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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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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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Ye J, Huang K, Xu Y, Chen N, Tu Y, Huang J, Shao L, Kong W, Zhao D, Xie Y. Clinical application of nanopore-targeted sequencing technology in bronchoalveolar lavage fluid from patients with pulmonary infections. Microbiol Spectr 2024; 12:e0002624. [PMID: 38687074 DOI: 10.1128/spectrum.00026-24] [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: 01/04/2024] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
The rapid and effective identification of pathogens in patients with pulmonary infections has posed a persistent challenge in medicine, with conventional microbiological tests (CMTs) proving time-consuming and less sensitive, hindering early diagnosis of respiratory infections. While there has been some research on the clinical performance of targeted sequencing technologies, limited focus has been directed toward bronchoalveolar lavage fluid (BALF). This study primarily evaluates the pathogen detection capabilities of nanopore-targeted sequencing (NTS) in BALF, providing a comprehensive analysis. The retrospective study, spanning from January 2022 to November 2023, includes 223 patients exclusively sourced from a single center. We conducted a detailed comparative analysis among NTS, targeted next-generation sequencing (tNGS), and CMTs. Initially, we compared the detection capabilities of NTS and tNGS and found no significant differences in their sensitivity and specificity. Specifically, we observed that the sensitivity of NTS was significantly higher than that of CMTs (74.83% vs 33.11%, P < 0.001). Furthermore, NTS exhibited a higher positivity rate in common pulmonary infections (62.88% vs. 23.48%) and in clinically suspected tuberculosis patients compared to CMTs (87.18% vs. 48.72%). Additionally, NTS showed less susceptibility to antibiotic interference, indicating a more sensitive detection capability, especially in detecting fastidious organisms. It complements GeneXpert in tuberculosis diagnosis and offers excellent advantages in identifying pathogens challenging for CMTs, such as non-tuberculous mycobacteria and viruses. Moreover, NTS significantly shortens the reporting time and is only a quarter of the cost of metagenomic next-generation sequencing. Clearly, NTS can facilitate faster and more cost-effective early diagnosis of respiratory infections.IMPORTANCEThis study holds paramount significance in advancing the field of respiratory infection diagnostics. By assessing the pathogen detection capabilities in bronchoalveolar lavage fluid (BALF) of patients with pulmonary infections, we illuminate the promising potential of nanopore-targeted sequencing (NTS). The findings underscore NTS as a comparable yet distinct alternative to traditional methods like comprehensive conventional microbiological tests (CMTs). Notably, NTS demonstrates a pivotal edge, expanding the spectrum of identified pathogens, particularly excelling in the detection of challenging entities like non-tuberculous mycobacteria and viruses. The study also highlights the complementary role of NTS alongside GeneXpert in the identification of tuberculosis, providing a comprehensive overview of the diagnostic landscape for respiratory infections. This insight carries significant implications for clinicians seeking rapid, cost-effective, and accurate diagnostic tools in the realm of pulmonary infections.
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Affiliation(s)
- Jiayuan Ye
- Health Science Center, Ningbo University, Ningbo, Zhejiang, China
- Department of Infectious Diseases, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Kai Huang
- Department of General Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Yaojiang Xu
- Department of Infectious Diseases, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Nan Chen
- Department of Infectious Diseases, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Yifei Tu
- Department of Radiology, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Jing Huang
- Department of Respiratory, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Longfei Shao
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Weiliang Kong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Dongdong Zhao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yilian Xie
- Department of Infectious Diseases, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
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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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Fu Y, Gu J, Chen LJ, Xiong M, Zhao J, Xiao X, Zhou J, Li Z, Li Y. A prospective study of nanopore-targeted sequencing in the diagnosis of central nervous system infections. Microbiol Spectr 2024; 12:e0331723. [PMID: 38294222 PMCID: PMC10913467 DOI: 10.1128/spectrum.03317-23] [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: 09/08/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Central nervous system (CNS) infections are a leading cause of death in patients. Nanopore-targeted sequencing (NTS) has begun to be used for pathogenic microbial detection. This study aims to evaluate the ability of NTS in the detection of pathogens in cerebrospinal fluid (CSF) through a prospective study. Fifty CSF specimens collected from 50 patients with suspected CNS infections went through three methods including NTS, metagenomic next-generation sequencing (mNGS), and microbial culture in parallel. When there was an inconsistency between NTS results and the results of the mNGS, the 16S rDNA gene was amplified followed by Sanger sequencing to further verify pathogens detected by NTS. Among 50 CSF specimens, 76% were NTS-positive, which is lower than mNGS (94.0%), yet higher than microbial culture (16.0%). The overall validation rate, diagnostic accordance rate (DAR), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of NTS were 86.7%, 50.0%, 71.0%, 15.8%, 57.9%, and 25.0%, respectively. In the CSF total nucleated cell (TNC) number ≤10 cells/µL, DAR, specificity, and PPV were 20%, 11.1%, and 11.1%, whereas in that with CSF TNC number >10 cells/µL, DAR, sensitivity, specificity, PPV, and NPV were 57.5%, 70.0%, 20.0%, 72.4%, and 18.2%, respectively. Although NTS has a higher microbial detection rate than microbial culture, it should combine CSF TNC result to evaluate the value of NTS for the diagnosis of CNS infections. IMPORTANCE This study aims to prospectively evaluate the ability of nanopore-targeted sequencing (NTS) in the detection of pathogens in cerebrospinal fluid (CSF). It was the first time combining mNGS and microbial culture to verify the NTS-positive results also using 16S rDNA amplification with Sanger sequencing. Although microbial culture was thought to be the gold standard for pathogens detection and diagnosis of infectious diseases, this study suggested that microbial culture of CSF is not the most appropriate way for diagnosing central nervous system (CNS) infection. NTS should be recommended to be used in CSF for diagnosing CNS infection. When evaluating the value of NTS for diagnosis of CNS infections, the results of CSF TNC should be combined, and NTS-positive result is observed to be more reliable in patients with CSF TNC level >10 cells/μL.
