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Lim FS, González-Cabrera J, Keilwagen J, Kleespies RG, Jehle JA, Wennmann JT. Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets. Sci Rep 2024; 14:8525. [PMID: 38609404 PMCID: PMC11014933 DOI: 10.1038/s41598-024-58768-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Rapid and reliable detection of pathogens is crucial to complement the growing industry of mass-reared insects, in order to safeguard the insect colonies from outbreak of diseases, which may cause significant economic loss. Current diagnostic methods are mainly based on conventional PCR and microscopic examination, requiring prior knowledge of disease symptoms and are limited to identifying known pathogens. Here, we present a rapid nanopore-based metagenomics approach for detecting entomopathogens from the European house cricket (Acheta domesticus). In this study, the Acheta domesticus densovirus (AdDV) was detected from diseased individuals using solely Nanopore sequencing. Virus reads and genome assemblies were obtained within twenty-four hours after sequencing. Subsequently, due to the length of the Nanopore reads, it was possible to reconstruct significantly large parts or even the entire AdDV genome to conduct studies for genotype identification. Variant analysis indicated the presence of three AdDV genotypes within the same house cricket population, with association to the vital status of the diseased crickets. This contrast provided compelling evidence for the existence of non-lethal AdDV genotypes. These findings demonstrated nanopore-based metagenomics sequencing as a powerful addition to the diagnostic tool kit for routine pathogen surveillance and diagnosis in the insect rearing industry.
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Affiliation(s)
- Fang Shiang Lim
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
- Department of Genetics and Institute BIOTECMED, Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain
| | - Joel González-Cabrera
- Department of Genetics and Institute BIOTECMED, Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain
| | - Jens Keilwagen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for the Safety of Biotechnological Processes in Plants, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Regina G Kleespies
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
| | - Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany.
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2
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Ali J, Johansen W, Ahmad R. Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing. Sci Rep 2024; 14:6534. [PMID: 38503770 PMCID: PMC10951244 DOI: 10.1038/s41598-024-55635-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Bloodstream infections (BSIs) and sepsis are major health problems, annually claiming millions of lives. Traditional blood culture techniques, employed to identify sepsis-causing pathogens and assess antibiotic susceptibility, usually take 2-4 days. Early and accurate antibiotic prescription is vital in sepsis to mitigate mortality and antibiotic resistance. This study aimed to reduce the wait time for sepsis diagnosis by employing shorter blood culture incubation times for BD BACTEC™ bottles using standard laboratory incubators, followed by real-time nanopore sequencing and data analysis. The method was tested on nine blood samples spiked with clinical isolates from the six most prevalent sepsis-causing pathogens. The results showed that pathogen identification was possible at as low as 102-104 CFU/mL, achieved after just 2 h of incubation and within 40 min of nanopore sequencing. Moreover, all the antimicrobial resistance genes were identified at 103-107 CFU/mL, achieved after incubation for 5 h and only 10 min to 3 h of sequencing. Therefore, the total turnaround time from sample collection to the information required for an informed decision on the right antibiotic treatment was between 7 and 9 h. These results hold significant promise for better clinical management of sepsis compared with current culture-based methods.
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Affiliation(s)
- Jawad Ali
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317, Hamar, Norway
| | - Wenche Johansen
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317, Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317, Hamar, Norway.
- Institute of Clinical Medicine, Faculty of Health Sciences, UiT - The Arctic University of Norway, Hansine Hansens Veg 18, 9019, Tromsø, Norway.
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3
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Liu Y, Xu Y, Xu X, Chen X, Chen H, Zhang J, Ma J, Zhang W, Zhang R, Chen J. Metagenomic identification of pathogens and antimicrobial-resistant genes in bacterial positive blood cultures by nanopore sequencing. Front Cell Infect Microbiol 2023; 13:1283094. [PMID: 38192400 PMCID: PMC10773726 DOI: 10.3389/fcimb.2023.1283094] [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: 08/25/2023] [Accepted: 10/30/2023] [Indexed: 01/10/2024] Open
Abstract
Nanopore sequencing workflows have attracted increasing attention owing to their fast, real-time, and convenient portability. Positive blood culture samples were collected from patients with bacterial bloodstream infection and tested by nanopore sequencing. This study compared the sequencing results for pathogen taxonomic profiling and antimicrobial resistance genes to those of species identification and phenotypic drug susceptibility using traditional microbiology testing. A total of 37 bacterial positive blood culture results of strain genotyping by nanopore sequencing were consistent with those of mass spectrometry. Among them, one mixed infection of bacteria and fungi was identified using nanopore sequencing and confirmatory quantitative polymerase chain reaction. The amount of sequencing data was 21.89 ± 8.46 MB for species identification, and 1.0 MB microbial strain data enabled accurate determination. Data volumes greater than or equal to 94.6 MB nearly covered all the antimicrobial resistance genes of the bacteria in our study. In addition, the results of the antimicrobial resistance genes were compared with those of phenotypic drug susceptibility testing for Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. Therefore, the nanopore sequencing platform for rapid identification of causing pathogens and relevant antimicrobial resistance genes complementary to conventional blood culture outcomes may optimize antimicrobial stewardship management for patients with bacterial bloodstream infection.
