GENOMIC SURVEILLANCE TO CONTROL PATHOGEN INFECTIONS IN AFRICA

Información del proyecto

GenPath Africa

Identificador del acuerdo de subvención: 101103171

DOI

10.3030/101103171

Fecha de la firma de la CE 28 Agosto 2023

Fecha de inicio 1 Mayo 2023

Fecha de finalización 30 Abril 2027

Financiado con arreglo a

• Health

Coste total

€ 4 999 170,25

Aportación de la UE

€ 4 999 170,25

Coordinado por

STELLENBOSCH UNIVERSITY
South Africa

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Publicaciones

Peer reviewed articles (25)

Isolation of viable <i>Mycobacterium bovis</i> from faeces of naturally infected free-ranging rural domestic cattle ( <i>Bos taurus</i> )

Autores: Rachiel Gumbo, Tristen Lourens, Deborah M Cooke, Tanya J Kerr, Robin M Warren, Michele A Miller, Giovanni Ghielmetti, Wynand J Goosen
Publicado en: Journal of Applied Microbiology, Edición 136, 2025, ISSN 1365-2672
Editor: Oxford University Press (OUP)
DOI: 10.1093/JAMBIO/LXAF281

A microbial safari: finding evidence of <i>Mycobacterium bovis</i> DNA in soil from the Kruger National Park, South Africa

Autores: M. C. Matthews, M. E. M. Toorians, T. J. Davies, R. D. Stewart, W. J. Goosen, M. A. Miller
Publicado en: Microbiology Spectrum, Edición 14, 2025, ISSN 2165-0497
Editor: American Society for Microbiology
DOI: 10.1128/SPECTRUM.01658-25

Detection of Mycobacterium bovis in nasal swabs from communal goats (Capra hircus) in rural KwaZulu-Natal, South Africa

Autores: Deborah M. Cooke; Charlene Clarke; Tanya J. Kerr; Robin M. Warren; Carmel Witte, Michele A. Miller; Wynand J. Goosen
Publicado en: Frontiers in Microbiology, Edición 15:1349163, 2024, ISSN 1664-302X
Editor: Frontiers Media S.A.
DOI: 10.3389/fmicb.2024.1349163

Genomic Surveillance of Climate-Amplified Cholera Outbreak, Malawi, 2022–2023

Autores: 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. WilliamWint, 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, Mathew Kagoli
Publicado en: Emerging Infectious Diseases, Edición 31, 2025, ISSN 1080-6040
Editor: Centers for Disease Control and Prevention (CDC)
DOI: 10.3201/EID3106.240930

Evaluation of DNA extraction methods from clinical Mycobacterium tuberculosis primary liquid culture for whole-genome sequencing

Autores: Emilyn Costa Conceição, Mishka Haffejee, Felicia Wells, Brendon Mann, Tim Heupink, Astrid Paulse, Jennifer Williams, Anzaan Dippenaar, Yonas Ghebrekristos, Megan Burger, Vincent Rennie, Miguel de Diego Fuertes, Ilham Al-Talib, Nabila Ismail, Melanie Grobbelaar, Elizabeth Maria Streicher, Túlio de Oliveira, Gian Van der Spuy, Annelies Van Rie, Robin Warren
Publicado en: BMC Genomics, 2026, ISSN 1471-2164
Editor: Springer Science and Business Media LLC
DOI: 10.1186/S12864-026-12812-W

CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation

Autores: Massimiliano S Tagliamonte, Abhinav Sharma, Alberto Riva, Monika Moir, Marco Salemi, Cheryl Baxter, Tulio de Oliveira, Carla N Mavian, Eduan Wilkinson
Publicado en: Bioinformatics, Edición 42, 2026, ISSN 1367-4811
Editor: Oxford University Press (OUP)
DOI: 10.1093/BIOINFORMATICS/BTAF665

The third era of genomics is at risk of being dismantled across the global south

Autores: Tulio de Oliveira
Publicado en: Science, Edición 386:6718, 2024, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.adt484

