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

Urinary tract infections (UTIs) are a common diagnosis in hospitals and are often treated empirically with broad-spectrum antibiotics. These broad-spectrum agents can select for resistance in these bacteria and co-colonizing organisms. The use of narrow-spectrum agents is desirable as an antibiotic stewardship measure; however, it is counterbalanced by the need for adequate therapy. Identification of causative organisms and their antibiotic susceptibility can help direct treatment; however, conventional testing requires days to produce actionable results. Methods to quickly and accurately predict susceptibility phenotypes for pathogens causing UTI could thus improve both patient outcomes and antibiotic stewardship. Here, expanding on previous work showing accurate prediction for certain Gram-positive pathogens, we demonstrate how the use of RASE from metagenomic sequencing can provide informative and rapid phenotype prediction results for common Gram-negative pathogens in UTI, highlighting the future potential of this method to be used in clinical settings to guide empiric antibiotic selection.

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Publication Details

Journal
Microbiology Spectrum
Published
2024-11-29
DOI
https://doi.org/10.1128/spectrum.01366-24
Citations
3
Primary Topic
Bacterial Identification and Susceptibility Testing
Type
article
Field-Weighted Citation Impact
1.14

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article

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

Angel Li, Allison McGeer, Derek R. MacFadden, Bryan A. Coburn et al.
3 citations
Microbiology Spectrum
Bacterial Identification and Susceptibility Testing
1.14
article

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

Angel Li, Allison McGeer, Derek R. MacFadden, Bryan A. Coburn, Karel Břinda, Leanne Mortimer, William P. Hanage, Amanda Carroll, Hiren Ghosh, Hajo Grundmann, Ashley M. Rooney, Sandra Reuter, Andrew Purssell, N. Yee, Martin Antonio, Aimee Paterson, Shola Able-Thomas
article en
3 citations

Abstract

Urinary tract infections (UTIs) are a common diagnosis in hospitals and are often treated empirically with broad-spectrum antibiotics. These broad-spectrum agents can select for resistance in these bacteria and co-colonizing organisms. The use of narrow-spectrum agents is desirable as an antibiotic stewardship measure; however, it is counterbalanced by the need for adequate therapy. Identification of causative organisms and their antibiotic susceptibility can help direct treatment; however, conventional testing requires days to produce actionable results. Methods to quickly and accurately predict susceptibility phenotypes for pathogens causing UTI could thus improve both patient outcomes and antibiotic stewardship. Here, expanding on previous work showing accurate prediction for certain Gram-positive pathogens, we demonstrate how the use of RASE from metagenomic sequencing can provide informative and rapid phenotype prediction results for common Gram-negative pathogens in UTI, highlighting the future potential of this method to be used in clinical settings to guide empiric antibiotic selection.

Microbiology SpectrumVol. 13(1)
University of London (GB), University Health Network (CA), Harvard University (US), University of Freiburg (DE), University of Toronto (CA), Ottawa Hospital (CA), Canada Research Chairs (CA), Institut de Recherche en Informatique et Systèmes Aléatoires (FR), Health Net (US), London School of Hygiene & Tropical Medicine (GB), MRC Unit the Gambia (GM), University of Education Freiburg (DE), Canadian Electricity Association (CA), Sinai Health System (CA), Sinai Health System (US), Ottawa Hospital Research Institute (CA), Université de Rennes (FR)
Pfizer, Joint Programming Initiative on Antimicrobial Resistance, Canadian Institutes of Health Research
Good health and well-being
Openalex Percentile: Top 21%
Bacterial Identification and Susceptibility Testing
1.14
DOIOpen Access PDFOpenAlex
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