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Affiliation(s)
- Yahui Liu
- Department of Laboratory Medicine, Shanghai Xuhui District Central Hospital & Fudan University Affiliated Xuhui Hospital, Shanghai, China
- Department of Laboratory Medicine, Shanghai Post and Telecommunication Hospital, Shanghai, China
| | - Yumei Xu
- Department of Laboratory Medicine, Shanghai Xuhui District Central Hospital & Fudan University Affiliated Xuhui Hospital, Shanghai, China
| | - Xinyu Xu
- Department of Laboratory Medicine, Shanghai Post and Telecommunication Hospital, Shanghai, China
| | - Xianghui Chen
- Shanghai Diabetes Institute, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongli Chen
- Shanghai Diabetes Institute, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingjing Zhang
- Precision Medicine Center, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiayu Ma
- Precision Medicine Center, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenrui Zhang
- Precision Medicine Center, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rong Zhang
- Shanghai Diabetes Institute, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Chen
- Department of Laboratory Medicine, Shanghai Post and Telecommunication Hospital, Shanghai, China
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Vidal-García M, Urrutikoetxea-Gutiérrez M, Forero Niampira JC, Basaras M, Cisterna R, Díaz de Tuesta Del Arco JL. Ultrafast detection of β-lactamase resistance in Klebsiella pneumoniae from blood culture by nanopore sequencing. Future Microbiol 2023; 18:1309-1317. [PMID: 37850345 DOI: 10.2217/fmb-2023-0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/25/2023] [Indexed: 10/19/2023] Open
Abstract
Aim: This study aimed to assess the ultra-fast method using MinION™ sequencing for rapid identification of β-lactamase-producing Klebsiella pneumoniae clinical isolates from positive blood cultures. Methods: Spiked-blood positive blood cultures were extracted using the ultra-fast method and automated DNA extraction for MinION sequencing. Raw reads were analyzed for β-lactamase resistance genes. Multilocus sequence typing and β-lactamase variant characterization were performed after assembly. Results: The ultra-fast method identified clinically relevant β-lactamase resistance genes in less than 1 h. Multilocus sequence typing and β-lactamase variant characterization required 3-6 h. Sequencing quality showed no direct correlation with pore number or DNA concentration. Conclusion: Nanopore sequencing, specifically the ultra-fast method, is promising for the rapid diagnosis of bloodstream infections, facilitating timely identification of multidrug-resistant bacteria in clinical samples.
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Affiliation(s)
- Matxalen Vidal-García
- Clinical Microbiology Department, Basurto University Hospital, 480132
- Clinical Microbiology & Infection Control, ISS Biocruces Bizkaia, 489033
| | - Mikel Urrutikoetxea-Gutiérrez
- Clinical Microbiology Department, Basurto University Hospital, 480132
- Clinical Microbiology & Infection Control, ISS Biocruces Bizkaia, 489033
| | - Juan C Forero Niampira
- Inmunology, Microbiology & Parasitology Department, University of the Basque Country, 48940
| | - Miren Basaras
- Inmunology, Microbiology & Parasitology Department, University of the Basque Country, 48940
| | - Ramón Cisterna
- Inmunology, Microbiology & Parasitology Department, University of the Basque Country, 48940
| | - José L Díaz de Tuesta Del Arco
- Clinical Microbiology Department, Basurto University Hospital, 480132
- Clinical Microbiology & Infection Control, ISS Biocruces Bizkaia, 489033
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Wang Y, Chen T, Zhang S, Zhang L, Li Q, Lv Q, Kong D, Jiang H, Ren Y, Jiang Y, Li Y, Huang W, Liu P. Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection. J Transl Med 2023; 21:762. [PMID: 37891586 PMCID: PMC10612365 DOI: 10.1186/s12967-023-04562-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Early availability of pathogen identification in urinary tract infections (UTIs) has critical importance in disease management. Metagenomic next-generation sequencing (mNGS) has the potential to transform how acute and serious infections are diagnosed by offering unbiased and culture-free pathogen detection. However, clinical experience with application of the mNGS test is relatively limited. METHODS We therefore established a MinION-based mNGS pathogens diagnostic platform and evaluated its potential for clinical implementation in UTIs with clinical samples. 213 urine samples from patients with suspected UTIs were included and subjected to mNGS testing using the MinION platform. mNGS results were compared to the gold standard of clinical culture and composite standard of combining clinical testing, confirmatory qPCR testing, and clinical adjudication by doctors. RESULTS The mNGS exhibited a sensitivity of 81.4% and a specificity of 92.3%, along with a positive predictive value of 96.6%, a negative predictive value of 64.9%, and an overall accuracy of 84.4%, all of which were determined based on the gold standard of routine culture results. When assessed against the composite standard, the sensitivity and specificity both increased to 89.9% and 100%, respectively, while the accuracy rose to 92.4%. Notably, the positive predictive value and negative predictive value also saw improvements, reaching 100% and 76.8%, respectively. Moreover, this diagnostic platform successfully identified dsDNA viruses. Among the 65 culture-negative samples, the viral detection rate reached 33.8% (22/65) and was subsequently validated through qPCR. Furthermore, the automatic bioinformatics pipeline we developed enabled one-click analysis from data to results, leading to a significant reduction in diagnosis time. CONCLUSION These results demonstrate that the pathogen detection performance of mNGS is sufficient for diagnostic testing in clinical settings. As the method is generally unbiased, it can improve diagnostic testing of UTIs and other microbial infections.
