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Liu S, Yang X, Li R, Wang S, Han Z, Yang M, Zhang Y. IS6 family insertion sequences promote optrA dissemination between plasmids varying in transfer abilities. Appl Microbiol Biotechnol 2024; 108:132. [PMID: 38229329 DOI: 10.1007/s00253-023-12858-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/25/2023] [Accepted: 11/13/2023] [Indexed: 01/18/2024]
Abstract
Plasmids are the primary vectors for intercellular transfer of the oxazolidinone and phenicol cross-resistance gene optrA, while insertion sequences (ISs) are mobile genetic elements that can mobilize plasmid-borne optrA intracellularly. However, little is known about how the IS-mediated intracellular mobility facilitates the dissemination of the optrA gene between plasmid categories that vary in transfer abilities, including non-mobilizable, mobilizable, and conjugative plasmids. Here, we performed a holistic genomic study of 52 optrA-carrying plasmids obtained from searches guided by the Comprehensive Antibiotic Resistance Database. Among the 132 ISs identified within 10 kbp from the optrA gene in the plasmids, IS6 family genes were the most prevalent (86/132). Homologous gene arrays containing IS6 family genes were shared between different plasmids, especially between mobilizable and conjugative plasmids. All these indicated the central role of IS6 family genes in disseminating plasmid-borne optrA. Thirty-three of the 52 plasmids were harbored by Enterococcus faecalis found mainly in humans and animals. By Nanopore sequencing and inverse PCR, the potential of the enterococcal optrA to be transmitted from a mobilizable plasmid to a conjugative plasmid mediated by IS6 family genes was further confirmed in Enterococcus faecalis strains recovered from the effluents of anaerobic digestion systems for treating chicken manure. Our findings highlight the increased intercellular transfer abilities and dissemination risk of plasmid-borne optrA gene caused by IS-mediated intracellular mobility, and underscore the importance of routinely monitoring the dynamic genetic contexts of clinically important antibiotic resistance genes to effectively control this critical public health threat. KEY POINTS: • IS6 was prevalent in optrA-plasmids varying in intercellular transfer abilities. • Enterococcal optrA-plasmids were widespread among human, animal, and the environment. • IS6 elevated the dissemination risk of enterococcal optrA-plasmids.
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Affiliation(s)
- Shihai Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Shaolin Wang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Lee AWT, Ng ICF, Wong EYK, Wong ITF, Sze RPP, Chan KY, So TY, Zhang Z, Ka-Yee Fung S, Choi-Ying Wong S, Tam WY, Lao HY, Lee LK, Leung JSL, Chan CTM, Ng TTL, Zhang J, Chow FWN, Leung PHM, Siu GKH. Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics. Food Microbiol 2024; 121:104493. [PMID: 38637066 DOI: 10.1016/j.fm.2024.104493] [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] [Received: 01/08/2024] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 04/20/2024]
Abstract
Foodborne pathogens, particularly antimicrobial-resistant (AMR) bacteria, remain a significant threat to global health. Given the limitations of conventional culture-based approaches, which are limited in scope and time-consuming, metagenomic sequencing of food products emerges as a promising solution. This method provides a fast and comprehensive way to detect the presence of pathogenic microbes and antimicrobial resistance genes (ARGs). Notably, nanopore long-read sequencing provides more accurate bacterial taxonomic classification in comparison to short-read sequencing. Here, we revealed the impact of food types and attributes (origin, retail place, and food processing methods) on microbial communities and the AMR profile using nanopore metagenomic sequencing. We analyzed a total of 260 food products, including raw meat, sashimi, and ready-to-eat (RTE) vegetables. Clostridium botulinum, Acinetobacter baumannii, and Vibrio parahaemolyticus were identified as the top three foodborne pathogens in raw meat and sashimi. Importantly, even with low pathogen abundance, higher percentages of samples containing carbapenem and cephalosporin resistance genes were identified in chicken and RTE vegetables, respectively. In parallel, our results demonstrated that fresh, peeled, and minced foods exhibited higher levels of pathogenic bacteria. In conclusion, this comprehensive study offers invaluable data that can contribute to food safety assessments and serve as a basis for quality indicators.
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Affiliation(s)
- Annie Wing-Tung Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Iain Chi-Fung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Evelyn Yin-Kwan Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Ivan Tak-Fai Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Rebecca Po-Po Sze
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Kit-Yu Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Tsz-Yan So
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Zhipeng Zhang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sharon Ka-Yee Fung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sally Choi-Ying Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Wing-Yin Tam
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Jiaying Zhang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China.
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3
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Vigil K, D'Souza N, Bazner J, Cedraz FMA, Fisch S, Rose JB, Aw TG. Long-term monitoring of SARS-CoV-2 variants in wastewater using a coordinated workflow of droplet digital PCR and nanopore sequencing. Water Res 2024; 254:121338. [PMID: 38430753 DOI: 10.1016/j.watres.2024.121338] [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] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/12/2024] [Accepted: 02/17/2024] [Indexed: 03/05/2024]
Abstract
Quantitative polymerase chain reaction (PCR) and genome sequencing are important methods for wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The reverse transcription-droplet digital PCR (RT-ddPCR) is a highly sensitive method for quantifying SARS-CoV-2 RNA in wastewater samples to track the trends of viral activity levels but cannot identify new variants. It also takes time to develop new PCR-based assays targeting variants of interest. Whole genome sequencing (WGS) can be used to monitor known and new SARS-CoV-2 variants, but it is generally not quantitative. Several short-read sequencing techniques can be expensive and might experience delayed turnaround times when outsourced due to inadequate in-house resources. Recently, a portable nanopore sequencing system offers an affordable and real-time method for sequencing SARS-CoV-2 variants in wastewater. This technology has the potential to enable swift response to disease outbreaks without relying on clinical sequencing results. In addressing concerns related to rapid turnaround time and accurate variant analysis, both RT-ddPCR and nanopore sequencing methods were employed to monitor the emergence of SARS-CoV-2 variants in wastewater. This surveillance was conducted at 23 sewer maintenance hole sites and five wastewater treatment plants in Michigan from 2020 to 2022. In 2020, the wastewater samples were dominated by the parental variants (20A, 20C and 20 G), followed by 20I (Alpha, B.1.1.7) in early 2021 and the Delta variant of concern (VOC) in late 2021. For the year 2022, Omicron variants dominated. Nanopore sequencing has the potential to validate suspected variant cases that were initially undetermined by RT-ddPCR assays. The concordance rate between nanopore sequencing and RT-ddPCR assays in identifying SARS-CoV-2 variants to the clade-level was 76.9%. Notably, instances of disagreement between the two methods were most prominent in the identification of the parental and Omicron variants. We also showed that sequencing wastewater samples with SARS-CoV-2 N gene concentrations of >104 GC/100 ml as measured by RT-ddPCR improve genome recovery and coverage depth using MinION device. RT-ddPCR was better at detecting key spike protein mutations A67V, del69-70, K417N, L452R, N501Y, N679K, and R408S (p-value <0.05) as compared to nanopore sequencing. It is suggested that RT-ddPCR and nanopore sequencing should be coordinated in wastewater surveillance where RT-ddPCR can be used as a preliminary quantification method and nanopore sequencing as the confirmatory method for the detection of variants or identification of new variants. The RT-ddPCR and nanopore sequencing methods reported here can be adopted as a reliable in-house analysis of SARS-CoV-2 in wastewater for rapid community level surveillance and public health response.
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Affiliation(s)
- Katie Vigil
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, United States
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States
| | - Julia Bazner
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States
| | - Fernanda Mac-Allister Cedraz
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, United States
| | - Samuel Fisch
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, United States
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, United States.
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Afflerbach AK, Albers A, Appelt A, Schweizer L, Paulus W, Bockmayr M, Schüller U, Thomas C. Nanopore sequencing from formalin-fixed paraffin-embedded specimens for copy-number profiling and methylation-based CNS tumor classification. Acta Neuropathol 2024; 147:74. [PMID: 38642165 PMCID: PMC11032293 DOI: 10.1007/s00401-024-02731-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/22/2024]
Affiliation(s)
- Ann-Kristin Afflerbach
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anne Albers
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Anton Appelt
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Leonille Schweizer
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt Am Main, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt Am Main, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Michael Bockmayr
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- bAIome - Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany.
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Fukuda Y, Suzuki T, Iwata KI, Haruta K, Yamaguchi M, Torii Y, Narita A, Muramatsu H, Takahashi Y, Kawada JI. Nanopore sequencing in distinguishing between wild-type and vaccine strains of Varicella-Zoster virus. Vaccine 2024; 42:2927-2932. [PMID: 38548526 DOI: 10.1016/j.vaccine.2024.03.046] [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] [Received: 11/03/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND The introduction of varicella vaccines into routine pediatric immunization programs has led to a considerable reduction in varicella incidence. However, there have been reports of varicella, herpes zoster, and meningitis caused by the vaccine strain of varicella-zoster virus (VZV), raising concerns. Establishing the relationship between the wild-type and vaccine strains in VZV infections among previously vaccinated individuals is crucial. Differences in the single nucleotide polymorphisms (SNPs) among vaccine strains can be utilized to identify the strain. In this study, we employed nanopore sequencing to identify VZV strains and analyzed clinical samples. METHODS We retrospectively examined vesicle and cerebrospinal fluid samples from patients with VZV infections. One sample each of the wild-type and vaccine strains, previously identified using allelic discrimination real-time PCR and direct sequencing, served as controls. Ten samples with undetermined VZV strains were included. After DNA extraction, a long PCR targeting the VZV ORF62 region was executed. Nanopore sequencing identified SNPs, allowing discrimination between the vaccine and wild-type strains. RESULTS Nanopore sequencing confirmed SNPs at previously reported sites (105,705, 106,262, 107,136, and 107,252), aiding in distinguishing between wild-type and vaccine strains. Among the ten unknown samples, nine were characterized as wild strains and one as a vaccine strain. Even in samples with low VZV DNA levels, nanopore sequencing was effective in strain identification. CONCLUSION This study validates that nanopore sequencing is a reliable method for differentiating between the wild-type and vaccine strains of VZV. Its ability to produce long-read sequences is remarkable, allowing simultaneous confirmation of known SNPs and the detection of new mutations. Nanopore sequencing can serve as a valuable tool for the swift and precise identification of wild-type and vaccine strains and has potential applications in future VZV surveillance.
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Affiliation(s)
- Yuto Fukuda
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Ken-Ichi Iwata
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
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Xu X, Deng Y, Ding J, Tang Q, Lin Y, Zheng X, Zhang T. High-resolution and real-time wastewater viral surveillance by Nanopore sequencing. Water Res 2024; 256:121623. [PMID: 38657304 DOI: 10.1016/j.watres.2024.121623] [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] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
Wastewater genomic sequencing stands as a pivotal complementary tool for viral surveillance in populations. While long-read Nanopore sequencing is a promising platform to provide real-time genomic data, concerns over the sequencing accuracy of the earlier Nanopore versions have somewhat restrained its widespread application in wastewater analysis. Here, we evaluate the latest improved version of Nanopore sequencing (R10.4.1), using SARS-CoV-2 as the model infectious virus, to demonstrate its effectiveness in wastewater viral monitoring. By comparing amplicon lengths of 400 bp and 1200 bp, we revealed that shorter PCR amplification is more suitable for wastewater samples due to viral genome fragmentation. Utilizing mock wastewater samples, we validated the reliability of Nanopore sequencing for variant identification by comparing it with Illumina sequencing results. The strength of Nanopore sequencing in generating real-time genomic data for providing early warning signals was also showcased, indicating that as little as 0.001 Gb of data can provide accurate results for variant prevalence. Our evaluation also identified optimal alteration frequency cutoffs (>50 %) for precise mutation profiling, achieving >99 % precision in detecting single nucleotide variants (SNVs) and insertions/deletions (indels). Monitoring two major wastewater treatment plants in Hong Kong from September 2022 to April 2023, covering over 4.5 million population, we observed a transition in dominant variants from BA.5 to XBB lineages, with XBB.1.5 being the most prevalent variants. Mutation detection also highlighted the potential of wastewater Nanopore sequencing in uncovering novel mutations and revealed links between signature mutations and specific variants. This study not only reveals the environmental implications of Nanopore sequencing in SARS-CoV-2 surveillance but also underscores its potential in broader applications including environmental health monitoring of other epidemic viruses, which could significantly enhance the field of wastewater-based epidemiology.
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Affiliation(s)
- Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Qinling Tang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Yunqi Lin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region; School of Public Health, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region.
