Geographical migration and fitness dynamics of Streptococcus pneumoniae

• 成果类型: Article
• 署名作者: Belman, Sophie; Lefrancq, Noemie; Nzenze, Susan; Downs, Sarah; du Plessis, Mignon; Lo, Stephanie W.; McGee, Lesley; Madhi, Shabir A.; von Gottberg, Anne; Bentley, Stephen D.; Salje, Henrik; Corso, Alejandra; Gagetti, Paula; Brooks, Abdullah W.; Hasanuzzaman, Md; Saha, Samir K.; Saha, Senjuti; Davydov, Alexander; Titov, Leonid; Grassi Almeida, Samanta Cristine; 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.; Noga, Varun Shamanna; 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; Munoz Almagro, Carmen; Redin Alonso, Alba; Henares, Desiree; Srifuengfung, Somporn; Kwambana-Adams, Brenda; Foster-Nyarko, Ebenezer; Bojang, Ebrima; Antonio, Martin; Tientcheu, Peggy-Estelle; Moisi, Jennifer; Nurse-Lucas, Michele; Akpaka, Patrick E.; Eser, Ozgen Koseoglu; 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.
• 署名单位: Wellcome Trust Sanger Institute; University of Cambridge; Universitat Politecnica de Catalunya; Barcelona Supercomputer Center (BSC-CNS); National Institute for Communicable Diseases (NICD); National Health Laboratory Service; University of Witwatersrand; University of Witwatersrand; National Institute for Communicable Diseases (NICD); National Health Laboratory Service; University of Bath; Centers for Disease Control & Prevention - USA; CDC National Center for Immunization & Respiratory Diseases (NCIRD); National Research Foundation - South Africa; University of Witwatersrand; University of Cape Town; International Centre for Diarrhoeal Disease Research (ICDDR); Belarusian State Medical University; Instituto Adolfo Lutz; Peking University; Chinese University of Hong Kong; Prince of Wales Hospital; University of Hong Kong; University of Hong Kong; University of California System; University of California San Francisco; University of California System; University of California San Francisco; Universite Paris-Est-Creteil-Val-de-Marne (UPEC); CHI Creteil; Institut National de la Sante et de la Recherche Medicale (Inserm); Universite Paris-Est-Creteil-Val-de-Marne (UPEC); Universite Paris-Est-Creteil-Val-de-Marne (UPEC); CHI Creteil; University of Ghana; Christian Medical College & Hospital (CMCH) Vellore; Kempegowda Institute of Medical Sciences (KIMS); Ben-Gurion University of the Negev; Kenya Medical Research Institute; Centers for Disease Control & Prevention - USA; CDC National Center for Immunization & Respiratory Diseases (NCIRD); University of Malawi; Malawi-Liverpool Wellcome Trust Clinical Research Programme; Khalifa University of Science & Technology; Khalifa University of Science & Technology; UCSI University; University of Southampton; University of Southampton; Centro de Investigacao em Saude de Manhica; University of Oxford; University of Sydney; Institute of Environmental Science & Research (ESR) - New Zealand; University of Alabama System; University of Alabama Birmingham; The Kids Research Institute Australia; University of Western Australia; Wesfarmers Limited; PNG Institute Of Medical Research; Universidad Peruana Cayetano Heredia; National Medicines Institute Lekow (NIL); Hamad Medical Corporation; G.N. Gabrichevsky Institute for Epidemiology & Microbiology; Universitat Internacional de Catalunya (UIC); University of Barcelona; CIBER - Centro de Investigacion Biomedica en Red; CIBERESP; Siam University; University of London; London School of Hygiene & Tropical Medicine; University of London; London School of Hygiene & Tropical Medicine; University of London; London School of Hygiene & Tropical Medicine; Pfizer; University West Indies Mona Jamaica; University West Indies Saint Augustine; Hacettepe University; University of London; London School of Hygiene & Tropical Medicine; University of Oxford; Imperial College London; European Molecular Biology Laboratory (EMBL); European Bioinformatics Institute; University of Oslo; Yale University; University of Birmingham; Bill & Melinda Gates Foundation; Utah System of Higher Education; University of Utah
• 刊物名称: Nature
• ISSN/ISSBN: 0028-5793
• DOI: 10.1038/s41586-024-07626-3
• 发表日期: 2024-07-11
• 页码: 386-+
• 关键词: vaccine; CHILDREN; disease

摘要

Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location(1,2). 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.