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Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection
BACKGROUND: Early availability of pathogen identification in urinary tract infections (UTIs) has critical importance in disease management. Metagenomic next-generation sequencing (mNGS) has the potential to transform how acute and serious infections are diagnosed by offering unbiased and culture-fre...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10612365/ https://www.ncbi.nlm.nih.gov/pubmed/37891586 http://dx.doi.org/10.1186/s12967-023-04562-0 |
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author | Wang, Ye Chen, Ting Zhang, Shengwei Zhang, Lei Li, Qian Lv, Qingyu Kong, Decong Jiang, Hua Ren, Yuhao Jiang, Yongqiang Li, Yan Huang, Wenhua Liu, Peng |
author_facet | Wang, Ye Chen, Ting Zhang, Shengwei Zhang, Lei Li, Qian Lv, Qingyu Kong, Decong Jiang, Hua Ren, Yuhao Jiang, Yongqiang Li, Yan Huang, Wenhua Liu, Peng |
author_sort | Wang, Ye |
collection | PubMed |
description | BACKGROUND: Early availability of pathogen identification in urinary tract infections (UTIs) has critical importance in disease management. Metagenomic next-generation sequencing (mNGS) has the potential to transform how acute and serious infections are diagnosed by offering unbiased and culture-free pathogen detection. However, clinical experience with application of the mNGS test is relatively limited. METHODS: We therefore established a MinION-based mNGS pathogens diagnostic platform and evaluated its potential for clinical implementation in UTIs with clinical samples. 213 urine samples from patients with suspected UTIs were included and subjected to mNGS testing using the MinION platform. mNGS results were compared to the gold standard of clinical culture and composite standard of combining clinical testing, confirmatory qPCR testing, and clinical adjudication by doctors. RESULTS: The mNGS exhibited a sensitivity of 81.4% and a specificity of 92.3%, along with a positive predictive value of 96.6%, a negative predictive value of 64.9%, and an overall accuracy of 84.4%, all of which were determined based on the gold standard of routine culture results. When assessed against the composite standard, the sensitivity and specificity both increased to 89.9% and 100%, respectively, while the accuracy rose to 92.4%. Notably, the positive predictive value and negative predictive value also saw improvements, reaching 100% and 76.8%, respectively. Moreover, this diagnostic platform successfully identified dsDNA viruses. Among the 65 culture-negative samples, the viral detection rate reached 33.8% (22/65) and was subsequently validated through qPCR. Furthermore, the automatic bioinformatics pipeline we developed enabled one-click analysis from data to results, leading to a significant reduction in diagnosis time. CONCLUSION: These results demonstrate that the pathogen detection performance of mNGS is sufficient for diagnostic testing in clinical settings. As the method is generally unbiased, it can improve diagnostic testing of UTIs and other microbial infections. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-023-04562-0. |
format | Online Article Text |
id | pubmed-10612365 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-106123652023-10-29 Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection Wang, Ye Chen, Ting Zhang, Shengwei Zhang, Lei Li, Qian Lv, Qingyu Kong, Decong Jiang, Hua Ren, Yuhao Jiang, Yongqiang Li, Yan Huang, Wenhua Liu, Peng J Transl Med Research BACKGROUND: Early availability of pathogen identification in urinary tract infections (UTIs) has critical importance in disease management. Metagenomic next-generation sequencing (mNGS) has the potential to transform how acute and serious infections are diagnosed by offering unbiased and culture-free pathogen detection. However, clinical experience with application of the mNGS test is relatively limited. METHODS: We therefore established a MinION-based mNGS pathogens diagnostic platform and evaluated its potential for clinical implementation in UTIs with clinical samples. 213 urine samples from patients with suspected UTIs were included and subjected to mNGS testing using the MinION platform. mNGS results were compared to the gold standard of clinical culture and composite standard of combining clinical testing, confirmatory qPCR testing, and clinical adjudication by doctors. RESULTS: The mNGS exhibited a sensitivity of 81.4% and a specificity of 92.3%, along with a positive predictive value of 96.6%, a negative predictive value of 64.9%, and an overall accuracy of 84.4%, all of which were determined based on the gold standard of routine culture results. When assessed against the composite standard, the sensitivity and specificity both increased to 89.9% and 100%, respectively, while the accuracy rose to 92.4%. Notably, the positive predictive value and negative predictive value also saw improvements, reaching 100% and 76.8%, respectively. Moreover, this diagnostic platform successfully identified dsDNA viruses. Among the 65 culture-negative samples, the viral detection rate reached 33.8% (22/65) and was subsequently validated through qPCR. Furthermore, the automatic bioinformatics pipeline we developed enabled one-click analysis from data to results, leading to a significant reduction in diagnosis time. CONCLUSION: These results demonstrate that the pathogen detection performance of mNGS is sufficient for diagnostic testing in clinical settings. As the method is generally unbiased, it can improve diagnostic testing of UTIs and other microbial infections. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-023-04562-0. BioMed Central 2023-10-27 /pmc/articles/PMC10612365/ /pubmed/37891586 http://dx.doi.org/10.1186/s12967-023-04562-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Wang, Ye Chen, Ting Zhang, Shengwei Zhang, Lei Li, Qian Lv, Qingyu Kong, Decong Jiang, Hua Ren, Yuhao Jiang, Yongqiang Li, Yan Huang, Wenhua Liu, Peng Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection |
title | Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection |
title_full | Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection |
title_fullStr | Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection |
title_full_unstemmed | Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection |
title_short | Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection |
title_sort | clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10612365/ https://www.ncbi.nlm.nih.gov/pubmed/37891586 http://dx.doi.org/10.1186/s12967-023-04562-0 |
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