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7
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Yuen ZWS, Shanmuganandam S, Stanley M, Jiang S, Hein N, Daniel R, McNevin D, Jack C, Eyras E. Profiling age and body fluid DNA methylation markers using nanopore adaptive sampling. Forensic Sci Int Genet 2024; 71:103048. [PMID: 38640705 DOI: 10.1016/j.fsigen.2024.103048] [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: 12/11/2023] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/21/2024]
Abstract
DNA methylation plays essential roles in regulating physiological processes, from tissue and organ development to gene expression and aging processes and has emerged as a widely used biomarker for the identification of body fluids and age prediction. Currently, methylation markers are targeted independently at specific CpG sites as part of a multiplexed assay rather than through a unified assay. Methylation detection is also dependent on divergent methodologies, ranging from enzyme digestion and affinity enrichment to bisulfite treatment, alongside various technologies for high-throughput profiling, including microarray and sequencing. In this pilot study, we test the simultaneous identification of age-associated and body fluid-specific methylation markers using a single technology, nanopore adaptive sampling. This innovative approach enables the profiling of multiple CpG marker sites across entire gene regions from a single sample without the need for specialized DNA preparation or additional biochemical treatments. Our study demonstrates that adaptive sampling achieves sufficient coverage in regions of interest to accurately determine the methylation status, shows a robust consistency with whole-genome bisulfite sequencing data, and corroborates known CpG markers of age and body fluids. Our work also resulted in the identification of new sites strongly correlated with age, suggesting new possible age methylation markers. This study lays the groundwork for the systematic development of nanopore-based methodologies in both age prediction and body fluid identification, highlighting the feasibility and potential of nanopore adaptive sampling while acknowledging the need for further validation and expansion in future research.
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Affiliation(s)
- Zaka Wing-Sze Yuen
- EMBL Australia Partner Laboratory Network, John Curtin School of Medical Research, The Australian National University, Canberra, Australia; The Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, The Australian National University, Canberra, Australia; The Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Somasundhari Shanmuganandam
- Department of Immunity, Inflammation and Infection, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia; Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra, ACT 2601, Australia
| | - Maurice Stanley
- Department of Immunity, Inflammation and Infection, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia; Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra, ACT 2601, Australia
| | - Simon Jiang
- Department of Immunity, Inflammation and Infection, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia; Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra, ACT 2601, Australia; Department of Renal Medicine, The Canberra Hospital, Canberra, ACT 2605, Australia
| | - Nadine Hein
- ACRF Department of Cancer Biology and Therapeutics and Division of Genome Sciences and Cancer, John Curtin School of Medical Research, Australian National University, Acton, Canberra, Australia
| | - Runa Daniel
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Queensland, Australia
| | - Dennis McNevin
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, Australia
| | - Cameron Jack
- ANU Bioinformatics Consultancy, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Eduardo Eyras
- EMBL Australia Partner Laboratory Network, John Curtin School of Medical Research, The Australian National University, Canberra, Australia; The Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, The Australian National University, Canberra, Australia; The Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
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8
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Hench J, Hultschig C, Brugger J, Mariani L, Guzman R, Soleman J, Leu S, Benton M, Stec IM, Hench IB, Hoffmann P, Harter P, Weber KJ, Albers A, Thomas C, Hasselblatt M, Schüller U, Restelli L, Capper D, Hewer E, Diebold J, Kolenc D, Schneider UC, Rushing E, Della Monica R, Chiariotti L, Sill M, Schrimpf D, von Deimling A, Sahm F, Kölsche C, Tolnay M, Frank S. EpiDiP/NanoDiP: a versatile unsupervised machine learning edge computing platform for epigenomic tumour diagnostics. Acta Neuropathol Commun 2024; 12:51. [PMID: 38576030 PMCID: PMC10993614 DOI: 10.1186/s40478-024-01759-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/11/2024] [Indexed: 04/06/2024] Open
Abstract
DNA methylation analysis based on supervised machine learning algorithms with static reference data, allowing diagnostic tumour typing with unprecedented precision, has quickly become a new standard of care. Whereas genome-wide diagnostic methylation profiling is mostly performed on microarrays, an increasing number of institutions additionally employ nanopore sequencing as a faster alternative. In addition, methylation-specific parallel sequencing can generate methylation and genomic copy number data. Given these diverse approaches to methylation profiling, to date, there is no single tool that allows (1) classification and interpretation of microarray, nanopore and parallel sequencing data, (2) direct control of nanopore sequencers, and (3) the integration of microarray-based methylation reference data. Furthermore, no software capable of entirely running in routine diagnostic laboratory environments lacking high-performance computing and network infrastructure exists. To overcome these shortcomings, we present EpiDiP/NanoDiP as an open-source DNA methylation and copy number profiling suite, which has been benchmarked against an established supervised machine learning approach using in-house routine diagnostics data obtained between 2019 and 2021. Running locally on portable, cost- and energy-saving system-on-chip as well as gpGPU-augmented edge computing devices, NanoDiP works in offline mode, ensuring data privacy. It does not require the rigid training data annotation of supervised approaches. Furthermore, NanoDiP is the core of our public, free-of-charge EpiDiP web service which enables comparative methylation data analysis against an extensive reference data collection. We envision this versatile platform as a useful resource not only for neuropathologists and surgical pathologists but also for the tumour epigenetics research community. In daily diagnostic routine, analysis of native, unfixed biopsies by NanoDiP delivers molecular tumour classification in an intraoperative time frame.
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Affiliation(s)
- Jürgen Hench
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland.
| | - Claus Hultschig
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Jon Brugger
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Luigi Mariani
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Raphael Guzman
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Jehuda Soleman
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Severina Leu
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Miles Benton
- Human Genomics, Institute of Environmental Science and Research (ESR), 5022, Porirua, Wellington, New Zealand
| | - Irenäus Maria Stec
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Ivana Bratic Hench
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Per Hoffmann
- Life&Brain GmbH, Venusberg-Campus 1, Gebäude 76, 53127, Bonn, Germany
| | - Patrick Harter
- Institute of Neuropathology, Center for Neuropathology and Prion Research, Feodor- Lynen-Str. 23, 81377, München, Germany
| | - Katharina J Weber
- Neurological Institute (Edinger Institute), University Hospital, Heinrich-Hoffmann- Straße 7, 60528, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Anne Albers
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Ulrich Schüller
- Forschungsinstitut Kinderkrebszentrum, Martinistrasse 52, 20251, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital Hamburg- Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Department of Neuropathology, Department of Neuropathology, Charité- Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Lisa Restelli
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - David Capper
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
| | - Ekkehard Hewer
- Institut universitaire de pathologie, Lausanne University Hospital (CHUV), University of Lausanne, Rue du Bugnon 25, 1011, Lausanne, Switzerland
| | - Joachim Diebold
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
| | - Danijela Kolenc
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
| | - Ulf C Schneider
- Klinik für Neurochirurgie, Luzerner Kantonsspital, Haus 31, 6000, 16, Spitalstrasse, Luzern, Switzerland
| | - Elisabeth Rushing
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
- Medica Pathologie Zentrum Zürich, Hottingerstrasse 9 / 11, 8032, Zürich, Switzerland
| | - Rosa Della Monica
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486 - 80145, Napoli, Italy
| | - Lorenzo Chiariotti
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486 - 80145, Napoli, Italy
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- , 23. DKFZ, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Christian Kölsche
- Pathologisches Institut der LMU, Thalkirchner Str. 36, 80337, München, Germany
| | - Markus Tolnay
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Stephan Frank
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland.
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Li H, Li C, Zhang Y, Jiang W, Zhang F, Tang X, Sun G, Xu S, Dong X, Shou J, Yang Y, Chen M. Comprehensive analysis of m 6 A methylome and transcriptome by Nanopore sequencing in clear cell renal carcinoma. Mol Carcinog 2024; 63:677-687. [PMID: 38362848 DOI: 10.1002/mc.23680] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/01/2023] [Accepted: 01/02/2024] [Indexed: 02/17/2024]
Abstract
N6 -methyladenosine (m6 A) is the most prevalent epigenetic modification on eukaryotic messenger RNAs. Recent studies have focused on elucidating the key role of m6 A modification patterns in tumor progression. However, the relationship between m6 A and transcriptional regulation remains elusive. Nanopore technology enables the quantification of m6 A levels at each genomic site. In this study, a pair of tumor tissues and adjacent normal tissues from clear cell renal cell carcinoma (ccRCC) surgical samples were collected for Nanopore direct RNA sequencing. We identified 9644 genes displaying anomalous m6 A modifications, with 5343 genes upregulated and 4301 genes downregulated. Among these, 5224 genes were regarded as dysregulated genes, encompassing abnormal regulation of both m6 A modification and RNA expression. Gene Set Enrichment Analysis revealed an enrichment of these genes in pathways related to renal system progress and fatty acid metabolic progress. Furthermore, the χ2 test demonstrated a significant association between the levels of m6 A in dysregulated genes and their transcriptional expression levels. Additionally, we identified four obesity-associated genes (FTO, LEPR, ADIPOR2, and NPY5R) among the dysregulated genes. Further analyses using public databases revealed that these four genes were all related to the prognosis and diagnosis of ccRCC. This study introduced the novel approach of employing conjoint analysis of m6 A modification and RNA expression based on Nanopore sequencing to explore potential disease-related genes. Our work demonstrates the feasibility of the application of Nanopore sequencing technology in RNA epigenetic regulation research and identifies new potential therapeutic targets for ccRCC.
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Affiliation(s)
- Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Chang Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuxiang Zhang
- Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weixing Jiang
- Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fubo Zhang
- Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaokun Tang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Gaoyuan Sun
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Siyuan Xu
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Dong
- Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianzhong Shou
- Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Yang
- Department of Oncology, Huai'an TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangsu, China
| | - Meng Chen
- Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Akkhasutthikun P, Kaewsapsak P, Nimsamer P, Klomkliew P, Visedthorn S, Chanchaem P, Teerapakpinyo C, Payungporn S, Luangdilok S. Tissue and Plasma-Based Highly Sensitive Blocker Displacement Amplicon Nanopore Sequencing for EGFR Mutations in Lung Cancer. Cancer Res Treat 2024; 56:455-463. [PMID: 37986562 PMCID: PMC11016658 DOI: 10.4143/crt.2023.1108] [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] [Received: 10/07/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023] Open
Abstract
PURPOSE The epidermal growth factor receptor (EGFR) mutation is a widely prevalent oncogene driver in non-small cell lung cancer (NSCLC) in East Asia. The detection of EGFR mutations is a standard biomarker test performed routinely in patients with NSCLC for the selection of targeted therapy. Here, our objective was to develop a portable new technique for detecting EGFR (19Del, T790M, and L858R) mutations based on Nanopore sequencing. MATERIALS AND METHODS The assay employed a blocker displacement amplification (BDA)-based polymerase chain reaction (PCR) technique combined with Nanopore sequencing to detect EGFR mutations. Mutant and wild-type EGFR clones were generated from DNA from H1650 (19Del heterozygous) and H1975 (T790M and L858R heterozygous) lung cancer cell lines. Then, they were mixed to assess the performance of this technique for detecting low variant allele frequencies (VAFs). Subsequently, formalin-fixed, paraffin-embedded (FFPE) tissue and cell-free DNA (cfDNA) from patients with NSCLC were used for clinical validation. RESULTS The assay can detect low VAF at 0.5% mutant mixed in wild-type EGFR. Using FFPE DNA, the concordance rates of EGFR 19Del, T790M, and L858R mutations between our method and Cobas real-time PCR were 98.46%, 100%, and 100%, respectively. For cfDNA, the concordance rates of EGFR 19Del, T790M, and L858R mutations between our method and droplet digital PCR were 94.74%, 100%, and 100%, respectively. CONCLUSION The BDA amplicon Nanopore sequencing is a highly accurate and sensitive method for the detection of EGFR mutations in clinical specimens.
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Affiliation(s)
- Patinya Akkhasutthikun
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pornchai Kaewsapsak
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pattaraporn Nimsamer
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pavit Klomkliew
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Suthida Visedthorn
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pragwalai Chanchaem
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sutima Luangdilok
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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11
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Brinkmann A, Pape K, Uddin S, Woelk N, Förster S, Jessen H, Michel J, Kohl C, Schaade L, Nitsche A. Genome sequencing of the mpox virus 2022 outbreak with amplicon-based Oxford Nanopore MinION sequencing. J Virol Methods 2024; 325:114888. [PMID: 38246565 DOI: 10.1016/j.jviromet.2024.114888] [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] [Received: 06/15/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
We present an amplicon-based assay for MinION Nanopore sequencing of mpox virus (MPXV) genomes from clinical specimens, obtaining high-quality results with an average genome coverage of 99% for Ct values of up to 25, and a genome coverage of 97.1% for Ct values from 25 to 30 which are challenging to sequence. This assay is easy to implement in PCR-based workflows and provides accurate genomic data within a short time.
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Affiliation(s)
- Annika Brinkmann
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany.
| | - Katharina Pape
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Steven Uddin
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Niklas Woelk
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Sophie Förster
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Heiko Jessen
- Praxis Jessen and Colleagues, Motzstraße 19, 10777 Berlin, Germany
| | - Janine Michel
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Claudia Kohl
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Lars Schaade
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Andreas Nitsche
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
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12
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Nakanishi H, Takada A, Yoneyama K, Hara M, Sakai K, Saito K. Estimating bloodstain age in the short term based on DNA fragment length using nanopore sequencer. Forensic Sci Int 2024; 358:112010. [PMID: 38581825 DOI: 10.1016/j.forsciint.2024.112010] [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: 01/07/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/08/2024]
Abstract
We used a nanopore sequencer to quantify DNA fragments > 10,000 bp in size and then evaluated their relationship with short-term bloodstain age. Moreover, DNA degradation was investigated after bloodstains were wetted once with water. Bloodstain samples on cotton gauze were stored at room temperature and low humidity for up to 6 months. Bloodstains stored for 1 day were wetted with nuclease-free water, allowed to dry, and stored at room temperature and low humidity for up to 1 week. The proportion of fragments > 20,000 bp in dry bloodstains tended to decrease over time, particularly for fragments > 50,000 bp in size. This trend was modeled using a power approximation curve, with the highest R2 value (0.6475) noted for fragments > 50,000 bp in size; lower values were recorded for shorter fragments. The proportion of longer fragments was significantly reduced in bloodstains that were dried after being wetted once, and there was significant difference in fragments > 50,000 bp between dry conditions and once-wetted. This result suggests that even temporary exposure to water causes significant DNA fragmentation, but not extensive degradation. Thus, bloodstains that appear fresh but have a low proportion of long DNA fragments may have been wetted previously. Our results indicate that evaluating the proportion of long DNA fragments yields information on both bloodstain age and the environment in which they were stored.