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Affiliation(s)
- Ye Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ting Chen
- Department of Critical Care Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Shengwei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Lei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Qian Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuhao Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yan Li
- Department of Critical Care Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China.
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
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Huang W, Qu S, Qin Q, Yang X, Han W, Lai Y, Chen J, Zhou S, Yang X, Zhou W. Nanopore Third-Generation Sequencing for Comprehensive Analysis of Hemoglobinopathy Variants. Clin Chem 2023; 69:1062-1071. [PMID: 37311260 DOI: 10.1093/clinchem/hvad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/03/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND Oxford Nanopore Technology (ONT) third-generation sequencing (TGS) is a versatile genetic diagnostic platform. However, it is nonetheless challenging to prepare long-template libraries for long-read TGS, particularly the ONT method for analysis of hemoglobinopathy variants involving complex structures and occurring in GC-rich and/or homologous regions. METHODS A multiplex long PCR was designed to prepare library templates, including the whole-gene amplicons for HBA2/1, HBG2/1, HBD, and HBB, as well as the allelic amplicons for targeted deletions and special structural variations. Library construction was performed using long-PCR products, and sequencing was conducted on an Oxford Nanopore MinION instrument. Genotypes were identified based on integrative genomics viewer (IGV) plots. RESULTS This novel long-read TGS method distinguished all single nucleotide variants and structural variants within HBA2/1, HBG2/1, HBD, and HBB based on the whole-gene sequence reads. Targeted deletions and special structural variations were also identified according to the specific allelic reads. The result of 158 α-/β-thalassemia samples showed 100% concordance with previously known genotypes. CONCLUSIONS This ONT TGS method is high-throughput, which can be used for molecular screening and genetic diagnosis of hemoglobinopathies. The strategy of multiplex long PCR is an efficient strategy for library preparation, providing a practical reference for TGS assay development.
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Affiliation(s)
- Weilun Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shoufang Qu
- Division of In Vitro Diagnostics for Non-infectious diseases, National Institutes for Food and Drug Control, Beijing, China
| | - Qiongzhen Qin
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xu Yang
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Wanqing Han
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Yongli Lai
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jiaqi Chen
- Department of Pediatrics, Southern Medical University Nanfang Hospital, Guangzhou, China
| | - Shihao Zhou
- Department of Genetics, Changsha Hospital for Maternal and Child Health Care, Changsha, China
| | - Xuexi Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Wanjun Zhou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Department of Laboratory Medicine, Southern Medical University Nanfang Hospital, Guangzhou, China
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7
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Nakamura A, Komatsu M. Performance evaluation of whole genome metagenomics sequencing with the MinION nanopore sequencer: Microbial community analysis and antimicrobial resistance gene detection. J Microbiol Methods 2023; 206:106688. [PMID: 36764487 DOI: 10.1016/j.mimet.2023.106688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
Recently, the human gut microbiota has been implicated in various diseases such as immunological and neuropsychiatric disorders, and comprehensive gut microbiota analysis by metagenomic analysis using next-generation sequencers has been attracting attention. In this study, we compared microbial communities of 16S rDNA metagenome sequencing (16S-meta) and whole genome metagenome sequencing (WG-meta) using the nanopore sequencer MinION and 16S-meta using the Illumina Miseq sequencer with simulated and fecal samples, and evaluated the ability of WG-meta to detect antimicrobial resistance genes. We used the commercial Microbial Community DNA Standard as the DNA standard and a simulated sample comprising 17 strains of 15 bacterial species. In the detection of antimicrobial resistance genes, we used a simulated sample and spiked fecal samples containing Escherichia coli carrying blaCTX-M-27, Klebsiella pneumoniae carrying blaOXA-48, and Staphylococcus aureus carrying mecA. WG-meta using MinION was superior to 16S-meta and could accurately analyze the microbial communities at the species level, but it underestimated or misidentified the Bacillus subtilis group, Cryptococcus neoformans, Shigella sonnei, and Campylobacter jejuni. WG-meta using MinION could analyze the microbial communities in 5 min, and antimicrobial resistance gene detection using WG-meta could be performed in >30 min in the simulated sample with fewer bacterial counts.
