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Related Experiment Video

Updated: May 24, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based

Samuel T Horsfield^1,2, Basil C T Fok³, Yuhan Fu³

¹MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W12 0BZ, United Kingdom; shorsfield@ebi.ac.uk.

Genome Research

|March 4, 2025

Summary

This summary is machine-generated.

Nanopore adaptive sampling (NAS) targeting the capsular biosynthetic locus (CBL) enables accurate Streptococcus pneumoniae serotyping, even with multiple strains. A new pangenome-graph algorithm, GNASTy, enhances novel serotype detection.

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Area of Science:

Microbiology and Genomics
Vaccine Development and Epidemiology

Background:

Serotype surveillance of Streptococcus pneumoniae (pneumococcus) is crucial for assessing vaccine effectiveness.
Current serotyping methods struggle with detecting multiple pneumococcal strains (co-carriage) and identifying new serotypes.

Purpose of the Study:

To develop a scalable, portable, and accurate method for direct pneumococcal serotyping from complex samples.
To overcome limitations of existing methods in detecting co-carriage and novel serotypes.

Main Methods:

Utilized nanopore adaptive sampling (NAS) for real-time, on-sequencer DNA enrichment.
Targeted the pneumococcal capsular biosynthetic locus (CBL) for specific serotype identification.
Developed and evaluated a novel pangenome-graph algorithm, GNASTy, for enhanced NAS sensitivity.

Main Results:

NAS targeting the CBL demonstrated high specificity and sensitivity for S. pneumoniae detection.
NAS significantly improved CBL coverage and accurately quantified serotype prevalence in co-carriage samples.
GNASTy outperformed linear alignment-based NAS in detecting serotypes absent from the target database.

Conclusions:

The developed NAS and GNASTy methods offer an improved approach for pneumococcal serotype surveillance.
These methods are fast, accurate, and feasible for low-resource settings, aiding novel serotype discovery.
Targeted enrichment using GNASTy optimizes serotype surveillance in complex clinical samples.