When PHF Science's health intelligence and surveillance team noticed a particular bacterial strain driving invasive pneumococcal disease in under-fives, they quickly built an evidence case that was used to change the national immunisation schedule – and cut childhood cases by more than half.
In late 2020, while the number of people contracting the flu and other notifiable diseases were tracking downward during the strict border closures due to Covid, scientist Dr Andy Anglemyer, senior epidemiologist at PHF Science, noticed something unusual.
He spotted a small increase in the number of children with invasive pneumococcal disease – among children all vaccinated against it. It was a faint signal that would have been easy to dismiss as a blip, but Anglemyer kept an eye on what he describes as “small numbers acting unusually”, raised it early with the Ministry of Health and infectious disease researchers, and kept tracking it as new cases came in.
Invasive pneumococcal disease is the most serious form of infection caused by the bacteria that causes pneumonia. It can cause meningitis, blood infections, and renal failure. Elderly and infants are most at risk, and it is the leading cause of vaccine-preventable deaths in children under five worldwide.
Unfortunately for the children affected and their families, cases continued to climb. The evidence became compelling and a strong collaboration sprang into action, recently recognised as winner of the ‘Collaboration for Impact’ award in the Science New Zealand Awards 2026. The PHF Science team worked with the Ministry of Health’s former Communicable Diseases team, Public Health Agency, National Public Health Service (Health NZ), Pharmac[AM1.1], Universities of Otago and Auckland and infectious disease specialists, and provided regular updates to the Immunisation Advisory Centre.
The compelling evidence led to urgent changes to the National Immunisation Programme, allowing the Ministry of Health to make a strong case to Pharmac to reinstate a broader coverage vaccine (PCV13) in December 2022.
The results were dramatic: invasive pneumococcal disease cases in under-5s dropped by more than 50% within two years. For Māori and Pasifika children, invasive pneumococcal disease caused by vaccine-preventable bacteria dropped by around 70%. This prevented an estimated three dozen hospitalisations for children under 5. Reduced disease in older age groups is anticipated over the coming years.
Anglemyer describes watching the numbers come down as a career highlight: “To see a vaccine working in real time is really cool. We learn a lot from textbooks and theories, we know that after vaccination, a population will reach herd immunity, and you'll see drops in disease. But this wasn't theory. This was empirical data looking at patients, realising that not only were we seeing a drop in numbers, but also that meant a drop in hospitalisations, morbidity, pain and life struggles, which was just awesome to see.
“That's job satisfaction.”
The Ministry of Health funds PHF Science to undertake surveillance of vaccine-preventable diseases, including invasive pneumococcal disease, to ensure the current vaccine matches the circulating strains. For invasive pneumococcal disease, PHF Science serotypes 80–90% of cases, runs whole-genome sequencing, and publishes a monthly dashboard.
Dr Harriette Carr, Deputy Director of Public Health, notes the importance of our networked and collaborative health system.
“This is a great example of the health system utilising the tools and levers available to ensure the best outcomes for our communities, from legislation for notifiable diseases, science and evidence to policy, funding and procurement.”
Most invasive pneumococcal disease is caused by about 20 different serotypes of pneumococcal bacteria. Between 2017 and December 2022, children in New Zealand had been vaccinated with a narrower pneumococcal vaccine targeting ten serotypes (PCV10).
This meant serotype 19A was no longer adequately covered – and had room to spread. (When a serotype that is not covered by a vaccine spreads, this is called serotype replacement, a known and monitored feature of vaccination programmes worldwide.) Within a few years, serotype 19A had taken hold, and dominated infections among New Zealand children.
PHF Science conducted genomic sequencing to identify the specific strain of bacteria within serotype 19a as ST-2062, which is resistant to penicillin and known to cause more illness. This finding is globally unique to New Zealand; this strain was not observed regularly in other countries that shifted from the PCV13 vaccine to PCV10.
The research team also found that serotype diversity for children under the age of two in NZ in 2022 was much lower than in other high-income countries since the early 2000s, a potential risk for increasing disease.
Because vaccines can have such locally unique consequences, ongoing surveillance is critical. Two serotypes (8 and 22F) are now being monitored, both covered by an even broader vaccine, PCV20, which Australia recently adopted.