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Affiliation(s)
- Yu Fu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jihong Gu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liang-Jun Chen
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mengyuan Xiong
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jin Zhao
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiao Xiao
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Junying Zhou
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yirong Li
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan, China
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Yang X, Zhou S, Chang Z, Xi X, Li J, Miao M, Chen Y, Chen W, Zhang H, Ding R, Hu Z. Nanopore targeted sequencing-based diagnosis of central nervous system infections in HIV-infected patients. Ann Clin Microbiol Antimicrob 2024; 23:22. [PMID: 38424544 PMCID: PMC10905896 DOI: 10.1186/s12941-024-00682-7] [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: 10/10/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Early and accurate etiological diagnosis is very important for improving the prognosis of central nervous system (CNS) infections in human immunodeficiency virus (HIV)-infected patients. The goal is not easily achieved by conventional microbiological tests. We developed a nanopore targeted sequencing (NTS) platform and evaluated the diagnostic performance for CNS infections in HIV-infected patients, with special focus on cryptococcal meningitis (CM). We compared the CM diagnostic performance of NTS with conventional methods and cryptococcal polymerase chain reaction (PCR). METHODS This study included 57 hospitalized HIV-infected patients with suspected CNS infections from September 2018 to March 2022. The diagnosis established during hospitalization includes 27 cases of CM, 13 CNS tuberculosis, 5 toxoplasma encephalitis, 2 cytomegalovirus (CMV) encephalitis and 1 Varicella-zoster virus (VZV) encephalitis. The 2 cases of CMV encephalitis also have co-existing CM. Target-specific PCR amplification was used to enrich pathogen sequences before nanopore sequencing. NTS was performed on stored cerebrospinal fluid (CSF) samples and the results were compared with the diagnosis during hospitalization. RESULTS 53 (93.0%) of the patients were male. The median CD4 cell count was 25.0 (IQR: 14.0-63.0) cells/uL. The sensitivities of CSF culture, India ink staining, cryptococcal PCR and NTS for CM were 70.4% (95%CI: 51.5 - 84.1%), 76.0% (95%CI: 56.6 - 88.5%), 77.8% (59.2 - 89.4%) and 85.2% (95%CI: 67.5 - 94.1%), respectively. All those methods had 100% specificity for CM. Our NTS platform could identify Cryptococcus at species level. Moreover, NTS was also able to identify all the 5 cases of toxoplasma encephalitis, 2 cases of CMV encephalitis and 1 VZV encephalitis. However, only 1 of 13 CNS tuberculosis cases was diagnosed by NTS, and so did Xpert MTB/RIF assay. CONCLUSIONS NTS has a good diagnostic performance for CM in HIV-infected patients and may have the ability of simultaneously detecting other pathogens, including mixed infections. With continuing improving of the NTS platform, it may be a promising alterative microbiological test for assisting with the diagnosis of CNS infections.
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Affiliation(s)
- Xihong Yang
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shuilian Zhou
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Pharmaceutical Co.,Ltd, Jiangsu Simcere Diagnostics Co.,Ltd., Nanjing, China
- Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Ziwei Chang
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaotong Xi
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Pharmaceutical Co.,Ltd, Jiangsu Simcere Diagnostics Co.,Ltd., Nanjing, China
- Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Jiahui Li
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Mengjiao Miao
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yaling Chen
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Chen
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongying Zhang
- Nanjing Center for Disease Control and Prevention, Nanjing Medical University, Nanjing, China.
| | - Ran Ding
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Pharmaceutical Co.,Ltd, Jiangsu Simcere Diagnostics Co.,Ltd., Nanjing, China.
- Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China.
| | - Zhiliang Hu
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China.
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
- Inovention Center for Infectious Disease of Jiangsu Province, Nanjing, China.
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Yu G, Shen Y, Yao L, Xu X. Evaluation of Nanopore Sequencing for Diagnosing Pulmonary Tuberculosis Using Negative Smear Clinical Specimens. Infect Drug Resist 2024; 17:673-682. [PMID: 38405053 PMCID: PMC10887957 DOI: 10.2147/idr.s442229] [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: 10/24/2023] [Accepted: 02/13/2024] [Indexed: 02/27/2024] Open
Abstract
Purpose This study aimed to evaluate the efficacy of nanopore sequencing for diagnosing pulmonary tuberculosis (PTB) using smear-negative clinical specimens. Methods We conducted a retrospective study based on a review of patient medical records to assess the accuracy of nanopore sequencing as a diagnostic tool for smear-negative PTB. Compared with clinical diagnosis, we determined the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the curve (AUC) of nanopore sequencing. Results A total of 647 patients were evaluated. Nanopore sequencing demonstrated an overall sensitivity of 91.7%, specificity of 85.3%, PPV of 95.1%, NPV of 76.4%, and AUC of 0.88. Notably, the overall diagnostic accuracy of nanopore sequencing was significantly higher than that of Mycobacterium tuberculosis (MTB) culture technique. Conclusion Nanopore sequencing exhibited satisfactory overall diagnostic accuracy for smear-negative PTB, regardless of MTB culture status. Therefore, if conditions permit, nanopore sequencing is recommended as a diagnostic method for smear-negative PTB.
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Affiliation(s)
- Guocan Yu
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Hangzhou Red Cross Hospital, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Yanqin Shen
- Department of Nursing, Hangzhou Red Cross Hospital, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Liwei Yao
- Department of Nursing, Hangzhou Red Cross Hospital, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Xudong Xu
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Hangzhou Red Cross Hospital, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
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Lin Q, Yao Y, Li X, Zhang S, Guo H, Ma X, Chen W, Ru C, Wang L, Wang B, Ma Q, Zhu J, Lin X, Chen Q, Lou H, Chen Q, Chen J, Zeng Z, Zhou J, Chen Y, Yu Y, Zhou H. The application of nanopore targeted sequencing for pathogen diagnosis in bronchoalveolar lavage fluid of patients with pneumonia: a prospective multicenter study. Infect Dis (Lond) 2024; 56:128-137. [PMID: 37934028 DOI: 10.1080/23744235.2023.2276785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023] Open
Abstract
OBJECTIVE To evaluate the value of nanopore targeted sequencing in diagnosing pneumonia pathogens. METHODS This large-scale multicentre prospective study performed in 8 hospitals across China from April to October 2022. Hospitalised patients with a diagnosis of pneumonia at admission were included. Complete clinical data were collected, and bronchoalveolar lavage fluid were obtained from each patient. These samples underwent simultaneous testing using conventional microbial testing, metagenomic next-generation sequencing, and nanopore targeted sequencing. RESULTS A total of 218 patients were included. Among the 168 cases of pulmonary infection, 246 strains of pathogens were confirmed. Nanopore targeted sequencing outperformed conventional microbial testing, identifying more pathogens with a sensitivity increase of 47.9% (77.2% vs. 29.3%). Metagenomic next-generation sequencing had a sensitivity of 82.9%. Total of 70.1% patients had consistent results in both metagenomic next-generation sequencing and nanopore targeted sequencing. Nanopore targeted sequencing exhibited significantly higher sensitivity in detecting Pneumocystis jiroveci, cytomegalovirus, Mycobacterium tuberculosis, Nontuberculous mycobacteria, Streptococcus pneumoniae, and Mycoplasma pneumoniae compared to conventional microbial testing. However, metagenomic next-generation sequencing demonstrated higher sensitivity than nanopore targeted sequencing for Aspergillus (88.5% vs. 53.8%). Regarding the detection of co-infections, nanopore targeted sequencing displayed significantly higher sensitivity than conventional microbial testing (76.7% vs. 28.7%) and was on par with metagenomic next-generation sequencing (76.7% vs. 82.9%). CONCLUSION Nanopore targeted sequencing performs equally well as metagenomic next-generation sequencing in bronchoalveolar lavage fluid for pathogen diagnosis in pneumonia, both methods showing higher sensitivity than conventional microbial testing. Nanopore targeted sequencing can be considered a reliable method for diagnosing pathogens in pneumonia.
