Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study.

Autor:	Janes VA; Department of Medical Microbiology, University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands. Electronic address: v.a.janes@amsterdamumc.nl., Matamoros S; Department of Medical Microbiology, University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands., Munk P; National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark., Clausen PTLC; National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark., Koekkoek SM; Department of Medical Microbiology, University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands., Koster LAM; Core Facility Genomics, Clinical Genetics, University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands., Jakobs ME; Core Facility Genomics, Clinical Genetics, University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands., de Wever B; Department of Medical Microbiology, University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands., Visser CE; Department of Medical Microbiology, University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands., Aarestrup FM; National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark., Lund O; National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark., de Jong MD; Department of Medical Microbiology, University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands., Bossuyt PMM; Department of Epidemiology and Data Science, University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands., Mende DR; Department of Medical Microbiology, University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands. Electronic address: d.r.mende@amsterdamumc.nl., Schultsz C; Department of Medical Microbiology, University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands; Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands.
Jazyk:	angličtina
Zdroj:	The Lancet. Microbe [Lancet Microbe] 2022 Aug; Vol. 3 (8), pp. e588-e597. Date of Electronic Publication: 2022 Jun 07.
DOI:	10.1016/S2666-5247(22)00088-X
Abstrakt:	Background: Semi-quantitative bacterial culture is the reference standard to diagnose urinary tract infection, but culture is time-consuming and can be unreliable if patients are receiving antibiotics. Metagenomics could increase diagnostic accuracy and speed by sequencing the microbiota and resistome directly from urine. We aimed to compare metagenomics to culture for semi-quantitative pathogen and resistome detection from urine. Methods: In this proof-of-concept study, we prospectively included consecutive urine samples from a clinical diagnostic laboratory in Amsterdam. Urine samples were screened by DNA concentration, followed by PCR-free metagenomic sequencing of randomly selected samples with a high concentration of DNA (culture positive and negative). A diagnostic index was calculated as the product of DNA concentration and fraction of pathogen reads. We compared results with semi-quantitative culture using area under the receiver operating characteristic curve (AUROC) analyses. We used ResFinder and PointFinder for resistance gene detection and compared results to phenotypic antimicrobial susceptibility testing for six antibiotics commonly used for urinary tract infection treatment: nitrofurantoin, ciprofloxacin, fosfomycin, cotrimoxazole, ceftazidime, and ceftriaxone. Findings: We screened 529 urine samples of which 86 were sequenced (43 culture positive and 43 culture negative). The AUROC of the DNA concentration-based screening was 0·85 (95% CI 0·81-0·89). At a cutoff value of 6·0 ng/mL, culture positivity was ruled out with a negative predictive value of 91% (95% CI 87-93; 26 of 297 samples), reducing the number of samples requiring sequencing by 56% (297 of 529 samples). The AUROC of the diagnostic index was 0·87 (95% CI 0·79-0·95). A diagnostic index cutoff value of 17·2 yielded a positive predictive value of 93% (95% CI 85-97) and a negative predictive value of 69% (55-80), correcting for a culture-positive prevalence of 66%. Gram-positive pathogens explained eight (89%) of the nine false-negative metagenomic test results. Agreement of phenotypic and genotypic antimicrobial susceptibility testing varied between 71% (22 of 31 samples) and 100% (six of six samples), depending on the antibiotic tested. Interpretation: This study provides proof-of-concept of metagenomic semi-quantitative pathogen and resistome detection for the diagnosis of urinary tract infection. The findings warrant prospective clinical validation of the value of this approach in informing patient management and care. Funding: EU Horizon 2020 Research and Innovation Programme. Competing Interests: Declaration of interests We declare no competing interests. (Copyright © 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)
Databáze:	MEDLINE
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