Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing.
Anti-Bacterial Agents
/ pharmacology
Bacterial Typing Techniques
/ methods
Databases, Factual
Drug Resistance, Multiple, Bacterial
/ drug effects
Genomics
Humans
Microbial Sensitivity Tests
/ methods
Molecular Epidemiology
Neisseria gonorrhoeae
/ drug effects
Phenotype
Sensitivity and Specificity
Streptococcus pneumoniae
/ drug effects
Journal
Nature microbiology
ISSN: 2058-5276
Titre abrégé: Nat Microbiol
Pays: England
ID NLM: 101674869
Informations de publication
Date de publication:
03 2020
03 2020
Historique:
received:
06
08
2019
accepted:
06
12
2019
pubmed:
12
2
2020
medline:
21
7
2020
entrez:
12
2
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 32042129
doi: 10.1038/s41564-019-0656-6
pii: 10.1038/s41564-019-0656-6
pmc: PMC7044115
mid: EMS85138
doi:
Substances chimiques
Anti-Bacterial Agents
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
455-464Subventions
Organisme : NIAID NIH HHS
ID : R01 AI106786
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI046645
Pays : United States
Organisme : Medical Research Council
ID : MR/N013956/1
Pays : United Kingdom
Organisme : Department of Health
ID : RP-PG-0514-20018
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : R01 AI128344
Pays : United States
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