resistance identified by NTS correlated with culture-confirmed phenotypic resistance. Using NTS, 95 % of samples can be tested and analyzed in approximately 7 h, allowing for early patient diagnosis. CONCLUSIONS NTS is rapid, sensitive, and efficient for detecting BSIs and drug-resistant genes, making it a potential preferred diagnostic tool for early infection identification in critically ill patients.
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Affiliation(s)
- Dongsheng Han
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, Zhejiang 310003, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Fei Yu
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, Zhejiang 310003, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Dan Zhang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, Zhejiang 310003, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Juan Hu
- Department of Critical Care Units, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Xuan Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Dairong Xiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Bin Lou
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, Zhejiang 310003, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yu Chen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, Zhejiang 310003, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.
| | - Shufa Zheng
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, Zhejiang 310003, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.
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Zhang H, Zhang P, Xiao Z, Gao Y, Han N, He X, Zhang J, Li Y. Hemophagocytic lymphohistiocytosis caused by herpes simplex virus type 1 in a young adult: a case report with literature review. J Hematop 2024; 17:91-96. [PMID: 38418769 DOI: 10.1007/s12308-024-00575-w] [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: 12/15/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
Hemophagocytic lymphohistiocytosis is a severe hyperinflammatory syndrome that can be potentially life-threatening without appropriate treatment. Although viral infection is the most common trigger of hemophagocytic lymphohistiocytosis, cases of herpes simplex virus type 1-induced hemophagocytic lymphohistiocytosis are rare in adults. This study aims to provide a comprehensive overview of the clinical characteristics and treatment outcomes associated with HSV-1-induced HLH. We herein report an adult case of hemophagocytic lymphohistiocytosis caused by herpes simplex virus type 1, diagnosed on the basis of peripheral blood metagenomic next-generation sequencing results. The patient exhibited a favorable response to treatment, involving dexamethasone, intravenous immunoglobulin, and acyclovir. Notably, etoposide administration was deemed unnecessary, and there has been no recurrence of the disease within the year following treatment. Early and sensitive recognition, rapid and precise diagnosis, and timely and appropriate treatment facilitated the successful treatment of this case.
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Affiliation(s)
- Hanqing Zhang
- Department of Hematology, General Hospital of Southern Theatre Command of PLA (People's Liberation Army), Guangzhou, 510010, China
- Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Peng Zhang
- Department of Hematology, General Hospital of Southern Theatre Command of PLA (People's Liberation Army), Guangzhou, 510010, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Zhifang Xiao
- Department of Hematology, General Hospital of Southern Theatre Command of PLA (People's Liberation Army), Guangzhou, 510010, China
| | - Yang Gao
- Department of Hematology, General Hospital of Southern Theatre Command of PLA (People's Liberation Army), Guangzhou, 510010, China
| | - Na Han
- Department of Hematology, General Hospital of Southern Theatre Command of PLA (People's Liberation Army), Guangzhou, 510010, China
| | - Xianjun He
- Department of Hematology, General Hospital of Southern Theatre Command of PLA (People's Liberation Army), Guangzhou, 510010, China
| | - Jinfeng Zhang
- Department of Hematology, General Hospital of Southern Theatre Command of PLA (People's Liberation Army), Guangzhou, 510010, China
| | - Yonghua Li
- Department of Hematology, General Hospital of Southern Theatre Command of PLA (People's Liberation Army), Guangzhou, 510010, China.
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, 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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Liu Y, Ma Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J Zhejiang Univ Sci B 2024; 25:471-484. [PMID: 38910493 PMCID: PMC11199093 DOI: 10.1631/jzus.b2300029] [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: 01/09/2023] [Accepted: 06/06/2023] [Indexed: 05/23/2024]
Abstract
Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
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Affiliation(s)
- Ying Liu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yongjun Ma
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China.
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Nurmukanova V, Matsvay A, Gordukova M, Shipulin G. Square the Circle: Diversity of Viral Pathogens Causing Neuro-Infectious Diseases. Viruses 2024; 16:787. [PMID: 38793668 PMCID: PMC11126052 DOI: 10.3390/v16050787] [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: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Neuroinfections rank among the top ten leading causes of child mortality globally, even in high-income countries. The crucial determinants for successful treatment lie in the timing and swiftness of diagnosis. Although viruses constitute the majority of infectious neuropathologies, diagnosing and treating viral neuroinfections remains challenging. Despite technological advancements, the etiology of the disease remains undetermined in over half of cases. The identification of the pathogen becomes more difficult when the infection is caused by atypical pathogens or multiple pathogens simultaneously. Furthermore, the modern surge in global passenger traffic has led to an increase in cases of infections caused by pathogens not endemic to local areas. This review aims to systematize and summarize information on neuroinvasive viral pathogens, encompassing their geographic distribution and transmission routes. Emphasis is placed on rare pathogens and cases involving atypical pathogens, aiming to offer a comprehensive and structured catalog of viral agents with neurovirulence potential.
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Affiliation(s)
- Varvara Nurmukanova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Alina Matsvay
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Maria Gordukova
- G. Speransky Children’s Hospital No. 9, 123317 Moscow, Russia
| | - German Shipulin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia
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Munson E. Biographical Feature: Charles Y. Chiu, M.D., Ph.D. J Clin Microbiol 2024; 62:e0140523. [PMID: 38619264 PMCID: PMC11077958 DOI: 10.1128/jcm.01405-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
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Osborn LJ, Fissel J, Gomez S, Mestas J, Flores-Vazquez J, Lee J, Hakimjavadi H, Costales C, Dien Bard J. Development of an automated amplicon-based next-generation sequencing pipeline for rapid detection of bacteria and fungi directly from clinical specimens. J Clin Microbiol 2024; 62:e0174923. [PMID: 38624235 PMCID: PMC11077995 DOI: 10.1128/jcm.01749-23] [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: 12/29/2023] [Accepted: 03/23/2024] [Indexed: 04/17/2024] Open
Abstract
The timely identification of microbial pathogens is essential to guide targeted antimicrobial therapy and ultimately, successful treatment of an infection. However, the yield of standard microbiology testing (SMT) is directly related to the duration of antecedent antimicrobial therapy as SMT culture methods are dependent on the recovery of viable organisms, the fastidious nature of certain pathogens, and other pre-analytic factors. In the last decade, metagenomic next-generation sequencing (mNGS) has been successfully utilized as a diagnostic tool for various applications within the clinical laboratory. However, mNGS is resource, time, and labor-intensive-requiring extensive laborious preliminary benchwork, followed by complex bioinformatic analysis. We aimed to address these shortcomings by developing a largely Automated targeted Metagenomic next-generation sequencing (tmNGS) PipeLine for rapId inFectIous disEase Diagnosis (AMPLIFIED) to detect bacteria and fungi directly from clinical specimens. Therefore, AMPLIFIED may serve as an adjunctive approach to complement SMT. This tmNGS pipeline requires less than 1 hour of hands-on time before sequencing and less than 2 hours of total processing time, including bioinformatic analysis. We performed tmNGS on 50 clinical specimens with concomitant cultures to assess feasibility and performance in the hospital laboratory. Of the 50 specimens, 34 (68%) were from true clinical infections. Specimens from cases of true infection were more often tmNGS positive compared to those from the non-infected group (82.4% vs 43.8%, respectively, P = 0.0087). Overall, the clinical sensitivity of AMPLIFIED was 54.6% with 85.7% specificity, equating to 70.6% and 75% negative and positive predictive values, respectively. AMPLIFIED represents a rapid supplementary approach to SMT; the typical time from specimen receipt to identification of potential pathogens by AMPLIFIED is roughly 24 hours which is markedly faster than the days, weeks, and months required to recover bacterial, fungal, and mycobacterial pathogens by culture, respectively. IMPORTANCE To our knowledge, this represents the first application of an automated sequencing and bioinformatics pipeline in an exclusively pediatric population. Next-generation sequencing is time-consuming, labor-intensive, and requires experienced personnel; perhaps contributing to hesitancy among clinical laboratories to adopt such a test. Here, we report a strong case for use by removing these barriers through near-total automation of our sequencing pipeline.
