期刊
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
卷 72, 期 1, 页码 104-114出版社
OXFORD UNIV PRESS
DOI: 10.1093/jac/dkw397
关键词
-
资金
- University of East Anglia
- Rosetrees Trust [A749]
- Norwich Research Park Translational Fund
- MRC [MR/N013956/1] Funding Source: UKRI
- Medical Research Council [MR/N013956/1] Funding Source: researchfish
- Rosetrees Trust [M468] Funding Source: researchfish
Objectives: The introduction of metagenomic sequencing to diagnostic microbiology has been hampered by slowness, cost and complexity. We explored whether MinION nanopore sequencing could accelerate diagnosis and resistance profiling, using complicated urinary tract infections as an exemplar. Methods: Bacterial DNA was enriched from clinical urines (n=10) and from healthy urines 'spiked' with multiresistant Escherichia coli (n=5), then sequenced by MinION. Sequences were analysed using external databases and bioinformatic pipelines or, ultimately, using integrated real-time analysis applications. Results were compared with Illumina data and resistance phenotypes. Results: MinION correctly identified pathogens without culture and, among 55 acquired resistance genes detected in the cultivated bacteria by Illumina sequencing, 51 were found by MinION sequencing directly from the urines; with three of the four failures in an early run with low genome coverage. Resistance-conferring mutations and allelic variants were not reliably identified. Conclusions: MinION sequencing comprehensively identified pathogens and acquired resistance genes from urine in a timeframe similar to PCR (4 h from sample to result). Bioinformatic pipeline optimization is needed to better detect resistances conferred by point mutations. Metagenomic-sequencing-based diagnosis will enable clinicians to adjust antimicrobial therapy before the second dose of a typical (i. e. every 8 h) antibiotic.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据