Mixed nontuberculous mycobacteria in an immunocompromised patient with probable progressive multifocal leukoencephalopathy

Autores: Christoffel Opperman, Janet Scott, Janre Steyn, Sarishna Singh, Yonas Ghebrekristos, Roland Croxford, Robin Warren, Aliasgar Esmail, Giovanni Ghielmetti, Wynand Goosen
Publicado en: IJID Regions, Edición 14, 2025, ISSN 2772-7076
Editor: Elsevier BV
DOI: 10.1016/J.IJREGI.2024.100502

Mycobacterium avium DNA extraction: Implications for NTM identification and amplicon sequencing

Autores: Christoffel J. Opperman, Salim Ben Amor, Greshan Kisten, Brendon C. Mann, Janré Steyn, Sarishna Singh, Yonas Ghebrekristos, Robin Warren, Wynand Goosen
Publicado en: Southern African Journal of Infectious Diseases, Edición 40, 2025, ISSN 2312-0053
Editor: AOSIS
DOI: 10.4102/SAJID.V40I1.717

Genomic Characterization of Circulating Dengue Virus, Ethiopia, 2022–2023

Autores: 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, null null
Publicado en: Emerging Infectious Diseases, Edición 31, 2025, ISSN 1080-6040
Editor: Centers for Disease Control and Prevention (CDC)
DOI: 10.3201/EID3103.240996

Dengue virus importation risks in Africa: a modelling study

Autores: 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
Publicado en: The Lancet Planetary Health, Edición 8, 2024, ISSN 2542-5196
Editor: Elsevier BV
DOI: 10.1016/S2542-5196(24)00272-9

Mycobacterium tuberculosis cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis

Autores: 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
Publicado en: Microbial Genomics, Edición Volume 11, Edición 11, 2025, ISSN 2057-5858
Editor: Microbiological Society
DOI: 10.1099/MGEN.0.001565

An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable for Genomic Surveillance Within Clinical Diagnostic Settings

Autores: 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
Publicado en: International Journal of Molecular Sciences, Edición 25, 2024, ISSN 1422-0067
Editor: MDPI AG
DOI: 10.3390/ijms252111702

Evidence of Mycobacterium bovis DNA in shared water sources at livestock–wildlife–human interfaces in KwaZulu-Natal, South Africa

Autores: 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
Publicado en: Frontiers in Veterinary Science, Edición 12, 2025, ISSN 2297-1769
Editor: Frontiers Media SA
DOI: 10.3389/FVETS.2025.1483162

A decade of dengue disease burden in Africa (2013–2023): a systematic review

Autores: Gaspary O. Mwanyika, Monika Moir, Abdualmoniem O. Musa, Jenicca Poongavanan, Graeme Dor, Eduan Wilkinson, Cheryl Baxter, Tulio de Oliveira, Houriiyah Tegally
Publicado en: Travel Medicine and Infectious Disease, Edición 67, 2025, ISSN 1477-8939
Editor: Elsevier BV
DOI: 10.1016/J.TMAID.2025.102897

Spatiotemporal patterns of Rift Valley fever virus in Africa: a retrospective genomic epidemiology and phylodynamic modelling study

Autores: John Juma, Houriiyah Tegally, Samson L Konongoi, Kristina Roesel, Rosemary Sang, Tulio de Oliviera, M Kariuki Njenga, Alan Christoffels, Bernard Bett, Simon Dellicour, Samuel O Oyola
Publicado en: The Lancet Microbe, Edición 7, 2026, ISSN 2666-5247
Editor: Elsevier BV
DOI: 10.1016/J.LANMIC.2025.101251

Insights into mycobacteriome composition in Mycobacterium bovis-infected African buffalo (Syncerus caffer) tissue samples

