Benchmarking Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms for whole genome sequencing of bacterial genomes and use in clinical microbiology.

ABSTRACT:

Background

In microbial diagnostics, whole-genome sequencing (WGS) is used to address key questions such as species identification, presence of antimicrobial resistance genes (ARGs), virulence genes, and outbreak detection. The choice of sequencing technology is crucial to ensure high-quality data, cost-effectiveness, and efficient reporting times. We aimed to compare Illumina (short-read) and ONT (long-read) sequencing methods for WGS on different bacterial species for base accuracy and reliable taxonomic and ARG identification.

Materials and methods

We used clinical isolates of ESKAPE pathogens (n = 12) and ATCC strains (n = 8) of varying %G + C. Illumina sequencing was performed on MiSeq (PE150) and ONT sequencing using GridION with R9.4.1 and R10.4.1 flowcells. Base-call

SUBMITTER: Purushothaman S 

PROVIDER: S-EPMC12903679 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature