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Zhang T, Li H, Ma S, Cao J, Liao H, Huang Q, Chen W. The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling. Appl Environ Microbiol 2023; 89:e0060523. [PMID: 37800969 PMCID: PMC10617388 DOI: 10.1128/aem.00605-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/04/2023] [Indexed: 10/07/2023] Open
Abstract
The long-read amplicon provides a species-level solution for the community. With the improvement of nanopore flowcells, the accuracy of Oxford Nanopore Technologies (ONT) R10.4.1 has been substantially enhanced, with an average of approximately 99%. To evaluate its effectiveness on amplicons, three types of microbiomes were analyzed by 16S ribosomal RNA (hereinafter referred to as "16S") amplicon sequencing using Novaseq, Pacbio sequel II, and Nanopore PromethION platforms (R9.4.1 and R10.4.1) in the current study. We showed the error rate, recall, precision, and bias index in the mock sample. The error rate of ONT R10.4.1 was greatly reduced, with a better recall in the case of the synthetic community. Meanwhile, in different types of environmental samples, ONT R10.4.1 analysis resulted in a composition similar to Pacbio data. We found that classification tools and databases influence ONT data. Based on these results, we conclude that the ONT R10.4.1 16S amplicon can also be used for application in environmental samples. IMPORTANCE The long-read amplicon supplies the community with a species-level solution. Due to the high error rate of nanopore sequencing early on, it has not been frequently used in 16S studies. Oxford Nanopore Technologies (ONT) introduced the R10.4.1 flowcell with Q20+ reagent to achieve more than 99% accuracy as sequencing technology advanced. However, there has been no published study on the performance of commercial PromethION sequencers with R10.4.1 flowcells on 16S sequencing or on the impact of accuracy improvement on taxonomy (R9.4.1 to R10.4.1) using 16S ONT data. In this study, three types of microbiomes were investigated by 16S ribosomal RNA (rRNA) amplicon sequencing using Novaseq, Pacbio sequel II, and Nanopore PromethION platforms (R9.4.1 and R10.4.1). In the mock sample, we displayed the error rate, recall, precision, and bias index. We observed that the error rate in ONT R10.4.1 is significantly lower, especially when deletions are involved. First and foremost, R10.4.1 and Pacific Bioscience platforms reveal a similar microbiome in environmental samples. This study shows that the R10.4.1 full-length 16S rRNA sequences allow for species identification of environmental microbiota.
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Affiliation(s)
- Tianyuan Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Wuhan Benagen Technology Co., Ltd., Wuhan, China
| | - Hanzhou Li
- Wuhan Benagen Technology Co., Ltd., Wuhan, China
| | - Silin Ma
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Jian Cao
- Wuhan Benagen Technology Co., Ltd., Wuhan, China
| | - Hao Liao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, China
| | - Wenli Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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2
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Ji X, Ni S, Tian G, Zhang L, Wang W. Detection of Microorganisms in Body Fluid Samples. Methods Mol Biol 2023; 2695:73-88. [PMID: 37450112 DOI: 10.1007/978-1-0716-3346-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Next-generation sequencing (NGS) has been widely applied to the identification of microbiome in body fluids. The methodology of 16S rRNA amplicon sequencing is simple, fast, and cost-effective. It overcomes the problem that some microorganisms cannot be isolated or cultured. Low abundant bacteria can also be amplified and sequenced, but the resolution of classification can hardly reach species or sub-species level; moreover, this methodology is mainly used to identify bacterial populations, and other microorganisms like viruses or fungi cannot be sequenced. On the other hand, the microbiome profiling obtained by shotgun metagenomic sequencing is more comprehensive with better resolution, and more accurate classification can be expected due to higher coverage of genomic sequences from microorganisms. By combining the capture-based method with metagenomic sequencing, we can further enrich and detect low abundant microorganisms and identify the viral integration sites in host gDNA at once.
