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

Whole Genome-Based Surveillance of Nasopharyngeal Pneumococcal Carriage and Serotype Distribution Among Vietnamese Children Hospitalized With Acute Respiratory Symptoms

This hospital-based cross-sectional study aims to determine the prevalence and serotype distribution of nasopharyngeal Streptococcus pneumoniae carriage among children aged 2-59 months hospitalized with acute respiratory symptoms at Vietnam National Children's Hospital (VNCH). Whole genome sequencing (WGS) will be used for serotype identification, antimicrobial resistance gene detection, and characterization of co-colonization patterns. The study will compare carriage prevalence and serotype distribution between previously healthy children and children with underlying comorbidities. Findings will inform pneumococcal vaccine policy and antimicrobial resistance surveillance in Vietnam.

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