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Affiliation(s)
- Qinqing Lin
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Critical Care Medicine, Affiliated Hospital of Shaoxing University, Shaoxing, China
| | - Yake Yao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xi Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Shanshan Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Respiratory and Critical Care Medicine, Beilun People's Hospital, Ningbo, China
| | - Huimin Guo
- Zhejiang Digena Diagnosis Technology CO., Ltd., Hangzhou, Zhejiang, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Xiaolong Ma
- Department of Respiratory and Critical Care Medicine, The First Hospital of JiaXing, JiaXing, China
| | - Wenyu Chen
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Chuhui Ru
- Department of Respiratory and Critical Care Medicine, Red Cross Society Hospital of Hangzhou, Hangzhou, China
| | - Limin Wang
- Department of Respiratory and Critical Care Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bin Wang
- Department of Respiratory and Critical Care Medicine, Huzhou Central Hospital, Huzhou, China
| | - Qiang Ma
- Department of Respiratory and Critical Care Medicine, The Second People's Hospital of Yuhang District, Hangzhou, China
| | - Junfei Zhu
- Department of Respiratory and Critical Care Medicine, Taizhou Central Hospital, Taizhou, China
| | - Xuemei Lin
- Department of Respiratory and Critical Care Medicine, Jiangshan People's Hospital, Quzhou, China
| | - Qi Chen
- Zhejiang Digena Diagnosis Technology CO., Ltd., Hangzhou, Zhejiang, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Hui Lou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Junjun Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhu Zeng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianying Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Chen
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Kuruwa S, Zade A, Shah S, Moidu R, Lad S, Chande C, Joshi A, Hirani N, Nikam C, Bhattacharya S, Poojary A, Kapoor M, Kondabagil K, Chatterjee A. An integrated method for targeted Oxford Nanopore sequencing and automated bioinformatics for the simultaneous detection of bacteria, fungi, and ARG. J Appl Microbiol 2024; 135:lxae037. [PMID: 38346849 DOI: 10.1093/jambio/lxae037] [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: 08/30/2023] [Revised: 01/26/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
AIMS The use of metagenomics for pathogen identification in clinical practice has been limited. Here we describe a workflow to encourage the clinical utility and potential of NGS for the screening of bacteria, fungi, and antimicrobial resistance genes (ARGs). METHODS AND RESULTS The method includes target enrichment, long-read sequencing, and automated bioinformatics. Evaluation of several tools and databases was undertaken across standard organisms (n = 12), clinical isolates (n = 114), and blood samples from patients with suspected bloodstream infections (n = 33). The strategy used could offset the presence of host background DNA, error rates of long-read sequencing, and provide accurate and reproducible detection of pathogens. Eleven targets could be successfully tested in a single assay. Organisms could be confidently identified considering ≥60% of best hits of a BLAST-based threshold of e-value 0.001 and a percent identity of >80%. For ARGs, reads with percent identity of >90% and >60% overlap of the complete gene could be confidently annotated. A kappa of 0.83 was observed compared to standard diagnostic methods. Thus, a workflow for the direct-from-sample, on-site sequencing combined with automated genomics was demonstrated to be reproducible. CONCLUSION NGS-based technologies overcome several limitations of current day diagnostics. Highly sensitive and comprehensive methods of pathogen screening are the need of the hour. We developed a framework for reliable, on-site, screening of pathogens.
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Affiliation(s)
- Sanjana Kuruwa
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Amrutraj Zade
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanchi Shah
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rameez Moidu
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shailesh Lad
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Chhaya Chande
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Ameeta Joshi
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Nilma Hirani
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Chaitali Nikam
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- Thyrocare Technologies Pvt. Ltd, Navi Mumbai 400703, India
| | - Sanjay Bhattacharya
- Department of Microbiology, Tata Medical Center, 14, MAR(E-W), DH Block (Newtown), Action Area I, Newtown, Kolkata, Chakpachuria 700160, India
| | - Aruna Poojary
- Department of Microbiology, Breach Candy Hospital and Research Center, Mumbai 400026, India
| | - Mahua Kapoor
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Kiran Kondabagil
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anirvan Chatterjee
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Yao Z, Liu Y, Zhan L, Qiu T, Li G, Chen Z, Fang X, Liu Z, Wu W, Liao Z, Xia W. The utilization of nanopore targeted sequencing proves to be advantageous in the identification of infections present in deceased donors. Front Microbiol 2023; 14:1238666. [PMID: 37664117 PMCID: PMC10469296 DOI: 10.3389/fmicb.2023.1238666] [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: 06/12/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023] Open
Abstract
Background Nanopore Target Sequencing (NTS) represents a novel iteration of gene sequencing technology; however, its potential utility in the detection of infection in deceased donors has yet to be documented. The present study endeavors to assess the applicability of NTS in this domain. Methods This retrospective study comprised a cohort of 71 patients who were under intensive care at Renmin Hospital of Wuhan University between June 2020 and January 2022. The specimens were subjected to microbiological tests utilizing NTS, culture, and other techniques, and subsequently, the diagnostic accuracy of NTS was compared with conventional methods. Results Blood NTS exhibited a better agreement rate of 52.11% and a greater positive rate of pathogen detection than blood culture (50.70% vs. 5.63%, p < 0.001). In NTS of deceased donors, Klebsiella pneumoniae, Escherichia coli, and Acinetobacter baumannii were the most frequently found bacteria, and Candida was the most frequently found fungus. Blood NTS had a considerably better sensitivity for detecting clinical bloodstream infection than blood culture (62.50%: 7.14%, p < 0.001). These findings were supported by comparisons between blood NTS and conventional microbial detection methods (such as blood culture, glucan testing, galactomannan testing, T cell spot testing for tuberculosis infection, smear, etc.). Conclusion The pathogen detection technology NTS has a high sensitivity and positive rate. It can more accurately and earlier detect infection in deceased donors, which could be very important for raising the donation conversion rate.
