Pneumococcal Carriage, Serotypes, and Antibiotic Resistance in Malaysian Children: A Multi-Centre Study

Overview

The goal of this observational study is to determine the prevalence, serotype distribution, and antimicrobial resistance patterns of nasopharyngeal carriage of Streptococcus pneumoniae in Malaysian children aged ≤5 years following the implementation of pneumococcal conjugate vaccines (PCVs). The study focuses on healthy and mildly symptomatic male and female children aged 0-60 months recruited from urban and semi-urban settings in Kuala Lumpur, Selangor, and Negeri Sembilan. The main questions it aims to answer are: 1. What is the overall and age-specific prevalence of nasopharyngeal pneumococcal carriage among children aged ≤5 years in Malaysia? 2. What are the circulating serotypes and antimicrobial resistance (AMR) profiles of pneumococcal isolates, and how are they associated with vaccination status and PCV valency coverage? Researchers will compare carriage prevalence, serotype distribution (vaccine-type vs non-vaccine-type), and antimicrobial resistance patterns across different states, vaccination statuses, and socioeconomic backgrounds to determine differences in transmission dynamics and potential serotype replacement patterns. Participants will: 1. Undergo a nasopharyngeal swab collection for pneumococcal detection. 2. Provide demographic and vaccination history information through a standardised case report form completed with parental/guardian consent. 3. Have their samples analysed using bacterial culture, antimicrobial susceptibility testing, and whole-genome sequencing (WGS) for serotyping and resistance profiling.

Nasopharyngeal colonisation with Streptococcus pneumoniae (Spn) is common in children under five and serves as a reservoir for transmission, a precursor to disease, and an indicator of circulating serotypes within communities. While often asymptomatic, pneumococcal carriage contributes to the development of respiratory tract infections and the spread of antimicrobial resistance (AMR). In Malaysia, pneumonia remains the third leading principal cause of death among children under five, and pneumococcal carriage is central to its pathogenesis. Spn is one of the primary bacterial agents responsible for childhood pneumonia and other serious infections, including otitis media, bacteremia, and meningitis. However, prior to causing disease, S. pneumoniae typically colonises the nasopharynx, particularly in young children, making nasopharyngeal carriage a key epidemiological marker for disease risk, serotype circulation, and transmission dynamics. The background of this study is rooted in the recent evolution of Malaysia's National Immunisation Programme (NIP). While pneumococcal conjugate vaccines (PCVs) have been available in the private sector for years, the Malaysian government officially introduced the vaccine into the NIP in December 2020, initially using the 10-valent vaccine (PCV10) before transitioning to the 13-valent version (PCV13) in 2023. This transition created a unique epidemiological landscape where different cohorts of children have received different vaccine formulations. Current surveillance in Malaysia has largely focused on invasive disease cases in hospital settings, leaving a significant "data gap" regarding how the vaccine is affecting the general population of children who carry the bacteria. Understanding this community carriage is essential because it reveals "serotype replacement"-a phenomenon where non-vaccine strains emerge to fill the ecological niche left by the strains targeted by the vaccine. Furthermore, the rising threat of antimicrobial resistance (AMR) in S. pneumoniae complicates treatment, as many strains are becoming less sensitive to common antibiotics like penicillin and erythromycin. The primary objective of this prospective, multi-centre, cross-sectional study is to establish a comprehensive baseline of pneumococcal carriage, serotype distribution, and antimicrobial resistance patterns among Malaysian children aged five years and below. By adopting a prospective cross-sectional design, the research aims to determine the point prevalence of carriage in both healthy and mildly symptomatic children across a specific temporal snapshot. Utilizing advanced laboratory techniques, the study intends to identify which specific serotypes are circulating in the community and evaluate the extent to which current vaccines (PCV13) cover these strains. Additionally, the study seeks to map the AMR profiles of these isolates to understand how resistance genes are distributed across different serotypes and geographic locations. A secondary but vital objective is to compare these findings across different urban and semi-urban settings in Kuala Lumpur, Selangor, and Negeri Sembilan to identify socioeconomic or regional variations in transmission. To achieve these goals, the study will recruit 600 children from diverse settings, including daycare centers and outpatient clinics, ensuring the data reflects the community rather than just the sickest patients in hospitals. Each participant will undergo a nasopharyngeal swab collection, and a standardized case report form will be used to record their demographic details and precise vaccination history. The collected samples will undergo rigorous analysis at the IMU Central Laboratory, employing both traditional bacterial culture and state-of-the-art Whole-Genome Sequencing (WGS). WGS allows for high-resolution serotyping and the detection of specific resistance markers, providing a level of detail that traditional methods cannot reach. By linking the genomic data of the bacteria with the vaccination status of the children within this prospective framework, the study will provide the evidence-based insights necessary for health authorities to decide on future strategies, such as the potential implementation of higher-valent vaccines like PCV15 or PCV20.