Geographical migration and fitness dynamics of Streptococcus pneumoniae

Sophie Belman (), Noémie Lefrancq, Susan Nzenze, Sarah Downs, Mignon Plessis, Stephanie W. Lo, Lesley McGee, Shabir A. Madhi, Anne Gottberg, Stephen D. Bentley and Henrik Salje
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Sophie Belman: Wellcome Sanger Institute
Noémie Lefrancq: University of Cambridge
Susan Nzenze: National Institute for Communicable Diseases of the National Health Laboratory Service
Sarah Downs: University of the Witwatersrand
Mignon Plessis: University of the Witwatersrand
Stephanie W. Lo: Wellcome Sanger Institute
Lesley McGee: Centers for Disease Control and Prevention
Shabir A. Madhi: University of the Witwatersrand
Anne Gottberg: University of the Witwatersrand
Stephen D. Bentley: Wellcome Sanger Institute
Henrik Salje: University of Cambridge

Nature, 2024, vol. 631, issue 8020, 386-392

Abstract: Abstract Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location1,2. The extent and mechanisms of spread and vaccine-driven changes in fitness and antimicrobial resistance remain largely unquantified. Here using geolocated genome sequences from South Africa (n = 6,910, collected from 2000 to 2014), we developed models to reconstruct spread, pairing detailed human mobility data and genomic data. Separately, we estimated the population-level changes in fitness of strains that are included (vaccine type (VT)) and not included (non-vaccine type (NVT)) in pneumococcal conjugate vaccines, first implemented in South Africa in 2009. Differences in strain fitness between those that are and are not resistant to penicillin were also evaluated. We found that pneumococci only become homogenously mixed across South Africa after 50 years of transmission, with the slow spread driven by the focal nature of human mobility. Furthermore, in the years following vaccine implementation, the relative fitness of NVT compared with VT strains increased (relative risk of 1.68; 95% confidence interval of 1.59–1.77), with an increasing proportion of these NVT strains becoming resistant to penicillin. Our findings point to highly entrenched, slow transmission and indicate that initial vaccine-linked decreases in antimicrobial resistance may be transient.

Date: 2024
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DOI: 10.1038/s41586-024-07626-3

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