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Meng B, Li G, Zeng Z, Zheng B, Xia Y, Li C, Li M, Wang H, Song Y, Yu S. Establishment of early diagnosis models for cervical precancerous lesions using large-scale cervical cancer screening datasets. Virol J 2022; 19:177. [PMID: 36335385 PMCID: PMC9636682 DOI: 10.1186/s12985-022-01908-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/24/2022] [Indexed: 11/08/2022] Open
Abstract
Background Human papilloma virus (HPV) DNA test was applied in cervical cancer screening as an effective cancer prevention strategy. The viral load of HPV generated by different assays attracted increasing attention on its potential value in disease diagnosis and progression discovery. Methods In this study, three HPV testing datasets were assessed and compared, including Hybrid Capture 2 (n = 31,954), Aptima HPV E6E7 (n = 3269) and HPV Cobas 4800 (n = 13,342). Logistic regression models for diagnosing early cervical lesions of the three datasets were established and compared. The best variable factor combination (VL + BV) and dataset (HC2) were used for the establishment of six machine learning models. Models were evaluated and compared, and the best-performed model was validated. Results Our results show that viral load value was significantly correlated with cervical lesion stages in all three data sets. Viral Load and Bacterial Vaginosis were the best variable factor combination for logistic regression model establishment, and models based on the HC2 dataset performed best compared with the other two datasets. Machine learning method Xgboost generated the highest AUC value of models, which were 0.915, 0.9529, 0.9557, 0.9614 for diagnosing ASCUS higher, ASC-H higher, LSIL higher, and HSIL higher staged cervical lesions, indicating the acceptable accuracy of the selected diagnostic model. Conclusions Our study demonstrates that HPV viral load and BV status were significantly associated with the early stages of cervical lesions. The best-performed models can serve as a useful tool to help diagnose cervical lesions early. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01908-w.
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Affiliation(s)
- Bo Meng
- Guangzhou KingMed Transformative Medicine Institute Co., Ltd., Guangzhou, Guangdong China
| | - Guibin Li
- Guangzhou KingMed Transformative Medicine Institute Co., Ltd., Guangzhou, Guangdong China
| | - Zhengyu Zeng
- grid.477337.3Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, Guangdong China
| | - Baowen Zheng
- grid.477337.3Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, Guangdong China
| | - Yuyue Xia
- grid.477337.3Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, Guangdong China
| | - Chen Li
- grid.477337.3Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, Guangdong China
| | - Minyu Li
- grid.477337.3Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, Guangdong China
| | - Hairong Wang
- grid.477337.3Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, Guangdong China
| | - Yuelong Song
- grid.477337.3Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, Guangdong China
| | - Shihui Yu
- Guangzhou KingMed Transformative Medicine Institute Co., Ltd., Guangzhou, Guangdong China ,grid.477337.3Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, Guangdong China
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Kerry-Barnard S, Zhou L, Phillips L, Furegato M, Witney AA, Sadiq ST, Oakeshott P. Vaginal microbiota in ethnically diverse young women who did or did not develop pelvic inflammatory disease: community-based prospective study. Sex Transm Infect 2022; 98:503-509. [PMID: 35086915 PMCID: PMC9613871 DOI: 10.1136/sextrans-2021-055260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES A lactobacilli-dominated vaginal microbiome may protect against pelvic inflammatory disease (PID), but one dominated by Gardnerella species might increase susceptibility. Not all lactobacilli are equally protective. Recent research suggests that D(-) isomer lactic acid producing lactobacilli (Lactobacillus crispatus, Lactobacillus jensenii and Lactobacillus gasseri) may protect against infection with Chlamydia trachomatis, an important cause of PID. Lactobacillus iners , which produces L(+) isomer lactic acid, may be less protective. We investigated the microbiome in stored vaginal samples from participants who did or did not develop PID during the prevention of pelvic infection (POPI) chlamydia screening trial. METHODS Long-read 16S rRNA gene nanopore sequencing was used on baseline vaginal samples (one per participant) from all 37 women who subsequently developed clinically diagnosed PID during 12-month follow-up, and 111 frequency matched controls who did not, matched on four possible risk factors for PID: age <20 versus ≥20, black ethnicity versus other ethnicity, chlamydia positive versus negative at baseline and ≥2 sexual partners in the previous year versus 0-1 partners. RESULTS Samples from 106 women (median age 19 years, 40% black ethnicity, 22% chlamydia positive, 54% reporting multiple partners) were suitable for analysis. Three main taxonomic clusters were identified dominated by L. iners, L. crispatus and Gardnerella vaginalis. There was no association between a more diverse, G. vaginalis dominated microbiome and subsequent PID, although increased Shannon diversity was associated with black ethnicity (p=0.002) and bacterial vaginosis (diagnosed by Gram stain p<0.0001). Women who developed PID had similar relative abundance of protective D(-) isomer lactic acid producing lactobacilli to women without PID, but numbers of PID cases were small. CONCLUSIONS In the first-ever community-based prospective study of PID, there was no clear association between the vaginal microbiome and subsequent development of PID. Future studies using serial samples may identify vaginal microbial communities that may predispose to PID.
