Clinical and laboratory investigations

Socio-demographic and clinical characteristics of the participants including age, gender, HIV exposure, history and type of previous treatment as well as clinical information at admission and discharge and treatment received were recorded in a standardized case report form [11]. Diagnosis at admission was based on clinical examination and systematic testing with a rapid diagnostic test for malaria (SD-Bioline Malaria Antigen P.f/Pan, Standard Diagnostics, Korea).

Final diagnosis was informed by biological investigations of blood and cerebrospinal fluid (CSF). Sample collection was performed systematically upon inclusion. Venous blood samples were collected aseptically into two single bottle blood-culture system (Signal Blood Culture System, Oxoid) and into EDTA tubes for hematological analyses. CSF was aseptically obtained by lumbar puncture into sterile CSF tubes. To diagnose bacterial pathogens, blood and CSF were analyzed at the Epicentre research laboratory on site following standardized bacteriology procedures [11]. Culture, staining, biochemical testing were used to identify any bacterial pathogens present. Drug susceptibility testing (DST) was done following the Comité De L’antibiogramme De La Société Francaise De Microbiologie (CA-SASFM 2006) guidelines [13]. We used the Kirby-Bauer disc diffusion method and E-tests to determine drug clearance zones and minimum inhibitory concentrations (MICs), respectively.

In addition, real-time polymerase chain reaction (qPCR) was performed systematically on CSF to look for the following bacterial pathogens: S. pneumoniae, H. influenzae type b (Hib), Salmonella, Listeria monocytogenes, as well as viral pathogens not presented here. These qPCRs were carried out initially at Epicentre Research Laboratory, Mbarara and later at APHM Laboratory, Marseille, France, on CSF stored and transported at -80°C following standardized procedures [11].

Thick and thin blood smears were prepared from EDTA blood, Giemsa-stained and examined by microscopy as recommended by the World Health Organization (WHO) to confirm malaria infection [14].