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Affiliation(s)
- Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495, Japan.
| | - Aya Takada
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495, Japan; Tokyo Medical Examiner's Office, Tokyo Metropolitan Government, 4-21-18, Otsuka, Bunkyo-Ku, Tokyo 112-0012, Japan
| | - Katsumi Yoneyama
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495, Japan
| | - Masaaki Hara
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495, Japan
| | - Kentaro Sakai
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan; Tokyo Medical Examiner's Office, Tokyo Metropolitan Government, 4-21-18, Otsuka, Bunkyo-Ku, Tokyo 112-0012, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495, Japan; Tokyo Medical Examiner's Office, Tokyo Metropolitan Government, 4-21-18, Otsuka, Bunkyo-Ku, Tokyo 112-0012, Japan
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13
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Krogsgaard LW, Benedetti G, Gudde A, Richter SR, Rasmussen LD, Midgley SE, Qvesel AG, Nauta M, Bahrenscheer NS, von Kappelgaard L, McManus O, Hansen NC, Pedersen JB, Haimes D, Gamst J, Nørgaard LS, Jørgensen ACU, Ejegod DM, Møller SS, Clauson-Kaas J, Knudsen IM, Franck KT, Ethelberg S. Results from the SARS-CoV-2 wastewater-based surveillance system in Denmark, July 2021 to June 2022. Water Res 2024; 252:121223. [PMID: 38310802 DOI: 10.1016/j.watres.2024.121223] [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] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/01/2023] [Accepted: 01/28/2024] [Indexed: 02/06/2024]
Abstract
The microbiological analysis of wastewater samples is increasingly used for the surveillance of SARS-CoV-2 globally. We described the setup process of the national SARS-CoV-2 wastewater-based surveillance system in Denmark, presented its main results during the first year of activities, from July 2021 to June 2022, and discussed their operational significance. The Danish SARS-CoV-2 wastewater-based surveillance system was designed to cover 85 % of the population in Denmark and it entailed taking three weekly samples from 230 sites. Samples were RT-qPCR tested for SARS-CoV-2 RNA, targeting the genetic markers N1, N2 and RdRp, and for two faecal indicators, Pepper Mild Mottle Virus and crAssphage. We calculated the weekly SARS-CoV-2 RNA concentration in the wastewater from each sampling site and monitored it in view of the results from individual testing, at the national and regional levels. We attempted to use wastewater results to identify potential local outbreaks, and we sequenced positive wastewater samples using Nanopore sequencing to monitor the circulation of viral variants in Denmark. The system reached its full implementation by October 2021 and covered up to 86.4 % of the Danish population. The system allowed for monitoring of the national and regional trends of SARS-CoV-2 infections in Denmark. However, the system contribution to the identification of potential local outbreaks was limited by the extensive information available from clinical testing. The sequencing of wastewater samples identified relevant variants of concern, in line with results from sequencing of human samples. Amidst the COVID-19 pandemic, Denmark implemented a nationwide SARS-CoV-2 wastewater-based surveillance system that integrated routine surveillance from individual testing. Today, while testing for COVID-19 at the community level has been discontinued, the system is on the frontline to monitor the occurrence and spread of SARS-CoV-2 in Denmark.
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Affiliation(s)
- Lene Wulff Krogsgaard
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Guido Benedetti
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark.
| | - Aina Gudde
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Stine Raith Richter
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Lasse Dam Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Sofie Elisabeth Midgley
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Amanda Gammelby Qvesel
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Maarten Nauta
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Naja Stolberg Bahrenscheer
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Lene von Kappelgaard
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Oliver McManus
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, Gustav III: s Boulevard 40, 16973 Solna, Sweden
| | - Nicco Claudio Hansen
- Test Centre Denmark, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Jan Bryla Pedersen
- Department of Finance, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Danny Haimes
- Danish Patient Safety Authority, Islands Brygge 67, 2300 Copenhagen, Denmark
| | - Jesper Gamst
- Eurofins Environment, Ladelundvej 85, 6600 Vejen, Denmark
| | | | | | | | | | - Jes Clauson-Kaas
- HOFOR - Greater Copenhagen Utility, Ørestads Boulevard 35, 2300 Copenhagen, Denmark
| | - Ida Marie Knudsen
- HOFOR - Greater Copenhagen Utility, Ørestads Boulevard 35, 2300 Copenhagen, Denmark
| | - Kristina Træholt Franck
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Steen Ethelberg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; Department of Public Health, Global Health Section, University of Copenhagen, Øster Farimagsgade 5, 1014 Copenhagen, Denmark
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Helal AA, Saad BT, Saad MT, Mosaad GS, Aboshanab KM. Benchmarking long-read aligners and SV callers for structural variation detection in Oxford nanopore sequencing data. Sci Rep 2024; 14:6160. [PMID: 38486064 PMCID: PMC10940726 DOI: 10.1038/s41598-024-56604-2] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Structural variants (SVs) are one of the significant types of DNA mutations and are typically defined as larger-than-50-bp genomic alterations that include insertions, deletions, duplications, inversions, and translocations. These modifications can profoundly impact the phenotypic characteristics and contribute to disorders like cancer, response to treatment, and infections. Four long-read aligners and five SV callers have been evaluated using three Oxford Nanopore NGS human genome datasets in terms of precision, recall, and F1-score statistical metrics, depth of coverage, and speed of analysis. The best SV caller regarding recall, precision, and F1-score when matched with different aligners at different coverage levels tend to vary depending on the dataset and the specific SV types being analyzed. However, based on our findings, Sniffles and CuteSV tend to perform well across different aligners and coverage levels, followed by SVIM, PBSV, and SVDSS in the last place. The CuteSV caller has the highest average F1-score (82.51%) and recall (78.50%), and Sniffles has the highest average precision value (94.33%). Minimap2 as an aligner and Sniffles as an SV caller act as a strong base for the pipeline of SV calling because of their high speed and reasonable accomplishment. PBSV has a lower average F1-score, precision, and recall and may generate more false positives and overlook some actual SVs. Our results are valuable in the comprehensive evaluation of popular SV callers and aligners as they provide insight into the performance of several long-read aligners and SV callers and serve as a reference for researchers in selecting the most suitable tools for SV detection.
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Affiliation(s)
- Asmaa A Helal
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt
| | - Bishoy T Saad
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt.
| | - Mina T Saad
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt
| | - Gamal S Mosaad
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt
| | - Khaled M Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Abassi, Cairo, 11566, Egypt.
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15
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Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson Z, Storz SHR, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. medRxiv 2024:2024.03.05.24303792. [PMID: 38496498 PMCID: PMC10942501 DOI: 10.1101/2024.03.05.24303792] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control datasets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project ONT Sequencing Consortium aims to generate LRS data from at least 800 of the 1000 Genomes Project samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37x and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs.
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Affiliation(s)
- Jonas A. Gustafson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Sophia B. Gibson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nikhita Damaraju
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Miranda PG Zalusky
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lei Yang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | | | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Nathan D. Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Human Technopole, Milan, Italy
| | - Qiuhui Li
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Angela L. Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Joy Goffena
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Zachery Anderson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sophie HR Storz
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sydney A. Ward
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Maisha Sinha
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Claudia Gonzaga-Jauregui
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México
| | - Wayne E. Clarke
- New York Genome Center, New York, NY, USA
- Outlier Informatics Inc., Saskatoon, SK, Canada
| | | | | | | | | | | | - Mahler Revsine
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Cate R. Paschal
- Department of Laboratories, Seattle Children’s Hospital, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Christina Zakarian
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Esther Robb
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | | | | | | | - Fritz J. Sedlazeck
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Justin M. Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mikhail Kolmogorov
- Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Richard N. McLaughlin
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Matt Loose
- Deep Seq, School of Life Sciences, University of Nottingham, Nottingham, England
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Khoury College of Computer Sciences, Northeastern University, Boston, MA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Danny E. Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
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16
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Sahın Vural G, Bolat H. Nanopore sequencing method for CTG18.1 expansion in TCF4 in late-onset Fuchs endothelial corneal dystrophy and a comparison of the structural features of cornea with first-degree relatives. Graefes Arch Clin Exp Ophthalmol 2024; 262:903-911. [PMID: 37747538 DOI: 10.1007/s00417-023-06243-6] [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] [Received: 03/23/2022] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND To evaluate the relationship between the number of trinucleotide repeats (TNR) in late-onset Fuchs corneal endothelial dystrophy (FCED) and to compare the endothelial properties of FCED, first-degree relatives, and controls. METHODS Blood samples were collected from FCEDs to determine TNR number. The FCED patients, first-degree relatives, and controls were examined with specular microscopy for central corneal thickness (CCT), endothelial cell density (ECD), pleomorphism and polymegatism, and with corneal topography for specific indicators such as (i) displacement of thinnest point of cornea, (ii) loss of isopachs, (iii) focal posterior surface depression towards anterior chamber. RESULTS This study included 92 patients with FCED, 92 first-degree relatives, and 96 controls. CCT was thickest in FCEDs (558.0 μm) (p < 0.05) while there was no difference between relatives (533.0 μm) and controls (530.4 μm) (p = 0.845). ECD was decreased in both FCED (2069.2 mm2) and relatives (2171.4 mm2) than controls (2822.9 mm2) (p < 0.05 in both). The presence of pleomorphism and polymegatism was significant in patients with FCED (93.4% and 93.4%, respectively), relatives (86.9% and 86.04%, respectively), and controls (8.33% and 1.04%, respectively) (p < 0.05). Specific topographic indicators differed among the groups (p < 0.05). The mean repeat number of the FCED patients was 17.48 ± 4.54 (12-25) times. The TNR number of FCED cases correlated with the relative CCT (p < 0.05, R = 0.615) and cell density (p = 0.009, R = -0.499). CONCLUSIONS A strong association between the corneal endothelium in relatives and TNR number of FCEDs was defined. Relatives tended to have fewer corneal endothelial cells, even though they did not have clinical findings.
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Affiliation(s)
- Gozde Sahın Vural
- Department of Ophthalmology, Balıkesir University Medicine Faculty, Balıkesir, Turkey.
- Department of Ophthalmology, Balıkesir University Medicine Faculty Hospital, Balıkesir, Turkey.
| | - Hilmi Bolat
- Department of Genetics, Balıkesir University Medicine Faculty, Balıkesir, Turkey
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17
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Gajski D, Wolff JO, Melcher A, Weber S, Prost S, Krehenwinkel H, Kennedy SR. Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing. Mol Phylogenet Evol 2024; 192:107988. [PMID: 38072140 DOI: 10.1016/j.ympev.2023.107988] [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] [Received: 08/03/2023] [Revised: 10/22/2023] [Accepted: 12/07/2023] [Indexed: 12/31/2023]
Abstract
Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.
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Affiliation(s)
- Domagoj Gajski
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czech Republic
| | - Jonas O Wolff
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, Greifswald 17489, Germany; School of Natural Sciences, Macquarie University, NSW 2109, Sydney, Australia
| | - Anja Melcher
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Sven Weber
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, Linnanmaa, Finland
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Susan R Kennedy
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany.
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18
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Polsomboon Nelson S, Ergunay K, Bourke BP, Reinbold-Wasson DD, Caicedo-Quiroga L, Kirkitadze G, Chunashvili T, Tucker CL, Linton YM. Nanopore-based metagenomics reveal a new Rickettsia in Europe. Ticks Tick Borne Dis 2024; 15:102305. [PMID: 38150911 DOI: 10.1016/j.ttbdis.2023.102305] [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] [Received: 04/18/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023]
Abstract
Accurate identification of tick-borne bacteria, including those associated with rickettsioses, pose significant challenges due to the polymicrobial and polyvectoral nature of the infections. We aimed to carry out a comparative evaluation of a non-targeted metagenomic approach by nanopore sequencing (NS) and commonly used PCR assays amplifying Rickettsia genes in field-collected ticks. The study included a total of 310 ticks, originating from Poland (44.2 %) and Bulgaria (55.8 %). Samples comprised 7 species, the majority of which were Ixodes ricinus (62.9 %), followed by Dermacentor reticulatus (21.2 %). Screening was carried out in 55 pools, using total nucleic acid extractions from individual ticks. NS and ompA/gltA PCRs identified Rickettsia species in 47.3 % and 54.5 % of the pools, respectively. The most frequently detected species were Rickettsia asiatica (27.2 %) and Rickettsia raoultii (21.8 %), followed by Rickettsia monacensis (3.6 %), Rickettsia helvetica (1.8 %), Rickettsia massiliae (1.8 %) and Rickettsia tillamookensis (1.8 %). Phylogeny construction on mutS, uvrD, argS and virB4 sequences and a follow-up deep sequencing further supported R. asiatica identification, documented in Europe for the first time. NS further enabled detection of Anaplasma phagocytophilum (9.1 %), Coxiella burnetii (5.4 %) and Neoehrlichia mikurensis (1.8 %), as well as various endosymbionts of Rickettsia and Coxiella. Co-detection of multiple rickettsial and non-rickettsial bacteria were observed in 16.4 % of the pools with chromosome and plasmid-based contigs. In conclusion, non-targeted metagenomic sequencing was documented as a robust strategy capable of providing a broader view of the tick-borne bacterial pathogen spectrum.
