Publications
C.D. October, B. Beko, A. Reuter, V. Rennie, N. Ismail, E.C. Conceicao, S. Tonsing, R.M. Warren, S.T. Malherbe, A. Van Rie, L. Viljoen
Real-world decision-making for post-exposure management of drug-resistant TB
IJTLD Open 2026; 3(6): 403–408. doi:10.5588/ijtldopen.26.0125.
Christoffel Johannes Opperman, Sarishna Singh, Yons Ghebrekristos, Michael Linström, Lourens Jacobsz, Wynand Goosen
Disseminated Mycobacterium avium: A multi-organ system investigation
International Journal of Infectious Diseases, Volume 165, 108475, April 2026. 10.1016/j.ijid.2026.108475.
Stepfan de Villiers, Kerwin Liedeman, Lucious Chabuka, Velda Wentzel, Tebogo Ramakutoane, Nondumiso Zakwe, Ottovan Dakurah, Eduan Wilkinson, Marije Hofstra, Lavanya Singh, Cheryl Baxter, Tulio De Oliveira
Viral Whole Genome Sequencing Using Illumina Microbial Amplicon Prep (iMAP) with ARTIC-Style Primer Schemes for RSV, SARS-CoV-2, and Dengue Virus (Serotypes 1–4)
Protocols.io, 28 April 2026. https://dx.doi.org/10.17504/protocols.io.36wgqxz4xlk5/v1.
Kerwin Liedeman, Stepfan de Villiers, Lucious Chabuka, Velda Wentzel, Tebogo Ramakutoane, Nondumiso Zakwe, Ottovon Dakurah, Eduan Wilkinson, Marije Hofstra, Cheryl Baxter, Lavanya Singh, Tulio De Oliveira
Influenza A and B virus WGS using Illumina Microbial Amplicon Prep (iMAP) half reaction
Protocols.io, 28 April 2026. https://dx.doi.org/10.17504/protocols.io.x54v9q49ql3e/v1.
Abisola Okunola, Johannes Loubser, Giovanni Ghielmetti, Rachiel Gumbo, Elizabeth M. Streicher, Pamela Ncube, Anzaan Dippenaar, Wynand J. Goosen, Ana Marcia Sá Guimarães, Robin M. Warren, Andre G. Loxton, Michele A. Miller, Tanya J. Kerr
Whole-genome sequencing reveals genetic diversity and transmission dynamics of Mycobacterium bovis in South African wildlife
Microbial Genomics, Volume 12, Issue 2, February 2026. doi:10.1099/mgen.0.001646.
Massimiliano S. Tagliamonte, Abhinav Sharma, Alberto Riva, Monika Moir, Marco Salemi, Cheryl Baxter, Tulio de Oliveira, Carla N. Mavian, Eduan Wilkinson
CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation
Bioinformatics, Volume 42, Issue 1, January 2026. https://doi.org/10.1093/bioinformatics/btaf665.
M. C. Matthews, M. E. M. Toorians, T. J. Davies, R. D. Stewart, W. J. Goosen, and M. A. Miller
A microbial safari: finding evidence of Mycobacterium bovis DNA in soil from the Kruger National Park, South Africa
Microbiology Spectrum, December 2025; 13. doi:10.1128/spectrum.01658-25.
Rachiel Gumbo, Tristen Lourens, Deborah M. Cooke, Tanya J. Kerr, Robin M. Warren, Michele A. Miller, Giovanni Ghielmetti, and Wynand J. Goosen
Isolation of viable Mycobacterium bovis from faeces of naturally infected free-ranging rural domestic cattle (Bos taurus)
Journal of Applied Microbiology, December 2025; 136(12): lxaf281. doi:10.1093/jambio/lxaf281.
Sinegugu Kholeka Mhlophe, Charlene Clarke, Giovanni Ghielmetti, Megan Matthews, Tanya Jane Kerr, Michele Ann Miller and Wynand Johan Goosen
Culture-independent detection of Mycobacterium tuberculosis complex DNA using targeted next generation sequencing in African buffalo (Syncerus caffer) oronasal swabs in South Africa
Frontiers in Veterinary Science, 2025; 12: 1523628. doi:10.3389/fvets.2025.1523628.
Emilyn C. Conceição, Felicia Wells, Abhinav Sharma, Mishka Haffejee, Brendon Mann, Justice T. Ngom, Shatha Omar, Johannes Loubser, Miguel de Diego Fuertes, Vincent Rennie, Anzaan Dippenaar, Tim Heupink, Túlio de Oliveira, Gian Van der Spuy, Annelies Van Rie, Robin M. Warren
Mycobacterium tuberculosis cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis
Microbial Genomics, Volume 11, Issue 11, 24 November 2025. doi.org:10.1099/mgen.0.001565.
Gaspary O. Mwanyika, Monika Moir, Abdualmoniem O. Musa, Jenicca Poongavanan, Graeme Dor, Eduan Wilkinson, Cheryl Baxter, Tulio de Oliveira, Houriiyah Tegally
A decade of dengue disease burden in Africa (2013–2023): a systematic review
Travel Medicine and Infectious Disease, Vol 67: 102897, October 2025 (available online 25 August 2925). doi:10.1016/j.tmaid.2025.102897.
Derek Tshiabuila, James E. San, Eduan Wilkinson, Graeme Dor, Houriiyah Tegally, Tongai G. Maponga, Marion Delphin, Philippa C. Matthews, Darren P. Martin, Cheryl Baxter and Tulio de Oliveira
Conserved recombination patterns across hepatitis B genotypes: a retrospective study
Virology Journal, July 2025 22:220. doi:10.1186/s12985-025-02829-0
Lucious Chabuka, Wonderful T. Choga, Carla N. Mavian, Monika Moir, Christian Morgenstern, Houriiyah Tegaly, Abhinav Sharma, Eduan Wilkinson, Yeshnee Naidoo, Rhys Inward, Samir Bhatt, G.R. William Wint, Kamran Khan, Isaac I. Bogoch, Moritz U.G. Kraemer, José Lourenço, Cheryl Baxter, Massimiliano Tagliamonte, Marco Salemi, Richard J. Lessells, Collins Mitambo, Ronald Chitatanga, Joseph Bitilinyu-Bango, Mabvuto Chiwaula, Yollamu Chavula, Mphatso Bukhu, Happy Manda, Moses Chitenje, Innocent Malolo, Alex Mwanyongo, Bernard Mvula, Mirrium Nyenje, Tulio de Oliveira, and Mathew Kagoli
Genomic surveillance of climate-amplified cholera outbreak, Malawi, 2022-2023
Emerging Infectious Diseases, 31(6):1090-1099, June 2025. doi:10.3201/eid3106.240930.
Christoffel J. Opperman, Salim Ben Amor, Greshan Kisten, Brendon C. Mann, Janré Steyn, Sarishna Singh, Yonas Ghebrekristos, Robin Warren, and Wynand Goosen
Mycobacterium avium DNA extraction: Implications for NTM identification and amplicon sequencing
South African Journal of Infectious Diseases, May 2025; 40(1): a717. doi:10.4102/sajid.v40i1.717.
John Juma, Samson Konongoi, Reuben Kimenji, Collins Muli, Paul Dobi, Shebbar Osiany, Edward Kiritu, Bernard Bett, Samuel Oyola
Targeted sequencing of Rift Valley fever virus (RVFV) on Oxford Nanopore MinION platform
Protocols.io, 28 April 2025. doi: 10.17504/protocols.io.rm7vz6y3xgx1/v1.
Christoffel Opperman, Janet Scott, Janre Steyn, Sarishna Singh, Yonas Ghebrekristos, Roland Croxford, Robin Warren, Aliasgar Esmail, Giovanni Ghielmetti, and Wynand Goosen
Mixed nontuberculous mycobacteria in an immunocompromised patient with probable progressive multifocal leukoencephalopathy
IJID Regions, 2025; 14: 100502. doi:10.1016/j.ijregi.2024.100502.
Megan C. Matthews, Deborah M. Cooke, Tanya J. Kerr, Andre G. Loxton, Robin M. Warren, Giovanni Ghielmetti, Elizabeth M. Streicher, Carmel S. Witte, Michele A. Miller, Wynand J. Goosen
Evidence of Mycobacterium bovis DNA in shared water sources at livestock – wildlife – human interfaces in KwaZulu-Natal, South Africa
Frontiers in Veterinary Science, Volume 12, 28 February 2025. doi:10.3389/fvets.2025.1483162.
