In:
Frontiers in Microbiology, Frontiers Media SA, Vol. 14 ( 2023-5-15)
Kurzfassung:
Genome-based analysis is crucial in monitoring antibiotic-resistant bacteria (ARB)and antibiotic-resistance genes (ARGs). Short-read sequencing is typically used to obtain incomplete draft genomes, while long-read sequencing can obtain genomes of multidrug resistance (MDR) plasmids and track the transmission of plasmid-borne antimicrobial resistance genes in bacteria. However, long-read sequencing suffers from low-accuracy base calling, and short-read sequencing is often required to improve genome accuracy. This increases costs and turnaround time. Methods In this study, a novel ONT sequencing method is described, which uses the latest ONT chemistry with improved accuracy to assemble genomes of MDR strains and plasmids from long-read sequencing data only. Three strains of Salmonella carrying MDR plasmids were sequenced using the ONT SQK-LSK114 kit with flow cell R10.4.1, and de novo genome assembly was performed with average read accuracy (Q & gt; 10) of 98.9%. Results and Discussion For a 5-Mb-long bacterial genome, finished genome sequences with accuracy of & gt;99.99% could be obtained at 75× sequencing coverage depth using Flye and Medaka software. Thus, this new ONT method greatly improves base-calling accuracy, allowing for the de novo assembly of high-quality finished bacterial or plasmid genomes without the need for short-read sequencing. This saves both money and time and supports the application of ONT data in critical genome-based epidemiological analyses. The novel ONT approach described in this study can take the place of traditional combination genome assembly based on short- and long-read sequencing, enabling pangenomic analyses based on high-quality complete bacterial and plasmid genomes to monitor the spread of antibiotic-resistant bacteria and antibiotic resistance genes.
Materialart:
Online-Ressource
ISSN:
1664-302X
DOI:
10.3389/fmicb.2023.1179966
DOI:
10.3389/fmicb.2023.1179966.s001
DOI:
10.3389/fmicb.2023.1179966.s002
DOI:
10.3389/fmicb.2023.1179966.s003
Sprache:
Unbekannt
Verlag:
Frontiers Media SA
Publikationsdatum:
2023
ZDB Id:
2587354-4
Permalink