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Affiliation(s)
- Lucas J. Osborn
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - John Fissel
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Samantha Gomez
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Javier Mestas
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Jessica Flores-Vazquez
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Jaehyeon Lee
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Jeollabukdo, South Korea
| | - Hesamedin Hakimjavadi
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Cristina Costales
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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Lee J, Jeong H, Kang HG, Park J, Choi EY, Lee CS, Byeon SH, Kim M. Rapid Pathogen Detection in Infectious Uveitis Using Nanopore Metagenomic Next-Generation Sequencing: A Preliminary Study. Ocul Immunol Inflamm 2024; 32:463-469. [PMID: 36758246 DOI: 10.1080/09273948.2023.2173243] [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: 05/04/2022] [Revised: 12/09/2022] [Accepted: 01/22/2023] [Indexed: 02/11/2023]
Abstract
PURPOSE We establish an accurate and rapid diagnostic method for pathogen detection in infectious uveitis using nanopore metagenomic next-generation sequencing (NGS). METHODS In eight patients with suspected infectious uveitis, we prospectively compared the accuracy and time taken for pathogen identification between conventional diagnostic methods, such as cultures and PCR, and nanopore metagenomic NGS. RESULTS All causative pathogens were identified using nanopore sequencing, while only five of the eight patients were confirmed positive for a specific pathogen using conventional methods. The overall sample-to-answer turnaround time of nanopore sequencing was much shorter than that of conventional methods in the bacterial and fungal infection (mean, 17 h vs. 4d, respectively; P = .028). The pathogens could be detected even when the quantity or quality of DNA was not optimal. CONCLUSION Nanopore metagenomic NGS is a promising diagnostic tool that can rapidly and accurately identify the causative pathogen in infectious uveitis.
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Affiliation(s)
- Junwon Lee
- Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Han Jeong
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Goo Kang
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Jinkyu Park
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Young Choi
- Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Christopher Seungkyu Lee
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Suk Ho Byeon
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Min Kim
- Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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Adewusi OO, Waldner CL, Hanington PC, Hill JE, Freeman CN, Otto SJG. Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review. J Vet Diagn Invest 2024; 36:400-417. [PMID: 38456288 PMCID: PMC11110769 DOI: 10.1177/10406387241235968] [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] [Indexed: 03/09/2024] Open
Abstract
Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.
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Affiliation(s)
- Olufunto O. Adewusi
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L. Waldner
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Janet E. Hill
- Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N. Freeman
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J. G. Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
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Sun J, Xu X, Gao S, Pan Q, Liu Z, Huang Y, Lian Y. Refractory pneumonia caused by Prevotella heparinolytica: a case report. J Med Case Rep 2024; 18:213. [PMID: 38685076 PMCID: PMC11059698 DOI: 10.1186/s13256-024-04538-8] [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: 10/26/2023] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Prevotella heparinolytica is a Gram-negative bacterium that is commonly found in the oral, intestinal, and urinary tracts. It has been extensively studied in lower respiratory tract infections in horses, which has heparinolytic activity and can secrete heparinase and further induces virulence factors in cells and causes disease. However, no such cases have been reported in humans. CASE PRESENTATION A 58-year-old male patient from China presented to the respiratory clinic in Suzhou with a productive cough producing white sputum for 20 days and fever for 3 days. Prior to this visit, a chest computed tomography scan was conducted, which revealed multiple patchy nodular opacities in both lungs. On admission, the patient presented with a temperature of 38.1 °C and a pulse rate of 110 beats per minute. Despite routine anti-infective treatment with moxifloxacin, his temperature fluctuated and the treatment was ineffective. The patient was diagnosed with Prevotella heparinolytica infection through metagenomic next-generation sequencing. Therefore, the antibiotics were switched to piperacillin-tazobactam in combination with ornidazole, which alleviated his symptoms; 1 week after discharge, the patient returned to the clinic for a follow-up chest computed tomography, and the opacities on the lungs continued to be absorbed. CONCLUSION Prevotella heparinolytica is an opportunistic pathogen. However, it has not been reported in human pneumonia. In refractory pneumonia, measures such as metagenomic next-generation sequencing can be used to identify pathogens and help guide antibiotic selection and early support.
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Affiliation(s)
- Jiongzhou Sun
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Xun Xu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China.
| | - Shiyuan Gao
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Qiong Pan
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Zian Liu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yiwen Huang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yixin Lian
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China.
