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Sequencing of mRNA from Whole Blood using Nanopore Sequencing
Published on: June 3, 2019
Genomic outbreak investigation of biosafety-level-3 pathogens using nanopore sequencing
Christine Francesca Thomas1,2, Hanka Brangsch1, Herbert Tomaso1
1Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany.
Microbial Genomics
|June 30, 2026
Summary
Oxford Nanopore Technologies (ONT) sequencing, especially with assembly-based SNP calling, reliably analyzes outbreaks of dangerous, low-diversity bacteria. This promising alternative offers high-resolution genotyping for infectious disease control.
Area of Science:
- Genomics and Bioinformatics
- Infectious Disease Epidemiology
- Microbial Pathogenesis
Background:
- Accurate outbreak analysis is crucial for controlling infectious diseases.
- Short-read Illumina sequencing is standard, but Oxford Nanopore Technologies (ONT) offers portability and real-time data.
- ONT's accuracy for SNP detection and cgMLST in high-containment pathogens needs characterization.
Purpose of the Study:
- Evaluate ONT sequencing for outbreak analysis of four biosafety-level-3 (BSL-3) bacterial species: *Bacillus anthracis*, *Brucella* spp., and *Francisella tularensis*.
- Compare ONT's SNP calling and cgMLST performance against existing Illumina data and epidemiological outbreaks.
- Assess the utility of different ONT analytical strategies (PACU, clair3, snippy) for bacterial genotyping.
Main Methods:
- Selected BSL-3 bacterial strains from defined outbreaks with prior Illumina data.
- Evaluated three SNP calling strategies: PACU, clair3, and assembly-based snippy.
- Performed core genome multilocus sequence typing (cgMLST) to compare genotyping resolution between ONT and Illumina.
Main Results:
- The assembly-based snippy approach yielded the highest F1 scores (0.96-0.99) for SNP calling across all species.
- Read-based callers (PACU, clair3) showed minor discrepancies, particularly with *F. tularensis* due to homopolymeric regions.
- cgMLST demonstrated high concordance between ONT and Illumina for *Brucella* spp., but greater variability for *Ba. anthracis* and *F. tularensis*.
Conclusions:
- ONT sequencing, particularly with assembly-based SNP calling, provides reliable outbreak analysis for highly pathogenic, low-diversity bacteria.
- Challenges exist for specific species and genomic features, but ONT is a viable alternative for high-resolution bacterial genotyping.
- ONT facilitates rapid and portable pathogen surveillance, enhancing infectious disease outbreak response capabilities.
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