Co-carriage of respiratory tract bacterial pathogens among under-5 children with pneumococcal carriage in Peninsular Malaysia

Streptococcus pneumoniae (SPN) is the commonest cause of bacterial childhood pneumonia, and adverse clinical outcomes have been associated with co-infections with other bacteria causing severe respiratory disease. We therefore conducted a study to look for evidence of other respiratory bacterial pathogens and to determine the prevalence and risk factors of co-carriage status among under-5 children in Peninsular Malaysia. This retrospective case-control study is part of a paediatric pneumonia surveillance study “MY-Pneumo” (NCT04923035. Registered on June 11, 2021) in young children across three sentinel sites in Peninsular Malaysia (Kelantan, Pahang, and Kuala Lumpur). Nasopharyngeal specimens of under-5 children with positive optochin sensitive SPN isolates (n = 154) were further tested for pneumococcal co-carriage status of SPN and six bacteria causing severe respiratory tract infections (Bordetella parapertussis (BPP), B. pertussis (BP), Chlamydophila pneumoniae (CP), Haemophilus influenzae (HI), Legionella pneumophila (LP), Mycoplasma pneumoniae (MP)) using multiplex real-time polymerase chain reaction (qPCR). Logistic regression analyses were fitted for paediatric bacterial co-carriage risk factors. Co-carriage was only present between SPN and HI in 54 children (35.1%). The majority were boys (n = 41, 75.9%) with a mean age of 19.26 (± 14.83) months. Co-carriage of SPN and HI (SPN-HI) were significantly associated with the sentinel site location (p = 0.037), gestation term (p = 0.004), and household size (p = 0.01). The predictors of positive co-carriage were household size of five to seven persons (aOR 3.70, 95% CI: 1.43–9.55, p = 0.007) and 8 or more persons (aOR 3.58, 95% CI: 1.06–12.12, p = 0.041). Our study revealed that co-carriage of SPN-HI was present in one third of children with pneumonia and was influenced by geographical area, and household size. Resource allocation should be targeted towards effective vaccination strategies and heightened awareness among healthcare providers to improve paediatric pneumonia interventions in the country. ClinicalTrials.gov, NCT04923035. Registered on June 11, 2021.