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Affiliation(s)
- Zhiyuan Yao
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yu Liu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
- Cardiovascular Research Institute of Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Cardiology, Wuhan, Hubei, China
| | - Liying Zhan
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Tao Qiu
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Guang Li
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhongbao Chen
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiaoyu Fang
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhou Liu
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wei Wu
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhaomin Liao
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wenfang Xia
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
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11
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Li X, Li Z, Wang M, Fu A, Hao X, Guo X, Gu J, Jin W, Yang A. The diagnostic utility of nanopore targeted sequencing in suspected endophthalmitis. Int Ophthalmol 2023; 43:2653-2668. [PMID: 36941506 PMCID: PMC10371907 DOI: 10.1007/s10792-023-02665-7] [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: 10/26/2022] [Accepted: 02/19/2023] [Indexed: 03/23/2023]
Abstract
PURPOSE This paper aimed to assess the diagnostic utility of a newly developed gene-based technology-nanopore targeted sequencing (NTS) in suspected endophthalmitis patients. METHODS This retrospective study included 43 patients (44 eyes) with suspected endophthalmitis. NTS was applied along with microbiological culture to detect unknown pathogens in intraocular fluid samples. The diagnostic utility of NTS was mainly evaluated from three aspects, including the positivity rate of bacterial/fungal presence, diagnostic turnaround time and the frequency of change in treatment based on etiology test results. Non-parametric, two-sided Wilcoxon rank sum test, the McNemar's test and the kappa statistic were used for statistical comparisons. RESULTS NTS showed significant advantages over traditional culture in positivity rates and diagnostic time (P < 0.001, kappa = 0.082; Z = -5.805, P < 0. 001). As regards antibiotic strategy, 17 patients (39.53%) and 5 patients (11.63%) underwent medication change following NTS and culture results respectively (P < 0.001, kappa = 0.335). With reasonable use of antibiotic and surgical intervention, most patients responded favorably, judged by significantly improved visual acuity (Z = -4.249, P < 0.001). The mean duration of hospitalization was 8.49 ± 2.45 days (range, 1-16 days). CONCLUSION The high efficiency feature of NTS in pathogen detection renders it a valuable supplementary to traditional culture. Additionally, it has facilitated patients' management for the early and precise diagnosis of endophthalmitis.
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Affiliation(s)
- Xuejie Li
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Ziyue Li
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Ming Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, China
| | - Aisi Fu
- Wuhan Dgensee Clinical Laboratory Co, Ltd. Wuhan 430075, Hubei Province, China
| | - Xinlei Hao
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Xinyang Guo
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China
| | - Jiashuang Gu
- Wuhan Dgensee Clinical Laboratory Co, Ltd. Wuhan 430075, Hubei Province, China
| | - Wei Jin
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China.
| | - Anhuai Yang
- Eye Center, Renmin Hospital of Wuhan University, Jiefang Road 238#, Wuhan, 430060, Hubei Province, China.
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12
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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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Ring N, Low AS, Wee B, Paterson GK, Nuttall T, Gally D, Mellanby R, Fitzgerald JR. Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections. Microb Genom 2023; 9:mgen001066. [PMID: 37471128 PMCID: PMC10438823 DOI: 10.1099/mgen.0.001066] [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: 02/16/2023] [Accepted: 06/18/2023] [Indexed: 07/21/2023] Open
Abstract
Antimicrobial resistance is a major threat to human and animal health. There is an urgent need to ensure that antimicrobials are used appropriately to limit the emergence and impact of resistance. In the human and veterinary healthcare setting, traditional culture and antimicrobial sensitivity testing typically requires 48-72 h to identify appropriate antibiotics for treatment. In the meantime, broad-spectrum antimicrobials are often used, which may be ineffective or impact non-target commensal bacteria. Here, we present a rapid, culture-free, diagnostics pipeline, involving metagenomic nanopore sequencing directly from clinical urine and skin samples of dogs. We have planned this pipeline to be versatile and easily implementable in a clinical setting, with the potential for future adaptation to different sample types and animals. Using our approach, we can identify the bacterial pathogen present within 5 h, in some cases detecting species which are difficult to culture. For urine samples, we can predict antibiotic sensitivity with up to 95 % accuracy. Skin swabs usually have lower bacterial abundance and higher host DNA, confounding antibiotic sensitivity prediction; an additional host depletion step will likely be required during the processing of these, and other types of samples with high levels of host cell contamination. In summary, our pipeline represents an important step towards the design of individually tailored veterinary treatment plans on the same day as presentation, facilitating the effective use of antibiotics and promoting better antimicrobial stewardship.
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Affiliation(s)
- Natalie Ring
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Alison S. Low
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Bryan Wee
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Gavin K. Paterson
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Tim Nuttall
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - David Gally
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Richard Mellanby
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
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14
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Șoldănescu I, Lobiuc A, Covașă M, Dimian M. Detection of Biological Molecules Using Nanopore Sensing Techniques. Biomedicines 2023; 11:1625. [PMID: 37371721 PMCID: PMC10295350 DOI: 10.3390/biomedicines11061625] [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: 05/16/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Modern biomedical sensing techniques have significantly increased in precision and accuracy due to new technologies that enable speed and that can be tailored to be highly specific for markers of a particular disease. Diagnosing early-stage conditions is paramount to treating serious diseases. Usually, in the early stages of the disease, the number of specific biomarkers is very low and sometimes difficult to detect using classical diagnostic methods. Among detection methods, biosensors are currently attracting significant interest in medicine, for advantages such as easy operation, speed, and portability, with additional benefits of low costs and repeated reliable results. Single-molecule sensors such as nanopores that can detect biomolecules at low concentrations have the potential to become clinically relevant. As such, several applications have been introduced in this field for the detection of blood markers, nucleic acids, or proteins. The use of nanopores has yet to reach maturity for standardization as diagnostic techniques, however, they promise enormous potential, as progress is made into stabilizing nanopore structures, enhancing chemistries, and improving data collection and bioinformatic analysis. This review offers a new perspective on current biomolecule sensing techniques, based on various types of nanopores, challenges, and approaches toward implementation in clinical settings.
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Affiliation(s)
- Iuliana Șoldănescu
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Stefan cel Mare University of Suceava, 720229 Suceava, Romania; (I.Ș.); (M.D.)
| | - Andrei Lobiuc
- Department of Biomedical Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Covașă
- Department of Biomedical Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Dimian
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Stefan cel Mare University of Suceava, 720229 Suceava, Romania; (I.Ș.); (M.D.)
- Department of Computer, Electronics and Automation, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
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15
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Qian P, He X, Yang M, Wei L, Zhang L, Xing X. Detection of Severe Murine Typhus by Nanopore Targeted Sequencing, China. Emerg Infect Dis 2023; 29:1275-1277. [PMID: 37209688 DOI: 10.3201/eid2906.221929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
We report a case of murine typhus in China caused by Rickettsia typhi and diagnosed by nanopore targeted sequencing of a bronchoalveolar lavage fluid sample. This case highlights that nanopore targeted sequencing can effectively detect clinically unexplained infections and be especially useful for detecting infections in patients without typical signs and symptoms.