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Affiliation(s)
- Akihiro Nakamura
- Department of Clinical Laboratory Science, Faculty of Health Care, Tenri Health Care University, Tenri, Japan.
| | - Masaru Komatsu
- Department of Clinical Laboratory Science, Faculty of Health Care, Tenri Health Care University, Tenri, Japan
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8
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Optimized Method for Bacterial Nucleic Acid Extraction from Positive Blood Culture Broth for Whole-Genome Sequencing, Resistance Phenotype Prediction, and Downstream Molecular Applications. J Clin Microbiol 2022; 60:e0101222. [PMID: 36314799 PMCID: PMC9667764 DOI: 10.1128/jcm.01012-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The application of direct metagenomic sequencing from positive blood culture broth may solve the challenges of sequencing from low-bacterial-load blood samples in patients with sepsis. Forty prospectively collected blood culture broth samples growing Gram-negative bacteria were extracted using commercially available kits to achieve high-quality DNA.
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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: 5.0] [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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10
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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: 1.0] [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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Pallerla SR, Van Dong D, Linh LTK, Van Son T, Quyen DT, Hoan PQ, Trung NT, The NT, Rüter J, Boutin S, Nurjadi D, Sy BT, Kremsner PG, Meyer CG, Song LH, Velavan TP. Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting. Ann Clin Microbiol Antimicrob 2022; 21:39. [PMID: 36064402 PMCID: PMC9443622 DOI: 10.1186/s12941-022-00530-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/11/2022] [Indexed: 11/21/2022] Open
Abstract
Aim The aim of the present study is to compare the performance of 16S rRNA Nanopore sequencing and conventional culture in detecting infectious pathogens in patients with suspected meningitis in a resource-limited setting without extensive bioinformatics expertise. Methods DNA was isolated from the cerebrospinal fluid (CSF) of 30 patients with suspected bacterial meningitis. The isolated DNA was subjected to 16S sequencing using MinION™. The data were analysed in real time via the EPI2ME cloud platform. The Nanopore sequencing was done in parallel to routine microbiological diagnostics. Results Nanopore sequencing detected bacterial pathogens to species level in 13 of 30 (43%) samples. CSF culture showed 40% (12/30) positivity. In 21 of 30 patients (70%) with suspected bacterial meningitis, both methods yielded concordant results. About nine of 30 samples showed discordant results, of these five were false positive and four were false negative. In five of the culture negative results, nanopore sequencing was able to detect pathogen genome, due to the higher sensitivity of the molecular diagnostics. In two other samples, the CSF culture revealed Cryptococcus neoformans and Streptococcus pneumoniae, which were not detected by Nanopore sequencing. Overall, using both the cultures and 16S Nanopore sequencing, positivity rate increased from 40% (12/30) to 57% (17/30). Conclusion Next-generation sequencing could detect pathogens within six hours and could become an important tool for both pathogen screening and surveillance in low- and middle-income countries (LMICs) that do not have direct access to extensive bioinformatics expertise. Supplementary Information The online version contains supplementary material available at 10.1186/s12941-022-00530-6.
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Affiliation(s)
- Srinivas Reddy Pallerla
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany
| | - Do Van Dong
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Le Thi Kieu Linh
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany.,Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Trinh Van Son
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Dao Thanh Quyen
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Phan Quoc Hoan
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Ngo Tat Trung
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon
| | - Nguyen Trong The
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon
| | - Jule Rüter
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Bui Tien Sy
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Department of Microbiology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Peter G Kremsner
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany.,Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon
| | - Christian G Meyer
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany.,Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Le Huu Song
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam. .,108 Military Central Hospital, Hanoi, Vietnam.
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany. .,Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.
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12
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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: 6] [Impact Index Per Article: 3.0] [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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13
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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: 5] [Impact Index Per Article: 2.5] [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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14
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Zhou M, Wu Y, Kudinha T, Jia P, Wang L, Xu Y, Yang Q. Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing. Front Genet 2021; 12:620009. [PMID: 33841495 PMCID: PMC8024499 DOI: 10.3389/fgene.2021.620009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Bloodstream infection is a major cause of morbidity and mortality worldwide. We explored whether MinION nanopore sequencing could accelerate diagnosis, resistance, and virulence profiling prediction in simulated blood samples and blood cultures. One milliliter of healthy blood samples each from direct spike (sample 1), anaerobic (sample 2), and aerobic (sample 3) blood cultures with initial inoculation of ∼30 CFU/ml of a clinically isolated Klebsiella pneumoniae strain was subjected to DNA extraction and nanopore sequencing. Hybrid assembly of Illumina and nanopore reads from pure colonies of the isolate (sample 4) was used as a reference for comparison. Hybrid assembly of the reference genome identified a total of 39 antibiotic resistance genes and 77 virulence genes through alignment with the CARD and VFDB databases. Nanopore correctly detected K. pneumoniae in all three blood samples. The fastest identification was achieved within 8 h from specimen to result in sample 1 without blood culture. However, direct sequencing in sample 1 only identified seven resistance genes (20.6%) but 28 genes in samples 2–4 (82.4%) compared to the reference within 2 h of sequencing time. Similarly, 11 (14.3%) and 74 (96.1%) of the virulence genes were detected in samples 1 and 2–4 within 2 h of sequencing time, respectively. Direct nanopore sequencing from positive blood cultures allowed comprehensive pathogen identification, resistance, and virulence genes prediction within 2 h, which shows its promising use in point-of-care clinical settings.