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Affiliation(s)
- Sarah Kerry-Barnard
- Population Health Research Institute, St George's, University of London, London, UK
| | - Liqing Zhou
- Applied Diagnostic Research and Evaluation Unit, St George's, University of London, London, UK
| | - Laura Phillips
- Applied Diagnostic Research and Evaluation Unit, St George's, University of London, London, UK
| | - Martina Furegato
- Applied Diagnostic Research and Evaluation Unit, St George's, University of London, London, UK
| | - Adam A Witney
- Institute for Infection and Immunity, St George's, University of London, London, UK
| | - S Tariq Sadiq
- Applied Diagnostic Research and Evaluation Unit, St George's, University of London, London, UK,Clinical Academic group in Infection and Immunity, St George’s University Hospitals NHS Foundation Trust, London, UK
| | - Pippa Oakeshott
- Population Health Research Institute, St George's, University of London, London, UK
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5
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Lüth T, Graspeuntner S, Neumann K, Kirchhoff L, Masuch A, Schaake S, Lupatsii M, Tse R, Griesinger G, Trinh J, Rupp J. Improving analysis of the vaginal microbiota of women undergoing assisted reproduction using nanopore sequencing. J Assist Reprod Genet 2022; 39:2659-2667. [PMID: 36223010 DOI: 10.1007/s10815-022-02628-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/25/2022] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Subclinical alterations of the vaginal microbiome have been described to be associated with female infertility and may serve as predictors for failure of in vitro fertilization treatment. While large prospective studies to delineate the role of microbial composition are warranted, integrating microbiome information into clinical management depends on economical and practical feasibility, specifically on a short duration from sampling to final results. The currently most used method for microbiota analysis is either metagenomics sequencing or amplicon-based microbiota analysis using second-generation methods such as sequencing-by-synthesis approaches (Illumina), which is both expensive and time-consuming. Thus, additional approaches are warranted to accelerate the usability of the microbiome as a marker in clinical praxis. METHODS Herein, we used a set of ten selected vaginal swabs from women undergoing assisted reproduction, comparing and performing critical optimization of nanopore-based microbiota analysis with the results from MiSeq-based data as a quality reference. RESULTS The analyzed samples carried varying community compositions, as shown by amplicon-based analysis of the V3V4 region of the bacterial 16S rRNA gene by MiSeq sequencing. Using a stepwise procedure to optimize adaptation, we show that a close approximation of the microbial composition can be achieved within a reduced time frame and at a minimum of costs using nanopore sequencing. CONCLUSIONS Our work highlights the potential of a nanopore-based methodical setup to support the feasibility of interventional studies and contribute to the development of microbiome-based clinical decision-making in assisted reproduction.
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Affiliation(s)
- Theresa Lüth
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany.
