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Reed GM, Strickland AK, Mutchler CT, Ochoa AR, Asin SN, Blackburn AN. Evaluating Nanopore Sequencing as a Respiratory Virus Diagnostic Tool for the Prehospital Setting. Mil Med 2025; 190:e1078-e1083. [PMID: 39953827 DOI: 10.1093/milmed/usaf046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 01/08/2025] [Accepted: 02/06/2025] [Indexed: 02/17/2025] Open
Abstract
INTRODUCTION Upper respiratory tract infections are a strain on military that results in lost duty days and an overall reduced readiness of the force. Improved diagnostic testing would enable better force health protection measures and earlier treatment of illness. Lightweight portable devices are preferred for diagnostic testing in austere environments where they are sometimes needed during military deployment. Current diagnostic testing is targeted to specific pathogens despite multiple pathogens that present with similar symptoms. In practice the pathogens that cause upper respiratory tract infections often go unidentified, which could be improved using agnostic or semi-agnostic diagnostic testing. Here, we performed an evaluation of shotgun metagenomic sequencing using the Oxford Nanopore Technologies (ONT) Rapid Sequencing Kit as a method for diagnostic testing of upper respiratory tract infections. This sequencing library preparation kit was chosen because of its ease of use and compatibility with the ONT MinION, a lightweight portable sequencer. MATERIALS AND METHODS Samples from patients with symptoms of upper respiratory tract infections were collected at Wilford Hall Ambulatory Surgical Center under an approved IRB protocol. Nasal rinse samples from 59 study participants were tested using the BioFire FilmArray Respiratory 2.1 Panel as well as shotgun metagenomic sequencing using ONT Rapid Sequencing Kit and ONT R9.4.1 flow cells. RESULTS A mixture of various viral pathogens was present among the 59 samples used in this study. We observed high specificity and modest sensitivity to detect the identified pathogens using shotgun metagenomic sequencing. Shotgun metagenomic sequencing detected additional pathogens that were missed by the BioFire FilmArray Respiratory 2.1 Panel, which are discussed. Lastly, we observe modest evidence of nonuniformity of the proportion of reads belonging to the pathogen during the duration of sequencing runs, which has implications for improving sensitivity by increasing the amount of sequencing performed. CONCLUSIONS Overall, ONT Rapid Sequencing Kit combined with alignment to a known panel of pathogens has shown great potential utility in our hands for quickly and accurately identifying viral respiratory pathogens. This, combined with its ease of use and portability, makes it a great candidate for further research and development toward a deployable agnostic diagnostic testing platform.
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Affiliation(s)
- Grace M Reed
- Office of the Chief Scientist, 59th Medical Wing, US Air Force, JBSA-Lackland, San Antonio, TX 78236, USA
| | - Amanda K Strickland
- Office of the Chief Scientist, 59th Medical Wing, US Air Force, JBSA-Lackland, San Antonio, TX 78236, USA
| | - Cameron T Mutchler
- Office of the Chief Scientist, 59th Medical Wing, US Air Force, JBSA-Lackland, San Antonio, TX 78236, USA
| | - Anna R Ochoa
- Office of the Chief Scientist, 59th Medical Wing, US Air Force, JBSA-Lackland, San Antonio, TX 78236, USA
| | - Susana N Asin
- Office of the Chief Scientist, 59th Medical Wing, US Air Force, JBSA-Lackland, San Antonio, TX 78236, USA
| | - August N Blackburn
- Office of the Chief Scientist, 59th Medical Wing, US Air Force, JBSA-Lackland, San Antonio, TX 78236, USA
- Applied Technology and Genomics, US Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, OH 45433, USA
