The science behind the shift: how ESR informed pneumococcal vaccine change

In December 2022, a critical shift in New Zealand’s National Immunisation Programme (NIP) took place—one that directly stemmed from work conducted by the Institute of Environmental Science and Research (ESR) on behalf of the Ministry of Health. ESR’s findings on the resurgence of invasive pneumococcal disease (IPD), particularly the rise of a serotype known as 19A, highlighted a concerning gap in protection within the existing childhood vaccination schedule.

The compelling evidence from ESR’s Health Intelligence and Surveillance Team, alongside the Invasive Pathogens Laboratory, allowed the Ministry of Health to make a strong case to the Pharmaceutical Management Agency (PHARMAC), which led to the reinstatement of the PCV13 vaccine. This move aimed to close the immunity gap left by earlier vaccine changes, addressing the rise of 19A head-on.

But how did ESR’s teams uncover this issue and what does this change mean for the future of childhood vaccinations in New Zealand? We take a closer look at the science, the impact and the decisions that shaped this crucial policy shift.

A global killer

Pneumococcal disease, caused by the bacteria Streptococcus pneumoniae (commonly called pneumococcus), was once responsible for nearly all cases of pneumonia before antibiotics became available. While drugs have helped reduce its impact, pneumococcus is still the leading cause of community-acquired pneumonia worldwide, especially in the colder months. Invasive pneumococcal disease (IPD) refers to the most severe end of the disease spectrum caused by this bacterium, including bloodstream infections and meningitis. Despite vaccines, IPD continues to take the lives of at least 300,000 children under five-years-old every year globally.

How the pneumococcal vaccination changed over time

There are many different types of pneumococcal bacteria (known as serotypes), but about 20 are responsible for most cases of serious illness. To tackle this, scientists develop vaccines to target specific serotypes.

These vaccination programs have played a key role in managing pneumococcal disease. The pneumococcal conjugate vaccine (PCV) was introduced in the early 2000s with PCV7, covering seven serotypes. This was followed by PCV10, which expanded coverage to 10 serotypes, and later PCV13, which further provided broadened protection.

In New Zealand, PCV7 was added to childhood immunisation schedules in 2008, followed by PCV10 in 2011 and PCV13 in 2014. However, in 2017, New Zealand switched back to PCV10, which meant losing reduced protection against some serotypes, including 19A. These vaccine shifts had a major impact on pneumococcal disease trends in the country.

The rise of 19A

In 2021, scientists at ESR noticed a rising number of 19A cases, even though overall cases of IPD remained low. Sometimes, when a vaccine lowers the incidence of disease from common serotypes, other serotypes not included in that vaccine become more common (a phenomenon called serotype replacement). In particular, cases of IPD in children under two-years had markedly increased, driven by increasing cases of 19A.[1]

New Zealand’s situation stands out

ESR researchers compared pneumococcal diversity in New Zealand and Australia from 2009 to 2022 using a measurement called the Simpson’s Diversity Index (SDI). This is similar to how scientists measure biodiversity—a lower SDI means one type of bacteria is taking over, which is a sign of an unhealthy microbial balance and a higher risk of disease.[2]

In New Zealand, pneumococcal diversity has steadily decreased since 2017, likely partly due to frequent vaccine schedule changes. By 2022, diversity was at its lowest, especially in children under two and adults over 65, highlighting the need for a more stable vaccination strategy.

A unique finding

Further research by ESR’s invasive pathogens lab revealed a surprising discovery when analysing pneumococcal samples from 2016 to 2022. The most common strain of serotype 19A in New Zealand was ST-2062, a strain not commonly seen in other countries.   

This was particularly concerning, because ST-2062 has been previously linked to invasive disease among people carrying the 19A bacteria. Its rise suggests that New Zealand may be facing unique public health risks compared to other nations.[3]

Conclusion

The teams at ESR have continued to monitor the impact of PCV13’s reintroduction. Since its return, cases of IPD caused by serotype 19A in children have significantly declined.

As seen with previous PCV vaccines, a similar decline in 19A-related disease is expected in older age groups over the coming years. However, with the potential rise of other serotypes and ongoing vaccine advancements, continued surveillance by ESR remains crucial. Monitoring that will help guide future vaccine strategies and public health decisions.