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Tang Z, Wang H, Liu Y, Wang C, Li X, Yang Q. Current status and new experimental diagnostic methods of invasive fungal infections after hematopoietic stem cell transplantation. Arch Microbiol 2024; 206:237. [PMID: 38678508 DOI: 10.1007/s00203-024-03905-9] [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: 01/24/2024] [Accepted: 02/19/2024] [Indexed: 05/01/2024]
Abstract
Invasive fungal infections (IFIs) are common and life-threatening complications in post-hematopoietic stem cell transplantation (post-HSCT) recipients, Severe IFIs can lead to systemic infection and organ damage, which results in high mortality in HSCT recipients. With the development of the field of fungal infection diagnosis, more and more advanced non-culture diagnostic tools have been developed, such as glip biosensors, metagenomic next-generation sequencing, Magnetic Nanoparticles and Identified Using SERS via AgNPs+ , and artificial intelligence-assisted diagnosis. The advanced diagnostic approaches contribute to the success of HSCT and improve the overall survival of post-HSCT leukemia patients by supporting therapeutical decisions. This review provides an overview of the characteristics of two high-incidence IFIs in post-HSCT recipients and discusses some of the recently developed IFI detection technologies. Additionally, it explores the potential application of cationic conjugated polymer fluorescence resonance energy transfer (CCP-FRET) technology for IFI detection. The aim is to offer insights into selecting appropriate IFI detection methods and gaining an understanding of novel fungal diagnostic approaches in laboratory settings.
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Affiliation(s)
- Zhenhua Tang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - HaiTao Wang
- Department of Hematology, The Fifth Medical Center of Chinese, PLA General Hospital, Beijing, 100071, China
| | - Yuankai Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Chen Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xinye Li
- Lanzhou Petrochemical General Hospital (The Fourth Affiliated Hospital of Gansu University of Chinese Medicine), Gansu, 730060, China.
| | - Qiong Yang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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Wang X, Zhang H, Zhang N, Zhang S, Shuai Y, Miao X, Liu Y, Qiu L, Ren S, Lai S, Han Y, Yao H, Zhang X, Fan F, Sun H, Yi H. Application value of metagenomic next-generation sequencing in hematological patients with high-risk febrile neutropenia. Front Cell Infect Microbiol 2024; 14:1366908. [PMID: 38725449 PMCID: PMC11079123 DOI: 10.3389/fcimb.2024.1366908] [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: 01/07/2024] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a novel non-invasive and comprehensive technique for etiological diagnosis of infectious diseases. However, its practical significance has been seldom reported in the context of hematological patients with high-risk febrile neutropenia, a unique patient group characterized by neutropenia and compromised immune responses. Methods This retrospective study evaluated the results of plasma cfDNA sequencing in 164 hematological patients with high-risk febrile neutropenia. We assessed the diagnostic efficacy and clinical impact of mNGS, comparing it with conventional microbiological tests. Results mNGS identified 68 different pathogens in 111 patients, whereas conventional methods detected only 17 pathogen types in 36 patients. mNGS exhibited a significantly higher positive detection rate than conventional methods (67.7% vs. 22.0%, P < 0.001). This improvement was consistent across bacterial (30.5% vs. 9.1%), fungal (19.5% vs. 4.3%), and viral (37.2% vs. 9.1%) infections (P < 0.001 for all comparisons). The anti-infective treatment strategies were adjusted for 51.2% (84/164) of the patients based on the mNGS results. Conclusions mNGS of plasma cfDNA offers substantial promise for the early detection of pathogens and the timely optimization of anti-infective therapies in hematological patients with high-risk febrile neutropenia.
