期刊
NATURE MICROBIOLOGY
卷 5, 期 3, 页码 455-+出版社
NATURE PORTFOLIO
DOI: 10.1038/s41564-019-0656-6
关键词
-
类别
资金
- Bill & Melinda Gates Foundation [GCGH GCE OPP1151010]
- NIH-National Institute of Allergy and Infectious Diseases [R01 AI106786-05]
- Canadian Institutes of Health Research [MFE 152448]
- NSF (GRFP)
- David and Lucile Packard Foundation
- National Institute for Health Research (NIHR) under its Programme Grants for Applied Research Programme [RP-PG-0514-20018]
- UK Antimicrobial Resistance Cross Council Initiative [MR/N013956/1]
- Rosetrees Trust [A749]
- Biotechnology and Biological Sciences Research Council (BBSRC) Institute Strategic Programme Microbes in the Food Chain [BB/R012504/1, BBS/E/F/000PR10348, BBS/E/F/000PR10349]
- NIH [R01 AI46645]
- University of East Anglia
- Oxford Nanopore Technologies
- Research Computing Group at Harvard Medical School
- Research Computing Group at Harvard Faculty of Arts and Sciences
- BBSRC [BBS/E/F/000PR10348] Funding Source: UKRI
- MRC [MR/N013956/1] Funding Source: UKRI
- National Institutes of Health Research (NIHR) [RP-PG-0514-20018] Funding Source: National Institutes of Health Research (NIHR)
Genomic neighbour typing can be used to infer the antimicrobial susceptibility and resistance of a bacterial sample based on the genomes of closest relatives. Combined with MinION sequencing, it can rapidly determine microbial resistance for clinical samples within 4 h. Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empirical antibiotic therapy. However, traditional molecular epidemiology does not typically occur on a timescale that could affect patient treatment and outcomes. Here, we present a method called 'genomic neighbour typing' for inferring the phenotype of a bacterial sample by identifying its closest relatives in a database of genomes with metadata. We show that this technique can infer antibiotic susceptibility and resistance for both Streptococcus pneumoniae and Neisseria gonorrhoeae. We implemented this with rapid k-mer matching, which, when used on Oxford Nanopore MinION data, can run in real time. This resulted in the determination of resistance within 10 min (91% sensitivity and 100% specificity for S. pneumoniae and 81% sensitivity and 100% specificity for N. gonorrhoeae from isolates with a representative database) of starting sequencing, and within 4 h of sample collection (75% sensitivity and 100% specificity for S. pneumoniae) for clinical metagenomic sputum samples. This flexible approach has wide application for pathogen surveillance and may be used to greatly accelerate appropriate empirical antibiotic treatment.
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