Aims Botswana is a country in Southern Africa with a UNAIDS estimated adult HIV prevalence of 25% but a PMTCT program that has limited mother-to-child transmission to an estimated 3%. Haemophilus influenza type B (Hib) vaccination was rolled out nationally in 2011, with WHO estimating coverage of 95% by 2012. This study aims to describe the culture-confirmed causes of meningitis in children in Botswana, a setting with high HIV prevalence and recent introduction of Hib vaccination.

Methods We conducted a retrospective laboratory-based surveillance study reviewing paediatric cerebrospinal fluid (CSF) records at the country’s main referral hospital. Microbiology reports from all CSF samples collected from inpatients aged 0–14 years between February 2012 and December 2014 were retrospectively reviewed.

Results Over the 3 year period, 1036 samples CSF samples were collected from patients aged 0–14 years. 67 samples were culture positive. Cryptococcus neoformans was the most commonly cultured organism, grown in 27 unique patients. This compared with 10 cases of culture-confirmed Streptococcus pneumoniae and 6 cases of Klebsiella pneumoniae. Haemophilus influenzae was not cultured from any CSF samples during this period. Half of all microbiologically confirmed cases of cryptococcal meningitis occurred in children aged 0–1 years.

Conclusion Cryptococcus neoformans was the most common microbiologically confirmed cause of meningitis in Botswana children. It was cultured twice as frequently as Streptococcus pneumoniae, traditionally the most common causative organism of paediatric meningitis. Literature is limited on the epidemiology of paediatric meningitis in settings of high HIV prevalence, although our single-centre study found this to be the predominant isolated pathogen. Following countrywide Hib vaccine rollout, no cases of Hib meningitis were observed during the surveillance period.