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16
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Jiang S, Wei Y, Ke H, Song C, Liao W, Meng L, Sun C, Zhou J, Wang C, Su X, Dong C, Xiong Y, Yang S. Building a nomogram plot based on the nanopore targeted sequencing for predicting urinary tract pathogens and differentiating from colonizing bacteria. Front Cell Infect Microbiol 2023; 13:1142426. [PMID: 37265501 PMCID: PMC10229875 DOI: 10.3389/fcimb.2023.1142426] [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: 01/11/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Background The identification of uropathogens (UPBs) and urinary tract colonizing bacteria (UCB) conduces to guide the antimicrobial therapy to reduce resistant bacterial strains and study urinary microbiota. This study established a nomogram based on the nanopore-targeted sequencing (NTS) and other infectious risk factors to distinguish UPB from UCB. Methods Basic information, medical history, and multiple urine test results were continuously collected and analyzed by least absolute shrinkage and selection operator (LASSO) regression, and multivariate logistic regression was used to determine the independent predictors and construct nomogram. Receiver operating characteristics, area under the curve, decision curve analysis, and calibration curves were used to evaluate the performance of the nomogram. Results In this study, the UPB detected by NTS accounted for 74.1% (401/541) of all urinary tract microorganisms. The distribution of ln(reads) between UPB and UCB groups showed significant difference (OR = 1.39; 95% CI, 1.246-1.551, p < 0.001); the reads number in NTS reports could be used for the preliminary determination of UPB (AUC=0.668) with corresponding cutoff values being 7.042. Regression analysis was performed to determine independent predictors and construct a nomogram, with variables ranked by importance as ln(reads) and the number of microbial species in the urinary tract of NTS, urine culture, age, urological neoplasms, nitrite, and glycosuria. The calibration curve showed an agreement between the predicted and observed probabilities of the nomogram. The decision curve analysis represented that the nomogram would benefit clinical interventions. The performance of nomogram with ln(reads) (AUC = 0.767; 95% CI, 0.726-0.807) was significantly better (Z = 2.304, p-value = 0.021) than that without ln(reads) (AUC = 0.727; 95% CI, 0.681-0.772). The rate of UPB identification of nomogram was significantly higher than that of ln(reads) only (χ2 = 7.36, p-value = 0.009). Conclusions NTS is conducive to distinguish uropathogens from colonizing bacteria, and the nomogram based on NTS and multiple independent predictors has better prediction performance of uropathogens.
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Affiliation(s)
- Shengming Jiang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yangyan Wei
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hu Ke
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chao Song
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wenbiao Liao
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lingchao Meng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chang Sun
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jiawei Zhou
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chuan Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaozhe Su
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Caitao Dong
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yunhe Xiong
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Sixing Yang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
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17
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Kamau E, Yang S. Metagenomic Sequencing of Positive Blood Culture Fluid for Accurate Bacterial and Fungal Species Identification: A Pilot Study. Microorganisms 2023; 11:1259. [PMID: 37317232 DOI: 10.3390/microorganisms11051259] [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: 04/03/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 06/16/2023] Open
Abstract
With blood stream infections (BSIs) representing a major cause of mortality and morbidity worldwide, blood cultures play a crucial role in diagnosis, but their clinical application is dampened by the long turn-around time and the detection of only culturable pathogens. In this study, we developed and validated a shotgun metagenomics next-generation sequencing (mNGS) test directly from positive blood culture fluid, allowing for the identification of fastidious or slow growing microorganisms more rapidly. The test was built based on previously validated next-generation sequencing tests, which rely on several key marker genes for bacterial and fungal identification. The new test utilizes an open-source metagenomics CZ-ID platform for the initial analysis to generate the most likely candidate species, which is then used as a reference genome for downstream, confirmatory analysis. This approach is innovative because it takes advantage of an open-source software's agnostic taxonomic calling capability while still relying on the more established and previously validated marker gene-based identification scheme, increasing the confidence in the final results. The test showed high accuracy (100%, 30/30) for both bacterial and fungal microorganisms. We further demonstrated its clinical utility especially for anaerobes and mycobacteria that are either fastidious, slow growing, or unusual. Although applicable in only limited settings, the Positive Blood Culture mNGS test provides an incremental improvement in solving the unmet clinical needs for the diagnosis of challenging BSIs.
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Affiliation(s)
- Edwin Kamau
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
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18
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Altindiş M, Kahraman Kilbaş EP. Managing Viral Emerging Infectious Diseases via Current and Future Molecular Diagnostics. Diagnostics (Basel) 2023; 13:diagnostics13081421. [PMID: 37189522 DOI: 10.3390/diagnostics13081421] [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: 03/29/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Emerging viral infectious diseases have been a constant threat to global public health in recent times. In managing these diseases, molecular diagnostics has played a critical role. Molecular diagnostics involves the use of various technologies to detect the genetic material of various pathogens, including viruses, in clinical samples. One of the most commonly used molecular diagnostics technologies for detecting viruses is polymerase chain reaction (PCR). PCR amplifies specific regions of the viral genetic material in a sample, making it easier to detect and identify viruses. PCR is particularly useful for detecting viruses that are present in low concentrations in clinical samples, such as blood or saliva. Another technology that is becoming increasingly popular for viral diagnostics is next-generation sequencing (NGS). NGS can sequence the entire genome of a virus present in a clinical sample, providing a wealth of information about the virus, including its genetic makeup, virulence factors, and potential to cause an outbreak. NGS can also help identify mutations and discover new pathogens that could affect the efficacy of antiviral drugs and vaccines. In addition to PCR and NGS, there are other molecular diagnostics technologies that are being developed to manage emerging viral infectious diseases. One of these is CRISPR-Cas, a genome editing technology that can be used to detect and cut specific regions of viral genetic material. CRISPR-Cas can be used to develop highly specific and sensitive viral diagnostic tests, as well as to develop new antiviral therapies. In conclusion, molecular diagnostics tools are critical for managing emerging viral infectious diseases. PCR and NGS are currently the most commonly used technologies for viral diagnostics, but new technologies such as CRISPR-Cas are emerging. These technologies can help identify viral outbreaks early, track the spread of viruses, and develop effective antiviral therapies and vaccines.
