TY - UNPB
T1 - Geographic migration and vaccine-induced fitness changes of Streptococcus pneumoniae
AU - Global Pneumococcal Sequencing Consortium
AU - Belman, Sophie
AU - Lefrancq, Noémie
AU - Nzenze, Susan
AU - Downs, Sarah
AU - du Plessis, Mignon
AU - Lo, Stephanie
AU - McGee, Lesley
AU - Madhi, Shabir A
AU - von Gottberg, Anne
AU - Bentley, Stephen D
AU - Salje, Henrik
PY - 2023/1/18
Y1 - 2023/1/18
N2 - UNLABELLED: Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location. The extent and mechanisms of spread, and vaccine-driven changes in fitness and antimicrobial resistance (AMR), remain largely unquantified. Using geolocated genome sequences from South Africa (N=6910, 2000-2014) 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 (vaccine type, VT) and are not (non-vaccine type, NVT) included in the vaccine, first implemented in 2009, as well as differences in strain fitness between those that are and are not resistant to penicillin. We estimated that pneumococci only become homogenously mixed across South Africa after about 50 years of transmission, with the slow spread driven by the focal nature of human mobility. Further, in the years following vaccine implementation the relative fitness of NVT compared to VT strains increased (RR: 1.29 [95% CI 1.20-1.37]) - with an increasing proportion of these NVT strains becoming penicillin resistant. Our findings point to highly entrenched, slow transmission and indicate that initial vaccine-linked decreases in AMR may be transient.ONE-SENTENCE SUMMARY: We describe geographic migration, and fitness dynamics conferred by NVT strains and AMR, for the globally endemic pathogen Streptococcus pneumoniae .
AB - UNLABELLED: Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location. The extent and mechanisms of spread, and vaccine-driven changes in fitness and antimicrobial resistance (AMR), remain largely unquantified. Using geolocated genome sequences from South Africa (N=6910, 2000-2014) 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 (vaccine type, VT) and are not (non-vaccine type, NVT) included in the vaccine, first implemented in 2009, as well as differences in strain fitness between those that are and are not resistant to penicillin. We estimated that pneumococci only become homogenously mixed across South Africa after about 50 years of transmission, with the slow spread driven by the focal nature of human mobility. Further, in the years following vaccine implementation the relative fitness of NVT compared to VT strains increased (RR: 1.29 [95% CI 1.20-1.37]) - with an increasing proportion of these NVT strains becoming penicillin resistant. Our findings point to highly entrenched, slow transmission and indicate that initial vaccine-linked decreases in AMR may be transient.ONE-SENTENCE SUMMARY: We describe geographic migration, and fitness dynamics conferred by NVT strains and AMR, for the globally endemic pathogen Streptococcus pneumoniae .
U2 - 10.1101/2023.01.18.524577
DO - 10.1101/2023.01.18.524577
M3 - Preprint
C2 - 36711799
T3 - bioRxiv
BT - Geographic migration and vaccine-induced fitness changes of Streptococcus pneumoniae
PB - bioRxiv
ER -