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Affiliation(s)
- Suppaluck Polsomboon Nelson
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USA
| | - Koray Ergunay
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USA; Hacettepe University, Faculty of Medicine, Ankara, Turkey.
| | - Brian P Bourke
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USA
| | | | - Laura Caicedo-Quiroga
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USA
| | - Giorgi Kirkitadze
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Tbilisi, Georgia
| | - Tamar Chunashvili
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Tbilisi, Georgia
| | - Cynthia L Tucker
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USA
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19
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Crispo M, Muñoz MC, Lacroix F, Kheyi MR, Delverdier M, Croville G, Dirat M, Gaide N, Guerin JL, Le Loc'h G. Pathological investigation of high pathogenicity avian influenza H5N8 in captive houbara bustards (Chlamydotis undulata), the United Arab Emirates 2020. Sci Rep 2024; 14:4235. [PMID: 38378877 PMCID: PMC10879111 DOI: 10.1038/s41598-024-54884-2] [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] [Received: 10/17/2023] [Accepted: 02/17/2024] [Indexed: 02/22/2024] Open
Abstract
At the end of 2020, an outbreak of HPAI H5N8 was registered in captive African houbara bustards (Chlamydotis undulata) in the United Arab Emirates. In order to better understand the pathobiology of this viral infection in bustards, a comprehensive pathological characterization was performed. A total of six birds were selected for necropsy, histopathology, immunohistochemistry, RNAscope in situ hybridization and RT-qPCR and nanopore sequencing on formalin-fixed and paraffin-embedded (FFPE) tissue blocks. Gross lesions included mottled and/or hemorrhagic pancreas, spleen and liver and fibrinous deposits on air sacs and intestine. Necrotizing pancreatitis, splenitis and concurrent vasculitis, hepatitis and fibrino-heterophilic peritonitis were identified, microscopically. Viral antigens (nucleoprotein) and RNAs (matrix gene) were both detected within necro-inflammatory foci, parenchymal cells, stromal cells and endothelial cells of affected organs, including the myenteric plexus. Molecular analysis of FFPE blocks successfully detected HPAI H5N8, further confirming its involvement in the lesions observed. In conclusion, HPAI H5N8 in African houbara bustards results in hyperacute/acute forms exhibiting marked pantropism, endotheliotropism and neurotropism. In addition, our findings support the use of FFPE tissues for molecular studies of poorly characterized pathogens in exotic and endangered species, when availability of samples is limited.
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Affiliation(s)
- Manuela Crispo
- IHAP, Université de Toulouse, ENVT, INRAE, 23 Chemin des Capelles, 31076, Toulouse Cedex 3, France.
| | - Mar Carrasco Muñoz
- Reneco International Wildlife Consultants LLC, PO Box 61741, Abu Dhabi, United Arab Emirates
| | - Frédéric Lacroix
- Reneco International Wildlife Consultants LLC, PO Box 61741, Abu Dhabi, United Arab Emirates
| | - Mohamed-Reda Kheyi
- Reneco International Wildlife Consultants LLC, PO Box 61741, Abu Dhabi, United Arab Emirates
| | - Maxence Delverdier
- IHAP, Université de Toulouse, ENVT, INRAE, 23 Chemin des Capelles, 31076, Toulouse Cedex 3, France
| | - Guillaume Croville
- IHAP, Université de Toulouse, ENVT, INRAE, 23 Chemin des Capelles, 31076, Toulouse Cedex 3, France
| | - Malorie Dirat
- IHAP, Université de Toulouse, ENVT, INRAE, 23 Chemin des Capelles, 31076, Toulouse Cedex 3, France
| | - Nicolas Gaide
- IHAP, Université de Toulouse, ENVT, INRAE, 23 Chemin des Capelles, 31076, Toulouse Cedex 3, France
| | - Jean Luc Guerin
- IHAP, Université de Toulouse, ENVT, INRAE, 23 Chemin des Capelles, 31076, Toulouse Cedex 3, France
| | - Guillaume Le Loc'h
- IHAP, Université de Toulouse, ENVT, INRAE, 23 Chemin des Capelles, 31076, Toulouse Cedex 3, France
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20
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Zhao JJ, Sun XY, Tian SN, Zhao ZZ, Yin MD, Zhao M, Zhang F, Li SA, Yang ZX, Wen W, Cheng T, Gong A, Zhang JP, Zhang XB. Decoding the complexity of on-target integration: characterizing DNA insertions at the CRISPR-Cas9 targeted locus using nanopore sequencing. BMC Genomics 2024; 25:189. [PMID: 38368357 PMCID: PMC10874558 DOI: 10.1186/s12864-024-10050-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/24/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND CRISPR-Cas9 technology has advanced in vivo gene therapy for disorders like hemophilia A, notably through the successful targeted incorporation of the F8 gene into the Alb locus in hepatocytes, effectively curing this disorder in mice. However, thoroughly evaluating the safety and specificity of this therapy is essential. Our study introduces a novel methodology to analyze complex insertion sequences at the on-target edited locus, utilizing barcoded long-range PCR, CRISPR RNP-mediated deletion of unedited alleles, magnetic bead-based long amplicon enrichment, and nanopore sequencing. RESULTS We identified the expected F8 insertions and various fragment combinations resulting from the in vivo linearization of the double-cut plasmid donor. Notably, our research is the first to document insertions exceeding ten kbp. We also found that a small proportion of these insertions were derived from sources other than donor plasmids, including Cas9-sgRNA plasmids, genomic DNA fragments, and LINE-1 elements. CONCLUSIONS Our study presents a robust method for analyzing the complexity of on-target editing, particularly for in vivo long insertions, where donor template integration can be challenging. This work offers a new tool for quality control in gene editing outcomes and underscores the importance of detailed characterization of edited genomic sequences. Our findings have significant implications for enhancing the safety and effectiveness of CRISPR-Cas9 gene therapy in treating various disorders, including hemophilia A.
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Affiliation(s)
- Juan-Juan Zhao
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Xin-Yu Sun
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | | | - Zong-Ze Zhao
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266000, China
| | - Meng-Di Yin
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Mei Zhao
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Feng Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Si-Ang Li
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Zhi-Xue Yang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Wei Wen
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - An Gong
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266000, China.
| | - Jian-Ping Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
- Tianjin Medical University, Tianjin, China.
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21
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LeBlanc NR, Harrigian FC. Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil. Microb Ecol 2024; 87:44. [PMID: 38367043 PMCID: PMC10874327 DOI: 10.1007/s00248-024-02361-8] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.
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Affiliation(s)
- Nicholas R LeBlanc
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, 1636 E. Alisal St, Salinas, CA, 93905, USA.
| | - Fiona C Harrigian
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, 1636 E. Alisal St, Salinas, CA, 93905, USA
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22
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Bertolo A, Valido E, Stoyanov J. Optimized bacterial community characterization through full-length 16S rRNA gene sequencing utilizing MinION nanopore technology. BMC Microbiol 2024; 24:58. [PMID: 38365589 PMCID: PMC10870487 DOI: 10.1186/s12866-024-03208-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/28/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Accurate identification of bacterial communities is crucial for research applications, diagnostics, and clinical interventions. Although 16S ribosomal RNA (rRNA) gene sequencing is a widely employed technique for bacterial taxonomic classification, it often results in misclassified or unclassified bacterial taxa. This study sought to refine the full-length 16S rRNA gene sequencing protocol using the MinION sequencer, focusing on the V1-V9 regions. Our methodological enquiry examined several factors, including the number of PCR amplification cycles, choice of primers and Taq polymerase, and specific sequence databases and workflows employed. We used a microbial standard comprising eight bacterial strains (five gram-positive and three gram-negative) in known proportions as a validation control. RESULTS Based on the MinION protocol, we employed the microbial standard as the DNA template for the 16S rRNA gene amplicon sequencing procedure. Our analysis showed that an elevated number of PCR amplification cycles introduced PCR bias, and the selection of Taq polymerase and primer sets significantly affected the subsequent analysis. Bacterial identification at genus level demonstrated Pearson correlation coefficients ranging from 0.73 to 0.79 when assessed using BugSeq, Kraken-Silva and EPI2ME-16S workflows. Notably, the EPI2ME-16S workflow exhibited the highest Pearson correlation with the microbial standard, minimised misclassification, and increased alignment accuracy. At the species taxonomic level, the BugSeq workflow was superior, with a Pearson correlation coefficient of 0.92. CONCLUSIONS These findings emphasise the importance of careful selection of PCR settings and a well-structured analytical framework for 16S rRNA full-length gene sequencing. The results showed a robust correlation between the predicted and observed bacterial abundances at both the genus and species taxonomic levels, making these findings applicable across diverse research contexts and with clinical utility for reliable pathogen identification.
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Affiliation(s)
- Alessandro Bertolo
- SCI Population Biobanking & Translational Research Group, Swiss Paraplegic Research, Nottwil, Switzerland
- Department of Orthopaedic Surgery, University of Bern, Bern Inselspital, Bern, Switzerland
| | - Ezra Valido
- SCI Population Biobanking & Translational Research Group, Swiss Paraplegic Research, Nottwil, Switzerland
| | - Jivko Stoyanov
- SCI Population Biobanking & Translational Research Group, Swiss Paraplegic Research, Nottwil, Switzerland.
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
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23
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Zhou L, Zou X, Hu Q, Hua H, Qi Q. Determination of the diagnostic accuracy of nanopore sequencing using bronchoalveolar lavage fluid samples from patients with sputum-scarce pulmonary tuberculosis. J Infect Chemother 2024; 30:98-103. [PMID: 37714266 DOI: 10.1016/j.jiac.2023.09.014] [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] [Received: 07/09/2023] [Revised: 08/22/2023] [Accepted: 09/13/2023] [Indexed: 09/17/2023]
Abstract
PURPOSE The early and efficient diagnosis of patients suspected of having pulmonary tuberculosis (PTB) remains challenging. This study aimed to evaluate the accuracy of nanopore sequencing for PTB diagnosis using bronchoalveolar lavage fluid (BALF) samples and compared it with other techniques such as acid-fast bacilli smear, culture, Xpert MTB/RIF, and CapitalBio Mycobacterium reverse transcription-polymerase chain reaction (MTB RT-PCR). METHODS We retrospectively analyzed the clinical data of 195 patients with suspected PTB who were admitted to our hospital. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the receiver operating characteristic curve (AUC) of these assays were calculated and compared. RESULTS The overall sensitivity, specificity, PPV, NPV, and AUC of nanopore sequencing were 90.70%, 84.85%, 92.13%, 82.35%, and 0.88; those of acid-fast bacilli smear were 12.40%, 98.48%, 94.12%, 36.52%, and 0.55; those of culture were 36.43%, 100%, 100%, 44.59%, and 0.68; those of Xpert MTB/RIF were 41.09%, 100%, 100%, 46.48%, and 0.71; and those of CapitalBio MTB RT-PCR were 34.88%, 98.48%, 97.83%, 43.62%, and 0.67, respectively. CONCLUSION The nanopore sequencing assay using BALF samples showed the best diagnostic accuracy for sputum-scarce PTB. Moreover, it can improve the clinical diagnosis of PTB.
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Affiliation(s)
- Lihong Zhou
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, No. 208 Huancheng East Road, Gongshu District, Hangzhou, Zhejiang, China.
| | - Xingwu Zou
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, No. 208 Huancheng East Road, Gongshu District, Hangzhou, Zhejiang, China.
| | - Qin Hu
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, No. 208 Huancheng East Road, Gongshu District, Hangzhou, Zhejiang, China.
| | - Haibo Hua
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, No. 208 Huancheng East Road, Gongshu District, Hangzhou, Zhejiang, China.
| | - Qi Qi
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, No. 208 Huancheng East Road, Gongshu District, Hangzhou, Zhejiang, China.
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24
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Vanhee M, Floré K, Vanthourenhout S, Hellemans J, Muyldermans A, Reynders M. Implementation of full-length 16S nanopore sequencing for bacterial identification in a clinical diagnostic setting. Diagn Microbiol Infect Dis 2024; 108:116156. [PMID: 38061217 DOI: 10.1016/j.diagmicrobio.2023.116156] [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] [Received: 08/16/2023] [Revised: 11/29/2023] [Accepted: 12/03/2023] [Indexed: 01/22/2024]
Abstract
This study describes the implementation of 16S nanopore sequencing in a diagnostic lab for pathogen identification without prior enrichment. First, the universality of the test and taxonomic resolution was evaluated for 78 clinically relevant bacteria (69 known and 9 unknown bacterial cultures). Next, the diagnostic value of the test was evaluated based on clinical samples. It was shown that 16S sequencing can be used both for identification of unknown cultures and to find bacteria directly in the clinical sample without cultivation. All culture-positive samples (n=11) tested positive with 16S sequencing directly performed on the sample, but bacteria were found as well in 15/30 culture-negative samples. Pathogenic bacteria were found in a background of commensal flora, and even complex polymicrobial infections could be unraveled. This study demonstrates the feasibility of implementing 16S nanopore sequencing in a clinical diagnostic setting and demonstrates its value for the diagnosis of culture-negative and polymicrobial infections.
