期刊
NATURE BIOTECHNOLOGY
卷 37, 期 7, 页码 783-+出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/s41587-019-0156-5
关键词
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资金
- National Institute for Health Research (NIHR) under its Program Grants for Applied Research Program [RP-PG-0514-20018]
- UK Antimicrobial Resistance Cross Council Initiative [MR/N013956/1]
- Rosetrees Trust [A749]
- University of East Anglia
- Oxford Nanopore Technologies
- Biotechnology and Biological Sciences Research Council (BBSRC) Institute Strategic Programme Microbes in the Food Chain [BB/R012504/1]
- MRC Doctoral Antimicrobial Research Training (DART) Industrial CASE Programme [MR/R015937/1]
- BBSRC [BB/N023196/1, BB/CSP17270/1]
- UK Medical Research Council [MR/L015080/1]
- [BBS/E/F/000PR10348]
- [BBS/E/F/000PR10349]
- National Institutes of Health Research (NIHR) [RP-PG-0514-20018] Funding Source: National Institutes of Health Research (NIHR)
- BBSRC [BBS/E/T/000PR9818, BBS/E/T/000PR6193, BB/N023196/1, BBS/E/T/000PR9817, BB/R022445/1, BBS/E/T/000PR5885, BBS/E/F/000PR10348] Funding Source: UKRI
- MRC [MR/N013956/1] Funding Source: UKRI
The gold standard for clinical diagnosis of bacterial lower respiratory infections (LRIs) is culture, which has poor sensitivity and is too slow to guide early, targeted antimicrobial therapy. Metagenomic sequencing could identify LRI pathogens much faster than culture, but methods are needed to remove the large amount of human DNA present in these samples for this approach to be feasible. We developed a metagenomics method for bacterial LRI diagnosis that features efficient saponin-based host DNA depletion and nanopore sequencing. Our pilot method was tested on 40 samples, then optimized and tested on a further 41 samples. Our optimized method (6 h from sample to result) was 96.6% sensitive and 41.7% specific for pathogen detection compared with culture and we could accurately detect antibiotic resistance genes. After confirmatory quantitative PCR and pathobiont-specific gene analyses, specificity and sensitivity increased to 100%. Nanopore metagenomics can rapidly and accurately characterize bacterial LRIs and might contribute to a reduction in broad-spectrum antibiotic use.
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