Geographical migration and fitness dynamics of Streptococcus pneumoniae
Authors: Belman Sophie , Lefrancq Noémie , Nzenze Susan , Downs Sarah , du Plessis Mignon , Lo Stephanie W. ,   The Global Pneumococcal Sequencing Consortium, Corso Alejandra , Gagetti Paula , Brooks Abdullah W. , Hasanuzzaman Md , Saha Samir K. , Saha Senjuti , Davydov Alexander , Titov Leonid , Almeida Samanta Cristine Grassi , Turner Paul , Zhao Chunjiang , Wang Hui , Ip Margaret , Ho Pak Leung , Law Pierra , Keenan Jeremy D. , Cohen Robert , Varon Emmanuelle , Sampane-Donkor Eric , Veeraraghavan Balaji , Nagaraj Geetha , Ravikumar K. L. , Yuvaraj J. , Shamanna Noga Varun , Benisty Rachel , Dagan Ron , Bigogo Godfrey , Verani Jennifer , Kiran Anmol , Everett Dean B. , Cornick Jennifer , Alaerts Maaike , Sekaran Shamala Devi , Clarke Stuart C. , Moiane Benild , Sigauque Betuel , Mucavele Helio , Pollard Andrew J. , Kandasamy Rama , Carter Philip E. , Obaro Stephen K. , Lehmann Deborah , Ford Rebecca , Ochoa Theresa J. , Skoczynska Anna , Sadowy Ewa , Hryniewicz Waleria , Puzia Weronika , Doiphode Sanjay , Egorova Ekaterina , Voropaeva Elena , Urban Yulia , Kastrin Tamara , Ndlangisa Kedibone , De Gouveia Linda , Ali Mushal , Wolter Nicole , Lekhuleni Cebile , Almagro Carmen Muñoz , Alonso Alba Redin , Henares Desiree , Srifuengfung Somporn , Kwambana-Adams Brenda , Foster-Nyarko Ebenezer , Bojang Ebrima , Antonio Martin , Tientcheu Peggy-Estelle , Moïsi Jennifer , Nurse-Lucas Michele , Akpaka Patrick E. , Eser Özgen Köseoglu , Scott Anthony , Aanensen David , Croucher Nicholas , Lees John A. , Gladstone Rebecca A. , Tonkin-Hill Gerry , Chaguza Chrispin , Cleary David , Mellor Kate , Beall Bernard , Klugman Keith P. , Rodgers Gail , Hawkins Paulina A. , Blaschke Anne J. , Pershing Nicole L. , McGee Lesley , Madhi Shabir A. , von Gottberg Anne , Bentley Stephen D. , Salje Henrik 
Published: July 2024

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.