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Affiliation(s)
- Menglan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yarong Wu
- Beijing Applied Biological Technologies Co., Ltd., Beijing, China
| | - Timothy Kudinha
- School of Biomedical Sciences, Charles Sturt University, Orange, NSW, Australia.,Pathology West, NSW Health Pathology, Orange, NSW, Australia
| | - Peiyao Jia
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Wang
- Beijing Applied Biological Technologies Co., Ltd., Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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15
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Ghosh PN, Brookes LM, Edwards HM, Fisher MC, Jervis P, Kappel D, Sewell TR, Shelton JM, Skelly E, Rhodes JL. Cross-Disciplinary Genomics Approaches to Studying Emerging Fungal Infections. Life (Basel) 2020; 10:E315. [PMID: 33260763 PMCID: PMC7761180 DOI: 10.3390/life10120315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/15/2020] [Accepted: 11/19/2020] [Indexed: 11/16/2022] Open
Abstract
Emerging fungal pathogens pose a serious, global and growing threat to food supply systems, wild ecosystems, and human health. However, historic chronic underinvestment in their research has resulted in a limited understanding of their epidemiology relative to bacterial and viral pathogens. Therefore, the untargeted nature of genomics and, more widely, -omics approaches is particularly attractive in addressing the threats posed by and illuminating the biology of these pathogens. Typically, research into plant, human and wildlife mycoses have been largely separated, with limited dialogue between disciplines. However, many serious mycoses facing the world today have common traits irrespective of host species, such as plastic genomes; wide host ranges; large population sizes and an ability to persist outside the host. These commonalities mean that -omics approaches that have been productively applied in one sphere and may also provide important insights in others, where these approaches may have historically been underutilised. In this review, we consider the advances made with genomics approaches in the fields of plant pathology, human medicine and wildlife health and the progress made in linking genomes to other -omics datatypes and sets; we identify the current barriers to linking -omics approaches and how these are being underutilised in each field; and we consider how and which -omics methodologies it is most crucial to build capacity for in the near future.
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Affiliation(s)
- Pria N. Ghosh
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
| | - Lola M. Brookes
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
- Institute of Zoology, Zoological Society of London, London NW1 4RY, UK
- Royal Veterinary College, Hawkshead Lane, North Mymms, Herts AL9 7TA, UK
| | - Hannah M. Edwards
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Phillip Jervis
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
- Institute of Zoology, Zoological Society of London, London NW1 4RY, UK
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Dana Kappel
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Thomas R. Sewell
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Jennifer M.G. Shelton
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
- UK Centre for Ecology & Hydrology, Wallingford OX10 8BB, UK
| | - Emily Skelly
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Johanna L. Rhodes
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
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16
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Latorre-Pérez A, Pascual J, Porcar M, Vilanova C. A lab in the field: applications of real-time, in situ metagenomic sequencing. Biol Methods Protoc 2020; 5:bpaa016. [PMID: 33134552 PMCID: PMC7585387 DOI: 10.1093/biomethods/bpaa016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 01/18/2023] Open
Abstract
High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.
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Affiliation(s)
| | | | - Manuel Porcar
- Darwin Bioprospecting Excellence SL, Valencia, Spain
- Institute for Integrative Systems Biology, I2SysBio, University of Valencia-CSIC, Valencia, Spain
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17
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Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing. Sci Rep 2020; 10:7622. [PMID: 32376847 PMCID: PMC7203151 DOI: 10.1038/s41598-020-64616-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/20/2020] [Indexed: 12/27/2022] Open
Abstract
Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1-2 days for identification of bacterial agent and an additional 2-3 days for phenotypic determination of antibiotic susceptibility pattern. With the escalating burden of antimicrobial resistance (AMR) rapid diagnostics becomes increasingly important to secure adequate antibiotic therapy. Real-time whole genome sequencing represents a genotypic diagnostic approach with the ability to rapidly identify pathogens and AMR-encoding genes. Here we have used nanopore sequencing of bacterial DNA extracted from positive blood cultures for identification of pathogens, detection of plasmids and AMR-encoding genes. To our knowledge, this is the first study to gather the above-mentioned information from nanopore sequencing and conduct a comprehensive analysis for diagnostic purposes in real-time. Identification of pathogens was possible after 10 minutes of sequencing and all predefined AMR-encoding genes and plasmids from monoculture experiments were detected within one hour using raw nanopore sequencing data. Furthermore, we demonstrate the correct identification of plasmids and blaCTX-M subtypes using de novo assembled nanopore contigs. Results from this study hold great promise for future applications in clinical microbiology and for health care surveillance purposes.