| | - Kay Neumann
- Department of Gynaecological Endocrinology and Reproductive Medicine, University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Laura Kirchhoff
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Antonia Masuch
- Department of Gynaecological Endocrinology and Reproductive Medicine, University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Susen Schaake
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Mariia Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Ronnie Tse
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Georg Griesinger
- Department of Gynaecological Endocrinology and Reproductive Medicine, University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany.,German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
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6
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Huang T, Zhang R, Li J. CRISPR-Cas-based techniques for pathogen detection: Retrospect, recent advances, and future perspectives. J Adv Res 2022:S2090-1232(22)00240-5. [PMID: 36367481 PMCID: PMC10403697 DOI: 10.1016/j.jare.2022.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/16/2022] [Accepted: 10/22/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Early detection of pathogen-associated diseases are critical for effective treatment. Rapid, specific, sensitive, and cost-effective diagnostic technologies continue to be challenging to develop. The current gold standard for pathogen detection, polymerase chain reaction technology, has limitations such as long operational cycles, high cost, and high technician and instrumentation requirements. AIM OF REVIEW This review examines and highlights the technical advancements of CRISPR-Cas in pathogen detection and provides an outlook for future development, multi-application scenarios, and clinical translation. KEY SCIENTIFIC CONCEPTS OF REVIEW Approaches enabling clinical detection of pathogen nucleic acids that are highly sensitive, specific, cheap, and portable are necessary. CRISPR-Cas9 specificity in targeting nucleic acids and "collateral cleavage" activity of CRISPR-Cas12/Cas13/Cas14 show significant promise in nucleic acid detection technology. These methods have a high specificity, versatility, and rapid detection cycle. In this paper, CRISPR-Cas-based detection methods are discussed in depth. Although CRISPR-Cas-mediated pathogen diagnostic solutions face challenges, their powerful capabilities will pave the way for ideal diagnostic tools.
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7
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Watanabe C, Kimizuka Y, Fujikura Y, Hamamoto T, Watanabe A, Yaguchi T, Sano T, Suematsu R, Kato Y, Miyata J, Matsukuma S, Kawana A. Mixed Infection of Cytomegalovirus and Pulmonary Nocardiosis Caused by Nocardia elegans Diagnosed Using Nanopore Sequencing Technology. Intern Med 2022; 61:1613-1617. [PMID: 34707041 PMCID: PMC9177376 DOI: 10.2169/internalmedicine.7639-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A 69-year-old woman who had undergone renal transplantation and was receiving sulfamethoxazole/trimethoprim (ST) developed pulmonary nocardiosis. To our knowledge, this is the first report of the identification of Nocardia elegans using nanopore sequencing, supported by 16S rDNA capillary sequencing findings. Chest computed tomography performed after ST initiation revealed significant improvement of the pulmonary shadows compared to previous findings. We herein report the value of nanopore sequencing for rapid identification of rare pathogens, such as Nocardia elegans. Furthermore, our findings suggest that Nocardia may infect even patients receiving ST, which is currently the most effective prophylactic drug.
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Affiliation(s)
- Chie Watanabe
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Yoshifumi Kimizuka
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Yuji Fujikura
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Takaaki Hamamoto
- Department of Laboratory Medicine, National Defense Medical College Hospital, Japan
| | - Akira Watanabe
- Division of Bio-resources, Medical Mycology Research Center, Chiba University, Japan
| | - Takashi Yaguchi
- Division of Bio-resources, Medical Mycology Research Center, Chiba University, Japan
| | - Tomoya Sano
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Ryohei Suematsu
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Yoshiki Kato
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Jun Miyata
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Susumu Matsukuma
- Department of Laboratory Medicine, National Defense Medical College Hospital, Japan
- Department of Pathology and Laboratory Medicine, National Defense Medical College, Japan
| | - Akihiko Kawana
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
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8
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Komiya S, Matsuo Y, Nakagawa S, Morimoto Y, Kryukov K, Okada H, Hirota K. MinION, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting. BMC Med Genomics 2022; 15:68. [PMID: 35337329 PMCID: PMC8953062 DOI: 10.1186/s12920-022-01218-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 02/14/2022] [Indexed: 01/13/2023] Open
Abstract
Background It has been suggested that the local microbiota in the reproductive organs is relevant to women's health and may also affect pregnancy outcomes. Analysis of partial 16S ribosomal RNA (rRNA) gene sequences generated by short-read sequencers has been used to identify vaginal and endometrial microbiota, but it requires a long time to obtain the results, making it unsuitable for rapid bacterial identification from a small specimen amount in a clinical context. Methods We developed a simple workflow using the nanopore sequencer MinION that allows high-resolution and rapid differentiation of vaginal microbiota. Vaginal samples collected from 18 participants were subjected to DNA extraction and full-length 16S rRNA gene sequencing with MinION. Results The principal coordinate analysis showed no differences in the bacterial compositions regardless of the sample collection method. The analysis of vaginal microbiota could be completed with a total analysis time of approximately four hours, allowing same-day results. Taxonomic profiling by MinION sequencing revealed relatively low diversity of the vaginal bacterial community, identifying the prevailing Lactobacillus species and several causative agents of bacterial vaginosis. Conclusions Full-length 16S rRNA gene sequencing analysis with MinION provides a rapid means for identifying vaginal bacteria with higher resolution. Species-level profiling of human vaginal microbiota by MinION sequencing can allow the analysis of associations with conditions such as genital infections, endometritis, and threatened miscarriage. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01218-8.