Adugna Abera, Houriiyah Tegally, Geremew Tasew, Eduan Wilkinson, Abraham Ali, Feyisa Regasa, Molalegne Bitew, Mahlet Belachew, Lucious Chabuka, Gaspary Mwanyika, Derek Tshiabuila, Jennifer Giandhari, Sureshnee Pillay, Jenicca Poogavanan, Monika Moir, Moritz U.G. Kraemer, Kamran Khan, Carmen Huber, Getachew Tollera, Tobias F. Rinke de Wit, Cheryl Baxter, Richard Lessells, Dawit Wolday, Dereje Beyene, Tulio de Oliveira, and CLIMADE Consortium
Genomic Characterization of Circulating Dengue Virus, Ethiopia, 2022 - 2023
Emerging Infectious Diseases, 31(3):516-525, March 2025. doi:10.3201/eid3103.240996.
Jenicca Poongavanan, José Lourenço, Joseph L-H Tsui, Vittoria Colizza, Yajna Ramphal, Cheryl Baxter, Moritz U G Kraemer, Marcel Dunaiski, Tulio de Oliveira, Houriiyah Tegally
Dengue virus importation risks in Africa: a modelling study
The Lancet Planetary Health, December 2024; 8(12): e1043–54. doi:10.1016/S2542-5196(24)00214-7
Derek Tshiabuila, Wonderful Choga, James E. San, Tongai Maponga, Gert Van Zyl, Jennifer Giandhari, Sureshnee Pillay, Wolfgang Preiser, Yeshnee Naidoo, Cheryl Baxter, Darren P. Martin, Tulio de Oliveira
An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable for Genomic Surveillance Within Clinical Diagnostic Settings
International Journal of Molecular Sciences, 25(21): 11702, 31 October 2024. doi:10.3390/ijms252111702.
Tulio de Oliveira
The third era of genomics is at risk of being dismantled across the global south
Science, vol 386, Issue 6718, 10 October 2024. doi:10.1126/science.adt4843.
Christoffel Opperman, Janré Steyn, Megan Ceris Matthews, Sarishna Singh, Yonas Ghebrekristos, Tanya Jane Kerr, Michele Miller, Aliasgar Esmail, Helen Cox, Robin Warren, Giovanni Ghielmetti, Wynand J. Goosen
Targeted deep sequencing of mycobacteria species from extrapulmonary sites not identified by routine line probe assays: a retrospective laboratory analysis of stored clinical cultures
IJID Regions, Volume 13, 100464, December 2024 (available online 24 September 2024). doi.org/10.1016/j.ijregi.2024.100464.
Isidore Nsengimana, John Juma, Kristina Roesel, Methode N. Gasana, Fabrice Ndayisenga, Claude M. Muvunyi, Emmanuel Hakizimana, Jean N. Hakizimana, Gillian Eastwood, Augustino A. Chengula, Bernard Bett, Christopher J. Kasanga, Samuel O. Oyola
Genomic epidemiology of Rift Valley Fever Virus involved in the 2018 and 2022 outbreaks in livestock in Rwanda
Viruses, 16, no. 7: 1148, 17 July 2024. doi.org/10.3390/v16071148.
Giovanni Ghielmetti, Tanya J. Kerr, Netanya Bernitz, Sinegugu K. Mhlophe, Elizma Streicher, Andre G. Loxton, Robin M. Warren, Michele A. Miller, Wynand J. Goosen
Insights into mycobacteriome composition in Mycobacterium bovis‑infected African buffalo (Syncerus caffer) tissue samples
Scientific Reports, 14, 17537, 30 July 2024, doi: 10.1038/s41598-024-68189-x.
Wynand J. Goosen, Sashen Moodley, Giovanni Ghielmetti, Yumna Moosa, Thando Zulu, Theresa Smit, Vukuzazi Team, Leanie Kleynhans, Tanya J. Kerr, Elizabeth M. Streicher, Willem A. Hanekom, Robin M. Warren, Emily B. Wong, Michele A. Miller
Identification and molecular characterization of Mycobacterium bovis DNA in GeneXpert® MTB/RIF ultra-positive, culture-negative sputum from a rural community in South Africa
One Health, 18, 100702, June 2024 (available online March 2024). doi: 10.1016/j.onehlt.2024.100702.
Deborah M. Cooke, Charlene Clarke, Tanya J. Kerr, Robin M. Warren, Carmel Witte, Michele A. Miller, Wynand J. Goosen
Detection of Mycobacterium bovis in nasal swabs from communal goats (Capra hircus) in rural KwaZulu-Natal, South Africa
Frontiers in Microbiology, 15:1349163, 14 February 2024. doi: 10.3389/fmicb.2024.1349163.