Linking Infectious disease Front-liners’ control Efforts with central public health authorities in The African Great Lakes Region

Resultado final

Initial and updated Data Management Plan to be executed. Reviews and any updates to the DMP will be done in Months 24 and 48.

Collaboration Agreement

Collaboration Agreement between projects

Tailored bioinformatic workflow created

The bioinfomratic workflow to be used in the frontline will be made publicly available on Github

Training in frontline sequencing and bioinformatics

Training conduced for project participants in nanopore sequencing and simple frontline bioinformatics

Publicaciones

Mpox: A case study for a one health approach to infectious disease prevention

Autores: David T.S. Hayman, Marion P.G. Koopmans, Andrew A. Cunningham, Salome A. Bukachi, Leandre Murhula Masirika, Wanda Markotter, Thomas C. Mettenleiter
Publicado en: One Health, Edición 20, 2026, ISSN 2352-7714
Editor: Elsevier BV
DOI: 10.1016/J.ONEHLT.2025.101059

Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations

Autores: Saria Otani, Marie Louise Jespersen, Christian Brinch, Frederik Duus Møller, Bo Pilgaard, Emilie Egholm Bruun Jensen, Pimlapas Leekitcharoenphon, Christina Aaby Svendsen, Amalie H. Aarestrup, Tolbert Sonda, Teresa J. Sylvina, Jeff Leach, Alexander Piel, Fiona Stewart, Panagiotis Sapountzis, Paul E. Kazyoba, Happiness Kumburu, Frank M. Aarestrup
Publicado en: Gut Microbes, Edición 17, 2025, ISSN 1949-0976
Editor: Informa UK Limited
DOI: 10.1080/19490976.2025.2484385

Monkeypox Clade Ib virus introduction into Burundi: first findings, July to mid-August 2024

Autores: Néhémie Nzoyikorera, Cassien Nduwimana, Leonard Schuele, David F Nieuwenhuijse, Marion Koopmans, Saria Otani, Frank M Aarestrup, Théogène Ihorimbere, Denis Niyomwungere, Armstrong Ndihokubwayo, Idrissa Diawara, Alexis Niyomwungere, Dionis Nizigiyimana, Marie Noelle Uwineza, Bas B Oude Munnink, Joseph Nyandwi
Publicado en: Eurosurveillance, Edición 29, 2024, ISSN 1560-7917
Editor: European Centre for Disease Control and Prevention (ECDC)
DOI: 10.2807/1560-7917.ES.2024.29.42.2400666

A Hadza-enriched <i>Prevotella/Segatella</i> xyloglucanase shows sequence conservation and functional specialization

Autores: Marie Louise Jespersen, Kamilla Kjærgaard Munk, Sune Fjermedal, Bo Pilgaard, Anne S. Meyer, Frank M. Aarestrup, Saria Otani
Publicado en: Gut Microbes Reports, Edición 3, 2026, ISSN 2993-3935
Editor: Informa UK Limited
DOI: 10.1080/29933935.2026.2673265

Real-time PCR assay to detect the novel Clade Ib monkeypox virus, September 2023 to May 2024

Autores: Leonard Schuele, Leandre Murhula Masirika, Jean Claude Udahemuka, Freddy Belesi Siangoli, Justin Bengehya Mbiribindi, Pacifique Ndishimye, Frank M Aarestrup, Marion Koopmans, Bas B Oude Munnink, Richard Molenkamp, null null
Publicado en: Eurosurveillance, Edición 29, 2024, ISSN 1560-7917
Editor: European Centre for Disease Control and Prevention (ECDC)
DOI: 10.2807/1560-7917.ES.2024.29.32.2400486

Genomic epidemiology reveals geographically structured co-circulation of AFR10 and AFR13 Vibrio cholerae lineages driving cholera outbreaks in Tanzania (2022–2024)

Autores: Ibrahim I. Mauki, Reuben Abednego, Lawrence Mapunda, Maria Ezekiely Kelly, Monica Fredrick Francis, Jackson Mushumbusi, Dennis Mrosso Kado, Feliciana Rawile, Boaz Wadugu, Hamisi Swalehe, Modest Benard, Edna Mgimba, Seif Abdul, Ambele Mwafulango, Tolbert Sonda, Calvin Sindato, Paul Kazyoba, Nyambura Moremi
Publicado en: Microbial Genomics, Edición 12, 2026, ISSN 2057-5858
Editor: Microbiology Society
DOI: 10.1099/MGEN.0.001813

Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics

Autores: Emilie Egholm Bruun Jensen, Néhémie Nzoyikorera, Mirena Ivanova, Pimlapas Leekitcharoenphon, Marie Noelle Uwineza, Idrissa Diawara, Joseph Nyandwi, Frank M. Aarestrup, Saria Otani
Publicado en: PLOS Neglected Tropical Diseases, Edición 20, 2026, ISSN 1935-2735
Editor: Public Library of Science (PLoS)
DOI: 10.1371/JOURNAL.PNTD.0014175

Capacity building for genomic surveillance of mpox and other emerging diseases in resource-limited settings within the African Great Lakes region

Autores: Leonard Schuele, Néhémie Nzoyikorera, Jean Claude Udahemuka, Hayley Cassidy, Leandre Murhula Masirika, David F. Nieuwenhuijse, Cassien Nduwimana, Richard Molenkamp, Joseph Nyandwi, Marjan Boter, Jules Minega Ndoli, Luca M. Zaeck, Jean Pierre Musabyimana, Rory D. de Vries, Justin Bengehya Mbiribindi, Freddy Belesi Siangoli, Saria Otani, Frank M. Aarestrup, Marion Koopmans, Pacifique Ndishimye, Bas B. Oude Munnink
Publicado en: Communications Medicine, Edición 6, 2026, ISSN 2730-664X
Editor: Springer Science and Business Media LLC
DOI: 10.1038/S43856-026-01713-4