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Affiliation(s)
- Mustafa Altindiş
- Medical Microbiology Department, Faculty of Medicine, Sakarya University, Sakarya 54050, Türkiye
| | - Elmas Pınar Kahraman Kilbaş
- Medical Laboratory Techniques, Vocational School of Health Services, Fenerbahce University, Istanbul 34758, Türkiye
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Chapman R, Jones L, D'Angelo A, Suliman A, Anwar M, Bagby S. Nanopore-Based Metagenomic Sequencing in Respiratory Tract Infection: A Developing Diagnostic Platform. Lung 2023; 201:171-179. [PMID: 37009923 PMCID: PMC10067523 DOI: 10.1007/s00408-023-00612-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/14/2023] [Indexed: 04/04/2023]
Abstract
Respiratory tract infection (RTI) remains a significant cause of morbidity and mortality across the globe. The optimal management of RTI relies upon timely pathogen identification via evaluation of respiratory samples, a process which utilises traditional culture-based methods to identify offending microorganisms. This process can be slow and often prolongs the use of broad-spectrum antimicrobial therapy, whilst also delaying the introduction of targeted therapy as a result. Nanopore sequencing (NPS) of respiratory samples has recently emerged as a potential diagnostic tool in RTI. NPS can identify pathogens and antimicrobial resistance profiles with greater speed and efficiency than traditional sputum culture-based methods. Increased speed to pathogen identification can improve antimicrobial stewardship by reducing the use of broad-spectrum antibiotic therapy, as well as improving overall clinical outcomes. This new technology is becoming more affordable and accessible, with some NPS platforms requiring minimal sample preparation and laboratory infrastructure. However, questions regarding clinical utility and how best to implement NPS technology within RTI diagnostic pathways remain unanswered. In this review, we introduce NPS as a technology and as a diagnostic tool in RTI in various settings, before discussing the advantages and limitations of NPS, and finally what the future might hold for NPS platforms in RTI diagnostics.
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Affiliation(s)
- Robert Chapman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK.
| | - Luke Jones
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Alberto D'Angelo
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Ahmed Suliman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Muhammad Anwar
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Stefan Bagby
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
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20
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Szoboszlay M, Schramm L, Pinzauti D, Scerri J, Sandionigi A, Biazzo M. Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required. Microorganisms 2023; 11:microorganisms11030804. [PMID: 36985377 PMCID: PMC10059749 DOI: 10.3390/microorganisms11030804] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows. To assess whether Nanopore with the improved error rate of the Kit 12 chemistry should be adopted as the preferred sequencing technology instead of Illumina for 16S amplicon sequencing of the gut microbiota, we used a mock community and human faecal samples to compare diversity, richness, and species-level community structure, as well as the replicability of the results. Nanopore had less noise, better accuracy with the mock community, a higher proportion of reads from the faecal samples classified to species, and better replicability. The difference between the Nanopore and Illumina results of the faecal bacterial community structure was significant but small compared to the variation between samples. The results show that Nanopore is a better choice for 16S rRNA gene amplicon sequencing when the focus is on species-level taxonomic resolution, the investigation of rare taxa, or an accurate estimation of richness. Illumina 16S sequencing should be reserved for communities with many unknown species, and for studies that require the resolution of amplicon sequence variants.
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Affiliation(s)
| | | | | | | | - Anna Sandionigi
- Department of Informatics, Systems and Communication, University of Milan Bicocca, 20126 Milan, Italy
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Nanopore-Targeted Sequencing Improves the Diagnosis and Treatment of Patients with Serious Infections. mBio 2023; 14:e0305522. [PMID: 36651731 PMCID: PMC9979620 DOI: 10.1128/mbio.03055-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Serious infections are characterized by rapid progression, poor prognosis, and difficulty in diagnosis. Recently, a new technique known as nanopore-targeted sequencing (NTS) was developed that facilitates the rapid and accurate detection of pathogenic microorganisms and is extremely suitable for patients with serious infections. The aim of our study was to evaluate the clinical application of NTS in the diagnosis and treatment of patients with serious infections. We developed an NTS technology that could detect microorganisms within a 6-h window based on the amplification of the 16S rRNA gene of bacteria, the internal transcribed spacer region of fungi, and the rpoB gene of Mycobacterium. The NTS detection results were compared with those of blood cultures and anal swabs from 50 patients with blood diseases suffering serious infections. The patient's condition before and after NTS was compared. The response rate and the infection-related mortality after the adjustment of antibiotics based on NTS were calculated. The positivity rate of pathogens was highest in NTS (90%), followed by blood culture (32.6%) and anal swabs (14.6%). After adjusting antibiotics for bacteria and fungi detected by NTS, the patients' condition improved significantly. Moreover, the response rate of anti-infective treatment based on NTS was 93.02% (40/43), and infection-related mortality was reduced to 0. NTS is an effective method to identify pathogens in the blood specimens of patients with serious infections and can guide anti-infection treatment and reduce infection-related mortality. IMPORTANCE We introduce the application of NTS in blood samples of patients with serious infections and expound the efficiency and accuracy of NTS in detecting pathogenic microorganisms. Our work builds on the considerable interest of the scientific community in the management of serious infection. This issue is becoming more pressing, especially since the incidence of blood diseases is increasing year by year and hematopoietic stem cell transplantation (HSCT) has been widely used in benign and malignant blood diseases in recent years. The infection progression of these patients is faster, and the study further demonstrates the effectiveness of NTS in guiding the diagnosis and treatment of patients with severe infections. We firmly believe that this method will guide clinicians to adjust anti-infection strategies and bring significant benefits to patients, and our study will have implications for the future clinical application of NTS in all kinds of patients with serious infections.
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Zhang H, Wang M, Han X, Wang T, Lei Y, Rao Y, Xu P, Wang Y, Gu H. The application of targeted nanopore sequencing for the identification of pathogens and resistance genes in lower respiratory tract infections. Front Microbiol 2022; 13:1065159. [PMID: 36620015 PMCID: PMC9822541 DOI: 10.3389/fmicb.2022.1065159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Objectives Lower respiratory tract infections (LRTIs) are one of the causes of mortality among infectious diseases. Microbial cultures commonly used in clinical practice are time-consuming, have poor sensitivity to unculturable and polymicrobial patterns, and are inadequate to guide timely and accurate antibiotic therapy. We investigated the feasibility of targeted nanopore sequencing (TNPseq) for the identification of pathogen and antimicrobial resistance (AMR) genes across suspected patients with LRTIs. TNPseq is a novel approach, which was improved based on nanopore sequencing for the identification of bacterial and fungal infections of clinical relevance. Methods This prospective study recruited 146 patients suspected of having LRTIs and with a median age of 61 years. The potential pathogens in these patients were detected by both TNPseq and the traditional culture workups. We compared the performance between the two methods among 146 LRTIs-related specimens. AMR genes were also detected by TNPseq to prompt the proper utilization of antibiotics. Results At least one pathogen was detected in 133 (91.1%) samples by TNPseq, but only 37 (25.3%) samples contained positive isolates among 146 cultured specimens. TNPseq possessed higher sensitivity than the conventional culture method (91.1 vs. 25.3%, P < 0.001) in identifying pathogens. It detected more samples with bacterial infections (P < 0.001) and mixed infections (P < 0.001) compared with the clinical culture tests. The most frequent AMR gene identified by TNPseq was bla TEM (n = 29), followed by bla SHV (n = 4), bla KPC (n = 2), bla CTX-M (n = 2), and mecA (n = 2). Furthermore, TNPseq discovered five possible multi-drug resistance specimens. Conclusion TNPseq is efficient to identify pathogens early, thus assisting physicians to conduct timely and precise treatment for patients with suspected LRTIs.