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18
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Bai B, Wang H, Li M, Ma X, Zheng J, Deng Q, Yu Z. Two Cases of Influenza B Virus-Related Fatal Fulminant Pneumonia Complicated With Staphylococcus aureus Infection in China Diagnosed Using Next-Generation Sequencing (2018). Front Public Health 2020; 8:121. [PMID: 32351925 PMCID: PMC7175880 DOI: 10.3389/fpubh.2020.00121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
Two rare cases of Chinese female patients with influenza B virus infection complicated with both fulminant pneumonia and septicemia caused by Panton–Valentine leukocidin(PVL) positive methicillin-sensitive Staphylococcus aureus (MASS) were reported for the first time in China through next-generation sequencing (NGS). An increasing body of evidence indicates that co-infection with influenza B virus and bacterial pneumonia is often fatal. Rapid and precise identification of the co-infection bacteria can guide the selection of treatment for patients with influenza virus infection in the clinical setting. In this study, next-generation sequencing (NGS) was applied for the rapid diagnosis of these two cases. Despite the unfavorable survival outcome of these patients, the application of next-generation sequencing showed promise as a diagnostic tool for the rapid diagnosis of unknown pathogens in patients with bacterial pneumonia and sepsis. This method can guide the administration of medications in such patients.
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Affiliation(s)
- Bing Bai
- Shenzhen Key Laboratory for Endogenous Infection, Department of Infectious Diseases, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Hongyan Wang
- Shenzhen Key Laboratory for Endogenous Infection, Department of Infectious Diseases, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Meng Li
- BGI Education Center, BGI Genomics and BGI-Shenzhen, University of Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoyu Ma
- Shenzhen Key Laboratory for Endogenous Infection, Department of Infectious Diseases, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Jinxin Zheng
- Shenzhen Key Laboratory for Endogenous Infection, Department of Infectious Diseases, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Qiwen Deng
- Shenzhen Key Laboratory for Endogenous Infection, Department of Infectious Diseases, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Zhijian Yu
- Shenzhen Key Laboratory for Endogenous Infection, Department of Infectious Diseases, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
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19
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Diagnosing Bacteremia in Real Time Using Next-Generation Sequencing-Based Technology. J Mol Diagn 2020; 22:301-303. [PMID: 31978560 DOI: 10.1016/j.jmoldx.2020.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 12/30/2019] [Accepted: 01/11/2020] [Indexed: 12/27/2022] Open
Abstract
This commentary highlights the article by Grumaz et al that describes the use of molecular sequencing for fast detection of pathogens directly from blood samples from septic patients.
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20
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Petersen LM, Martin IW, Moschetti WE, Kershaw CM, Tsongalis GJ. Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing. J Clin Microbiol 2019; 58:e01315-19. [PMID: 31619531 PMCID: PMC6935936 DOI: 10.1128/jcm.01315-19] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, the length of time to results, and the need for technical and bioinformatics expertise. However, the recent technological innovation of nanopore sequencing from Oxford Nanopore Technologies (ONT) has the potential to address these challenges. ONT sequencing is an attractive platform for clinical laboratories to adopt due to its low cost, rapid turnaround time, and user-friendly bioinformatics pipelines. However, this method still faces the problem of base-calling accuracy compared to other platforms. This review highlights the general challenges of pathogen detection in clinical specimens by metagenomic sequencing, the advantages and disadvantages of the ONT platform, and how research to date supports the potential future use of nanopore sequencing in infectious disease diagnostics.
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Affiliation(s)
- Lauren M Petersen
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, New Hampshire, USA
| | - Isabella W Martin
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, New Hampshire, USA
| | - Wayne E Moschetti
- Dartmouth-Hitchcock Medical Center, Department of Orthopaedics and Sports Medicine, Lebanon, New Hampshire, USA
| | - Colleen M Kershaw
- Dartmouth-Hitchcock Medical Center, Department of Infectious Disease and International Health, Lebanon, New Hampshire, USA
| | - Gregory J Tsongalis
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, New Hampshire, USA
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21
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A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer. Biotechniques 2019; 68:72-78. [PMID: 31849245 DOI: 10.2144/btn-2019-0072] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Oxford Nanopore Technologies MinION™ sequencer holds the capability to generate long amplicon reads; however, only a small amount of information is available regarding methodological approaches and the ability to identify a broad diversity of fungal taxa. To assess capabilities, three fungal mock communities were sequenced, each of which had varying ratios of 16 taxa. The data were processed through our selected pipeline. The MinION recovered all mock community members, when mixed at equal ratios. When a taxon was represented at a lower ratio, it was not recovered or decreased in relative abundance. Despite high error rates, highly accurate consensus sequences can be derived. This methodological approach identified all mock community taxa, demonstrating the MinION can be used as a practical alternative to profile fungal communities.
