Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics

Stephen D Bentley, Stephanie W Lo

Research output: Contribution to journalReview articlepeer-review

13 Citations (SciVal)


Vaccines are powerful agents in infectious disease prevention but often designed to protect against some strains that are most likely to spread and cause diseases. Most vaccines do not succeed in eradicating the pathogen and thus allow the potential emergence of vaccine evading strains. As with most evolutionary processes, being able to capture all variations across the entire genome gives us the best chance of monitoring and understanding the processes of vaccine evasion. Genomics is being widely adopted as the optimum approach for pathogen surveillance with the potential for early and precise identification of high-risk strains. Given sufficient longitudinal data, genomics also has the potential to forecast the emergence of such strains enabling immediate or pre-emptive intervention. In this review, we consider the strengths and challenges for pathogen genomic surveillance using the experience of the Global Pneumococcal Sequencing (GPS) project as an early example. We highlight the multifaceted nature of genome data and recent advances in genome-based tools to extract useful information relevant to inform vaccine strategies and treatment options. We conclude with future perspectives for genomic pathogen surveillance.

Original languageEnglish
Pages (from-to)84
JournalGenome Medicine
Issue number1
Publication statusPublished - 17 May 2021

Bibliographical note

The Bill and Melinda Gates Foundation (Investment ID INV-003570)


  • Antigens, Bacterial/genetics
  • Databases, Genetic
  • Disease Susceptibility
  • Genome, Bacterial
  • Genomics/methods
  • Global Health
  • Humans
  • Incidence
  • Pneumococcal Infections/epidemiology
  • Pneumococcal Vaccines/genetics
  • Population Surveillance
  • Serogroup
  • Streptococcus pneumoniae/classification
  • Vaccination/methods
  • Vaccines, Conjugate/immunology


Dive into the research topics of 'Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics'. Together they form a unique fingerprint.

Cite this