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Affiliation(s)
- Merijn Vanhee
- Department of Laboratory Medicine, General Hospital Sint-Jan Brugge, Ruddershove 10, 8000, Brugge, Belgium.
| | - Katelijne Floré
- Department of Laboratory Medicine, General Hospital Sint-Jan Brugge, Ruddershove 10, 8000, Brugge, Belgium
| | - Sanne Vanthourenhout
- Department of Laboratory Medicine, General Hospital Sint-Jan Brugge, Ruddershove 10, 8000, Brugge, Belgium
| | - Jorn Hellemans
- Department of Laboratory Medicine, General Hospital Sint-Jan Brugge, Ruddershove 10, 8000, Brugge, Belgium
| | - Astrid Muyldermans
- Department of Laboratory Medicine, General Hospital Sint-Jan Brugge, Ruddershove 10, 8000, Brugge, Belgium
| | - Marijke Reynders
- Department of Laboratory Medicine, General Hospital Sint-Jan Brugge, Ruddershove 10, 8000, Brugge, Belgium
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25
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Acevedo AM, Postic L, Curiel M, Gondard M, Bréard E, Zientara S, Vorimore F, Tran ML, Turpaud M, Savini G, Lorusso A, Marcacci M, Vitour D, Dujardin P, Perera CL, Díaz C, Obret Y, Sailleau C. Detection, Characterization and Sequencing of BTV Serotypes Circulating in Cuba in 2022. Viruses 2024; 16:164. [PMID: 38275974 PMCID: PMC10819738 DOI: 10.3390/v16010164] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
In Cuba, despite a high sero-prevalence of bluetongue virus (BTV), circulating serotypes remain unknown. The aim of this study was to identify circulating BTV serotypes in farms throughout the western region of Cuba. Blood samples were collected from 200 young cattle and sheep between May and July 2022 for virological analyses (PCR, viral isolation and virus neutralization) and genome sequencing. The results confirmed viral circulation, with viro-prevalence of 25% for BTV. The virus was isolated from 18 blood samples and twelve BTV serotypes were identified by sequencing RT-PCR products targeting the segment 2 of the BTV genome (BTV-1, 2, 3, 6, 10, 12, 13, 17, 18, 19, 22 and 24). Finally, the full genome sequences of 17 Cuban BTV isolates were recovered using a Sequence Independent Single Primer Amplification (SISPA) approach combined to MinION Oxford Nanopore sequencing technology. All together, these results highlight the co-circulation of a wide diversity of BTV serotypes in a quite restricted area and emphasize the need for entomological and livestock surveillance, particularly in light of recent changes in the global distribution and nature of BTV infections.
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Affiliation(s)
- Ana María Acevedo
- National Center for Animal and Plant Health (CENSA), Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San José de las Lajas, San José de las Lajas 32700, Cuba; (A.M.A.); (M.C.); (C.L.P.); (C.D.); (Y.O.)
| | - Lydie Postic
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Maray Curiel
- National Center for Animal and Plant Health (CENSA), Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San José de las Lajas, San José de las Lajas 32700, Cuba; (A.M.A.); (M.C.); (C.L.P.); (C.D.); (Y.O.)
| | - Mathilde Gondard
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Emmanuel Bréard
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Stéphan Zientara
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Fabien Vorimore
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (F.V.); (M.-L.T.)
| | - Mai-Lan Tran
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (F.V.); (M.-L.T.)
| | - Mathilde Turpaud
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Giovanni Savini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy; (G.S.); (A.L.); (M.M.)
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy; (G.S.); (A.L.); (M.M.)
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy; (G.S.); (A.L.); (M.M.)
| | - Damien Vitour
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Pascal Dujardin
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Carmen Laura Perera
- National Center for Animal and Plant Health (CENSA), Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San José de las Lajas, San José de las Lajas 32700, Cuba; (A.M.A.); (M.C.); (C.L.P.); (C.D.); (Y.O.)
| | - Cristian Díaz
- National Center for Animal and Plant Health (CENSA), Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San José de las Lajas, San José de las Lajas 32700, Cuba; (A.M.A.); (M.C.); (C.L.P.); (C.D.); (Y.O.)
| | - Yalainne Obret
- National Center for Animal and Plant Health (CENSA), Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San José de las Lajas, San José de las Lajas 32700, Cuba; (A.M.A.); (M.C.); (C.L.P.); (C.D.); (Y.O.)
| | - Corinne Sailleau
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
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26
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Konings M, Gerrits van den Ende B, Raats MWJ, Fahal AH, van de Sande WWJ, Hagen F. Complete Genome Sequence of the Itraconazole Decreased Susceptible Madurella fahalii Type-Strain CBS 129176. Mycopathologia 2024; 189:6. [PMID: 38231295 PMCID: PMC10794591 DOI: 10.1007/s11046-023-00807-0] [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] [Received: 03/07/2023] [Accepted: 10/04/2023] [Indexed: 01/18/2024]
Abstract
Madurella fahalii is a causative agent of the implantation mycosis mycetoma with decreased susceptibility to itraconazole, the preferred therapeutic drug to combat mycetoma. Here, we report the M. fahalii type-strain CBS 129176 genome assembly and annotation to identify a glutamic acid insert near the azole-binding pocket in the Cyp51A protein.
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Affiliation(s)
- Mickey Konings
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | | | - Mirthe W J Raats
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | | | - Wendy W J van de Sande
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystems Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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27
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Duarte F, Cordero E, Calderon M, Godinez A, Ross B, Allard M, Gonzalez-Escalona N. Closed genomes of four multidrug resistance Salmonella enterica serotype Infantis isolated in Costa Rica. Microbiol Resour Announc 2024; 13:e0025723. [PMID: 38019019 DOI: 10.1128/mra.00257-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
Here, we report the complete genome of four S. enterica Infantis isolated in Costa Rica from human, poultry rinse, and raw chicken meat from 2017 to 2019. All genomes belonged to ST32 and carried a 310-kb plasmid with many antimicrobial resistance genes including the bla CTX-M65 gene.
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Affiliation(s)
- Francisco Duarte
- Costa Rican Institute for Research and Education in Nutrition and Health (INCIENSA), National Reference Center for Microbiological Food Safety , Cartago, Costa Rica
| | - Estela Cordero
- Costa Rican Institute for Research and Education in Nutrition and Health (INCIENSA), National Reference Center for Microbiological Food Safety , Cartago, Costa Rica
| | - Melany Calderon
- Costa Rican Institute for Research and Education in Nutrition and Health (INCIENSA), National Reference Center for Microbiological Food Safety , Cartago, Costa Rica
| | - Adriana Godinez
- Costa Rican Institute for Research and Education in Nutrition and Health (INCIENSA), National Reference Center for Microbiological Food Safety , Cartago, Costa Rica
| | - Bruce Ross
- Latin America Regional Office, Office of Global Policy and Strategy, Food and Drug Administration Santiago , Santiago, Chile
| | - Marc Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland, USA
| | - Narjol Gonzalez-Escalona
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland, USA
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28
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Lao HY, Wong LLY, Hui Y, Ng TTL, Chan CTM, Lo HWH, Yau MCY, Leung ECM, Wong RCW, Ho AYM, Yip KT, Lam JYW, Chow VCY, Luk KS, Que TL, Chow FWN, Siu GKH. The clinical utility of Nanopore 16S rRNA gene sequencing for direct bacterial identification in normally sterile body fluids. Front Microbiol 2024; 14:1324494. [PMID: 38264489 PMCID: PMC10803466 DOI: 10.3389/fmicb.2023.1324494] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024] Open
Abstract
The prolonged incubation period of traditional culture methods leads to a delay in diagnosing invasive infections. Nanopore 16S rRNA gene sequencing (Nanopore 16S) offers a potential rapid diagnostic approach for directly identifying bacteria in infected body fluids. To evaluate the clinical utility of Nanopore 16S, we conducted a study involving the collection and sequencing of 128 monomicrobial samples, 65 polymicrobial samples, and 20 culture-negative body fluids. To minimize classification bias, taxonomic classification was performed using 3 analysis pipelines: Epi2me, Emu, and NanoCLUST. The result was compared to the culture references. The limit of detection of Nanopore 16S was also determined using simulated bacteremic blood samples. Among the three classifiers, Emu demonstrated the highest concordance with the culture results. It correctly identified the taxon of 125 (97.7%) of the 128 monomicrobial samples, compared to 109 (85.2%) for Epi2me and 102 (79.7%) for NanoCLUST. For the 230 cultured species in the 65 polymicrobial samples, Emu correctly identified 188 (81.7%) cultured species, compared to 174 (75.7%) for Epi2me and 125 (54.3%) for NanoCLUST. Through ROC analysis on the monomicrobial samples, we determined a threshold of relative abundance at 0.058 for distinguishing potential pathogens from background in Nanopore 16S. Applying this threshold resulted in the identification of 107 (83.6%), 117 (91.4%), and 114 (91.2%) correctly detected samples for Epi2me, Emu, and NanoCLUST, respectively, in the monomicrobial samples. Nanopore 16S coupled with Epi2me could provide preliminary results within 6 h. However, the ROC analysis of polymicrobial samples exhibited a random-like performance, making it difficult to establish a threshold. The overall limit of detection for Nanopore 16S was found to be about 90 CFU/ml.
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Affiliation(s)
- Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Lily Lok-Yee Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Yan Hui
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Hazel Wing-Hei Lo
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Miranda Chong-Yee Yau
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong SAR, China
| | - Eddie Chi-Man Leung
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong SAR, China
| | - River Chun-Wai Wong
- Department of Microbiology, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Alex Yat-Man Ho
- Department of Pathology, Princess Margaret Hospital, Kowloon, Hong Kong SAR, China
| | - Kam-Tong Yip
- Department of Clinical Pathology, Tuen Mun Hospital, Tuen Mun, Hong Kong SAR, China
| | - Jimmy Yiu-Wing Lam
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong SAR, China
| | - Viola Chi-Ying Chow
- Department of Microbiology, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Kristine Shik Luk
- Department of Pathology, Princess Margaret Hospital, Kowloon, Hong Kong SAR, China
| | - Tak-Lun Que
- Department of Clinical Pathology, Tuen Mun Hospital, Tuen Mun, Hong Kong SAR, China
| | - Franklin Wang Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
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Teng H, Stoiber M, Bar-Joseph Z, Kingsford C. Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework. bioRxiv 2024:2024.01.06.574484. [PMID: 38260359 PMCID: PMC10802372 DOI: 10.1101/2024.01.06.574484] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Direct nanopore-based RNA sequencing can be used to detect post-transcriptional base modifications, such as m6A methylation, based on the electric current signals produced by the distinct chemical structures of modified bases. A key challenge is the scarcity of adequate training data with known methylation modifications. We present Xron, a hybrid encoder-decoder framework that delivers a direct methylation-distinguishing basecaller by training on synthetic RNA data and immunoprecipitation-based experimental data in two steps. First, we generate data with more diverse modification combinations through in silico cross-linking. Second, we use this dataset to train an end-to-end neural network basecaller followed by fine-tuning on immunoprecipitation-based experimental data with label-smoothing. The trained neural network basecaller outperforms existing methylation detection methods on both read-level and site-level prediction scores. Xron is a standalone, end-to-end m6A-distinguishing basecaller capable of detecting methylated bases directly from raw sequencing signals, enabling de novo methylome assembly.
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Affiliation(s)
- Haotian Teng
- Computational Biology Department, Carnegie Mellon Univeristy, Pittsburgh PA 15213, USA
| | | | - Ziv Bar-Joseph
- Computational Biology Department, Carnegie Mellon Univeristy, Pittsburgh PA 15213, USA
| | - Carl Kingsford
- Computational Biology Department, Carnegie Mellon Univeristy, Pittsburgh PA 15213, USA
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Delannoy E, Liehrmann A, Castandet B. The Use of Nanopore Sequencing to Analyze the Chloroplast Transcriptome Part II: Bioinformatic Analyzes and Virtual RNA Blots. Methods Mol Biol 2024; 2776:259-267. [PMID: 38502510 DOI: 10.1007/978-1-0716-3726-5_16] [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: 03/21/2024]
Abstract
Nanopore sequencing of full-length cDNAs offers unprecedented details of the plastid RNA metabolism. After the generation of the nanopore reads, several bioinformatic steps are required to analyze the data. In this chapter, we describe in a few simple command lines the processing and mapping of the reads as well as the generation of virtual Northern blots as a simple and familiar way to visualize Nanopore sequencing data.
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Affiliation(s)
- Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France.