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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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Wang JZ, Yuan D, Yang XH, Sun CH, Hou LL, Zhang Y, Gao YX. Etiology of lower respiratory tract in pneumonia based on metagenomic next-generation sequencing: a retrospective study. Front Cell Infect Microbiol 2024; 13:1291980. [PMID: 38264726 PMCID: PMC10803656 DOI: 10.3389/fcimb.2023.1291980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Pneumonia are the leading cause of death worldwide, and antibiotic treatment remains fundamental. However, conventional sputum smears or cultures are still inefficient for obtaining pathogenic microorganisms.Metagenomic next-generation sequencing (mNGS) has shown great value in nucleic acid detection, however, the NGS results for lower respiratory tract microorganisms are still poorly studied. Methods This study dealt with investigating the efficacy of mNGS in detecting pathogens in the lower respiratory tract of patients with pulmonary infections. A total of 112 patients admitted at the First Affiliated Hospital of Zhengzhou University between April 30, 2018, and June 30, 2020, were enrolled in this retrospective study. The bronchoalveolar lavage fluid (BALF) was obtained from lower respiratory tract from each patient. Routine methods (bacterial smear and culture) and mNGS were employed for the identification of pathogenic microorganisms in BALF. Results The average patient age was 53.0 years, with 94.6% (106/112) obtaining pathogenic microorganism results. The total mNGS detection rate of pathogenic microorganisms significantly surpassed conventional methods (93.7% vs. 32.1%, P < 0.05). Notably, 75% of patients (84/112) were found to have bacteria by mNGS, but only 28.6% (32/112) were found to have bacteria by conventional approaches. The most commonly detected bacteria included Acinetobacter baumannii (19.6%), Klebsiella pneumoniae (17.9%), Pseudomonas aeruginosa (14.3%), Staphylococcus faecium (12.5%), Enterococcus faecium (12.5%), and Haemophilus parainfluenzae (11.6%). In 29.5% (33/112) of patients, fungi were identified using mNGS, including 23 cases of Candida albicans (20.5%), 18 of Pneumocystis carinii (16.1%), and 10 of Aspergillus (8.9%). However, only 7.1 % (8/112) of individuals were found to have fungi when conventional procedures were used. The mNGS detection rate of viruses was significantly higher than the conventional method rate (43.8% vs. 0.9%, P < 0.05). The most commonly detected viruses included Epstein-Barr virus (15.2%), cytomegalovirus (13.4%), circovirus (8.9%), human coronavirus (4.5%), and rhinovirus (4.5%). Only 29.4% (33/112) of patients were positive, whereas 5.4% (6/112) of patients were negative for both detection methods as shown by Kappa analysis, indicating poor consistency between the two methods (P = 0.340; Kappa analysis). Conclusion Significant benefits of mNGS have been shown in the detection of pathogenic microorganisms in patients with pulmonary infection. For those with suboptimal therapeutic responses, mNGS can provide an etiological basis, aiding in precise anti-infective treatment.
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Affiliation(s)
- Jin-zhu Wang
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ding Yuan
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiang-hong Yang
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Chang-hua Sun
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lin-lin Hou
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Zhang
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan-xia Gao
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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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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Chen T, Zhang L, Huang W, Zong H, Li Q, Zheng Y, Lv Q, Kong D, Ren Y, Jiang Y, Li Y, Liu P. Detection of Pathogens and Antimicrobial Resistance Genes in Ventilator-Associated Pneumonia by Metagenomic Next-Generation Sequencing Approach. Infect Drug Resist 2023; 16:923-936. [PMID: 36814827 PMCID: PMC9939671 DOI: 10.2147/idr.s397755] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/26/2023] [Indexed: 02/16/2023] Open
Abstract
Background The early identification of pathogens and their antibiotic resistance are essential for the management and treatment of patients affected by ventilator-associated pneumonia (VAP). However, microbiological culture may be time-consuming and has a limited culturability of many potential pathogens. In this study, we developed a rapid nanopore-based metagenomic next-generation sequencing (mNGS) diagnostic assay for detection of VAP pathogens and antimicrobial resistance genes (ARGs). Patients and Methods Endotracheal aspirate (ETA) samples from 63 patients with suspected VAP were collected between November 2021 and July 2022. Receiver operating characteristic (ROC) curves were established to compare the pathogen identification performance of the target pathogen reads, reads percent of microbes (RPM) and relative abundance (RA). The evaluation of the accuracy of mNGS was