Whole Genome-Based Surveillance of Nasopharyngeal Pneumococcal Carriage in Vietnamese Children

Nasopharyngeal colonization with Streptococcus pneumoniae is a prerequisite for invasive pneumococcal disease. In Vietnam, PCV10 and PCV13 have been introduced in the private sector; however, updated surveillance data reflecting post-vaccine serotype dynamics are limited.

This study will enroll 530 children aged 2 months to 59 months hospitalized with acute respiratory symptoms. Participants will be categorized into:

• Group 1: Previously healthy children
• Group 2: Children with chronic underlying conditions Nasopharyngeal swabs will be collected at enrollment. Streptococcus pneumoniae isolates will undergo culture, identification using MALDI-TOF MS, and whole genome sequencing using the Illumina NextSeq platform. Bioinformatic analysis will include in silico serotyping, MLST typing, resistance gene detection, and co-colonization assessment.

The study will evaluate associations between pneumococcal carriage and demographic, clinical, vaccination, and environmental factors.

Inclusion criteria

• Age 2 months to 59 months
• Hospitalized with acute respiratory symptoms (≤14 days duration)
• Parent or legal guardian provides written informed consent

Acute respiratory symptoms defined as one or more of:

• Cough
• Rhinorrhea
• Nasal obstruction
• Sore throat
• Tachypnea
• Wheeze
• Retraction

Exclusion criteria

• Confirmed pneumococcal infection within the past 30 days