Episode 43: Why use genomics in an epidemic? with Sam Sheppard

In this episode of the microbinfie podcast, Sam Sheppard explores the evolution of molecular epidemiology, highlighting how genomic technologies have transformed our understanding of pathogen strain identification and outbreak tracking.

Presenter: Sam Sheppard, University of Bath
Event: ARTICnetwork & CLIMB-BIG-DATA Workshop on COVID-19 Data Analysis

Key Points

• Use of Genomics in Epidemics:
  Sam Sheppard discussed the importance of integrating genomics in the study and management of epidemics, focusing on its application in understanding COVID-19.

• Background on Typing Schemes:
  He provided an overview of different typing schemes that can be used for bacterial and viral pathogens and their relevance in tracking the spread of diseases.

• Sequencing Methods:
  The presentation covered various sequencing techniques, highlighting their benefits and constraints, and how these can be applied to study pathogens at a genomic level.

• Challenges in Genomic Data Analysis:
  Sheppard addressed the issues faced while analyzing large volumes of genomic data. This includes data storage, computational requirements, and the complexity of interpreting results.

Resources

• Sheppard Lab Website
• ARTIC and CLIMB-BIG-DATA Joint Workshop

These resources offer further insights into the applications of genomics in monitoring and controlling emerging infectious diseases.

Extra notes

• Microbial Typing and Strain Differentiation:

  • The podcast discusses various methodologies for distinguishing between microbial strains, emphasizing the need to differentiate pathogenic strains from commensal organisms.
  • Traditional typing techniques include serotyping, phage typing, restriction fragment length polymorphism (RFLP), and pulse-field gel electrophoresis (PFGE).
  • Multi-locus sequence typing (MLST) is highlighted as a method where usually seven genes are sequenced to differentiate between strains.

• Evolution of Typing Approaches:

  • The transition from older methods to genomic epidemiology has been driven by decreasing sequencing costs, making whole-genome sequencing the preferred approach for typing and tracking pathogen strains.

• Current Sequencing Technologies:

  • The use of Illumina sequencing platforms, particularly the MiSeq, is commonplace in many laboratories, enabling more accessible genomic sequencing and data sharing across labs.
  • The podcast notes the "democratization" and "mobilization" of sequencing with the advent of portable Oxford Nanopore sequencers, facilitating in-field or small-space laboratory sequencing operations.

• Challenges and Collaboration:

  • The complexity of analyzing and interpreting vast amounts of genome data represents a significant challenge.
  • The podcast mentions collaborative efforts, such as the Climb platform, which offer shared computational resources and support for managing large genomic datasets.

• Data Sharing and Standardization:

  • Genome sequencing allows for easier data sharing between laboratories globally, facilitated by open-access databases.
  • The importance of standardized analyses for comparative genomic epidemiology was emphasized.

• Applications in Molecular Epidemiology:

  • Genomic epidemiology aids in understanding the relationships between strains, tracking outbreaks, and hypothesizing about pathogen evolution.
  • Insights gained can be applied to comprehend the transmission and emergence of new strains, including those related to significant pathogens like coronaviruses.

• Technical and Analytical Infrastructure:

  • The session discusses advancements in data infrastructure and computational power, enabling the use of genomic epidemiology to map the spread and evolution of pathogens with greater accuracy.

Key Points

1. Evolution of Microbial Typing

• Traditional typing methods included serotyping, phage typing, and multi-locus sequence typing
• Older techniques were limited by resolution and complexity of strain differentiation
• Decreasing sequencing costs have made whole-genome sequencing the preferred approach

2. Technological Democratization of Genomic Sequencing

• Shift from centralized sequencing services to community and field-based sequencing
• Illumina MiSeq platforms widely adopted in laboratories worldwide
• Oxford Nanopore technologies enabling portable, mobile sequencing capabilities

3. Genomic Epidemiology Applications

• Enables standardized data sharing and comparative analysis across laboratories
• Supports understanding of pathogen transmission, evolution, and outbreak dynamics
• Provides framework for hypothesis generation about strain relationships and emergence

Take-Home Messages

• Whole-genome sequencing has revolutionized molecular epidemiology
• Collaborative platforms like CLIMB enable large-scale genomic data analysis
• Genomic technologies provide unprecedented insights into pathogen evolution