performed comparing with the gold standard and the composite standard, respectively. Then, the ARGs were analyzed by mNGS. Results ROC curves showed that RA has the highest diagnostic value and the corresponding threshold was 9.93%. The sensitivity and specificity of mNGS test were 91.3% and 78.3%, respectively, based on the gold standard, while the sensitivity and specificity of mNGS test were 97.4% and 100%, respectively, based on the composite standard. A total of 13 patients were virus-positive based on mNGS results, while the coinfection rate increased from 27% to 46% compared to the rate obtained based on clinical findings. The mNGS test also performed well at predicting antimicrobial resistance phenotypes. Patients with a late-onset VAP had a significantly greater proportion of ARGs in their respiratory microbiome compared to those with early-onset VAP (P = 0.041). Moreover, the median turnaround time of mNGS was 4.43 h, while routine culture was 72.00 h. Conclusion In this study, we developed a workflow that can accurately detect VAP pathogens and enable prediction of antimicrobial resistance phenotypes within 5 h of sample receipt by mNGS.
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Affiliation(s)
- Ting Chen
- The PLA 307 Clinical College of Anhui Medical University, The Fifth Clinical Medical College of Anhui Medical University, Hefei, People’s Republic of China,Department of Critical Care Medicine, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100071, People’s Republic of China
| | - Lei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Huijun Zong
- The PLA 307 Clinical College of Anhui Medical University, The Fifth Clinical Medical College of Anhui Medical University, Hefei, People’s Republic of China,Department of Critical Care Medicine, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100071, People’s Republic of China
| | - Qian Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Yuhao Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Yan Li
- The PLA 307 Clinical College of Anhui Medical University, The Fifth Clinical Medical College of Anhui Medical University, Hefei, People’s Republic of China,Department of Critical Care Medicine, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100071, People’s Republic of China,Correspondence: Yan Li, The PLA 307 Clinical College of Anhui Medical University, The Fifth Clinical Medical College of Anhui Medical University, Hefei, 230032, People’s Republic of China, Email
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China,Peng Liu, Beijing Institute of Microbiology and Epidemiology, Dongdajie Road 20, Beijing, 100071, People’s Republic of China, Tel +86-010-66948487, Email
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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: 0.7] [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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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: 10] [Impact Index Per Article: 3.3] [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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Ju Y, Pu M, Sun K, Song G, Geng J. Nanopore Electrochemistry for Pathogen Detection. Chem Asian J 2022; 17:e202200774. [PMID: 36069587 DOI: 10.1002/asia.202200774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/06/2022] [Indexed: 11/05/2022]
Abstract
Pathogen infections have seriously threatened human health, and there is an urgent demand for rapid and efficient pathogen identification to provide instructions in clinical diagnosis and therapeutic intervention. Recently, nanopore technology, a rapidly maturing technology which delivers ultrasensitive sensing and high throughput in real-time and at low cost, has achieved success in pathogen detection. Furthermore, the remarkable development of nanopore sequencing, for example, the MinION sequencer from Oxford Nanopore Technologies (ONT) as a competitive sequencing technology, has facilitated the rapid analysis of disease-related microbiomes at the whole-genome level and on a large scale. Here, we highlighted recent advances in nanopore approaches for pathogen detection at the single-molecule level. We also overviewed the applications of nanopore sequencing in pathogenic bacteria identification and diagnosis. In the end, we discussed the challenges and future developments of nanopore technology as promising tools for the management of infections, which may be helpful to aid understanding as well as decision-making.
