Epidemiology of viral and atypical bacterial respiratory infections among children hospitalised at a Kenyan tertiary referral centre: a cross sectional multiplex PCR study.

BACKGROUND: Severe acute respiratory infections (SARIs) cause high paediatric morbidity and mortality particularly in sub-Saharan Africa. Understanding contemporary trends in SARI aetiology is needed to inform prevention strategies. We aimed to determine the current aetiology, severity and seasonality of SARIs based on pathogens detected by multiplex quantitative real-time polymerase chain reaction (qRT-PCR) tests, BioFire® respiratory panel 2.0 (RP 2) and 2.1plus (RP2.1plus). METHODS: We conducted a retrospective cross-sectional analytic study among Kenyan children aged 0-18 years hospitalised between March 2018 and March 2023, with SARI and a positive nasopharyngeal swab multiplex qRT-PCR test. Cases were analyzed for their clinical characteristics, radiological features, laboratory data, seasonality of the respiratory pathogens and risk factors for severe infection. RESULTS: A total of 545 pathogens were detected in 382 cases,123 (22.5%) had polymicrobial detection, 14 (4%) had severe illness and three (0.8%) died. Rhinovirus (24%) and respiratory syncytial virus (21%) were the most common viral pathogens identified whereas Mycoplasma pneumoniae (2.4%) and Bordetella pertussis (1.8%) were the most common atypical pathogens detected. Infections peaked during the first dry season and the short rainy season. Lower respiratory tract infections and presence of co-morbidities like asthma,vitamin D deficiency and iron deficiency anaemia were associated with disease severity independent of age, sex and seasonality. CONCLUSIONS: Viruses accounted for majority of respiratory infections. Infections had two distinct peaks: the first dry season and the short rainy season, suggesting that respiratory vaccines should be scheduled prior to their onset.