Autores: Giovanni Ghielmetti; Tanya J. Kerr; Netanya Bernit; Sinegugu K. Mhlophe; Elizma Streicher; Andre G. Loxton; Robin M. Warren; Michele A. Miller; Wynand J. Goosen
Publicado en: Scientific Reports, Edición 14:17537, 2024, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-024-68189-x

Hyperendemicity of Rift Valley Fever in Southwestern Uganda Associated With the Rapidly Evolving Lineage C Viruses

Autores: Barnabas Bakamutumaho, John Juma, Erin Clancey, Luke Nyakarahuka, Silvia Situma, Raymond Odinoh, Jeanette Dawa, Carolyne Nasimiyu, Evan A Eskew, Stephen Balinandi, Sophia Mulei, John Kayiwa, John D Klena, Trevor R Shoemaker, Shannon L M Whitmer, Joel M Montgomery, John Schieffelin, Julius Lutwama, Allan Muruta, Henry Kyobe Bosa, Scott L Nuismer, Samuel O Oyola, Robert F Breiman, M Kariuki Njenga
Publicado en: The Journal of Infectious Diseases, Edición 233, 2026, ISSN 0022-1899
Editor: Oxford University Press (OUP)
DOI: 10.1093/INFDIS/JIAF417

Whole-genome sequencing reveals genetic diversity and transmission dynamics of Mycobacterium bovis in South African wildlife

Autores: 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
Publicado en: Microbial Genomics, Edición 12, 2026, ISSN 2057-5858
Editor: Microbiology Society
DOI: 10.1099/MGEN.0.001646

Disseminated Mycobacterium avium: A multi-organ system investigation

Autores: Christoffel Johannes Opperman, Sarishna Singh, Yons Ghebrekristos, Michael Linström, Lourens Jacobsz, Wynand Goosen
Publicado en: International Journal of Infectious Diseases, Edición 165, 2026, ISSN 1201-9712
Editor: Elsevier BV
DOI: 10.1016/J.IJID.2026.108475

Genomic Epidemiology of Rift Valley Fever Virus Involved in the 2018 and 2022 Outbreaks in Livestock in Rwanda

Autores: 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
Publicado en: Viruses, Edición 16(7):1148, 2024, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v16071148

Identification and molecular characterization of Mycobacterium bovis DNA in GeneXpert® MTB/RIF ultra-positive, culture-negative sputum from a rural community in South Africa

Autores: 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
Publicado en: One Health, Edición 18:100702, 2024, ISSN 2352-7714
Editor: Elsevier
DOI: 10.1016/j.onehlt.2024.100702

Culture-independent detection of Mycobacterium tuberculosis complex DNA using targeted next generation sequencing in African buffalo (Syncerus caffer) oronasal swabs in South Africa

Autores: Sinegugu Kholeka Mhlophe, Charlene Clarke, Giovanni Ghielmetti, Megan Matthews, Tanya Jane Kerr, Michele Ann Miller, Wynand Johan Goosen
Publicado en: Frontiers in Veterinary Science, Edición 12, 2025, ISSN 2297-1769
Editor: Frontiers Media SA
DOI: 10.3389/FVETS.2025.1523628

Conserved recombination patterns across hepatitis B genotypes: a retrospective study

Autores: Derek Tshiabuila, James E. San, Eduan Wilkinson, Graeme Dor, Houriiyah Tegally, Tongai G. Maponga, Marion Delphin, Philippa C. Matthews, Darren P. Martin, Cheryl Baxter, Tulio de Oliveira
Publicado en: Virology Journal, Edición 22, 2025, ISSN 1743-422X
Editor: Springer Science and Business Media LLC
DOI: 10.1186/S12985-025-02829-0

Targeted deep sequencing of mycobacteria species from extrapulmonary sites not identified by routine line probe assays: a retrospective laboratory analysis of stored clinical cultures

Autores: 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 Goosen
Publicado en: IJID Regions, 2024, ISSN 2772-7076
Editor: Elsevier BV
DOI: 10.1016/j.ijregi.2024.100464