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, France.
| | - Arnaud Liehrmann
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, France
- Laboratoire de Mathématiques et de Modélisation d'Evry (LaMME), Université d'Evry-Val-d'Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, Evry, France
| | - Benoît Castandet
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, France
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Skiada S, Launay-Avon A, Liehrmann A, Delannoy E, Castandet B. The Use of Nanopore Sequencing to Analyze the Chloroplast Transcriptome Part I: Library Preparation. Methods Mol Biol 2024; 2776:243-257. [PMID: 38502509 DOI: 10.1007/978-1-0716-3726-5_15] [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: 03/21/2024]
Abstract
Global understanding of plastid gene expression has always been impaired by its complexity. RNA splicing, editing, and intercistronic processing create multiple transcripts isoforms that can hardly be resolved using traditional molecular biology techniques. During the last decade, the wide adoption of RNA-seq-based techniques has, however, allowed an unprecedented understanding of all the different steps of chloroplast gene expression, from transcription to translation. Current strategies are nonetheless unable to identify and quantify full length transcripts isoforms, a limitation that can now be overcome using Nanopore Sequencing. We here provide a complete protocol to produce, from total leaf RNA, cDNA libraries ready for Nanopore sequencing. While most Nanopore protocols take advantage of the mRNA polyA tail we here first ligate an RNA adapter to the 3' ends of the RNAs and use it to initiate the template switching reverse transcription. The cDNA is then prepared and indexed for use with the regular Oxford Nanopore v14 chemistry. This protocol is of particular interest to researchers willing to simultaneously study the multiple post-transcriptional processes prevalent in the chloroplast.
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Affiliation(s)
- Sébastien Skiada
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France
| | - Alexandra Launay-Avon
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France
- Laboratoire de Mathématiques et de Modélisation d'Evry (LaMME), Université d'Evry-Val-d'Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, Evry, France
| | - Arnaud Liehrmann
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France
- Laboratoire de Mathématiques et de Modélisation d'Evry (LaMME), Université d'Evry-Val-d'Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, Evry, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France
| | - Benoît Castandet
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, France.
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Krawczyk PS, Tudek A, Mroczek S, Dziembowski A. Transcriptome-Wide Analysis of mRNA Adenylation Status in Yeast Using Nanopore Sequencing. Methods Mol Biol 2024; 2723:193-214. [PMID: 37824072 DOI: 10.1007/978-1-0716-3481-3_12] [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: 10/13/2023]
Abstract
There are multiple methods for studying deadenylation, either in vitro or in vivo, which allow for observation of mRNA abundance or poly(A) tail dynamics. However, direct RNA sequencing using the Oxford Nanopore Technologies (ONT) platform makes it possible to conduct transcriptome-wide analyses at the single-molecule level without the PCR bias introduced by other methods. In this chapter, we provide a protocol to measure both RNA levels and poly(A)-tail lengths in the yeast Saccharomyces cerevisiae using ONT.
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Affiliation(s)
- Pawel S Krawczyk
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Seweryn Mroczek
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Dziembowski
- International Institute of Molecular and Cell Biology, Warsaw, Poland.
- Faculty of Biology, University of Warsaw, Warsaw, Poland.
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Zaragosi LE, Gouleau A, Delin M, Lebrigand K, Arguel MJ, Girard-Riboulleau C, Rios G, Redman E, Plaisant M, Waldmann R, Magnone V, Marcet B, Barbry P, Ponzio G. Combination of CRISPR-Cas9-RNP and Single-Cell RNAseq to Identify Cell State-Specific FOXJ1 Functions in the Human Airway Epithelium. Methods Mol Biol 2024; 2725:1-25. [PMID: 37856015 DOI: 10.1007/978-1-0716-3507-0_1] [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: 10/20/2023]
Abstract
The study of the airway epithelium in vitro is routinely performed using air-liquid culture (ALI) models from nasal or bronchial basal cells. These 3D experimental models allow to follow the regeneration steps of fully differentiated mucociliary epithelium and to study gene function by performing gene invalidation. Recent progress made with CRISPR-based techniques has overcome the experimental difficulty of this approach, by a direct transfection of ribonucleoprotein complexes combining a mix of synthetic small guide RNAs (sgRNAs) and recombinant Cas9. The approach shows more than 95% efficiency and does not require any selection step. A limitation of this approach is that it generates cell populations that contain heterogeneous deletions, which makes the evaluation of invalidation efficiency difficult. We have successfully used Flongle sequencing (Nanopore) to quantify the number of distinct deletions. We describe the use of CRISPR-Cas9 RNP in combination with single-cell RNA sequencing to functionally characterize the impact of gene invalidation in ALI cultures. The complex ecosystem of the airway epithelium, composed of many cell types, makes single-cell approaches particularly relevant to study cell type, or cell state-specific events. This protocol describes the invalidation of FOXJ1 in ALI cultures through the following steps: (1) Establishment of basal cell cultures from nasal turbinates, (2) CRISPR-Cas9 RNP invalidation of FOXJ1, (3) Quantification of FOXJ1 invalidation efficiency by Nanopore sequencing, (4) Dissociation of ALI cultures and single-cell RNAseq, (5) Analysis of single-cell RNAseq data from FOXJ1-invalidated cells.We confirm here that FOXJ1 invalidation impairs the final differentiation step of multiciliated cells and provides a framework to explore other gene functions.
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Affiliation(s)
| | - Alizé Gouleau
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Margot Delin
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | | | | | - Geraldine Rios
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Elisa Redman
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Magali Plaisant
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Rainer Waldmann
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | | | - Brice Marcet
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Gilles Ponzio
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
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Pecman A, Mehle N, Kutnjak D. Detection of Plant Viruses Using Nanopore Sequencing Based Metagenomic Approach. Methods Mol Biol 2024; 2732:251-264. [PMID: 38060130 DOI: 10.1007/978-1-0716-3515-5_17] [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] [Indexed: 12/08/2023]
Abstract
Nanopore sequencing has proven to be a useful tool for the generic detection of plant viruses, especially in laboratories working with small number of samples. In this chapter, we describe the steps prior to library preparation as well as the library preparation itself, which we found provides comparable results to Illumina sequencing.
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Affiliation(s)
- Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- School for Viticulture and Enology, University of Nova Gorica, Vipava, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
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Liu J, Li S, Su Y, Wen Y, Qin L, Zhao M, Hui M, Jiang L, Chen X, Hou Y, Wang Z. A proof-of-principle study: The potential application of MiniHap biomarkers in ancestry inference based on the QNome nanopore sequencing. Forensic Sci Int Genet 2024; 68:102947. [PMID: 37862770 DOI: 10.1016/j.fsigen.2023.102947] [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] [Received: 06/14/2023] [Revised: 09/25/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023]
Abstract
Haplotyped SNPs convey forensic-related information, and microhaplotypes (MHs), as the most representative of this kind of marker, have proved the potential value for human forensics. In recent years, nanopore sequencing technology has developed rapidly, with its outstanding ability to sequence long continuous DNA fragments and obtain phase information, making the detection of longer haplotype marker possible. In this proof-of-principle study, we proposed a new type of forensic marker, MiniHap, based on five or more SNPs within a molecular distance less than 800 bp, and investigated the haplotype data of 56 selected MiniHaps in five Chinese populations using the QNome nanopore sequencing. The sequencing performance, allele (haplotype) frequencies, forensic parameters, effective number of alleles (Ae), and informativeness (In) were subsequently calculated. In addition, we performed principal component analysis (PCA), phylogenetic tree, and structure analysis to investigate the population genetic relationships and ancestry components among the five investigated populations and 26 worldwide populations. MiniHap-04 exhibited remarkable forensic efficacy, with 148 haplotypes reported and the Ae was 66.9268. In addition, the power of discrimination (PD) was 0.9934, the probability of exclusion (PE) was 0.9898, and the In value was 0.7893. Of the 56 loci, 85.71% had PD values above 0.85, 66.07% had PE values above 0.54, 67.86% had Ae values over 7.0%, and 55.36% were with In values above 0.2 across all samples, indicating that most of the MiniHaps are suitable for individual identification, paternity testing, mixture deconvolution, and ancestry inference. Moreover, the results of PCA, phylogenetic tree and structure analysis demonstrated that this MiniHap panel had the competency in continental population ancestry inference, but the differentiation within intracontinental/linguistically restricted subpopulations was not ideal. Such findings suggested that the QNome device for MiniHap detection was feasible and this novel marker has the potential in ancestry inference. Yet, the establishment of a more comprehensive database with sufficient reference population data remains necessary to screen more suitable MiniHaps.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu 610041, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Liu Qin
- Qitan Technology Ltd., Chengdu 610044, China
| | - Mengyao Zhao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Minxiao Hui
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Putzeys L, Intizar D, Lavigne R, Boon M. Obtaining Detailed Phage Transcriptomes Using ONT-Cappable-Seq. Methods Mol Biol 2024; 2793:207-235. [PMID: 38526733 DOI: 10.1007/978-1-0716-3798-2_14] [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: 03/27/2024]
Abstract
Detailed transcription maps of bacteriophages are not usually explored, limiting our understanding of molecular phage biology and restricting their exploitation and engineering. The ONT-cappable-seq method described here brings phage transcriptomics to the accessible nanopore sequencing platform and provides an affordable and more detailed overview of transcriptional features compared to traditional RNA-seq experiments. With ONT-cappable-seq, primary transcripts are specifically capped, enriched, and prepared for long-read sequencing on the nanopore sequencing platform. This enables end-to-end sequencing of unprocessed transcripts covering both phage and host genome, thus providing insight on their operons. The subsequent analysis pipeline makes it possible to rapidly identify the most important transcriptional features such as transcription start and stop sites. The obtained data can thus provide a comprehensive overview of the transcription by your phage of interest.
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Affiliation(s)
- Leena Putzeys
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Danish Intizar
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium.
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
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Cuevas-Ferrando E, Sánchez G, Pérez-Cataluña A. SARS-CoV-2 Detection and Genome Sequencing in Urban Wastewaters. Methods Mol Biol 2024; 2732:119-131. [PMID: 38060121 DOI: 10.1007/978-1-0716-3515-5_8] [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] [Indexed: 12/08/2023]
Abstract
Due to the excretion of SARS-CoV-2 in faeces, the use of wastewater-based epidemiology (WBE) is a useful tool for virus surveillance in large populations. The analysis of this virus includes a concentration step prior to virus detection by RT-qPCR. In addition, the use of massive sequencing allows the detection of specific mutations of clinical importance, as well as the detection of the introduction of new lineages in a specific population. In this chapter, we describe the analysis of SARS-CoV-2 in urban wastewater by the concentration of the samples by precipitation with aluminum chloride, the detection, and quantification of SARS-CoV-2 RNA by RT-qPCR and the genomic sequencing using two different sequencing platforms.
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Affiliation(s)
- Enric Cuevas-Ferrando
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Valencia, Paterna, Spain
| | - Gloria Sánchez
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Valencia, Paterna, Spain
| | - Alba Pérez-Cataluña
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Valencia, Paterna, Spain.
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Giraudo P, Simonnot Q, Pflieger D, Peter J, Gagliardi D, Zuber H. Nano3'RACE: A Method to Analyze Poly(A) Tail Length and Nucleotide Additions at the 3' Extremity of Selected mRNAs Using Nanopore Sequencing. Methods Mol Biol 2024; 2723:233-252. [PMID: 37824074 DOI: 10.1007/978-1-0716-3481-3_14] [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: 10/13/2023]
Abstract
Deadenylation is a major process that regulates gene expression by shaping the length of mRNA poly(A) tails. Deadenylation is controlled by factors in trans that recruit or impede deadenylases, by the incorporation of non-adenosines during poly(A) tail synthesis, and by the posttranscriptional addition of 3' nucleotides to poly(A) tails. Deciphering the regulation of poly(A) tail shortening requires both transcriptome-wide approaches and more targeted methodologies, allowing deep analyses of specific mRNAs. In this chapter, we present Nano3'RACE, a nanopore-based cDNA sequencing method that allows in-depth analysis to precisely measure poly(A) tail length and detect 3' terminal nucleotide addition, such as uridylation, for mRNAs of interest.
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Affiliation(s)
- Pietro Giraudo
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Quentin Simonnot
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Jackson Peter
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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Heberle BA, Brandon JA, Page ML, Nations KA, Dikobe KI, White BJ, Gordon LA, Fox GA, Wadsworth ME, Doyle PH, Williams BA, Fox EJ, Shantaraman A, Ryten M, Goodwin S, Ghiban E, Wappel R, Mavruk-Eskipehlivan S, Miller JB, Seyfried NT, Nelson PT, Fryer JD, Ebbert MTW. Using deep long-read RNAseq in Alzheimer's disease brain to assess medical relevance of RNA isoform diversity. bioRxiv 2023:2023.08.06.552162. [PMID: 37609156 PMCID: PMC10441303 DOI: 10.1101/2023.08.06.552162] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Due to alternative splicing, human protein-coding genes average over eight RNA isoforms, resulting in nearly four distinct protein coding sequences per gene. Long-read RNAseq (IsoSeq) enables more accurate quantification of isoforms, shedding light on their specific roles. To assess the medical relevance of measuring RNA isoform expression, we sequenced 12 aged human frontal cortices (6 Alzheimer's disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. Our study uncovered 53 new high-confidence RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. Specific examples include WDR4 (61%; microcephaly), MYL3 (44%; hypertrophic cardiomyopathy), and MTHFS (25%; major depression, schizophrenia, bipolar disorder). Other notable genes with new high-confidence isoforms include CPLX2 (10%; schizophrenia, epilepsy) and MAOB (9%; targeted for Parkinson's disease treatment). We identified 1,917 medically relevant genes expressing multiple isoforms in human frontal cortex, where 1,018 had multiple isoforms with different protein coding sequences, demonstrating the need to better understand how individual isoforms from a single gene body are involved in human health and disease, if at all. Exactly 98 of the 1,917 genes are implicated in brain-related diseases, including Alzheimer's disease genes such as APP (Aβ precursor protein; five), MAPT (tau protein; four), and BIN1 (eight). As proof of concept, we also found 99 differentially expressed RNA isoforms between Alzheimer's cases and controls, despite the genes themselves not exhibiting differential expression. Our findings highlight the significant knowledge gaps in RNA isoform diversity and their medical relevance. Deep long-read RNA sequencing will be necessary going forward to fully comprehend the medical relevance of individual isoforms for a "single" gene.
