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ONT Genomic Epidemiology (Prokaryotic)

 
 
Microsynth's ONT Genomic Epidemiology service offers a specialized analysis pipeline designed for in-depth investigation of prokaryotic genomes. By combining cutting-edge sequencing technologies with advanced bioinformatics, this service provides comprehensive insights into antimicrobial resistance (AMR), virulence factors, and genomic variations.

Features and Benefits


Our ONT Genomic Epidemiology service provides:

  • Extensive Epidemiologic Analysis: Access detailed information about species identity, homologues of resistance and virulence genes, and plasmid presence.
  • Reference-Based Insights: Uncover genomic variations relative to a provided reference sequence.
  • Plasmid Detection and Recovery: Reconstruct plasmid sequences to analyze their roles in resistance and virulence.
  • Advanced Taxonomic Analysis: Determine taxonomic identity with ANI (Average Nucleotide Identity) and MLST (Multi-Locus Sequence Typing), if available.
  • High-Throughput Capabilities: Ideal for genomic epidemiology studies in clinical, environmental, or industrial settings.
 

Workflow

Our streamlined workflow ensures high-quality and reliable results:

DNA Isolation
High-molecular-weight (HMW) DNA is critical for optimal long-read sequencing results. Our protocols handle challenging samples effectively and can incorporate custom isolation procedures as needed.

DNA Library Preparation
Libraries are prepared using the appropriate sequencing kit to optimize sequencing performance.

Sequencing
We recommend >100x read coverage to achieve comprehensive genomic data. Coverage can be adjusted based on project-specific needs.

Bioinformatics Analysis
Our sophisticated genomic epidemiology pipeline includes:

  • De-novo Assembly: Reconstruct the genome from raw sequencing data.
  • Gene Prediction and Annotation: Identify and characterize genes across the genome.
  • Plasmid Detection and Recovery: Reconstruct plasmids where possible for further analysis.
  • Homology Search: Screen for known AMR and virulence genes.
  • Variant Calling: Detect genomic variations relative to a provided reference sequence.
  • Taxonomic Analysis: Determine ANI and conduct MLST analysis (if available in PubMLST).

Results


You will receive detailed and actionable results, including:

Comprehensive Tables and Visualizations:
  • If a reference sequence is provided (e.g., NCBI Accession), results include comparisons similar to our ONT Resequencing service.
  • If no reference genome is provided, a de novo assembly is conducted.


Included Analyses:

  • MLST analysis (if schema available in PubMLST)
  • Plasmid recovery
  • Screening for AMR and virulence genes

 

Turnaround Time


Results delivered within 3 to 7 days of sample receipt.