PneumoTRACE

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Overview

PneumoTRACE Overview

The PneumoTRACE system is designed to provide real-time insights into the epidemiology of pneumococcus. PneumoTRACE uses active sampling of carriage across a broad range of ages, combined with local data on invasive pneumococcal disease and custom analytics, to provide a more complete picture of changes in the frequency of serotypes circulating in the population and causing severe disease. Sampling started in January 2026 and continues on a rolling basis, with reports issued roughly every 6 months.

Pneumococcal carriage prevalence and notable serotype patterns

In this first report, we are sharing data from the first 6 months of sampling, which includes data from ~1500 samples collected January-June 2026. The report includes data on overall pneumococcal carriage prevalence across age groups. As expected, carriage prevalence was ~20-30% in children and ~5-10% in older adults, with 245 pneumococcal-positive samples. Pneumococcal detection was notably more common among individuals who had a virus detected in their sample. Among children, the prevalence was twice as high among children who had a virus detected. Overall carriage positivity was similar across the study period. Explore the data in the ‘Carriage Data’ section.

Despite the small numbers to date, the serotype patterns in carriage have already yielded some intriguing findings. Notably, serotype 19F, which has re-emerged as a cause of IPD, is detected in carriage in infants, toddlers, and adults. This could point towards a need to more effectively suppress carriage in children. You can explore the data in the ‘Serotype patterns in carriage’ section.

Nowcasts of IPD

An important goal of PneumoTRACE is to provide up-to-date estimates of serotype distributions in IPD. We do this in two complementary ways. First, we generate time series forecasts using only the CDC’s reported IPD data, stratified by age and serotype. Based on this, we also estimate what proportion of the IPD cases in each year could be prevented by a number of current and future vaccines. Complementary to the time series modeling, we use data on serotype-specific carriage prevalence among children, combined with a published statistical approach for inferring serotype patterns in IPD from carriage data. In the current report, we compare these estimates head-to-head, which highlights the areas of agreement and disagreement. In future reports as we accrue more data, we will formally synthesize these estimates to have a more robust nowcast, and we will generate additional nowcasts based on the adult carriage data. Explore the data in the ‘Nowcasts of IPD serotype patterns’ section

What’s next

We are excited by the data we have been able to collect so far and are continuing to collect samples at a steady rate. Alongside sample collection, we are continuing to refine our serotyping methods and statistical approach, which will inform additional analytics in future reports. In parallel to PneumoTRACE, we have started collecting samples among children <10 years for an NIH-funded study, which will allow us to further boost the numbers of serotyped samples for future reports. We are continuing to work with our partners at Yale New Haven Hospital to transfer clinical metadata, including the reason for the visit, race/ethnicity, and other demographic information, as well as vaccine history. We will issue an update to this report as soon as those supplemental data are available.

We expect the next complete report will be released in January 2027.

Feel free to reach out to Dr. Weinberger (daniel.weinberger@yale.edu) with any questions or feedback.