Strain Level Streptococcus Colonization Patterns during the First Year of Life.

Area of Science:

• Microbiology
• Genomics
• Vaccinology

Background:

• Pneumococcal pneumonia mortality remains high in infants in developing countries despite pneumococcal conjugate vaccine (PCV) implementation.
• The nasopharyngeal (NP) microbiome plays a crucial role in infant health and susceptibility to infections.

Purpose of the Study:

• To characterize the nasopharyngeal microbiome during the first year of life in infants from the Philippines and South Africa.
• To develop and apply informatic tools for identifying Streptococcus species and Streptococcus pneumoniae serotypes from metagenomic data.
• To investigate co-colonization dynamics and identify virulence/drug resistance elements in the infant NP microbiome.

Main Methods:

• Utilized lytA qPCR assay for Streptococcus sp. carriage determination.
• Performed whole metagenomic sequencing and 16S rRNA amplicon profiling.
• Developed in silico tools for Streptococcus community composition and S. pneumoniae serotyping from metagenomic data.

Main Results:

• Streptococcus sp. carriage (lytA+) increased with infant age, ranging from 24-85%.
• In silico serotyping identified known serotypes in 28/51 samples, with 5 samples showing co-occurrence of serotypes.
• Multiple Streptococcus species, potential pathogens (e.g., S. aureus), virulence factors, and drug resistance elements were identified in the NP microbiome.

Conclusions:

• Nasopharyngeal colonization by S. pneumoniae is a dynamic process involving multiple serotypes and species in infants.
• In silico serotype analysis is a powerful tool for determining S. pneumoniae carriage serotypes.
• Findings can inform the development of targeted vaccines to prevent invasive pneumococcal disease (IPD) in developing countries.