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Affiliation(s)
- Yuan Ju
- Sichuan University, Sichuan University Library, CHINA
| | - Mengjun Pu
- Sichuan University, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, CHINA
| | - Ke Sun
- Sichuan University, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, CHINA
| | - Guiqin Song
- North Sichuan Medical College [Search North Sichuan Medical College]: North Sichuan Medical University, Shool of Basic Medical Sciences and Forensic Medicine, CHINA
| | - Jia Geng
- Sichuan University, State Key Laboratory of Biotherapy, No 17 Section 3 of South Renmin Rd, 610040, Chengdu, CHINA
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9
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Bhar A. The application of next generation sequencing technology in medical diagnostics: a perspective. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [PMCID: PMC9395867 DOI: 10.1007/s43538-022-00098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid isolation, characterization, and identification are prerequisites of any successful medical intervention to infectious disease treatment. This is a real challenge to the scientific as well as a medical community to find out a proper and robust method of pathogen detection. Classical cultural, as well as biochemical test-based identification, has its own limitations to their time-consuming and ineffectiveness for closely related pathovars. Molecular diagnostics became a popular alternative to classical techniques for the past couple of decades but it required some prior information to detect the pathogen successfully. Recently, with the advent of next-generation sequencing (NGS) technology identification, and characterization of almost all the pathogenic bacteria become possible without any information a priori. Metagenomic next generation sequencing is another specialized type of NGS that is profoundly utilized in medical biotechnology and diagnostics now a days. Therefore, the present review is focused on a brief introduction to NGS technology, its application in medical microbiology, and possible future aspects for the development of medical sciences.
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Affiliation(s)
- Anirban Bhar
- Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata 700118 India
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10
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Bouchiat C, Ginevra C, Benito Y, Gaillard T, Salord H, Dauwalder O, Laurent F, Vandenesch F. Improving the Diagnosis of Bacterial Infections: Evaluation of 16S rRNA Nanopore Metagenomics in Culture-Negative Samples. Front Microbiol 2022; 13:943441. [PMID: 35910644 PMCID: PMC9329087 DOI: 10.3389/fmicb.2022.943441] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/17/2022] [Indexed: 11/29/2022] Open
Abstract
While 16S rRNA PCR-Sanger sequencing has paved the way for the diagnosis of culture-negative bacterial infections, it does not provide the composition of polymicrobial infections. We aimed to evaluate the performance of the Nanopore-based 16S rRNA metagenomic approach, using both partial and full-length amplification of the gene, and to explore its feasibility and suitability as a routine diagnostic tool for bacterial infections in a clinical laboratory. Thirty-one culture-negative clinical samples from mono- and polymicrobial infections based on Sanger-sequencing results were sequenced on MinION using both the in-house partial amplification and the Nanopore dedicated kit for the full-length amplification of the 16S rRNA gene. Contamination, background noise definition, bacterial identification, and time-effectiveness issues were addressed. Cost optimization was also investigated with the miniaturized version of the flow cell (Flongle). The partial 16S approach had a greater sensitivity compared to the full-length kit that detected bacterial DNA in only 24/31 (77.4%) samples. Setting a threshold of 1% of total reads overcame the background noise issue and eased the interpretation of clinical samples. Results were obtained within 1 day, discriminated polymicrobial samples, and gave accurate bacterial identifications compared to Sanger-based results. We also found that multiplexing and using Flongle flow cells was a cost-effective option. The results confirm that Nanopore technology is user-friendly as well as cost- and time-effective. They also indicate that 16S rRNA targeted metagenomics is a suitable approach to be implemented for the routine diagnosis of culture-negative samples in clinical laboratories.
