GENOMIC SURVEILLANCE TO CONTROL PATHOGEN INFECTIONS IN AFRICA

Informacje na temat projektu

GenPath Africa

Identyfikator umowy o grant: 101103171

DOI

10.3030/101103171

Data podpisania przez KE 28 Sierpnia 2023

Data rozpoczęcia 1 Maja 2023

Data zakończenia 30 Kwietnia 2027

Finansowanie w ramach

• Health

Koszt całkowity

€ 4 999 170,25

Wkład UE

€ 4 999 170,25

Koordynowany przez

STELLENBOSCH UNIVERSITY
South Africa

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Publikacje

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> )

Autorzy: Rachiel Gumbo, Tristen Lourens, Deborah M Cooke, Tanya J Kerr, Robin M Warren, Michele A Miller, Giovanni Ghielmetti, Wynand J Goosen
Opublikowane w: Journal of Applied Microbiology, Numer 136, 2025, ISSN 1365-2672
Wydawca: 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

Autorzy: M. C. Matthews, M. E. M. Toorians, T. J. Davies, R. D. Stewart, W. J. Goosen, M. A. Miller
Opublikowane w: Microbiology Spectrum, Numer 14, 2025, ISSN 2165-0497
Wydawca: 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

Autorzy: Deborah M. Cooke; Charlene Clarke; Tanya J. Kerr; Robin M. Warren; Carmel Witte, Michele A. Miller; Wynand J. Goosen
Opublikowane w: Frontiers in Microbiology, Numer 15:1349163, 2024, ISSN 1664-302X
Wydawca: Frontiers Media S.A.
DOI: 10.3389/fmicb.2024.1349163

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

Autorzy: 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
Opublikowane w: Emerging Infectious Diseases, Numer 31, 2025, ISSN 1080-6040
Wydawca: 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

Autorzy: 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
Opublikowane w: BMC Genomics, 2026, ISSN 1471-2164
Wydawca: 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

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

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

Autorzy: Tulio de Oliveira
Opublikowane w: Science, Numer 386:6718, 2024, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.adt484

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

Autorzy: Christoffel Opperman, Janet Scott, Janre Steyn, Sarishna Singh, Yonas Ghebrekristos, Roland Croxford, Robin Warren, Aliasgar Esmail, Giovanni Ghielmetti, Wynand Goosen
Opublikowane w: IJID Regions, Numer 14, 2025, ISSN 2772-7076
Wydawca: Elsevier BV
DOI: 10.1016/J.IJREGI.2024.100502

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

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

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

Autorzy: 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
Opublikowane w: Emerging Infectious Diseases, Numer 31, 2025, ISSN 1080-6040
Wydawca: Centers for Disease Control and Prevention (CDC)
DOI: 10.3201/EID3103.240996

Dengue virus importation risks in Africa: a modelling study

Autorzy: 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
Opublikowane w: The Lancet Planetary Health, Numer 8, 2024, ISSN 2542-5196
Wydawca: 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

Autorzy: 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
Opublikowane w: Microbial Genomics, Numer Volume 11, Numer 11, 2025, ISSN 2057-5858
Wydawca: 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

Autorzy: 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
Opublikowane w: International Journal of Molecular Sciences, Numer 25, 2024, ISSN 1422-0067
Wydawca: 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

Autorzy: 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
Opublikowane w: Frontiers in Veterinary Science, Numer 12, 2025, ISSN 2297-1769
Wydawca: Frontiers Media SA
DOI: 10.3389/FVETS.2025.1483162

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

Autorzy: Gaspary O. Mwanyika, Monika Moir, Abdualmoniem O. Musa, Jenicca Poongavanan, Graeme Dor, Eduan Wilkinson, Cheryl Baxter, Tulio de Oliveira, Houriiyah Tegally
Opublikowane w: Travel Medicine and Infectious Disease, Numer 67, 2025, ISSN 1477-8939
Wydawca: 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

Autorzy: 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
Opublikowane w: The Lancet Microbe, Numer 7, 2026, ISSN 2666-5247
Wydawca: Elsevier BV
DOI: 10.1016/J.LANMIC.2025.101251

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

Autorzy: Giovanni Ghielmetti; Tanya J. Kerr; Netanya Bernit; Sinegugu K. Mhlophe; Elizma Streicher; Andre G. Loxton; Robin M. Warren; Michele A. Miller; Wynand J. Goosen
Opublikowane w: Scientific Reports, Numer 14:17537, 2024, ISSN 2045-2322
Wydawca: 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

Autorzy: 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
Opublikowane w: The Journal of Infectious Diseases, Numer 233, 2026, ISSN 0022-1899
Wydawca: 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

Autorzy: 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
Opublikowane w: Microbial Genomics, Numer 12, 2026, ISSN 2057-5858
Wydawca: Microbiology Society
DOI: 10.1099/MGEN.0.001646

Disseminated Mycobacterium avium: A multi-organ system investigation

Autorzy: Christoffel Johannes Opperman, Sarishna Singh, Yons Ghebrekristos, Michael Linström, Lourens Jacobsz, Wynand Goosen
Opublikowane w: International Journal of Infectious Diseases, Numer 165, 2026, ISSN 1201-9712
Wydawca: 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

Autorzy: 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
Opublikowane w: Viruses, Numer 16(7):1148, 2024, ISSN 1999-4915
Wydawca: 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

Autorzy: 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
Opublikowane w: One Health, Numer 18:100702, 2024, ISSN 2352-7714
Wydawca: 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

Autorzy: Sinegugu Kholeka Mhlophe, Charlene Clarke, Giovanni Ghielmetti, Megan Matthews, Tanya Jane Kerr, Michele Ann Miller, Wynand Johan Goosen
Opublikowane w: Frontiers in Veterinary Science, Numer 12, 2025, ISSN 2297-1769
Wydawca: Frontiers Media SA
DOI: 10.3389/FVETS.2025.1523628

Conserved recombination patterns across hepatitis B genotypes: a retrospective study

Autorzy: 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
Opublikowane w: Virology Journal, Numer 22, 2025, ISSN 1743-422X
Wydawca: 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

Autorzy: 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
Opublikowane w: IJID Regions, 2024, ISSN 2772-7076
Wydawca: Elsevier BV
DOI: 10.1016/j.ijregi.2024.100464