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Affiliation(s)
- Hongying Zhang
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China,*Correspondence: Hongying Zhang ✉
| | - Meng Wang
- Institute of Health Education, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Ximei Han
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Ting Wang
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Yanjuan Lei
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Yu Rao
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Peisong Xu
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Yunfei Wang
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,Graduate School, University of Science and Technology of China, Hefei, China,Hongcang Gu ✉
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Huggins LG, Colella V, Atapattu U, Koehler AV, Traub RJ. Nanopore Sequencing Using the Full-Length 16S rRNA Gene for Detection of Blood-Borne Bacteria in Dogs Reveals a Novel Species of Hemotropic Mycoplasma. Microbiol Spectr 2022; 10:e0308822. [PMID: 36250862 PMCID: PMC9769565 DOI: 10.1128/spectrum.03088-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/26/2022] [Indexed: 01/09/2023] Open
Abstract
Dogs across the globe are afflicted by diverse blood- and vector-borne bacteria (VBB), many of which cause severe disease and can be fatal. Diagnosis of VBB infections can be challenging due to the low concentration of bacteria in the blood, the frequent occurrence of coinfections, and the wide range of known, emerging, and potentially novel VBB species encounterable. Therefore, there is a need for diagnostics that address these challenges by being both sensitive and capable of detecting all VBB simultaneously. We detail the first employment of a nanopore-based sequencing methodology conducted on the Oxford Nanopore Technologies (ONT) MinION device to accurately elucidate the "hemobacteriome" from canine blood through sequencing of the full-length 16S rRNA gene. We detected a diverse range of important canine VBB, including Ehrlichia canis, Anaplasma platys, Mycoplasma haemocanis, Bartonella clarridgeiae, "Candidatus Mycoplasma haematoparvum", a novel species of hemotropic mycoplasma, and Wolbachia endosymbionts of filarial worms, indicative of filariasis. Our nanopore-based protocol was equivalent in sensitivity to both quantitative PCR (qPCR) and Illumina sequencing when benchmarked against these methods, achieving high agreement as defined by the kappa statistics (k > 0.81) for three key VBB. Utilizing the ability of the ONT' MinION device to sequence long read lengths provides an excellent alternative diagnostic method by which the hemobacteriome can be accurately characterized to the species level in a way previously unachievable using short reads. We envision our method to be translatable to multiple contexts, such as the detection of VBB in other vertebrate hosts, including humans, while the small size of the MinION device is highly amenable to field use. IMPORTANCE Blood- and vector-borne bacteria (VBB) can cause severe pathology and even be lethal for dogs in many regions across the globe. Accurate characterization of all the bacterial pathogens infecting a canine host is critical, as coinfections are common and emerging and novel pathogens that may go undetected by traditional diagnostics frequently arise. Deep sequencing using devices from Oxford Nanopore Technologies (ONT) provides a solution, as the long read lengths achievable provide species-level taxonomic identification of pathogens that previous short-read technologies could not accomplish. We developed a protocol using ONT' MinION sequencer to accurately detect and classify a wide spectrum of VBB from canine blood at a sensitivity comparable to that of regularly used diagnostics, such as qPCR. This protocol demonstrates great potential for use in biosurveillance and biosecurity operations for the detection of VBB in a range of vertebrate hosts, while the MinION sequencer's portability allows this method to be used easily in the field.
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Affiliation(s)
- Lucas G. Huggins
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Vito Colella
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Ushani Atapattu
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Anson V. Koehler
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
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Jing D, Jiang X, Ren X, Su J, Huang C, Yang J, Hao R, Li X. Metagenomic nanopore sequencing of ocular microbiome in patients with meibomian gland dysfunction. Front Med (Lausanne) 2022; 9:1045990. [PMID: 36438054 PMCID: PMC9682043 DOI: 10.3389/fmed.2022.1045990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/26/2022] [Indexed: 07/30/2023] Open
Abstract
PURPOSE To explore the composition of the ocular microbiome in patients with Meibomian gland dysfunction (MGD) using metagenomic nanopore sequencing. METHODS A total of 98 participants were recruited from September to December 2021, including 86 patients with MGD and 12 controls. Symptoms and signs of dry eye were assessed, and bacterial samples in the conjunctival sac (CS) and meibomian gland (MG) secretions were then identified by bacterial culture identification and metagenomic nanopore sequencing. RESULTS The positive rate of CS bacterial culture in the MGD group was significantly higher than that in the normal group. A more complex composition of bacterial genera was detected in the mild and moderate MGD groups than in the control. However, the severe MGD groups had the simplest composition of bacteria. Metagenomic nanopore sequencing detected more species of bacteria than traditional culture. CONCLUSION The CS and MG of MGD patients may have different degrees of bacterial microbiota imbalance. Metagenomic nanopore sequencing technology provides a new way for us to understand the composition of "real-world" ocular surface microorganisms.
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Affiliation(s)
- Dalan Jing
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Xiaodan Jiang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Xiaotong Ren
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Jie Su
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Chen Huang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
- Medical Research Center, Peking University Third Hospital, Beijing, China
| | - Jiarui Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Ran Hao
- Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xuemin Li
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
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25
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Player R, Verratti K, Staab A, Forsyth E, Ernlund A, Joshi MS, Dunning R, Rozak D, Grady S, Goodwin B, Sozhamannan S. Optimization of Oxford Nanopore Technology Sequencing Workflow for Detection of Amplicons in Real Time Using ONT-DART Tool. Genes (Basel) 2022; 13:genes13101785. [PMID: 36292670 PMCID: PMC9602318 DOI: 10.3390/genes13101785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/17/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022] Open
Abstract
An optimized, well-tested and validated targeted genomic sequencing-based high-throughput assay is currently not available ready for routine biodefense and biosurveillance applications. Earlier, we addressed this gap by developing and establishing baseline comparisons of a multiplex end-point Polymerase Chain Reaction (PCR) assay followed by Oxford Nanopore Technology (ONT) based amplicon sequencing to real time PCR and customized data processing. Here, we expand upon this effort by identifying the optimal ONT library preparation method for integration into a novel software platform ONT-DART (ONT-Detection of Amplicons in Real-Time). ONT-DART is a dockerized, real-time, amplicon-sequence analysis workflow that is used to reproducibly process and filter read data to support actionable amplicon detection calls based on alignment metrics, within sample statistics, and no-template control data. This analysis pipeline was used to compare four ONT library preparation protocols using R9 and Flongle (FL) flow cells. The two 4-Primer methods tested required the shortest preparation times (5.5 and 6.5 h) for 48 libraries but provided lower fidelity data. The Native Barcoding and Ligation methods required longer preparation times of 8 and 12 h, respectively, and resulted in higher overall data quality. On average, data derived from R9 flow cells produced true positive calls for target organisms more than twice as fast as the lower throughput FL flow cells. These results suggest that utilizing the R9 flowcell with an ONT Native Barcoding amplicon library method in combination with ONT-DART platform analytics provides the best sequencing-based alternative to current PCR-based biodetection methods.
