Molecular characterisation of nontypeable Streptococcus pneumoniae in South Africa

Abstract

Streptococcus pneumoniae colonises the nasopharynx and is also a significant pathogen causing diseases such as meningitis and pneumonia. The capsular polysaccharide is an important virulence determinant and a target for current pneumococcal vaccines. However, pneumococci showing no serological evidence of capsule expression (nontypeable pneumococci [NTPn]) have been identified, mainly in carriage studies and rarely in invasive disease. NTPn are not targeted by current vaccines and are believed to play an important role in the evolution of Streptococcus species. Limited data exist which describe NTPn and their population structure, especially from the African continent. Our aim was to describe, characterise and compare invasive and carriage NTPn isolates from South Africa.

Invasive NTPn were detected through national, laboratory-based surveillance for invasive pneumococcal disease in South Africa between 2003 and 2013. Carriage NTPn were obtained from cross-sectional studies assessing the impact of pneumococcal conjugate vaccine (PCV) on nasopharyngeal colonisation in South Africa between 2009 and 2012. Isolates were characterised by capsular locus sequence analysis, multilocus sequence typing and whole genome phylogenetic analysis. Antimicrobial non-susceptibility patterns and potentially inactivating capsule mutations were determined. We also performed comparative genomic analysis of invasive and carriage NTPn isolates.

The prevalence of invasive and carriage NTPn was 0.1% (39/32,824) and 3.7% (137/3721) (P <0.01), respectively. Carriage NTPn increased from 3.0% (60/2015) to 4.5% (77/1706) (P = 0.02), post-PCV7. Five percent (2/39) and 24.0% (33/137) (P <0.01) of invasive and carriage NTPn were co-infected and co-colonised with encapsulated pneumococci, respectively. Non susceptibility to cotrimoxazole [84.0% (112/133) vs. 44.0% (17/39)], penicillin [77.0% vi (102/133) vs. 36.0% (14/39)], erythromycin [53.0% (70/133) vs. 31.0% (12/39)] and clindamycin [36.0% (48/133) vs. 18.0% (7/39)] were significantly higher (P ≤0.03) among carriage than invasive NTPn.

Fifty-six percent (22/39) of invasive and 9.0% (13/137) of carriage NTPn isolates (P <0.01) had at least partial capsule genes (Group I). The remaining invasive (17/39, 44.0%) and carriage (124/137, 91.0%) (P <0.01) NTPn had complete deletion of the capsular locus (Group II). We identified a variety of potentially inactivating capsule mutations in Group I invasive and carriage NTPn. Invasive NTPn were more diverse (Simpson’s diversity index [D] = 0.97 [95.0% CI: 0.947 - 0.996]) than carriage NTPn (D = 0.92 [95.0% CI: 0.899 - 0.945]). Seventy nine percent (31/39) of invasive NTPn belonged to a lineage that was related to encapsulated pneumococci compared carriage NTPn, where 67.0% (92/137) belonged to a lineage exclusive to NTPn strains. We identified 275 genes that were significantly associated with invasive NTPn compared to carriage NTPn.

In conclusion, carriage NTPn were frequently isolated and had higher rates of antimicrobial non-susceptibility than invasive NTPn. Carriage NTPn were also less diverse, with the majority belonging to classical lineage and lacking capsule genes, whereas invasive NTPn were more diverse and the majority belonged to a lineage related to encapsulated pneumococci. Comparative genomic analysis revealed genes that may be responsible for capsule-independent virulence mechanisms of invasive NTPn.