Case-fatality and sequelae following acute bacterial meningitis in South Africa, 2016 through 2020.

OBJECTIVES: Providing country-specific estimates of case fatality and sequelae from bacterial meningitis (BM) is important to evaluate and monitor progress toward the World Health Organization's roadmap to "defeating meningitis by 2030". METHODS: From 2016-2020, GERMS-SA conducted enhanced surveillance at 26 hospitals across South Africa. Episodes of laboratory-confirmed BM due to Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis were included. Risk factors for in-hospital death and sequelae at hospital discharge among survivors were analyzed. RESULTS: Of 12,717 invasive bacterial infections reported nationally, 39% (4980) were from enhanced surveillance sites, including 4159 pneumococcal, 640 H. influenzae, and 181 meningococcal infections. BM accounted for 32% (1319/4159) of pneumococcal, 21% (136/640) of H. influenzae, and 83% (151/181) of meningococcal invasive diseases. Clinical data were available for 91% (1455/1606) of BM: 26% (376/1455) were aged <5 years, 50% (726/1455) were female, and 62% (723/1171) with known HIV results, were HIV-infected. In-hospital case fatality was 37% (534/1455), and 24% (222/921) of survivors had adverse sequelae. Risk factors for death included altered mental status, HIV infection, and comorbidities. Risk factors for adverse sequelae included altered mental status and antimicrobial nonsusceptibility. CONCLUSION: BM in South Africa has a high case fatality, and adverse sequelae frequently occur among survivors. Those with comorbidities (including HIV) are at the highest risk.

Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae.

Serotype 1 Streptococcus pneumoniae is a leading cause of invasive pneumococcal disease (IPD) worldwide, with the highest burden in developing countries. We report the whole-genome sequencing analysis of 448 serotype 1 isolates from 27 countries worldwide (including 11 in Africa). The global serotype 1 population shows a strong phylogeographic structure at the continental level, and within Africa there is further region-specific structure. Our results demonstrate that region-specific diversification within Africa has been driven by limited cross-region transfer events, genetic recombination and antimicrobial selective pressure. Clonal replacement of the dominant serotype 1 clones circulating within regions is uncommon; however, here we report on the accessory gene content that has contributed to a rare clonal replacement event of ST3081 with ST618 as the dominant cause of IPD in the Gambia.

Invasive disease due to Haemophilus influenzae serotype b ten years after routine vaccination, South Africa, 2003-2009.

INTRODUCTION: South Africa started routine infant immunization against Haemophilus influenzae serotype b (Hib) disease in 1999 with an accelerated three-dose schedule of Hib conjugate vaccine (HibCV) without a booster dose. Following initial declines in Hib disease, national surveillance has identified increasing numbers of Hib disease episodes in fully vaccinated children. MATERIALS AND METHODS: We reviewed national laboratory-based surveillance data from 2003 through 2009 for invasive Hib disease episodes among children <5 years, including HIV status and vaccination histories. We defined HibCV failures as invasive Hib disease in children at least four months of age who had received all recommended doses of HibCV. RESULTS: Despite high HibCV vaccination coverage, detection rates of Hib disease in children <5 years increased from 0.7 per 100,000 population in 2003 to 1.3/100,000 in 2009 (p<0.001). Among 263 episodes of invasive Hib disease among children with known vaccination status, 135 (51%) were classified as vaccine failures. Of vaccine failures, 55% occurred among case patients ≥18 months old. HIV status was documented for 90 children with vaccine failure; 53% were not HIV infected. DISCUSSION AND CONCLUSIONS: Vaccine failures, which occurred in both HIV-infected and -uninfected children, comprised half of the rise in invasive Hib disease detected in South African children 10 years after national introduction of Hib vaccine. These findings suggest that HibCV recommendations may require revision. In November 2010, children in South Africa began receiving a booster dose of HibCV as part of a pentavalent vaccine.