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Please use this identifier to cite or link to this item:
http://ir.nhri.org.tw/handle/3990099045/16957
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| Title: | Streamlining whole genome sequencing for clinical diagnostics with ONT technology |
| Authors: | Wu, HC;Chiu, YT;Wu, IC;Liou, CH;Cheng, HW;Kuo, SC;Lauderdale, TL;Sytwu, HK;Liao, YC;Chen, FJ |
| Contributors: | National Institute of Infectious Diseases and Vaccinology;Institute of Population Health Sciences |
| Abstract: | Recent advances in whole-genome sequencing (WGS) have increased the accessibility of this tool, offering substantial potential for pathogen surveillance, outbreak response, and diagnostics. However, the routine clinical adoption of WGS is hindered by factors such as high costs, technical complexity, and the requirement for bioinformatics expertise for data analysis. To address these challenges, we propose RapidONT, a workflow designed for cost-effective and accessible WGS-based pathogen analysis. RapidONT employs a mechanical shearing–based DNA extraction protocol, followed by library construction by using a multiplexing Oxford nanopore technologies (ONT) rapid barcoding kit. Flye software is used for de novo assembly without manual intervention, followed by basic assembly polishing using Medaka and Homopolish. The polished assemblies are then analyzed using the user-friendly web-based platform Pathogenwatch, which facilitates species identification, molecular typing, and antimicrobial resistance (AMR) prediction, all while requiring minimal bioinformatics expertise. The efficacy of RapidONT was evaluated using nine clinically relevant pathogens, encompassing a total of 90 gram-positive and gram-negative bacterial strains. The workflow demonstrated high accuracy in critical tasks such as multilocus sequence typing (MLST) and AMR identification, using only ONT R9.4.1 flowcell data. Notably, limitations were observed with Salmonella spp. and Neisseria gonorrhoeae. Furthermore, RapidONT enabled the generation of genomic information for 48 bacterial isolates by using a single flow cell, significantly reducing sequencing costs. This approach eliminates the need for extensive experimentation in obtaining crucial genomic information. This workflow facilitates broader WGS implementation in clinical pathogen analysis and diagnostics. © The Author(s) 2025. |
| Date: | 2025-02-20 |
| Relation: | Scientific Reports. 2025 Feb 20;15:Article number 6270. |
| Link to: | http://dx.doi.org/10.1038/s41598-025-90127-8 |
| JIF/Ranking 2023: | http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=NHRI&SrcApp=NHRI_IR&KeyISSN=2045-2322&DestApp=IC2JCR |
| Cited Times(Scopus): | https://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=85218693002 |
| Appears in Collections: | [陳逢叡] 期刊論文
[司徒惠康] 期刊論文
[楊采菱] 期刊論文
[郭書辰] 期刊論文
[廖玉潔] 期刊論文
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| SCP85218693002.pdf | 3924Kb | Adobe PDF | 35 | View/Open |
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