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Group B streptococcus (GBS) is a leading cause of neonatal sepsis. Sortase-dependent pilus-like structures have been identified on the surface of GBS, and have been found to be important in the adhesion and attachment of GBS to host cells. Three pilus island alleles, PI-1, PI-2a and PI-2b, have been described, and their proteins are being explored as vaccine candidates. The pilus islands from 541 colonization isolates and 284 invasive isolates were characterized by PCR. All isolates carried at least one pilus island, and they were identified alone or in combinations at the following overall frequencies: PI-2a, 29.8 %; PI-2b, 0.2 %; PI-1+PI-2a, 24.8 %; and PI-1+PI-2b, 45.1 %. A combination of PI-1+PI-2a (28.7 vs 17.6 %) was more common among colonizing compared with invasive isolates. Conversely, a combination of PI-1+PI-2b (37.2 vs 60.2 %) was more frequently associated with invasive disease compared to colonization. There was a strong association between pilus islands when adjusted for serotype distribution, PI-2a was identified in 92.6 % of colonizing and 90.0 % of invasive serotype Ia isolates, whereas serotype III was associated with co-expression of a PI-1 and PI-2b among 84.6 % of colonizing and 96.5 % of invasive isolates. Based on this homogeneity of pilus island distribution, a pilus-based vaccine developed for Europe and the USA will have similar coverage in South Africa.