Dr Courtney Olwagen

Senior Scientist


Dr Courtney Olwagen is a senior research scientist at the Vaccine and Infectious Diseases Analytics Research Unit (VIDA) of the University of the Witwatersrand. She has been involved in clinical microbiology and infectious disease research for the past 10 years, with a specific focus on reducing under-5 childhood morbidity and mortality. She is the principal investigator on a project that is evaluating the association of HIV infection and density of nasopharyngeal bacterial colonizers in PCV-immunised children and is the co-principal investigator on a grant-funded project investigating the temporal changes of drug-resistant Streptococcus pneumoniae. Her work on pneumococcal disease also encompasses a molecular diagnostic program for Streptococcus pneumonia in which she is the lead scientist. As part of this work, Courtney has developed a nanofluidic assay that can simultaneously detect 90 different pneumococcal serotypes together with other common bacterial and viral respiratory pathogens. The development of this assay has allowed the unit to serotype pneumococcus in several ongoing projects including a clinical trial that is investigating pneumococcal colonisation in children receiving different schedules of different PCV vaccine formulations.

To better understand the interaction of different pathogens causing disease in children, Courtney’s research portfolio also includes studies that are investigating the maternal vaginal microbiome composition that is associated with adverse pregnancy outcomes (including neonatal deaths and stillbirths) and a longitudinal study of the nasopharyngeal microbiome in infants with lower respiratory tract infections. Further, she is the co-principal investigator on a grant-funded study that is applying next-generation sequencing to identify pathogens causing infection-related neonatal deaths and stillbirths.

During her time at Wits VIDA, Courtney’s work has resulted in numerous publications as well as presentations at both international and local conferences. She is the recipient of the Robert Austrian research award and is a member of the Golden Key International Honour Society. She has also reviewed publications for several different scientific journals.


Baillie VL; Madhi SA; Ahyong V; Olwagen CP, 2023. Metagenomic sequencing of post-mortem tissue samples for the identification of pathogens associated with neonatal deaths.  Nat Commun 14(1):5373

Downs SL; Olwagen CP; Van Der Merwe L; Nzenze SA; Nunes MC; Madhi SA, 2023. Streptococcus pneumoniae and other bacterial nasopharyngeal colonization seven years post-introduction of 13-valent pneumococcal conjugate vaccine in South African children.  Int J Infect Dis 134:45-52

Izu A; Nunes MC; Solomon F; Baillie V; Serafin N; Verwey C; Moore DP; Laubscher M; Ncube M; Olwagen C; Dangor Z; Madhi SA, 2023. All-cause and pathogen-specific lower respiratory tract infection hospital admissions in children younger than 5 years during the COVID-19 pandemic (2020-22) compared with the pre-pandemic period (2015-19) in South Africa: an observational study.  Lancet Infect Dis 23(9):1031-1041

Khan S; Madhi SA; Olwagen C, 2023. In-silico identification of potential inhibitors against FabI protein in Klebsiella pneumoniae.  J Biomol Struct Dyn.

Downs SL; Madhi SA; van der Merwe L; Nunes MC; Olwagen CP, 2023. Optimization of a high-throughput nanofluidic real-time PCR to detect and quantify of 15 bacterial species and 92 Streptococcus pneumoniae serotypes.  Sci Rep 13(1):4588

Olwagen CP; Izu A; Mutsaerts EAML; Jose L; Koen A; Downs SL; Van Der Merwe L; Laubscher M; Nana AJ; Moultrie A; Cutland CL; Dorfman JR; Madhi SA, 2023. Single priming and booster dose of ten-valent and 13-valent pneumococcal conjugate vaccines and Streptococcus pneumoniae colonisation in children in South Africa: a single-centre, open-label, randomised trial.  Lancet Child Adolesc Health 7(5):326-335

Javaid N; Olwagen C; Nzenze S; Hawkins P; Gladstone R; McGee L; Breiman RF; Bentley SD; Madhi SA; Lo S, 2022. Population genomics of pneumococcal carriage in South Africa following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) immunization.  Microb Genom 8.

Downs SL; Madhi SA; Van der Merwe L; Nunes MC; Olwagen CP, 2021. High-throughput nanofluidic real-time PCR to discriminate Pneumococcal Conjugate Vaccine (PCV)-associated serogroups 6, 18, and 22 to serotypes using modified oligonucleotides.  Sci Rep 11(1):23728

Olwagen CP; Adrian PV; Madhi SA, 2020. Evaluation of the impact of HIV-1 infection and density of common nasopharyngeal bacterial colonizers in South African children immunized with 7-valent pneumococcal conjugate vaccine.  Vaccine 38(7):1762-1769

Olwagen CP; Adrian PV; Madhi SA, 2019. Performance of the Biomark HD real-time qPCR System (Fluidigm) for the detection of nasopharyngeal bacterial pathogens and Streptococcus pneumoniae typing.  Sci Rep 9(1):6494

Baillie VL; Olwagen CP; Madhi SA, 2018. Review on Clinical and Molecular Epidemiology of Human Rhinovirus-Associated Lower Respiratory Tract Infections in African and Southeast Asian Children.  Pediatr Infect Dis J 37(7):e185-e194

Olwagen CP; Adrian PV; Nunes MC; Madhi SA, 2018. Evaluation of the association of pneumococcal conjugate vaccine immunization and density of nasopharyngeal bacterial colonization using a multiplex quantitative polymerase chain reaction assay.  Vaccine 36(23):3278-3285

Olwagen CP; Adrian PV; Nunes MC; Groome MJ; Cotton MF; Violari A; Madhi SA, 2017. Use of Multiplex Quantitative PCR To Evaluate the Impact of Pneumococcal Conjugate Vaccine on Nasopharyngeal Pneumococcal Colonization in African Children.  mSphere 2.

Olwagen CP; Adrian PV; Madhi SA, 2017. Comparison of traditional culture and molecular qPCR for detection of simultaneous carriage of multiple pneumococcal serotypes in African children.  Sci Rep 7(1):4628

Publication list retrieved from NCBI using ImpactPubs