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Affiliation(s)
- Shinnosuke Komiya
- Department of Obstetrics and Gynecology, Kansai Medical University Graduate School of Medicine, Osaka, Japan.,HORAC Grand Front Osaka Clinic, Osaka, Japan
| | - Yoshiyuki Matsuo
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan.
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | | | - Kirill Kryukov
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
| | - Hidetaka Okada
- Department of Obstetrics and Gynecology, Kansai Medical University Graduate School of Medicine, Osaka, Japan
| | - Kiichi Hirota
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
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9
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Ohshiro T. Nanodevices for Biological and Medical Applications: Development of Single-Molecule Electrical Measurement Method. Applied Sciences 2022; 12:1539. [DOI: 10.3390/app12031539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A comprehensive detection of a wide variety of diagnostic markers is required for the realization of personalized medicine. As a sensor to realize such personalized medicine, a single molecule electrical measurement method using nanodevices is currently attracting interest for its comprehensive simultaneous detection of various target markers for use in biological and medical application. Single-molecule electrical measurement using nanodevices, such as nanopore, nanogap, or nanopipette devices, has the following features:; high sensitivity, low-cost, high-throughput detection, easy-portability, low-cost availability by mass production technologies, and the possibility of integration of various functions and multiple sensors. In this review, I focus on the medical applications of single- molecule electrical measurement using nanodevices. This review provides information on the current status and future prospects of nanodevice-based single-molecule electrical measurement technology, which is making a full-scale contribution to realizing personalized medicine in the future. Future prospects include some discussion on of the current issues on the expansion of the application requirements for single-mole-cule measurement.
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10
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Usyk M, Schlecht NF, Pickering S, Williams L, Sollecito CC, Gradissimo A, Porras C, Safaeian M, Pinto L, Herrero R, Strickler HD, Viswanathan S, Nucci-Sack A, Diaz A, Burk RD. molBV reveals immune landscape of bacterial vaginosis and predicts human papillomavirus infection natural history. Nat Commun 2022; 13:233. [PMID: 35017496 PMCID: PMC8752746 DOI: 10.1038/s41467-021-27628-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/30/2021] [Indexed: 12/16/2022] Open
Abstract
Bacterial vaginosis (BV) is a highly prevalent condition that is associated with adverse health outcomes. It has been proposed that BV’s role as a pathogenic condition is mediated via bacteria-induced inflammation. However, the complex interplay between vaginal microbes and host immune factors has yet to be clearly elucidated. Here, we develop molBV, a 16 S rRNA gene amplicon-based classification pipeline that generates a molecular score and diagnoses BV with the same accuracy as the current gold standard method (i.e., Nugent score). Using 3 confirmatory cohorts we show that molBV is independent of the 16 S rRNA region and generalizable across populations. We use the score in a cohort without clinical BV states, but with measures of HPV infection history and immune markers, to reveal that BV-associated increases in the IL-1β/IP-10 cytokine ratio directly predicts clearance of incident high-risk HPV infection (HR = 1.86, 95% CI: 1.19-2.9). Furthermore, we identify an alternate inflammatory BV signature characterized by elevated TNF-α/MIP-1β ratio that is prospectively associated with progression of incident infections to CIN2 + (OR = 2.81, 95% CI: 1.62-5.42). Thus, BV is a heterogeneous condition that activates different arms of the immune response, which in turn are independent risk factors for HR-HPV clearance and progression. Clinical Trial registration number: The CVT trial has been registered under: NCT00128661. Here, Burk et al. develop an algorithm to diagnose bacterial vaginosis (BV) using the 16S rRNA gene, called molBV, which they use to profile the inflammatory landscape of BV and predict progression of human papillomavirus infection to cervical pre-cancer.