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Affiliation(s)
- Coralie Bouchiat
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
- Equipe Inserm U1111, Centre International de Recherche en Infectiologie, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- *Correspondence: Coralie Bouchiat
| | - Christophe Ginevra
- Centre National de Référence des Légionelles, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Yvonne Benito
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
| | - Tiphaine Gaillard
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
- Laboratoire de biologie médicale, Hôpital d'Instruction des Armées Desgenettes, Service de Santé des Armées, Lyon, France
| | - Hélène Salord
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
| | - Olivier Dauwalder
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Laurent
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
- Equipe Inserm U1111, Centre International de Recherche en Infectiologie, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - François Vandenesch
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
- Equipe Inserm U1111, Centre International de Recherche en Infectiologie, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
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11
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Hoang MTV, Irinyi L, Hu Y, Schwessinger B, Meyer W. Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections. Front Microbiol 2022; 12:708550. [PMID: 35069461 PMCID: PMC8770865 DOI: 10.3389/fmicb.2021.708550] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on culturing and cell propagation to isolate and identify the causative pathogen. These techniques are limited by the ability and the time required to grow or propagate an agent in vitro and the facts that identification based on morphological traits are non-specific, insensitive, and reliant on technical expertise. The evolution of next-generation sequencing has revolutionized genomic studies to generate more data at a cheaper cost. These are divided into short- and long-read sequencing technologies, depending on the length of reads generated during sequencing runs. Long-read sequencing also called third-generation sequencing emerged commercially through the instruments released by Pacific Biosciences and Oxford Nanopore Technologies, although relying on different sequencing chemistries, with the first one being more accurate both platforms can generate ultra-long sequence reads. Long-read sequencing is capable of entirely spanning previously established genomic identification regions or potentially small whole genomes, drastically improving the accuracy of the identification of pathogens directly from clinical samples. Long-read sequencing may also provide additional important clinical information, such as antimicrobial resistance profiles and epidemiological data from a single sequencing run. While initial applications of long-read sequencing in clinical diagnosis showed that it could be a promising diagnostic technique, it also has highlighted the need for further optimization. In this review, we show the potential long-read sequencing has in clinical diagnosis of fungal infections and discuss the pros and cons of its implementation.
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Affiliation(s)
- Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
| | - Yiheng Hu
- Research School of Biology, Australia National University, Canberra, ACT, Australia
| | | | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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12
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Wu N, Ranjan P, Tao C, Liu C, Yang E, He B, Erb-Downward JR, Bo S, Zheng J, Guo C, Liu B, Sun L, Yan W, Wang M, Wang W, Wen J, Yang P, Yang L, Tian Q, Dickson RP, Shen N. Rapid identification of pathogens associated with ventilator-associated pneumonia by Nanopore sequencing. Respir Res 2021; 22:310. [PMID: 34893078 PMCID: PMC8665642 DOI: 10.1186/s12931-021-01909-3] [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: 06/08/2021] [Accepted: 11/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aetiology detection is crucial in the diagnosis and treatment of ventilator-associated pneumonia (VAP). However, the detection method needs improvement. In this study, we used Nanopore sequencing to build a quick detection protocol and compared the efficiency of different methods for detecting 7 VAP pathogens. METHODS The endotracheal aspirate (ETA) of 83 patients with suspected VAP from Peking University Third Hospital (PUTH) was collected, saponins were used to deplete host genomes, and PCR- or non-PCR-amplified library construction methods were used and compared. Sequence was performed with MinION equipment and local data analysis methods were used for sequencing and data analysis. RESULTS Saponin depletion effectively removed 11 of 12 human genomes, while most pathogenic bacterial genome results showed no significant difference except for S. pneumoniae. Moreover, the average sequence time decreased from 19.6 h to 3.62 h. The non-PCR amplification method and PCR amplification method for library build has a similar average sensitivity (85.8% vs. 86.35%), but the non-PCR amplification method has a better average specificity (100% VS 91.15%), and required less time. The whole method takes 5-6 h from ETA extraction to pathogen classification. After analysing the 7 pathogens enrolled in our study, the average sensitivity of metagenomic sequencing was approximately 2.4 times higher than that of clinical culture (89.15% vs. 37.77%), and the average specificity was 98.8%. CONCLUSIONS Using saponins to remove the human genome and a non-PCR amplification method to build libraries can be used for the identification of pathogens in the ETA of VAP patients within 6 h by MinION, which provides a new approach for the rapid identification of pathogens in clinical departments.