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Affiliation(s)
- Xiao Wang
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Huiye Zhang
- School of Pharmacy, Chengdu Medical College, Chengdu, China
- Department of Pharmacy, Chengdu Eighth People’s Hospital, Chengdu, China
| | - Nan Zhang
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Shan Zhang
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Yanrong Shuai
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Xiaojuan Miao
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Yilan Liu
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Ling Qiu
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Shihui Ren
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Sihan Lai
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Ying Han
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Hao Yao
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Xupai Zhang
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Fangyi Fan
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Haoping Sun
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Hai Yi
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
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Wu MY, Chen L, Liu LC, Liu MJ, Li YF, Zheng HY, Leng L, Zou YJ, Chen WJ, Li J. Using circulating microbial cell-free DNA to identify persistent Treponema pallidum infection in serofast syphilis patients. iScience 2024; 27:109399. [PMID: 38523794 PMCID: PMC10959656 DOI: 10.1016/j.isci.2024.109399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/06/2024] [Accepted: 02/28/2024] [Indexed: 03/26/2024] Open
Abstract
The question of whether serofast status of syphilis patients indicates an ongoing low-grade Treponema pallidum (T. pallidum) infection remains unanswered. To address this, we developed a machine learning model to identify T. pallidum in cell-free DNA (cfDNA) using next-generation sequencing (NGS). Our findings showed that a TP_rate cut-off of 0.033 demonstrated superior diagnostic performance for syphilis, with a specificity of 92.3% and a sensitivity of 71.4% (AUROC = 0.92). This diagnosis model predicted that 20 out of 92 serofast patients had a persistent low-level infection. Based on these predictions, re-treatment was administered to these patients and its efficacy was evaluated. The results showed a statistically significant decrease in RPR titers in the prediction-positive group compared to the prediction-negative group after re-treatment (p < 0.05). These findings provide evidence for the existence of T. pallidum under serofast status and support the use of intensive treatment for serofast patients at higher risk in clinical practice.
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Affiliation(s)
- Meng Yin Wu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lu Chen
- Beijing Macro & Micro-test Bio-Tech Co., Ltd, Beijing 100083, China
| | - Li Cheng Liu
- Beijing Macro & Micro-test Bio-Tech Co., Ltd, Beijing 100083, China
| | - Ming Juan Liu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yan Feng Li
- Department of Neurology, Peking Union Medical College Hospital, Beijing 100730, China
| | - He Yi Zheng
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Ling Leng
- State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yi Jun Zou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Jun Chen
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Li
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Gu Y, Wang Z, Xia X, Zhao G. Nocardia farcinica brain abscess with torque teno virus co-infection: A case report. Heliyon 2024; 10:e28632. [PMID: 38590894 PMCID: PMC11000006 DOI: 10.1016/j.heliyon.2024.e28632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Background Brain abscesses caused by Nocardia are rare and difficult to diagnose. Nocardia farcinica is among the most common species; however, the conventional diagnosis of N. farcinica infection consists of cerebrospinal fluid (CSF) and blood culture and Gram staining. These procedures prolong the time to diagnosis and initiating treatment. Case presentation A 69-year-old woman with diabetes mellitus presented with headaches and dizziness persisting for 2 weeks, which was initially diagnosed as a brain abscess. Due to the unusual presentation and rapid progression of symptoms, she underwent surgical resection of the brain abscess. No pathogens were detected in blood or CSF cultures. However, metagenomic next-generation sequencing (mNGS) identified N. farcinica and Torque teno virus in pus extracted from the abscesses. The patient received appropriate antibiotic therapy and recovered fully without any residual neurological deficits. Conclusion mNGS useful for prompt diagnosis and selection of antibiotic therapy for brain abscesses caused by Nocardia. Surgical intervention is necessary in some cases.
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Affiliation(s)
- Yuting Gu
- Department of Emergency Medicine, The First People's Hospital of Kunshan, Kunshan, 215300, Jiangsu, China
- The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Zide Wang
- The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xiaohua Xia
- Department of Emergency Medicine, The First People's Hospital of Kunshan, Kunshan, 215300, Jiangsu, China
| | - Guang Zhao
- Department of Emergency Medicine, The First People's Hospital of Kunshan, Kunshan, 215300, Jiangsu, China
- The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
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Zhang D, Li X, Wang Y, Zhao Y, Zhang H. The clinical importance of metagenomic next-generation sequencing in detecting disease-causing microorganisms in cases of sepsis acquired in the community or hospital setting. Front Microbiol 2024; 15:1384166. [PMID: 38686114 PMCID: PMC11056561 DOI: 10.3389/fmicb.2024.1384166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024] Open