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Affiliation(s)
- Bernardo Aguzzoli Heberle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | | | - Madeline L. Page
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Kayla A. Nations
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Ketsile I. Dikobe
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Brendan J. White
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Lacey A. Gordon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Grant A. Fox
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | - Mark E. Wadsworth
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Patricia H. Doyle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | - Brittney A. Williams
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY
| | - Edward J. Fox
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Mina Ryten
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Elena Ghiban
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Robert Wappel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | | | - Justin B. Miller
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Peter T. Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - John D. Fryer
- Department of Neuroscience, Mayo Clinic, Scottsdale, Arizona
| | - Mark T. W. Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
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Braga PRC, Dos Santos CA, Bertani AMDJ, Vieira T, Amarante AF, Reis AD, Sacchi CT, Camargo CH, Ribeiro MG, Borges AS, Tiba-Casas MR. Detection and genomic characterization of a multidrug-resistant Salmonella Newport co-harbouring bla CMY-2, qnrB19 and mcr-9 from the diarrheic faeces of a foal. J Glob Antimicrob Resist 2023; 35:198-201. [PMID: 37805072 DOI: 10.1016/j.jgar.2023.09.019] [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] [Received: 09/15/2022] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/09/2023] Open
Abstract
OBJECTIVES This study reports the genomic characterization of the multidrug resistant Salmonella Newport strain 195_20 recovered from the diarrheic faeces of a foal in Brazil and co-harbouring the mcr-9, blaCMY-2 and qnrB19 antibiotic resistance genes. METHODS Bacterial isolate positive for mobile colistin resistance gene (mcr-9) was submitted to antimicrobial susceptibility testing by disk diffusion and broth microdilution for colistin and polymyxin B. The isolate was submitted to whole genome sequencing by Illumina technology and Nanopore Sequencing. Conjugation assays, plasmid sizes determined by S1-PFGE and plasmid content were investigated by hybrid assembly after MinIon long reads sequencing. RESULTS Isolate 195_20 was identified as sequence type ST45, resistant to penicillin and cephalosporins (ampicillin, ceftazidime, ceftriaxone and cefotaxime), aminoglycosides (streptomycin and gentamicin), phenicol (chloramphenicol), quinolones and fluoroquinolones (nalidixic acid, ciprofloxacin, and pefloxacin), folate pathway antagonists (sulfonamides and trimethoprim-sulfamethoxazole), and tetracycline. A transferable IncHI2/IncHI2A plasmid sized ca. 262kb was found to carry the mcr-9 gene in a module consisting of IS903-mcr-9-wbuC-IS26. In addition, an 174kb IncC and a 48kb IncN plasmid were also identified in the 195_20 isolate, carrying blaCMY-2 and qnrB19, respectively. CONCLUSIONS Not surprisingly, isolate 195_20 was susceptible to polymyxins, possibly due to absence of qseBC regulatory operon. Presence of mobile colistin resistance (mcr-9), third-generation cephalosporins (blaCMY-2) and quinolone (qnrB19) resistance determinants in zoonotic pathogens from animals in close contact with humans alerts for the possible route of transmission between these different reservoirs.
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Affiliation(s)
- Pollyana Rennó Campos Braga
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, SP, Brazil
| | | | | | | | | | | | | | | | - Marcio Garcia Ribeiro
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, SP, Brazil
| | - Alexandre Secorun Borges
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, SP, Brazil
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Treagus S, Lowther J, Longdon B, Gaze W, Baker-Austin C, Ryder D, Batista FM. Metabarcoding of Hepatitis E Virus Genotype 3 and Norovirus GII from Wastewater Samples in England Using Nanopore Sequencing. Food Environ Virol 2023; 15:292-306. [PMID: 37910379 PMCID: PMC7615314 DOI: 10.1007/s12560-023-09569-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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
Norovirus is one of the largest causes of gastroenteritis worldwide, and Hepatitis E virus (HEV) is an emerging pathogen that has become the most dominant cause of acute viral hepatitis in recent years. The presence of norovirus and HEV has been reported within wastewater in many countries previously. Here we used amplicon deep sequencing (metabarcoding) to identify norovirus and HEV strains in wastewater samples from England collected in 2019 and 2020. For HEV, we sequenced a fragment of the RNA-dependent RNA polymerase (RdRp) gene targeting genotype three strains. For norovirus, we sequenced the 5' portion of the major capsid protein gene (VP1) of genogroup II strains. Sequencing of the wastewater samples revealed eight different genotypes of norovirus GII (GII.2, GII.3, GII.4, GII.6, GII.7, GII.9, GII.13 and GII.17). Genotypes GII.3 and GII.4 were the most commonly found. The HEV metabarcoding assay was able to identify HEV genotype 3 strains in some samples with a very low viral concentration determined by RT-qPCR. Analysis showed that most HEV strains found in influent wastewater were typed as G3c and G3e and were likely to have originated from humans or swine. However, the small size of the HEV nested PCR amplicon could cause issues with typing, and so this method is more appropriate for samples with high CTs where methods targeting longer genomic regions are unlikely to be successful. This is the first report of HEV RNA in wastewater in England. This study demonstrates the utility of wastewater sequencing and the need for wider surveillance of norovirus and HEV within host species and environments.
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Affiliation(s)
- Samantha Treagus
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK.
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Penryn Campus, Cornwall, UK.
- UK Health Security Agency, Manor Farm Road, Porton Down, SP4 0JG, Wiltshire, UK.
| | - James Lowther
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Ben Longdon
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Penryn Campus, Cornwall, UK
| | - William Gaze
- Faculty of Health and Life Sciences, University of Exeter Medical School, Penryn Campus, Cornwall, UK
| | | | - David Ryder
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
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42
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Simon SA, Schmidt K, Griesdorn L, Soares AR, Bornemann TLV, Probst AJ. Dancing the Nanopore limbo - Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction. BMC Genomics 2023; 24:727. [PMID: 38041056 PMCID: PMC10693096 DOI: 10.1186/s12864-023-09853-w] [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: 03/03/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing has increasingly been used in microbial metagenomics as long reads greatly improve the assembly quality of MAGs, the recommended DNA quantity usually exceeds the recoverable amount of DNA of environmental samples. Here, we evaluated lower-than-recommended DNA quantities for Nanopore library preparation by determining sequencing quality, community composition, assembly quality and recovery of MAGs. RESULTS We generated 27 Nanopore metagenomes using the commercially available ZYMO mock community and varied the amount of input DNA from 1000 ng (the recommended minimum) down to 1 ng in eight steps. The quality of the generated reads remained stable across all input levels. The read mapping accuracy, which reflects how well the reads match a known reference genome, was consistently high across all libraries. The relative abundance of the species in the metagenomes was stable down to input levels of 50 ng. High-quality MAGs (> 95% completeness, ≤ 5% contamination) could be recovered from metagenomes down to 35 ng of input material. When combined with publicly available Illumina reads for the mock community, Nanopore reads from input quantities as low as 1 ng improved the quality of hybrid assemblies. CONCLUSION Our results show that the recommended DNA amount for Nanopore library preparation can be substantially reduced without any adverse effects to genome recovery and still bolster hybrid assemblies when combined with short-read data. We posit that the results presented herein will enable studies to improve genome recovery from low-biomass environments, enhancing microbiome understanding.
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Affiliation(s)
- Sophie A Simon
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany.
| | - Katharina Schmidt
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
| | - Lea Griesdorn
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
| | - André R Soares
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Till L V Bornemann
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany.
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
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Son H, Moon J, Ha EJ, Kim N, Kim EY, Lee HS, Koh EJ, Phi JH, Park CK, Kim JE, Kim SK, Lee ST, Jung KH, Lee SK, Cho WS, Chu K. Identification of bacterial pathogens in brain abscesses by metagenomic approach using nanopore 16S amplicon sequencing. Diagn Microbiol Infect Dis 2023; 107:116041. [PMID: 37741170 DOI: 10.1016/j.diagmicrobio.2023.116041] [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] [Received: 03/09/2023] [Revised: 06/30/2023] [Accepted: 07/22/2023] [Indexed: 09/25/2023]
Abstract
Brain abscess is medically challenging. In this study, we applied nanopore sequencing for 16S rRNA analysis and investigated its efficacy and diagnostic value for patients with brain abscesses. Genomic DNA was extracted from the pus samples (n = 27) of brain abscess, and 16S rRNA genes were amplified by PCR. Sequencing libraries were generated using a rapid barcoding kit, and the generated reads were analyzed using the EPI2ME16S workflow. A conventional culture study was performed. More sensitive identification of pathogens was made by 16S sequencing, faster than the culture study. The proportion of anaerobic bacteria identified by 16S sequencing was higher (75%) than that obtained by culturing (32%). Polymicrobial infections were identified in 10 cases (40%) by 16S sequencing, while the culture study identified multiple bacteria in only 2 cases (8%). 16S sequencing was useful for identifying the composition of polymicrobial infections, including rare pathogens, and for the initial diagnosis of space-occupying lesions.
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Affiliation(s)
- Hyoshin Son
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea; Department of Neurology, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Jangsup Moon
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea; Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Eun Jin Ha
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Narae Kim
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea
| | - Eun-Young Kim
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea; Department of Neurology, Chungnam National University Sejong Hospital, Sejong, Korea
| | - Han Sang Lee
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea; Center of Hospital Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Eun Jung Koh
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea; Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea; Center of Hospital Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Ji Hoon Phi
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea; Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Jeong Eun Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Seung-Ki Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea; Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea
| | - Soon-Tae Lee
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea
| | - Keun-Hwa Jung
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea
| | - Sang Kun Lee
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea
| | - Won-Sang Cho
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Kon Chu
- Department of Neurology, Laboratory for Neurotherapeutics, Biomedical Research Institute, College of Medicine Seoul National University, Seoul National University Hospital, Seoul, South Korea.
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Drag MH, Debes KP, Franck CS, Flethøj M, Lyhne MK, Møller JE, Ludvigsen TP, Jespersen T, Olsen LH, Kilpeläinen TO. Nanopore sequencing reveals methylation changes associated with obesity in circulating cell-free DNA from Göttingen Minipigs. Epigenetics 2023; 18:2199374. [PMID: 37032646 PMCID: PMC10088973 DOI: 10.1080/15592294.2023.2199374] [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] [Received: 11/22/2022] [Revised: 01/29/2023] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
Profiling of circulating cell-free DNA (cfDNA) by tissue-specific base modifications, such as 5-methylcytosines (5mC), may enable the monitoring of ongoing pathophysiological processes. Nanopore sequencing allows genome-wide 5mC detection in cfDNA without bisulphite conversion. The aims of this study were: i) to find differentially methylated regions (DMRs) of cfDNA associated with obesity in Göttingen minipigs using Nanopore sequencing, ii) to validate a subset of the DMRs using methylation-specific PCR (MSP-PCR), and iii) to compare the cfDNA DMRs with those from whole blood genomic DNA (gDNA). Serum cfDNA and gDNA were obtained from 10 lean and 7 obese Göttingen Minipigs both with experimentally induced myocardial infarction and sequenced using Oxford Nanopore MinION. A total of 1,236 cfDNA DMRs (FDR<0.01) were associated with obesity. In silico analysis showed enrichment of the adipocytokine signalling, glucagon signalling, and cellular glucose homoeostasis pathways. A strong cfDNA DMR was discovered in PPARGC1B, a gene linked to obesity and type 2 diabetes. The DMR was validated using MSP-PCR and correlated significantly with body weight (P < 0.05). No DMRs intersected between cfDNA and gDNA, suggesting that cfDNA originates from body-wide shedding of DNA. In conclusion, nanopore sequencing detected differential methylation in minute quantities (0.1-1 ng/µl) of cfDNA. Future work should focus on translation into human and comparing 5mC from somatic tissues to pinpoint the exact location of pathology.
