Policy recommendations on pertussis vaccination need to be guided by data, which are limited from low- and middle-income countries. We aimed to describe the epidemiology of pertussis in South Africa, a country with high HIV prevalence and routine pertussis vaccination for six decades including the acellular vaccine since 2009.
Hospitalized patients of all ages were enrolled at five sentinel sites as part of a pneumonia surveillance program from January 2013 through December 2018. Nasopharyngeal specimens and induced sputum were tested by PCR for Bordetella pertussis. In addition, demographic and clinical information were collected. Incidence rates were calculated for 2013-2016, and multivariable logistic regression performed to identify factors associated with pertussis.
Over the six-year period 19429 individuals were enrolled, of which 239 (1.2%) tested positive for B. pertussis. Detection rate was highest in infants aged <6 months (2.8%, 155/5524). Mean annual incidence was 17 cases per 100,000 population, with the highest incidence in children <1 year of age (228 per 100,000). Age-adjusted incidence was 65.9 per 100,000 in HIV-infected individuals compared to 8.5 per 100,000 in HIV-uninfected individuals (risk ratio 30.4, 95% confidence interval 23.0-40.2). Ten individuals (4.2%) with pertussis died; of which 7 were infants aged <6 months and 3 were immunocompromised adults.
Pertussis continues to be a significant cause of illness and hospitalization in South Africa, despite routine vaccination. The highest burden of disease and death occurred in infants; however, HIV-infected adults were also identified as an important group at risk of B. pertussis infection.

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