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Affiliation(s)
- Nan Wu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Piyush Ranjan
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Changyu Tao
- Department of Human Anatomy and Histology and Embryology, Peking University, Beijing, 100191, People's Republic of China
| | - Chao Liu
- Department of Infectious Diseases, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Ence Yang
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, People's Republic of China
| | - Bei He
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - John R Erb-Downward
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Shining Bo
- Intensive Care Unit, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Jiajia Zheng
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Chenxia Guo
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Beibei Liu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Lina Sun
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Wei Yan
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Meng Wang
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Wenting Wang
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Jianing Wen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Ping Yang
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Lin Yang
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Qiaoshan Tian
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Robert P Dickson
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ning Shen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, 100191, People's Republic of China.
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13
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Goelz H, Wetzel S, Mehrbarzin N, Utzolino S, Häcker G, Badr MT. Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients. Cells 2021; 10:3226. [PMID: 34831447 PMCID: PMC8617993 DOI: 10.3390/cells10113226] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Infections of the ascitic fluid are serious conditions that require rapid diagnosis and treatment. Ascites is often accompanied by other critical pathologies such as gastrointestinal bleeding and bowel perforation, and infection increases the risk of mortality in intensive care patients. Owing to a relatively low success rate of conventional culture methods in identifying the responsible pathogens, new methods may be helpful to guide antimicrobial therapy and to refine empirical regimens. Here, we aim to assess outcomes and to identify responsible pathogens in ascitic fluid infections, in order to improve patients' care and to guide empirical therapy. METHODS Between October 2019 and March 2021, we prospectively collected 50 ascitic fluid samples from ICU patients with suspected infection. Beside standard culture-based microbiology methods, excess fluid underwent DNA isolation and was analyzed by next- and third-generation sequencing (NGS) methods. RESULTS NGS-based methods had higher sensitivity in detecting additional pathogenic bacteria such as E. faecalis and Klebsiella in 33 out of 50 (66%) ascitic fluid samples compared with culture-based methods (26%). Anaerobic bacteria were especially identified by sequencing-based methods in 28 samples (56%), in comparison with only three samples in culture. Analysis of clinical data showed a correlation between sequencing results and various clinical parameters such as peritonitis and hospitalization outcomes. CONCLUSIONS Our results show that, in ascitic fluid infections, NGS-based methods have a higher sensitivity for the identification of clinically relevant pathogens than standard microbiological culture diagnostics, especially in detecting hard-to-culture anaerobic bacteria. Patients with such infections may benefit from the use of NGS methods by the possibility of earlier and better targeted antimicrobial therapy, which has the potential to lower the high morbidity and mortality in critically ill patients with ascitic bacterial infection.
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Affiliation(s)
- Hanna Goelz
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
| | - Simon Wetzel
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
| | - Negin Mehrbarzin
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
| | - Stefan Utzolino
- Center of Surgery, Department of General and Visceral Surgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany;
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
- IMM-PACT-Program, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
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14
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Chew KL, Octavia S, Jureen R, Lin RTP, Teo JWP. Targeted amplification and MinION nanopore sequencing of key azole and echinocandin resistance determinants of clinically relevant Candida spp. from blood culture bottles. Lett Appl Microbiol 2021; 73:286-293. [PMID: 34060660 DOI: 10.1111/lam.13516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/29/2021] [Accepted: 05/21/2021] [Indexed: 12/19/2022]
Abstract
The objective of the study was to evaluate the use of targeted multiplex Nanopore MinION amplicon re-sequencing of key Candida spp. from blood culture bottles to identify azole and echinocandin resistance associated SNPs. Targeted PCR amplification of azole (ERG11 and ERG3) and echinocandin (FKS) resistance-associated loci was performed on positive blood culture media. Sequencing was performed using MinION nanopore device with R9.4.1 Flow Cells. Twenty-eight spiked blood cultures (ATCC strains and clinical isolates) and 12 prospectively collected positive blood cultures with candidaemia were included. Isolate species included Candida albicans, Candida glabrata, Candida krusei, Candida parapsilosis, Candida tropicalis and Candida auris. SNPs that were identified on ERG and FKS genes using Snippy tool and CLC Genomic Workbench were correlated with phenotypic testing by broth microdilution (YeastOne™ Sensititre). Illumina whole-genome-sequencing and Sanger-sequencing were also performed as confirmatory testing of the mutations identified from nanopore sequencing data. There was a perfect agreement of the resistance-associated mutations detected by MinION-nanopore-sequencing compared to phenotypic testing for acquired resistance (16 with azole resistance; 3 with echinocandin resistance), and perfect concordance of the nanopore sequence mutations to Illumina and Sanger data. Mutations with no known association with phenotypic drug resistance and novel mutations were also detected.