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Affiliation(s)
- Markus Hodal Drag
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Conservation, Copenhagen Zoo, Frederiksberg, Denmark
| | | | - Clara Sandkamm Franck
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Flethøj
- Research & Early Development, Novo Nordisk A/S, Måløv, Denmark
| | - Mille Kronborg Lyhne
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Eifer Møller
- Department of Cardiology, Copenhagen University Hospital and Odense University Hospital, Odense, Denmark
| | | | - Thomas Jespersen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lisbeth Høier Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tuomas O. Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Guo Y, Li Z, Li L, Li S, Sun L, Yang X, Dai Y, Gu J, Yang L, Liu X, Lu B, Han J, Chang K, Gu L, Yin Y, Sun S, Jing C, Chen H, Liu M, Xu H, Liu R, Ren Y, Guo H, Wang H. A dual-process of targeted and unbiased Nanopore sequencing enables accurate and rapid diagnosis of lower respiratory infections. EBioMedicine 2023; 98:104858. [PMID: 37925777 PMCID: PMC10652131 DOI: 10.1016/j.ebiom.2023.104858] [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] [Received: 09/18/2023] [Revised: 10/15/2023] [Accepted: 10/15/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Nanopore metagenomics has been used for infectious disease diagnosis for bacterial pathogens. However, this technology currently lacks comprehensive performance studies in clinical settings for simultaneous detection of bacteria, fungi, and viruses. METHODS We developed a dual-process of Nanopore sequencing for one sample, with unbiased metagenomics in Meta process and target enrichment in Panel process (Nanopore Meta-Panel process, NanoMP) and prospectively enrolled 450 respiratory specimens from multiple centers. The filter system of pathogen detection was established with machine learning and receiver operator characteristic (ROC) curve to optimize the detection accuracy based on orthogonal test of 21 species. Antimicrobial resistance (AMR) genes were identified based on the Comprehensive Antibiotic Resistance Database (CARD) and single-nucleotide polymorphism matrix. FINDINGS Our approach showed high sensitivity in Meta process, with 82.9%, 88.7%, and 75.0% for bacteria, fungi (except Aspergillus), and Mycobacterium tuberculosis groups, respectively. Moreover, target amplification improved the sensitivity of virus (>80.0% vs. 39.4%) and Aspergillus (81.8% vs. 42.3%) groups in Panel process compared with Meta process. Overall, NanoMP achieved 80.2% sensitivity and 98.8% specificity compared with the composite reference standard, and we were able to accurately detect AMR genes including blaKPC-2, blaOXA-23 and mecA and distinguish their parent organisms in patients with mixed infections. INTERPRETATION We combined metagenomic and enriched Nanopore sequencing for one sample in parallel. Our NanoMP approach simultaneously covered bacteria, viruses and fungi in respiratory specimens and demonstrated good diagnostic performance in real clinical settings. FUNDING National Key Research and Development Program of China and National Natural Science Foundation of China.
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Affiliation(s)
- Yifan Guo
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Zhenzhong Li
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China; Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Lijuan Li
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, National Center for Clinical Research on Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Shan Li
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China; Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Lingxiao Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Xinfang Yang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China; Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Yan Dai
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China; Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Ju Gu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China; Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Lan Yang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China; Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Xue Liu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China; Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Binghuai Lu
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, National Center for Clinical Research on Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Jiajing Han
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, National Center for Clinical Research on Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Kang Chang
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, National Center for Clinical Research on Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Li Gu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao Yang Hospital, Capital Medical University, Beijing, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shijun Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Chendi Jing
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Manjiao Liu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China; Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Hui Xu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China; Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Ryon Liu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China; Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Yong Ren
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China; Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Hao Guo
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China; Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China.
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China.
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Sanderson H, McCarthy MC, Nnajide CR, Sparrow J, Rubin JE, Dillon JAR, White AP. Identification of plasmids in avian-associated Escherichia coli using nanopore and illumina sequencing. BMC Genomics 2023; 24:698. [PMID: 37990161 PMCID: PMC10664647 DOI: 10.1186/s12864-023-09784-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Avian pathogenic Escherichia coli (APEC) are the causative agents of colibacillosis in chickens, a disease which has significant economic impact on the poultry industry. Large plasmids detected in APEC are known to contribute to strain diversity for pathogenicity and antimicrobial resistance, but there could be other plasmids that are missed in standard analysis. In this study, we determined the impact of sequencing and assembly factors for the detection of plasmids in an E. coli whole genome sequencing project. RESULTS Hybrid assembly (Illumina and Nanopore) combined with plasmid DNA extractions allowed for detection of the greatest number of plasmids in E. coli, as detected by MOB-suite software. In total, 79 plasmids were identified in 19 E. coli isolates. Hybrid assemblies were robust and consistent in quality regardless of sequencing kit used or if long reads were filtered or not. In contrast, long read only assemblies were more variable and influenced by sequencing and assembly parameters. Plasmid DNA extractions allowed for the detection of physically smaller plasmids, but when averaged over 19 isolates did not significantly change the overall number of plasmids detected. CONCLUSIONS Hybrid assembly can be reliably used to detect plasmids in E. coli, especially if researchers are focused on large plasmids containing antimicrobial resistance genes and virulence factors. If the goal is comprehensive detection of all plasmids, particularly if smaller sized vectors are desired for biotechnology applications, the addition of plasmid DNA extractions to hybrid assemblies is prudent. Long read sequencing is sufficient to detect many plasmids in E. coli, however, it is more prone to errors when expanded to analyze a large number of isolates.
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Affiliation(s)
- Haley Sanderson
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Madeline C McCarthy
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
- Current address: Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Chinenye R Nnajide
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jessica Sparrow
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Joseph E Rubin
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jo-Anne R Dillon
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Aaron P White
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.
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Patterson EC, Lall GM, Neumann R, Ottolini B, Batini C, Sacchini F, Foster AP, Wetton JH, Jobling MA. Mitogenome sequences of domestic cats demonstrate lineage expansions and dynamic mutation processes in a mitochondrial minisatellite. BMC Genomics 2023; 24:690. [PMID: 37978434 PMCID: PMC10655372 DOI: 10.1186/s12864-023-09789-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND As a population genetic tool, mitochondrial DNA is commonly divided into the ~ 1-kb control region (CR), in which single nucleotide variant (SNV) diversity is relatively high, and the coding region, in which selective constraint is greater and diversity lower, but which provides an informative phylogeny. In some species, the CR contains variable tandemly repeated sequences that are understudied due to heteroplasmy. Domestic cats (Felis catus) have a recent origin and therefore traditional CR-based analysis of populations yields only a small number of haplotypes. RESULTS To increase resolution we used Nanopore sequencing to analyse 119 cat mitogenomes via a long-amplicon approach. This greatly improves discrimination (from 15 to 87 distinct haplotypes in our dataset) and defines a phylogeny showing similar starlike topologies within all major clades (haplogroups), likely reflecting post-domestication expansion. We sequenced RS2, a CR tandem array of 80-bp repeat units, placing RS2 array structures within the phylogeny and increasing overall haplotype diversity. Repeat number varies between 3 and 12 (median: 4) with over 30 different repeat unit types differing largely by SNVs. Five SNVs show evidence of independent recurrence within the phylogeny, and seven are involved in at least 11 instances of rapid spread along repeat arrays within haplogroups. CONCLUSIONS In defining mitogenome variation our study provides key information for the forensic genetic analysis of cat hair evidence, and for the first time a phylogenetically informed picture of tandem repeat variation that reveals remarkably dynamic mutation processes at work in the mitochondrion.
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Affiliation(s)
- Emily C Patterson
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Gurdeep Matharu Lall
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Barbara Ottolini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Present Address: Oxford Nanopore Technologies Plc., Oxford Science Park, Edmund Halley Rd, Oxford, OX4 4DQ, UK
| | - Chiara Batini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Present Address: Department of Population Health Sciences, University of Leicester, Leicester, UK
- Biomedical Research Centre, Leicester National Institute for Health and Care Research, Glenfield Hospital, Leicester, UK
| | - Federico Sacchini
- IDEXX Laboratories Italia S.R.L., Via Guglielmo Silva, 36-20149, Milano, MI, Italy
| | - Aiden P Foster
- Bristol Veterinary School, University of Bristol, Langford House, Langford, BS40 5DU, North Somerset, UK
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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Li J, Yang L, Wang K, Gao Z, Li P, Lin Y, Jia L, Wang Q, Song H, Li P. Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols. Virol J 2023; 20:263. [PMID: 37964283 PMCID: PMC10647158 DOI: 10.1186/s12985-023-02224-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023] Open
Abstract
Human astroviruses (HAstV) are etiologic agents of acute gastroenteritis that most often afflict young children and elderly adults. Most studies of HAstV have focused on epidemiology. In this study, we collected 10 stool samples from a diarrhea outbreak from a diarrhea sentinel surveillance hospital in Beijing. Samples were evaluated immediately using parallel multiplex RT-qPCR and nanopore sequencing, and were then amplified by designed primers and Sanger sequencing to obtain whole genome sequences. Six isolates were categorized as HAstV-5 and subjected to whole genome analysis to characterize their genetic variation and evolution. Full genome analysis revealed low genetic variation (99.38-100% identity) among isolates. Phylogenetic analysis showed that all isolates were closely related to domestic strains Yu/1-CHN and 2013/Fuzhou/85. The recombination breakpoint of the six isolates was located at 2741 bp in the overlap region of ORF1a and ORF1b, similar to those of Yu/1-CHN and 2013/Fuzhou/85. Overall, our study highlights the combined use of RT-qPCR and sequencing as an important tool in rapid diagnosis and acquisition of whole genome sequences of HAstV.
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Affiliation(s)
- Jinhui Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Lang Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kaiying Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Zhiyong Gao
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Peihan Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- Huadong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Yanfeng Lin
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- Huadong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Leili Jia
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, Beijing, China.
| | - Hongbin Song
- Chinese PLA Center for Disease Control and Prevention, Beijing, China.
| | - Peng Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China.
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Li X, Wei X, Liu X, Wang N, Xu F, Liu X, Li Y, Zhou Y, Tang H, Bian M, Hou Y, Zhang L, Wang W, Liu Q. The analysis of HPV integration sites based on nanopore sequencing and the profiling changes along the course of photodynamic therapy. BMC Cancer 2023; 23:1052. [PMID: 37914994 PMCID: PMC10621124 DOI: 10.1186/s12885-023-11538-2] [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: 05/25/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
OBJECTIVE To detect the HPV genotype and integration sites in patients with high-risk HPV infection at different stages of photodynamic therapy using nanopore technology and to evaluate the treatment effect. METHODS Four patients with HPV infection were selected and subjected to photodynamic therapy, and cervical exfoliated cell was sampled at before treatment, after three courses of treatment and six courses of treatment, their viral abundance and insertion sites were analyzed by nanopore technology, and pathological examinations were performed before and after treatment. In this study, we developed a novel assay that combined viral sequence enrichment and Nanopore sequencing for identification of HPV genotype and integration sites at once. The assay has obvious advantages over qPCR or NGS-based methods, as it has better sensitivity after viral sequences enrichment and can generate long-reads (kb to Mb) for better detection rate of structure variations, moreover, fast turn-around time for real-time viral sequencing and analysis. RESULTS The pathological grade was reduced in all four patients after photodynamic therapy. Virus has been cleared in two cases after treatment, the virus amount reduced after treatment but not completely cleared in one case, and two type viruses were cleared and one type virus persisted after treatment in the last patient with multiple infection. Viral abundance and the number of integration sites were positively correlated. Gene enrichment analysis showed complete viral clearance in 1 patient and 3 patients required follow-up. CONCLUSION Nanopore sequencing can effectively monitor the abundance of HPV viruses and integration sites to show the presence status of viruses, and combined with the results of gene enrichment analysis, the treatment effect can be dynamically assessed.
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Affiliation(s)
- Xiulan Li
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xiaoke Wei
- Geneis, Bldg A, 5 Guangshun North Street, Beijing, 100102, China
| | - Xin Liu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Nan Wang
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Fuqiang Xu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xingyu Liu
- Geneis, Bldg A, 5 Guangshun North Street, Beijing, 100102, China
| | - Yanmei Li
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Yuxiang Zhou
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Huadong Tang
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Meina Bian
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Ying Hou
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Lili Zhang
- Geneis, Bldg A, 5 Guangshun North Street, Beijing, 100102, China.
| | - Weiwei Wang
- Geneis, Bldg A, 5 Guangshun North Street, Beijing, 100102, China.
| | - Qing Liu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
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50
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Casanova-Adán L, Mosquera-Miguel A, González-Bao J, Ambroa-Conde A, Ruiz-Ramírez J, Cabrejas-Olalla A, González-Martín E, Freire-Aradas A, Rodríguez-López A, Phillips C, Lareu MV, de la Puente M. Adapting an established Ampliseq microhaplotype panel to nanopore sequencing through direct PCR. Forensic Sci Int Genet 2023; 67:102937. [PMID: 37812882 DOI: 10.1016/j.fsigen.2023.102937] [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] [Received: 07/19/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
We have adapted an established Ampliseq microhaplotype panel for nanopore sequencing with the Oxford Nanopore Technologies (ONT) system, as a cost-effective and highly scalable solution for forensic genetics applications. For this purpose, we designed a protocol combining direct PCR amplification from unextracted DNA with ONT library construction and sequencing using the MinION device and workflow. The analysis of reference samples at input amounts of 5-10 ng of DNA demonstrates stable coverage patterns, allele balance, and strand bias, reaching profile completeness and concordance rates of ∼95%. Similar levels were achieved when using direct-PCR from blood, buccal and semen swabs. Dilution series results indicate sensitivity is maintained down to 250 pg of input DNA, and informative profiles are produced down to 62.5 pg. Finally, we demonstrated the forensic utility of the nanopore workflow by analyzing two third degree pedigrees that showed low likelihood ratio values after the analysis of an extended panel of 38 STRs, achieving likelihood ratios 2-3 orders of magnitude higher when testing with the MinION-based haplotype data.
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Affiliation(s)
- L Casanova-Adán
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - J González-Bao
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - J Ruiz-Ramírez
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Cabrejas-Olalla
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - E González-Martín
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Rodríguez-López
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain.
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