William Hanage, United States of America
Harvard T.H. Chan School of Public Health Center for Communicable Disease DynamicsPoster Author Of 1 e-Poster
RAPID INFERENCE OF ANTIBIOTIC RESISTANCE AND SUSCEPTIBILITY BY GENOMIC NEIGHBOR TYPING
Author Of 2 Presentations
SPATIAL DISTANCE IS A KEY DETERMINANT OF PNEUMOCOCCAL STRAIN SHARING AND THE SUSTAINED CARRIAGE OF SHARED STRAINS (ID 957)
- Madikay Senghore, United States of America
- Chrispin Chaguza, United Kingdom
- Ebrima Bojang,
- Peggy-Estelle Tientcheu,
- Rowan Bancroft, Côte d'Ivoire
- Stephanie Lo, United Kingdom
- Rebecca Gladstone, Norway
- Lesley McGee, United States of America
- Archibald Worwui,
- Ebenezer Foster-Nyarko,
- Fatima Ceesay,
- Catherine Okoi,
- Keith P. Klugman, United States of America
- Robert F Breiman, United States of America
- Richard Adegbola,
- Stephen D. Bentley, United Kingdom
- William Hanage, United States of America
- Martin Antonio, Gambia
- Brenda Kwambana-Adams, United Kingdom
RAPID INFERENCE OF ANTIBIOTIC RESISTANCE AND SUSCEPTIBILITY BY GENOMIC NEIGHBOR TYPING (ID 1213)
Abstract
Background
Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empiric antibiotic therapy. However, traditional molecular epidemiology does not typically occur on a timescale that could impact patient treatment and outcomes.
Methods
We developed a method called ‘genomic neighbor typing’ for inferring the phenotype of a bacterial sample by identifying its closest relatives in a database of genomes with metadata. We implemented this with rapid k-mer matching, which can be used on Oxford Nanopore MinION data and run in real time. We adopted the method for pneumococcus using a database of 616 genomes from a carriage study in Massachusetts children and five antibiotics. Finally, we evaluated the method using isolates and metagenomes from geographically distinct regions.
Results
We show that genomic neighbor typing can infer antibiotic resistance and susceptibility of S. pneumoniae isolates within five minutes of sequencing starting (sens/spec 91%/100%) and for clinical metagenomic sputum samples within four hours of sample collection (75%/100%). We also show how the method can be adopted for custom species and drugs.
Conclusions
Genomic neighbor typing has wide application to pathogen surveillance and may be used to greatly accelerate appropriate empirical antibiotic treatment.