The impact of applying various de novo assembly and correction tools on the identification of genome characterization, drug resistance, and virulence factors of clinical isolates using ONT sequencing

BMC Biotechnology

Research

Rehab Al-Ajmi¹  Abu Salim Mustafa¹  Wadha Alfouzan²  Hussain A. Safar³  Kother Nasser⁴  Fatemah Alatar⁴ 

[1] Department of Microbiology, Faculty of Medicine, Kuwait University, Hawalli Governorate, Kuwait;Department of Microbiology, Faculty of Medicine, Kuwait University, Hawalli Governorate, Kuwait;Microbiology Unit, Farwaniya Hospital, Ministry of Health, Al Farwaniyah Governorate, Kuwait;OMICS Research Unit, Health Science Centre, Kuwait University, Hawalli Governorate, Kuwait;Serology and Molecular Microbiology Reference Laboratory, Mubarak Al-Kabeer Hospital, Ministry of Health, Hawalli Governorate, Kuwait;

关键词: Genome assembly;    ONT;    E. coli;    WGS;   

DOI  :  10.1186/s12896-023-00797-3

 received in 2023-02-02, accepted in 2023-07-21,  发布年份 2023

来源: Springer

【 摘 要 】

Oxford Nanopore sequencing technology (ONT) is currently widely used due to its affordability, simplicity, and reliability. Despite the advantage ONT has over next-generation sequencing in detecting resistance genes in mobile genetic elements, its relatively high error rate (10–15%) is still a deterrent. Several bioinformatic tools are freely available for raw data processing and obtaining complete and more accurate genome assemblies. In this study, we evaluated the impact of using mix-and-matched read assembly (Flye, Canu, Wtdbg2, and NECAT) and read correction (Medaka, NextPolish, and Racon) tools in generating complete and accurate genome assemblies, and downstream genomic analysis of nine clinical Escherichia coli isolates. Flye and Canu assemblers were the most robust in genome assembly, and Medaka and Racon correction tools significantly improved assembly parameters. Flye functioned well in pan-genome analysis, while Medaka increased the number of core genes detected. Flye, Canu, and NECAT assembler functioned well in detecting antimicrobial resistance genes (AMR), while Wtdbg2 required correction tools for better detection. Flye was the best assembler for detecting and locating both virulence and AMR genes (i.e., chromosomal vs. plasmid). This study provides insight into the performance of several read assembly and read correction tools for analyzing ONT sequencing reads for clinical isolates.

【 授权许可】

CC BY   
© The Author(s) 2023

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