Abstract
Objectives Although metagenomic next-generation sequencing (mNGS) is commonly used for diagnosing infectious diseases, clinicians face limited options due to the high costs that are not covered by basic medical insurance. The goal of this research is to challenge this bias through a thorough examination and evaluation of the clinical importance of mNGS in precisely identifying pathogenic microorganisms in cases of sepsis acquired in the community or in hospitals. Methods A retrospective observational study took place at a tertiary teaching hospital in China from January to December 2021. Data on 308 sepsis patients were collected, and the performance of etiological examination was compared between mNGS and traditional culture method. Results Two hundred twenty-nine cases were observed in the community-acquired sepsis (CAS) group and 79 cases in the hospital-acquired sepsis (HAS) group. In comparison with conventional culture, mNGS showed a significantly higher rate of positivity in both the CAS group (88.21% vs. 25.76%, adj.P < 0.001) and the HAS group (87.34% vs. 44.30%, adj.P < 0.001), particularly across various infection sites and specimens, which were not influenced by factors like antibiotic exposure or the timing and frequency of mNGS technology. Sepsis pathogens detected by mNGS were broad, especially viruses, Mycobacterium tuberculosis, and atypical pathogens, with mixed pathogens being common, particularly bacterial-viral co-detection. Based on the optimization of antimicrobial therapy using mNGS, 58 patients underwent antibiotic de-escalation, two patients were switched to antiviral therapy, and 14 patients initiated treatment for tuberculosis, resulting in a reduction in antibiotic overuse but without significant impact on sepsis prognosis. The HAS group exhibited a critical condition, poor prognosis, high medical expenses, and variations in etiology, yet the mNGS results did not result in increased medical costs for either group. Conclusions mNGS demonstrates efficacy in identifying multiple pathogens responsible for sepsis, with mixed pathogens of bacteria and viruses being prevalent. Variability in microbiological profiles among different infection setting underscores the importance of clinical vigilance. Therefore, the adoption of mNGS for microbiological diagnosis of sepsis warrants acknowledgment and promotion.
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Affiliation(s)
| | | | | | | | - Hong Zhang
- Department of Emergency Medicine, The First Affiliated Hospital of Anhui Medical University, Anhui, Hefei, China
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Gan M, Zhang Y, Yan G, Wang Y, Lu G, Wu B, Chen W, Zhou W. Antimicrobial resistance prediction by clinical metagenomics in pediatric severe pneumonia patients. Ann Clin Microbiol Antimicrob 2024; 23:33. [PMID: 38622723 PMCID: PMC11020437 DOI: 10.1186/s12941-024-00690-7] [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: 11/08/2023] [Accepted: 03/26/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a major threat to children's health, particularly in respiratory infections. Accurate identification of pathogens and AMR is crucial for targeted antibiotic treatment. Metagenomic next-generation sequencing (mNGS) shows promise in directly detecting microorganisms and resistance genes in clinical samples. However, the accuracy of AMR prediction through mNGS testing needs further investigation for practical clinical decision-making. METHODS We aimed to evaluate the performance of mNGS in predicting AMR for severe pneumonia in pediatric patients. We conducted a retrospective analysis at a tertiary hospital from May 2022 to May 2023. Simultaneous mNGS and culture were performed on bronchoalveolar lavage fluid samples obtained from pediatric patients with severe pneumonia. By comparing the results of mNGS detection of microorganisms and antibiotic resistance genes with those of culture, sensitivity, specificity, positive predictive value, and negative predictive value were calculated. RESULTS mNGS detected bacterial in 71.7% cases (86/120), significantly higher than culture (58/120, 48.3%). Compared to culture, mNGS demonstrated a sensitivity of 96.6% and a specificity of 51.6% in detecting pathogenic microorganisms. Phenotypic susceptibility testing (PST) of 19 antibiotics revealed significant variations in antibiotics resistance rates among different bacteria. Sensitivity prediction of mNGS for carbapenem resistance was higher than penicillins and cephalosporin (67.74% vs. 28.57%, 46.15%), while specificity showed no significant difference (85.71%, 75.00%, 75.00%). mNGS also showed a high sensitivity of 94.74% in predicting carbapenem resistance in Acinetobacter baumannii. CONCLUSIONS mNGS exhibits variable predictive performance among different pathogens and antibiotics, indicating its potential as a supplementary tool to conventional PST. However, mNGS currently cannot replace conventional PST.
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Affiliation(s)
- Mingyu Gan
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China
| | - Yanyan Zhang
- Department of Neonatology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Gangfeng Yan
- Department of Critical Care Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China
| | - Yixue Wang
- Department of Critical Care Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China
| | - Guoping Lu
- Department of Critical Care Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China
| | - Weiming Chen
- Department of Critical Care Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China.
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China.
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510005, China.
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