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Loit K, Adamson K, Bahram M, Puusepp R, Anslan S, Kiiker R, Drenkhan R, Tedersoo L. Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens. Appl Environ Microbiol 2019; 85:e01368-19. [PMID: 31444199 PMCID: PMC6803294 DOI: 10.1128/aem.01368-19] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/18/2019] [Indexed: 02/06/2023] Open
Abstract
Culture-based molecular identification methods have revolutionized detection of pathogens, yet these methods are slow and may yield inconclusive results from environmental materials. The second-generation sequencing tools have much-improved precision and sensitivity of detection, but these analyses are costly and may take several days to months. Of the third-generation sequencing techniques, the portable MinION device (Oxford Nanopore Technologies) has received much attention because of its small size and possibility of rapid analysis at reasonable cost. Here, we compare the relative performances of two third-generation sequencing instruments, MinION and Sequel (Pacific Biosciences), in identification and diagnostics of fungal and oomycete pathogens from conifer (Pinaceae) needles and potato (Solanum tuberosum) leaves and tubers. We demonstrate that the Sequel instrument is efficient for metabarcoding of complex samples, whereas MinION is not suited for this purpose due to a high error rate and multiple biases. However, we find that MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms and other associated organisms from plant tissues following both amplicon-based and PCR-free metagenomics approaches. Using the metagenomics approach with shortened DNA extraction and incubation times, we performed the entire MinION workflow, from sample preparation through DNA extraction, sequencing, bioinformatics, and interpretation, in 2.5 h. We advocate the use of MinION for rapid diagnostics of pathogens and potentially other organisms, but care needs to be taken to control or account for multiple potential technical biases.IMPORTANCE Microbial pathogens cause enormous losses to agriculture and forestry, but current combined culturing- and molecular identification-based detection methods are too slow for rapid identification and application of countermeasures. Here, we develop new and rapid protocols for Oxford Nanopore MinION-based third-generation diagnostics of plant pathogens that greatly improve the speed of diagnostics. However, due to high error rate and technical biases in MinION, the Pacific BioSciences Sequel platform is more useful for in-depth amplicon-based biodiversity monitoring (metabarcoding) from complex environmental samples.
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Affiliation(s)
- Kaire Loit
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Kalev Adamson
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rasmus Puusepp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sten Anslan
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Riinu Kiiker
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Rein Drenkhan
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Natural History Museum, University of Tartu, Tartu, Estonia
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Arastehfar A, Wickes BL, Ilkit M, Pincus DH, Daneshnia F, Pan W, Fang W, Boekhout T. Identification of Mycoses in Developing Countries. J Fungi (Basel) 2019; 5:E90. [PMID: 31569472 PMCID: PMC6958481 DOI: 10.3390/jof5040090] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/22/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
Extensive advances in technology offer a vast variety of diagnostic methods that save time and costs, but identification of fungal species causing human infections remains challenging in developing countries. Since the echinocandins, antifungals widely used to treat invasive mycoses, are still unavailable in developing countries where a considerable number of problematic fungal species are present, rapid and reliable identification is of paramount importance. Unaffordability, large footprints, lack of skilled personnel, and high costs associated with maintenance and infrastructure are the main factors precluding the establishment of high-precision technologies that can replace inexpensive yet time-consuming and inaccurate phenotypic methods. In addition, point-of-care lateral flow assay tests are available for the diagnosis of Aspergillus and Cryptococcus and are highly relevant for developing countries. An Aspergillus galactomannan lateral flow assay is also now available. Real-time PCR remains difficult to standardize and is not widespread in countries with limited resources. Isothermal and conventional PCR-based amplification assays may be alternative solutions. The combination of real-time PCR and serological assays can significantly increase diagnostic efficiency. However, this approach is too expensive for medical institutions in developing countries. Further advances in next-generation sequencing and other innovative technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic tools may lead to efficient, alternate methods that can be used in point-of-care assays, which may supplement or replace some of the current technologies and improve the diagnostics of fungal infections in developing countries.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
| | - Brian L Wickes
- The Department of Microbiology, Immunology, and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana 01330, Turkey.
| | | | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
| | - Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1012 WX Amsterdam, The Netherlands.