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Affiliation(s)
- Mykhaylo Usyk
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, Bronx, USA.,Department of Epidemiology and Population Health, NYU School of Medicine, New York, USA
| | - Nicolas F Schlecht
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, USA.,Department of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Sarah Pickering
- Department of Pediatrics, Mount Sinai Adolescent Health Center, Icahn School of Medicine at Mount Sinai, Manhattan, NY, USA
| | - LaShanda Williams
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, Bronx, USA
| | - Christopher C Sollecito
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, Bronx, USA
| | - Ana Gradissimo
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, Bronx, USA
| | - Carolina Porras
- Agencia Costarricense de Investigaciones Biomédicas, Fundación INCIENSA, Costa Rica, USA
| | | | - Ligia Pinto
- HPV Serology Laboratory, Frederick National Laboratory for Cancer Research, Fredrick, MD, USA
| | - Rolando Herrero
- Agencia Costarricense de Investigaciones Biomédicas, Fundación INCIENSA, Costa Rica, USA
| | - Howard D Strickler
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, USA
| | - Shankar Viswanathan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, USA
| | - Anne Nucci-Sack
- Department of Pediatrics, Mount Sinai Adolescent Health Center, Icahn School of Medicine at Mount Sinai, Manhattan, NY, USA
| | - Angela Diaz
- Department of Pediatrics, Mount Sinai Adolescent Health Center, Icahn School of Medicine at Mount Sinai, Manhattan, NY, USA
| | | | - Robert D Burk
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, Bronx, USA. .,Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, USA. .,Departments of Microbiology and Immunology, and Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA.
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11
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Abstract
In the past several years, nanopore sequencing technology from Oxford Nanopore Technologies (ONT) and single-molecule real-time (SMRT) sequencing technology from Pacific BioSciences (PacBio) have become available to researchers and are currently being tested for cancer research. These methods offer many advantages over most widely used high-throughput short-read sequencing approaches and allow the comprehensive analysis of transcriptomes by identifying full-length splice isoforms and several other posttranscriptional events. In addition, these platforms enable structural variation characterization at a previously unparalleled resolution and direct detection of epigenetic marks in native DNA and RNA. Here, we present a comprehensive summary of important applications of these technologies in cancer research, including the identification of complex structure variants, alternatively spliced isoforms, fusion transcript events, and exogenous RNA. Furthermore, we discuss the impact of the newly developed nanopore direct RNA sequencing (RNA-Seq) approach in advancing epitranscriptome research in cancer. Although the unique challenges still present for these new single-molecule long-read methods, they will unravel many aspects of cancer genome complexity in unprecedented ways and present an encouraging outlook for continued application in an increasing number of different cancer research settings.
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Affiliation(s)
- Zhiao Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
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12
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Abstract
This minireview will discuss the improvements in Oxford Nanopore (Oxford; sequencing technology that make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the increase in sequence accuracy from 65 to 96.5% during the last 5 years, the ability to obtain a quantifiable/predictive signal from the MinION with respect to target molecule abundance, simple-to-use GUI-based pathways for data analysis and the modest additional equipment needs for sequencing in the field. Coupling these recent improvements with the low capital costs for equipment and the reasonable per sample cost makes MinION sequencing an attractive option for virtually any laboratory.
