AdventHealth Streptococcus pneumoniae Surveillance Initiative. Preliminary Results

Streptococcus pneumoniae remains a major cause of morbidity and mortality worldwide. Despite widespread use of pneumococcal conjugate vaccines (PCVs), this pathogen is responsible for a significant burden of disease in children under 5 and adults over 65, particularly through pneumonia, meningitis, and bacteremia. According to the CDC, pneumococcal disease continues to result in over 150,000 hospitalizations in the United States annually, with invasive pneumococcal disease (IPD) leading to nearly 3,250 deaths per year.

The Forgotten Role of Serotyping and Genotyping

Monitoring the serotype and genotype of S. pneumoniae is essential for evaluating vaccine effectiveness, understanding transmission dynamics, and detecting capsular switching, a phenomenon where strains acquire new serotypes, sometimes evading vaccine-induced immunity, but serotype testing is gone from routine clinical labs. Serotype data informs whether infections are caused by vaccine-covered strains or represent breakthroughs, while sequence types (STs) provide insight into the clonal spread, antimicrobial resistance patterns, and hypervirulence potential of circulating strains. Serotype data can guide providers in post-infection management decisions, such as recommending a vaccine booster. More importantly, it provides the necessary context to help patients and parents understand why an infection may occur even after vaccination.

The AdventHealth Approach

At AdventHealth Central Florida Orlando Microbiology Lab, we have integrated next-generation sequencing (NGS) using Oxford Nanopore Technologies into routine diagnostics for invasive pneumococcal isolates, including respiratory sources. All isolates are first cultured, then sequenced, and analyzed via the Pasteur MLST database.

• For pediatric patients (<=14 years): all isolates from blood, CSF, and respiratory specimens undergo NGS-based serotyping and genotyping.
• For adult patients (>14 years): sequencing is limited to isolates from blood and CSF.

The turnaround time from isolate to reported result is just 24 hours, with data directly published into the Epic system, including both serotype and sequence type (ST). Following the identification of the organism, antimicrobial susceptibility testing and NGS-based serotyping/genotyping are performed in sequence.

Preliminary Findings

A total of 20 S. pneumoniae isolates have been analyzed since March 2025:

• Pediatric group (<=14 years): 6 isolates
• Adult group (>14 years): 14 isolates

• Blood: 15 isolates
• Respiratory: 3 isolates (pediatrics only)
• CSF: 2 isolates

Age-stratified visualization shows the highest burden in very young children but predominantly in older adults, demonstrating the classic bimodal distribution of S. pneumoniae disease.

Serotype Distribution and Vaccine Coverage

We identified a total of 11 distinct serotypes among the isolates:

• 19A (4 isolates)
• 35B (3 isolates)
• 15BC, 19F, 3 (each seen in 2 isolates)
• 15A, 16F, 22F, 38, 8, 9N, 9V (each seen in 1 isolate)

Vaccine Coverage Analysis: 

• PCV13-covered serotypes (1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, 23F): 4/11 serotypes detected in our dataset (36.4%)
• PCV15-covered serotypes (PCV13 serotypes plus 22F, 33F): 5/11 serotypes detected (45.5%)
• PCV20-covered serotypes (PCV15 serotypes plus 8, 10A, 11A, 12F, 15B): 6/11 serotypes detected (54.5%)
• PPSV23-covered serotypes (PCV20 serotypes plus 2, 9N, 17F, 20): 7/11 serotypes detected (63.6%)
• Not covered by any FDA-approved vaccines: 4/11 serotypes detected (36.4%)

These findings emphasize the rise of non-vaccine serotypes, suggesting vaccine escape or serotype replacement. Notably, 16F and 35B, which are absent from PCV20 and PPSV23, were prevalent.

Sequence Type (ST) and Serotype Correlation

Using Pasteur MLST analysis, several notable correlations were observed:

• ST320: Linked to 19A, known for multidrug resistance (MDR)
• ST156: Associated with 35B, historically linked to clonal expansion
• ST393: Correlated with serotype 38

These associations are crucial, as ST320 and ST156 have been implicated in prior studies as MDR or hypervirulent lineages. The knowledge of the presence of these strains regionally circulating is the waking call for reinforcing and improving our laboratory approach to S. pneumoniae workup and clinical management. 

This heatmap illustrates clonal distribution, showing which STs dominate specific serotypes, aiding in early detection of potential outbreak clones or capsular switching events.

Conclusion and Implications for Surveillance

The prevalence of serotype 19A and 35B in our dataset highlights important epidemiological and clinical dynamics. Serotype 19A, once rare, emerged as a dominant strain following early pneumococcal vaccine introductions and has been associated with vaccine breakthrough infections, especially prior to the inclusion of 19A in PCV13. Despite now being covered in PCV13, its continued presence, along with its association with multidrug-resistant ST320, reinforces its relevance in both pediatric and adult cases. In contrast, serotype 35B is not covered by PCV13, PCV15, or PCV20, nor by PPSV23, and has been increasingly associated with the clonal lineage ST156, which has also demonstrated resistance patterns in multiple studies. Its rising detection suggests capsular switching or selection pressure favoring non-vaccine serotypes, a concerning trend in the post-vaccine era.

Several serotypes in our analysis, such as 15A, 16F, and 38, are not currently covered by any FDA-approved pneumococcal vaccines. These strains, although historically considered of lower virulence, are now more frequently detected in clinical isolates, suggesting an ecological shift following widespread PCV implementation. Their presence emphasizes the importance of ongoing genomic surveillance to inform future vaccine development. These emerging non-vaccine serotypes could eventually become more prevalent or acquire virulence and resistance traits through recombination or clonal expansion. Therefore, tracking their circulation at the molecular level is essential to staying ahead of pneumococcal evolution and ensuring vaccines remain aligned with real-world epidemiology.

Routine sequencing of S. pneumoniae provides critical insights into the evolving landscape of pneumococcal disease. By integrating rapid NGS with MLST and serotyping, we enable real-time surveillance that can inform clinical decisions, infection control, and public health interventions.

The growing prevalence of non-vaccine serotypes underscores the need for updated vaccines and continuous monitoring. Additionally, genotype data helps detect hypervirulent or resistant clones, supporting antimicrobial stewardship and outbreak preparedness.

Our work at AdventHealth is just beginning...

This work wouldn't be possible without the motivated and dedicated team of microbiologists at AdventHealth, Daniel Navas , Hershey Jade Miraballes, MLS (ASCPi) , Loong Fai Ho , Dustin Evans .

References:

1. CDC. Pneumococcal Disease Surveillance and Reporting. https://www.cdc.gov/pneumococcal/index.html
2. European Centre for Disease Prevention and Control. https://www.ecdc.europa.eu/en/pneumococcal-disease/facts
3. CLSI M45 Guidelines – Streptococcus pneumoniae AST Reporting
4. Pasteur MLST Database: https://bigsdb.pasteur.fr
5. Oligbu et al. "Effectiveness of pneumococcal vaccines on invasive pneumococcal disease in high-income settings." Lancet Infect Dis. 2019
6. Moore MR et al. “Population snapshot of emergent pneumococcal serotype 19A in the United States.” J Infect Dis. 2008
7. Chochua S et al. “Bacterial Genomics Reveal the Emergence of Multidrug-Resistant ST156 Serotype 35B Pneumococci.” mBio. 2017

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