RT Journal Article
SR Electronic
T1 Nanopore-Based Enrichment of Antimicrobial Resistance Genes – A Case-Based Study
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.08.29.458107
DO 10.1101/2021.08.29.458107
A1 Adrian Viehweger
A1 Mike Marquet
A1 Martin Hölzer
A1 Nadine Dietze
A1 Mathias W. Pletz
A1 Christian Brandt
YR 2023
UL http://biorxiv.org/content/early/2023/01/04/2021.08.29.458107.abstract
AB Rapid screening of hospital admissions to detect asymptomatic carriers of resistant bacteria can prevent pathogen outbreaks. However, the resulting isolates rarely have their genome sequenced due to cost constraints and long turn-around times to get and process the data, limiting their usefulness to the practitioner. Here we use real-time, on-device target enrichment (“adaptive”) sequencing as a highly multiplexed assay covering 1,147 antimicrobial resistance genes. We compare its utility against standard and metagenomic sequencing, focusing on an isolate of Raoultella ornithinolytica harbouring three carbapenemases (NDM, KPC, VIM). Based on this experimental data, we then model the influence of several variables on the enrichment results and predict a large effect of nucleotide identity (higher is better) and read length (shorter is better). Lastly, we show how all relevant resistance genes are detected using adaptive sequencing on a miniature (“Flongle”) flow cell, motivating its use in a clinical setting to monitor similar cases and their surroundings.Competing Interest StatementThe authors have declared no competing interest.ARGantimicrobial resistance geneORFopen reading frameMAGmetagenome-assembled genomeFNRfalse negative rate