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Affiliation(s)
- Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
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13
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Oberle A, Urban L, Falch-Leis S, Ennemoser C, Nagai Y, Ashikawa K, Ulm PA, Hengstschläger M, Feichtinger M. 16S rRNA long-read nanopore sequencing is feasible and reliable for endometrial microbiome analysis. Reprod Biomed Online 2021; 42:1097-1107. [PMID: 33849786 DOI: 10.1016/j.rbmo.2021.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 01/09/2023]
Abstract
RESEARCH QUESTION Full-length 16S rRNA gene sequencing using nanopore technology is a fast alternative to conventional short-read 16S rRNA gene sequencing with low initial investment costs that has been used for various microbiome studies but has not yet been investigated as an alternative approach for endometrial microbiome analysis. Is in-situ 16S rRNA gene long-read sequencing using portable nanopore sequencing technology feasible and reliable for endometrial microbiome analysis? DESIGN A prospective experimental study based on 33 patients seeking infertility treatment between January and October 2019. A 16S rRNA gene long-read nanopore sequencing protocol for analysing endometrial microbiome samples was established, including negative controls for contamination evaluation and positive controls for bias evaluation. Contamination caused by kit and exterior sources was identified and excluded from the analysis. Endometrial samples from 33 infertile patients were sequenced using the optimized long-read nanopore sequencing protocol and compared with conventional short-read sequencing carried out by external laboratories. RESULTS Of the 33 endometrial patient samples, 23 successfully amplified (69.7%) and their microbiome was assessed using nanopore sequencing. Of those 23 samples, 14 (60.9%) were Lactobacillus-dominated (>80% of reads mapping to Lactobacillus), with 10 samples resulting in more than 90% Lactobacillus reads. Our long-read nanopore sequencing revealed results similar to two conventional short-read sequencing approaches and to long-read sequencing validation carried out in external laboratories. CONCLUSION In this pilot study, 16S rRNA gene long-read nanopore sequencing was established to analyse the endometrial microbiome in situ that could be widely applied owing to its cost efficiency and portable character.
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Affiliation(s)
- Anna Oberle
- Wunschbaby Institut Feichtinger, Lainzerstrasse 6, Vienna 1130, Austria
| | - Lara Urban
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Department of Anatomy, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Stefanie Falch-Leis
- Tyrolpath, Pathologielabor Dr. Obrist Dr. Brunhuber, Hauptplatz 4, Zams 6511, Austria
| | - Chiara Ennemoser
- Tyrolpath, Pathologielabor Dr. Obrist Dr. Brunhuber, Hauptplatz 4, Zams 6511, Austria
| | - Yoko Nagai
- Varinos, Inc., Dai 2 Gotanda Fujikoshi Bldg., 6F 5-23-1 Higashigotanda, Shinagawa-ku Tokyo, Japan
| | - Kyota Ashikawa
- Varinos, Inc., Dai 2 Gotanda Fujikoshi Bldg., 6F 5-23-1 Higashigotanda, Shinagawa-ku Tokyo, Japan
| | - Patricia A Ulm
- Wunschbaby Institut Feichtinger, Lainzerstrasse 6, Vienna 1130, Austria
| | | | - Michael Feichtinger
- Wunschbaby Institut Feichtinger, Lainzerstrasse 6, Vienna 1130, Austria; Department of Oncology - Pathology, Karolinska Institutet, Karolinska vägen, A2:07171 64 Solna Stockholm, Sweden.
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14
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Lippert J, Bønløkke S, Utke A, Knudsen BR, Sorensen BS, Steiniche T, Stougaard M. Targeted next generation sequencing panel for HPV genotyping in cervical cancer. Exp Mol Pathol 2020; 118:104568. [PMID: 33171155 DOI: 10.1016/j.yexmp.2020.104568] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/24/2020] [Accepted: 11/03/2020] [Indexed: 02/08/2023]
Abstract
Cervical cancer are generally caused by a persistent infection with the oncogenic virus, HPV. Patients with HPV integration are more prone to develop cervical cancer than patients without integration. In this proof-of-concept study, we aimed to develop a sensitive method based on targeted amplicon based NGS for early and precise detection of high-risk HPV-genotypes that are highly associated with the development of cervical cancer. Furthermore, we aimed to investigate if amplicon based NGS allowed for HPV genotyping in cervical lesions and whether it could detect HPV integration. The cohort included a group of CIN3+ biopsies (n = 64), CIN2 samples that progressed (n = 5), CIN2 samples that regressed (n = 3), healthy controls (n = 10), and plasma samples (n = 10) from cervical cancer patients. Sequencing was performed using a custom targeted NGS panel designed to detect all 25 high-risk and probably high-risk and two low-risk HPV genotypes. The method was validated by the SPF10 PCR-DEIA-LiPA25 assay. In the cohort, the following HPV genotypes were identified: HPV-16, 18, 31, 33, 35, 45, 51, 52, 56, 58, and 59. When comparing the results from the SPF10 PCR-DEIA-LiPA25 analyses with the NGS analyses, there was close to a perfect agreement (K = 0.92) among the genotyped HPV types, while in the two cases with complete disagreement, a third assay was applied, and here the results of the NGS analyses were confirmed. Whereas multiple HPV types were detected by the SPF10 PCR-DEIA-LiPA25 assay, the NGS analysis clearly suggest that there is one predomentant HPV type. The NGS assay was capable of detecting HPV-16 in a previous false-negative sample classified by the INNO-LiPA assay, emphasizing the importance of including multiple regions of the HPV genome when genotyping. For the 10 plasma samples, our NGS analyses showed full agreement with the digital droplet PCR (ddPCR) analyses of HPV positive as well as negative plasma samples. Lastly, the custom panel was capable of detecting the integration of HPV-16 in the SiHa cell line. The HPV panel provides a highly cost-effective method for HPV detection and genotyping, as exemplified by a list price of around 75 € per sample. In conclusion, the current study demonstrates that targeted NGS is capable of detecting and genotyping HPV in both FFPE biopsies and plasma samples. This method provides for early diagnosis and prognosis of cervical cancer disease progression, thereby optimizing the potential of recovery and survival for these patients.
