Streptococcus pneumoniae (the pneumococcus) is a major cause of death in children below 5 years old in developing countries, where carriage rates as high as 93% have been reported for this age group. Although several studies have revealed a high prevalence of prophages in clinical isolates from different countries, there are no published reports indicating how pneumococcal bacteriophages (pneumophages) influence the Sub-Saharan African pneumococcal populations. Consequently our research has focused on exploring the contribution of bacteriophages to the high carriage and disease rates of the pneumococcus in The Gambia.

To do this 123 nasopharyngeal swabs (NPS) collected from healthy children below 5 years old and their mothers were enriched for pneumophages. Phage characterization was conducted by transmission electron microscopy and genome sequencing. Presence of active prophages in eight Gambian isolates, from highly prevalent clones, was assessed by determination of Mitomycin C minimum inhibitory concentration (MitC-MIC) and prediction of phage-derived regions in their genomes. Genomic sequences of phages identified here were compared to sequences of previously characterized pneumophages that formed the basis of a prophage typing system.

SpGS-1, a temperate siphovirus with lytic properties was isolated. Its 37631 bp genome has 53 putative CDS organized in five modules. Genome comparisons revealed that SpGS-1 is closely related to pneumophages belonging to group 3, where phage MM1 (associated with the multi-antibiotic resistant Spain23F-1 lineage) is found. All Gambian isolates tested had significantly lower MitC-MIC compared to a set of non prophage-containing pneumococci. Eleven complete prophages were detected in the genomes analysed and all fit the pneumococcal prophage classification system previously reported, however two new integration sites were identified for group 2 pneumophages. Overall we show that temperate pneumophages are prevalent and diverse among pneumococci associated with high carriage rates in The Gambia. Work is underway to determine their ecological role within this population.