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Summary Background Over the last decade Streptococcus pneumoniae has emerged as the most common bacterial pathogen for meningitis in all age groups, beyond the neonatal period. Objective To determine the epidemiological and clinical characteristics; and risk factors for mortality of pneumoccocal meningitis in children in a developing transitional country. Materials and methods A retrospective study that included patients <15 years of age admitted at the Instituto de Medicina Tropical of Paraguay, from January 1990 until December 2003 with the diagnosis of bacterial meningitis caused by S. pneumoniae. Clinical and laboratory data were collected and analysed in order to identify risk factors associated with morbidity and mortality outcomes of this infection. Results Seventy-two patients (between the ages of 35 days and 14 years) were identified. Forty-two per cent of patients had seizures prior to or at the time of admission, 36% were admitted in a comatose state, and 19% with shock. Mortality was 33% (24/72), and 18% of the survivors (11/60) developed severe sequelae. Upon admission, the following variables were strongly correlated with mortality: age <12 months (P = 0.007), the presence of seizures (P = 0.0001) or development of seizures 48 h after admission (P = 0.01), a cerebrospinal fluid (CSF) glucose level of <10 mg/dl (P = 0.01), CSF albumin >200 mg/dl (P = 0.0003), an absolute blood neutrophil count <2000/mm3 (P = 0.006) and a haemoglobin value of <9 g/dl (P = 0.0001). Conclusions This study confirms the high morbidity and mortality associated with S. pneumoniae meningitis in Paraguay. Certain clinical parameters and laboratory findings in blood and CSF at the time of admission could be used as predictors for mortality or severe sequelae among survivors.