Antimicrobial resistance trends and lineage distribution among invasive pneumococcal disease isolates pre- and post-pneumococcal conjugate vaccine introduction, South Africa.

OBJECTIVES

Pneumococcal conjugate vaccines (PCV) have reduced antimicrobial-resistant invasive pneumococcal disease (IPD) globally. We evaluated trends in antimicrobial-resistant IPD and pneumococcal lineages before and after PCV13 introduction in South Africa.

METHODS

We analysed national, laboratory-based IPD surveillance reported cases (2005-2020) and compared the incidence of resistant-IPD pre- and post-PCV introduction. Antimicrobial susceptibility testing was performed for six antibiotics, and penicillin-multidrug resistance (penicillin-MDR) was defined as penicillin nonsusceptibility plus resistance to ≥2 additional antibiotic classes. Whole-genome sequencing was used to determine serotypes, sequence types, global pneumococcal sequence clusters (GPSC), and antimicrobial resistance (AMR) determinants.

RESULTS

Following PCV introduction, overall IPD and AMR IPD incidence declined substantially. Penicillin-cotrimoxazole nonsusceptible and penicillin-MDR IPD incidence decreased from 5.6 to 0.8 per 100,000 population (percentage decrease -86.5%, confidence intervals [CI] -90.5% to -81.4%) and 5.5 to 0.4 (-93.0%, -95.7% to -89.1%), respectively, in children <5 years, with smaller but significant reductions in the ≥5 years old. Despite these declines, residual PCV13 serotypes, particularly 19A and 19F, continued to contribute notably to penicillin-cotrimoxazole nonsusceptible and penicillin-MDR IPD, respectively, after PCV13 introduction. Non-vaccine serotypes (10A, 15A, 15B/C, 16F, 23B, and 35B) increasingly contributed to resistant IPD in the post-PCV13 era through the expansion of both vaccine-type and non-vaccine-type GPSC lineages.

CONCLUSION

PCVs substantially reduced AMR IPD in South Africa, but persistent PCV13 serotypes and expanding resistant non-vaccine-type lineages highlight the potential benefit of higher-valency PCVs, including PCV20.