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Belman, Sophie, Lefrancq, Noémie, Nzenze, Susan, Downs, Sarah, du Plessis, Mignon, Lo, Stephanie W., 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, 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. and Salje, Henrik (2024) 'Geographical migration and fitness dynamics of Streptococcus pneumoniae'. Nature, Vol 631, Issue 8020, pp. 386-392.
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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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | NOT_LSTM |
| Subjects: | WC Communicable Diseases > WC 20 Research (General) WC Communicable Diseases > Infection. Bacterial Infections > Bacterial Infections > WC 210 Streptococcal infections (General or not elsewhere classified) |
| Faculty: Department: | Clinical Sciences & International Health > Clinical Sciences Department |
| Digital Object Identifer (DOI): | https://doi.org/10.1038/s41586-024-07626-3 |
| Depositing User: | Lynn Roberts-Maloney |
| Date Deposited: | 18 Jul 2024 08:24 |
| Last Modified: | 18 Jul 2024 08:24 |
| URI: | https://archive.lstmed.ac.uk/id/eprint/24950 |
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