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Affiliation(s)
- K L Chew
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - S Octavia
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - R Jureen
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - R T P Lin
- Department of Laboratory Medicine, National University Hospital, Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - J W P Teo
- Department of Laboratory Medicine, National University Hospital, Singapore
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15
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The impact of smoking different tobacco types on the subgingival microbiome and periodontal health: a pilot study. Sci Rep 2021; 11:1113. [PMID: 33441919 PMCID: PMC7806658 DOI: 10.1038/s41598-020-80937-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023] Open
Abstract
Smoking is a risk factor for periodontal disease, and a cause of oral microbiome dysbiosis. While this has been evaluated for traditional cigarette smoking, there is limited research on the effect of other tobacco types on the oral microbiome. This study investigates subgingival microbiome composition in smokers of different tobacco types and their effect on periodontal health. Subgingival plaques were collected from 40 individuals, including smokers of either cigarettes, medwakh, or shisha, and non-smokers seeking dental treatment at the University Dental Hospital in Sharjah, United Arab Emirates. The entire (~ 1500 bp) 16S rRNA bacterial gene was fully amplified and sequenced using Oxford Nanopore technology. Subjects were compared for the relative abundance and diversity of subgingival microbiota, considering smoking and periodontal condition. The relative abundances of several pathogens were significantly higher among smokers, such as Prevotella denticola and Treponema sp. OMZ 838 in medwakh smokers, Streptococcus mutans and Veillonella dispar in cigarette smokers, Streptococcus sanguinis and Tannerella forsythia in shisha smokers. Subgingival microbiome of smokers was altered even in subjects with no or mild periodontitis, probably making them more prone to severe periodontal diseases. Microbiome profiling can be a useful tool for periodontal risk assessment. Further studies are recommended to investigate the impact of tobacco cessation on periodontal disease progression and oral microbiome.
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16
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Zhu X, Yan S, Yuan F, Wan S. The Applications of Nanopore Sequencing Technology in Pathogenic Microorganism Detection. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2020; 2020:6675206. [PMID: 33488885 PMCID: PMC7790562 DOI: 10.1155/2020/6675206] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/04/2020] [Accepted: 12/18/2020] [Indexed: 12/23/2022]
Abstract
Infectious diseases are major threats to human health and lead to a serious public health burden. The emergence of new pathogens and the mutation of known pathogens challenge our ability to diagnose and control infectious diseases. Nanopore sequencing technology exhibited versatile applications in pathogenic microorganism detection due to its flexible data throughput. This review article introduced the applications of nanopore sequencing in clinical microbiology and infectious diseases management, including the monitoring of emerging infectious diseases outbreak, identification of pathogen drug resistance, and disease-related microbial communities characterization.
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Affiliation(s)
- Xiaojian Zhu
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
| | - Shanshan Yan
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- Department of Publication Health and Health Management, Gannan Medical University, Ganzhou 341000, China
| | - Fenghua Yuan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
| | - Shaogui Wan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
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