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Affiliation(s)
- Robert Player
- Applied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA
- Datirium, LLC, Cincinnati, OH 45226, USA
| | - Kathleen Verratti
- Applied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA
| | - Andrea Staab
- Naval Surface Warfare Center, Dahlgren, VA 22448, USA
| | - Ellen Forsyth
- Applied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA
| | - Amanda Ernlund
- Applied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA
| | - Mihir S. Joshi
- Applied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA
| | - Rebecca Dunning
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD 21702, USA
| | - David Rozak
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD 21702, USA
| | - Sarah Grady
- Applied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA
| | - Bruce Goodwin
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), JPL-Enabling Biotechnologies, Frederick, MD 21702, USA
| | - Shanmuga Sozhamannan
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), JPL-Enabling Biotechnologies, Frederick, MD 21702, USA
- Logistics Management Institute, Tysons, VA 22102, USA
- Correspondence:
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Deng Q, Cao Y, Wan X, Wang B, Sun A, Wang H, Wang Y, Wang H, Gu H. Nanopore-based metagenomic sequencing for the rapid and precise detection of pathogens among immunocompromised cancer patients with suspected infections. Front Cell Infect Microbiol 2022; 12:943859. [PMID: 36204638 PMCID: PMC9530710 DOI: 10.3389/fcimb.2022.943859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer patients are at high risk of infections and infection-related mortality; thereby, prompt diagnosis and precise anti-infectives treatment are critical. This study aimed to evaluate the performance of nanopore amplicon sequencing in identifying microbial agents among immunocompromised cancer patients with suspected infections. This prospective study enlisted 56 immunocompromised cancer patients with suspected infections. Their body fluid samples such as sputum and blood were collected, and potential microbial agents were detected in parallel by nanopore amplicon sequencing and the conventional culture method. Among the 56 body fluid samples, 47 (83.9%) samples were identified to have at least one pathogen by nanopore amplicon sequencing, but only 25 (44.6%) samples exhibited a positive finding by culture. Among 31 culture-negative samples, nanopore amplicon sequencing successfully detected pathogens in 22 samples (71.0%). Nanopore amplicon sequencing showed a higher sensitivity in pathogen detection than that of the conventional culture method (83.9% vs. 44.6%, P<0.001), and this advantage both existed in blood samples (38.5% vs. 0%, P=0.039) and non-blood samples (97.7% vs. 58.1%, P<0.001). Compared with the culture method, nanopore amplicon sequencing illustrated more samples with bacterial infections (P<0.001), infections from fastidious pathogens (P=0.006), and co-infections (P<0.001). The mean turnaround time for nanopore amplicon sequencing was about 17.5 hours, which was shorter than that of the conventional culture assay. This study suggested nanopore amplicon sequencing as a rapid and precise method for detecting pathogens among immunocompromised cancer patients with suspected infections. The novel and high-sensitive method will improve the outcomes of immunocompromised cancer patients by facilitating the prompt diagnosis of infections and precise anti-infectives treatment.
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Affiliation(s)
- Qingmei Deng
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Yongqing Cao
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Xiaofeng Wan
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Bin Wang
- Zhejiang ShengTing Biotechnology Company, Hangzhou, China
| | - Aimin Sun
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Huanzhong Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotechnology Company, Hangzhou, China
| | - Hongzhi Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
- *Correspondence: Hongzhi Wang, ; Hongcang Gu,
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
- *Correspondence: Hongzhi Wang, ; Hongcang Gu,
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27
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Wang Y, Hu X, Yang L, Chen C, Cheng H, Hu H, Liang W, Tong Y, Wang M, Wang H. Application of High-Throughput Sequencing Technology in the Pathogen Identification of Diverse Infectious Diseases in Nephrology Departments. Diagnostics (Basel) 2022; 12:diagnostics12092128. [PMID: 36140529 PMCID: PMC9497786 DOI: 10.3390/diagnostics12092128] [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: 07/07/2022] [Revised: 08/21/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Objective: The purpose of this study was to explore the clinical applications of high-throughput sequencing (HTS) in the identification of pathogens in patients with urinary tract infection (UTI), peritoneal dialysis-associated peritonitis (PDAP), central venous catheter related blood infections (CRBIs), and lung infections in the nephrology department. Methods: Midstream urine samples from 112 patients with UTI, peritoneal fluid samples from 67 patients with PDAP, blood samples from 15 patients with CRBI, and sputum specimens from 53 patients with lung infection were collected. The HTS and ordinary culture methods were carried out in parallel to identify the pathogens in each sample. Pathogen detection positive rate and efficacy were compared between the two methods. Results: The pathogen positive detection rates of HTS in UTI, PDAP, CRBI, and lung infection were strikingly higher than those of the culture method (84.8% vs. 35.7, 71.6% vs. 23.9%, 75% vs. 46.7%, 84.9% vs. 5.7%, p < 0.05, respectively). HTS was superior to the culture method in the sensitivity of detecting bacteria, fungi, atypical pathogens, and mixed microorganisms in those infections. In patients who had empirically used antibiotics before the test being conducted, HTS still exhibited a considerably higher positive rate than the culture method (81.6% vs. 39.0%, 68.1% vs. 14.9%, 72.7% vs. 36.4%, 83.3% vs. 4.2%, p < 0.05, respectively). Conclusions: HTS is remarkably more efficient than the culture method in detecting pathogens in diverse infectious diseases in nephrology, and is particularly potential in identifying the pathogens that are unable to be identified by the common culture method, such as in cases of complex infection with specific pathogens or subclinical infection due to preemptive use of antibiotics.
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Affiliation(s)
- Yujuan Wang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Xiaoyi Hu
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Lianhua Yang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Cheng Chen
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Hui Cheng
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Haiyun Hu
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Wei Liang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Yongqing Tong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Ming Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
- Correspondence: (M.W.); (H.W.)
| | - Huiming Wang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
- Correspondence: (M.W.); (H.W.)
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