Invasive pneumococcal disease

National insight into the genomic epidemiology of Invasive Pneumococcal Disease

Invasive pneumococcal disease (IPD) has been nationally notifiable since 2001 and is monitored through the Enhanced Invasive Pneumococcal Disease Surveillance Program (EIPDSP), part of the National Notifiable Diseases Surveillance System. National surveillance is overseen by the Enhanced IPD Surveillance Working Group, a subcommittee of the Communicable Diseases Network of Australia. Key aims of the surveillance is to inform the prevention and management of IPD, especially the nationally coordinated immunisation program in children and adults. National genomic analysis of IPD cases is an opportunity to further enhance and strengthen this program.
 
A range of multi-valent vaccines are effective preventative measures for pneumococcal disease, but also impose a selective pressure on both pathogenic and commensal bacterial populations, providing niches for non-vaccine serotypes to proliferate. Due to the genomic plasticity of the organism, monitoring of capsular switching events and serotype replacement is needed to ensure continued effectiveness of vaccination programs. Additionally, any systemic antibiotic use, regardless of the target pathogen, further adds selective pressure on Streptococcus pneumoniae as a successful coloniser of the respiratory tract, and may result in the emergence and establishment of vaccine evasive antibiotic resistant strains.
 
Whole genome sequencing has the capability of providing high-resolution information on the phylogenetic relationship of isolates to contextualise serotype data and unravel the evolutionary dynamics of pneumococcal populations, while simultaneously providing a comprehensive genome-wide view of AMR determinants. Full realisation of the value of a genomics informed surveillance system would be through integration with key epidemiological data sources, such the Australian Immunisation Registry (AIR), NINDSS and electronic medical records.

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Project Aims

Specific aims are to: Develop a framework to inform the best stategy for national genomic surveillance of IPD and integration into AusTrakka

1. Implement harmonised national analysis methodologies in AusTrakka

2. Undertake national comprehensive snapshot over a 12-month period to define the genomic epidemiology of IPD and contextualisation of Australian cases globally.

3. Explore integration models with existing national epidemiological surveillance systems.