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The NVT pneumococcal strains were most abundant in 53.6 % (15/28) of multiple carriage events that occurred with VT strains.
In those multiple carriage events, 61%% (28/46) co-carried at least one VT and an NVT, 15%% (7/46) carried VT only and 24%% (11/46) carried NVT only.
Since conventional serotyping methods are biased towards detection of the most abundant serotype, the VTs present at low abundance in multiple carriage events may not have been detected in these samples, which could have resulted in poor estimation of the vaccine coverage.
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The effect of HIV infection on multiple carriage was also investigated.
Carriage of two or more serotypes is defined as multiple carriage.
The association between age and multiple carriage was also investigated.
Carriage of either single or multiple pneumococcal serotypes (multiple carriage) is a prerequisite for developing invasive pneumococcal disease.
The proportion of multiple carriage, i.e. samples with more than one isolate was 13% (8/62).
Minority serotypes 5, 6A, 6C, 9N, 13, 22F were only detected as part of multiple carriage.
The high multiple carriage in Malawian children provides opportunities for genetic exchange through horizontal gene transfer.
Complete genome level analyses of multiple carriage strains of S. aureus will be important in clarifying molecular determinants of S. aureus nasal carriage.
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