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Affiliation(s)
- J Lippert
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark
| | - S Bønløkke
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark; Aarhus University Hospital, Department of Pathology, Aarhus, Denmark
| | - A Utke
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark
| | - B R Knudsen
- Aarhus University, Department of Molecular Biology and Genetics, Aarhus, Denmark
| | - B S Sorensen
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark; Aarhus University Hospital, Department of Clinical Biochemistry, Aarhus, Denmark
| | - T Steiniche
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark; Aarhus University Hospital, Department of Pathology, Aarhus, Denmark
| | - M Stougaard
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark; Aarhus University Hospital, Department of Pathology, Aarhus, Denmark.
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15
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Yang W, Liu Y, Dong R, Liu J, Lang J, Yang J, Wang W, Li J, Meng B, Tian G. Accurate Detection of HPV Integration Sites in Cervical Cancer Samples Using the Nanopore MinION Sequencer Without Error Correction. Front Genet 2020; 11:660. [PMID: 32714374 PMCID: PMC7344299 DOI: 10.3389/fgene.2020.00660] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/29/2020] [Indexed: 12/14/2022] Open
Abstract
During the carcinogenesis of cervical cancer, the DNA of human papillomavirus (HPV) is frequently integrated into the human genome, which might be a biomarker for the early diagnosis of cervical cancer. Although the detection sensitivity of virus infection status increased significantly through the Illumina sequencing platform, there were still disadvantages remain for further improvement, including the detection accuracy and the complex integrated genome structure identification, etc. Nanopore sequencing has been proven to be a fast yet accurate technique of detecting pathogens in clinical samples with significant longer sequencing length. However, the identification of virus integration sites, especially HPV integration sites was seldom carried out by using nanopore platform. In this study, we evaluated the feasibility of identifying HPV integration sites by nanopore sequencer. Specifically, we re-sequenced the integration sites of a previously published sample by both nanopore and Illumina sequencing. After analyzing the results, three points of conclusions were drawn: first, 13 out of 19 previously published integration sites were found from all three datasets (i.e., nanopore, Illumina, and the published data), indicating a high overlap rate and comparability among the three platforms; second, our pipeline of nanopore and Illumina data identified 66 unique integration sites compared with previous published paper with 13 of them being verified by Sanger sequencing, indicating the higher integration sites detection sensitivity of our results compared with published data; third, we established a pipeline which could be used in HPV integration site detection by nanopore sequencing data without doing error correction analysis. In summary, a new nanopore data analysis method was tested and proved to be reliable in integration sites detection compared with methods of existing Illumina data analysis pipeline with less sequencing data required. It provides a solid evidence and tool to support the potential application of nanopore in virus status identification.
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Affiliation(s)
| | - Ying Liu
- Laboratory of Genetics, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ruyi Dong
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Jia Liu
- Geneis (Beijing) Co., Ltd., Beijing, China
| | | | | | | | - Jingjing Li
- The Precision Medicine Centre of Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Bo Meng
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd., Beijing, China
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
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