Rapid inference of antibiotic susceptibility phenotype of uropathogens using metagenomic sequencing with neighbor typing.

doi:10.1128/spectrum.01366-24

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Article

Rapid inference of antibiotic susceptibility phenotype of uropathogens using metagenomic sequencing with neighbor typing.

Microbiology spectrum - 7 Jan 2025

Carroll Amanda C, Mortimer Leanne, Ghosh Hiren, Reuter Sandra, Grundmann Hajo, Brinda Karel, Hanage William P, Li Angel, Paterson Aimee, Purssell Andrew, Rooney Ashley, Yee Noelle R, Coburn Bryan, Able-Thomas Shola, Antonio Martin, McGeer Allison, MacFadden Derek R

Abstract excerpt

Timely diagnostic tools are needed to improve antibiotic treatment. Pairing metagenomic sequencing with genomic neighbor typing algorithms may support rapid clinically actionable results. We created resistance-associated sequence elements (RASE) databases for Escherichia coli and Klebsiella spp. and used them to predict antibiotic susceptibility in directly sequenced (Oxford Nanopore) urine specimens from...

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Topics

Humans
Anti-Bacterial Agents
Urinary Tract Infections
Metagenomics
Klebsiella

Methodology Data sources Editorial policy Privacy Delete account & data About Contact Helena Bioinformatics

Microbial Sensitivity Tests

Escherichia coli

Phenotype

Multilocus Sequence Typing

Drug Resistance, Bacterial

Escherichia coli Infections

Klebsiella Infections

Bacterial Typing Techniques

Source

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Identifiers

PMID: 39611823
DOI: 10.1128/spectrum.01366-24
PMCID: PMC11705937

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