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An identification protocol for ESBL-producing Gram-negative bacteria bloodstream infections using a MinION nanopore sequencer. J Med Microbiol 2019; 68:1219-1226. [PMID: 31237534 DOI: 10.1099/jmm.0.001024] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE The new third-generation sequencing platform MinION is an attractive maintenance-free and disposable portable tool that can perform long-read and real-time sequencing. In this study, we validated this technology for the identification of pathogens from positive blood culture (BC) bottles. METHODOLOGY A total of 38 positive BC bottles were collected from patients with bloodstream infections, and 18 isolates of Gram-negative (GN) bacteria and 20 isolates of Gram-positive (GP) bacteria were identified from these using 16S rRNA sequencing and then used in this study. DNA was extracted from each aliquot using an extraction protocol that combined glass bead beating and chemical lysis. Up to 200 ng of each purified DNA sample was processed for library preparation and whole-genome sequencing was performed on up to 12 samples through a single MinION flow cell. RESULTS All GN bacteria identifications made by MinION sequencing for 30 min using the What's In My Pot? (WIMP) workflow via EPI2ME on the basis of the most frequent classified reads were consistent with those made by 16S rRNA sequencing. On the other hand, for GP bacteria specimens, the identification results for 16S rRNA sequencing and MinION were only in agreement in 12 out of 20 (60.0 %) cases. ARMA analysis was able to detect extended-spectrum β-lactamase (ESBL)-associated genes among various antimicrobial resistance-related genes. CONCLUSION We demonstrated the potential of the MinION sequencer for the identification of GN bacteria from positive BC bottles and the confirmation of an ESBL phenotype. This innovative sequence technology and its application could lead to a breakthrough in the diagnosis of infectious diseases.
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Abstract
Objective: Sepsis is a deadly infection that causes injury to tissues and organs. Infection and anti-infective treatment are the eternal themes of sepsis. The successful control of infection is a key factor of resuscitation for sepsis and septic shock. This review examines evidence for the treatment of sepsis. This evidence is combined with clinical experiments to reveal the rules and a standard flowchart of anti-infection therapy for sepsis. Data Sources: We retrieved information from the PubMed database up to October 2018 using various search terms and their combinations, including sepsis, septic shock, infection, antibiotics, and anti-infection. Study Selection: We included data from peer-reviewed journals printed in English on the relationships between infections and antibiotics. Results: By combining the literature review and clinical experience, we propose a 6Rs rule for sepsis and septic shock management: right patients, right time, right target, right antibiotics, right dose, and right source control. This rule encompasses rational decisions regarding the timing of treatment, the identification of the correct pathogen, the selection of appropriate antibiotics, the formulation of a scientifically based antibiotic dosage regimen, and the adequate control of infectious foci. Conclusions: This review highlights how to recognize and treat sepsis and septic shock and provides rules and a standard flowchart for anti-infection therapy for sepsis and septic shock for use in the clinical setting.
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Carleton HA, Besser J, Williams-Newkirk AJ, Huang A, Trees E, Gerner-Smidt P. Metagenomic Approaches for Public Health Surveillance of Foodborne Infections: Opportunities and Challenges. Foodborne Pathog Dis 2019; 16:474-479. [PMID: 31170005 PMCID: PMC6653786 DOI: 10.1089/fpd.2019.2636] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Foodborne disease surveillance in the United States is at a critical point. Clinical and diagnostic laboratories are using culture-independent diagnostic tests (CIDTs) to identify the pathogen causing foodborne illness from patient specimens. CIDTs are molecular tests that allow doctors to rapidly identify the bacteria causing illness within hours. CIDTs, unlike previous gold standard methods such as bacterial culture, do not produce an isolate that can be subtyped as part of the national molecular subtyping network for foodborne disease surveillance, PulseNet. Without subtype information, cases can no longer be linked using molecular data to identify potentially related cases that are part of an outbreak. In this review, we discuss the public health needs for a molecular subtyping approach directly from patient specimen and highlight different approaches, including amplicon and shotgun metagenomic sequencing.
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Affiliation(s)
- Heather A Carleton
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John Besser
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Amanda J Williams-Newkirk
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Andrew Huang
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Eija Trees
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Peter Gerner-Smidt
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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Ellwanger JH, Kaminski VDL, Chies JAB. Emerging infectious disease prevention: Where should we invest our resources and efforts? J Infect Public Health 2019; 12:313-316. [PMID: 30928239 DOI: 10.1016/j.jiph.2019.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/25/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023] Open
Abstract
Strategies focused on the prevention of emerging infectious disease outbreaks are currently in the spotlight of discussions among researchers committed to infectious disease control. In this mini-review, we provided a brief update on this discussion and characterized the three main targets for investments in emerging infectious disease prevention: animals, human sentinels for spillover events, and the general human population. Furthermore, the pros and cons of each target are highlighted. Despite the particularities of the proposed targets, each of them can fill different gaps in the surveillance of infectious diseases. When all three targets are focused on together, they create a powerful strategy of emerging infectious disease prevention.
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Affiliation(s)
- Joel H Ellwanger
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Valéria de Lima Kaminski
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - José A B Chies
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil.
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