Ongoing mpox outbreak in Kamituga, South Kivu province, associated with monkeypox virus of a novel Clade I sub-lineage, Democratic Republic of the Congo, 2024

Autores: Leandre Murhula Masirika, Jean Claude Udahemuka, Leonard Schuele, Pacifique Ndishimye, Saria Otani, Justin Bengehya Mbiribindi, Jean M. Marekani, Léandre Mutimbwa Mambo, Nadine Malyamungu Bubala, Marjan Boter, David F. Nieuwenhuijse, Trudie Lang, Ernest Balyahamwabo Kalalizi, Jean Pierre Musabyimana, Frank M. Aarestrup, Marion Koopmans, Bas B. Oude Munnink, Freddy Belesi Siangoli
Publicado en: Eurosurveillance, Edición 29, 2024, ISSN 1560-7917
Editor: European Centre for Disease Control and Prevention (ECDC)
DOI: 10.2807/1560-7917.ES.2024.29.11.2400106

Genomic monitoring and tracking of mpox virus clade Ib in Burundi between july to september 2024

Autores: Néhémie Nzoyikorera, Leonard Schuele, David F. Nieuwenhuijse, Cassien Nduwimana, Théogène Ihorimbere, Denis Niyomwungere, Hayley Cassidy, Marjan Boter, Celestin Nibogora, Armstrong Ndihokubwayo, Alexis Niyomwungere, Dionis Nizigiyimana, Marie Noelle Uwineza, Idrissa Diawara, Saria Otani, Frank M. Aarestrup, Marion Koopmans, Joseph Nyandwi, Bas B. Oude Munnink
Publicado en: Communications Medicine, Edición 5, 2025, ISSN 2730-664X
Editor: Springer Science and Business Media LLC
DOI: 10.1038/S43856-025-01199-6

Improved ability to utilize lactose and grow in milk as a potential explanation for emergence of the novel bovine Staphylococcus aureus ST5477

Autores: Frank M. Aarestrup, Egon B. Hansen, Happiness H. Kumburu, Tutu Mzee, Saria Otani
Publicado en: International Journal of Medical Microbiology, Edición 317, 2024, ISSN 1438-4221
Editor: Elsevier BV
DOI: 10.1016/j.ijmm.2024.151637

Epidemiological and genomic evolution of the ongoing outbreak of clade Ib mpox virus in the eastern Democratic Republic of the Congo

Autores: Leandre Murhula Masirika, Jean Claude Udahemuka, Leonard Schuele, David F. Nieuwenhuijse, Pacifique Ndishimye, Marjan Boter, Justin Bengehya Mbiribindi, Cris Kacita, Trudie Lang, Christian Gortázar, Jean Pierre Musabyimana, Saria Otani, Frank M. Aarestrup, Freddy Belesi Siangoli, Bas B. Oude Munnink, Marion Koopmans
Publicado en: Nature Medicine, 2025, ISSN 1078-8956
Editor: Springer Science and Business Media LLC
DOI: 10.1038/S41591-025-03582-1

Serological evidence of clade Ib Mpox transmission by sex workers and within household in South Kivu, DRC

Autores: Leandre Murhula Masirika, Luca M. Zaeck, Pacifique Ndishimye, Jean Claude Udahemuka, Saria Otani, Frank M. Aarestrup, Leonard Schuele, Babs E. Verstrepen, Scott Jones, Ashley Otter, Corine H. GeurtsvanKessel, Jean Pierre Musabyimana, Justin Bengehya Mbiribindi, Jules Minega Ndoli, Bas B. Oude Munnink, Freddy Siangoli Belesi, Marion P. G. Koopmans, Rory D. de Vries
Publicado en: Nature Communications, Edición 16, 2025, ISSN 2041-1723
Editor: Springer Science and Business Media LLC
DOI: 10.1038/S41467-025-62064-7

Prevalence, Etiology, and Treatment of Diarrheal Diseases in Kenya: A Scoping Review

Autores: Fredrick Ogumbo, Latifah Benta, Brian Kimutai, Joseph Mugah, Eddy Johnson, Vanessa Onyonyi, Caroline Dande, Lillian Musila, Steve Wandiga
Publicado en: American Journal of Epidemiology and Infectious Disease, Edición 12, 2024, ISSN 2333-116X
Editor: Science and Education Publishing Co., Ltd.
DOI: 10.12691/ajeid-12-4-1

NanoMGT: Marker gene typing of low complexity mono-species metagenomic samples using noisy long reads

Autores: Malte B Hallgren, Philip T L C Clausen, Frank M Aarestrup
Publicado en: Biology Methods and Protocols, Edición 9, 2024, ISSN 2396-8923
Editor: Oxford University Press (OUP)
DOI: 10.1093/BIOMETHODS/BPAE057

Persistent circulation of Rift Valley fever virus lineage C in Rwanda, 2022–2025

Autores: Jean Claude Udahemuka, Hayley Cassidy, Leonard Schuele, Evodie Uwibambe, Methode Gasana Ngabo, Leandre Murhula Masirika, Reuben Sindayiheba, Saria Otani, Misbah Gashegu, Jean-Claude Twizere, Frank Aarestrup, Fabrice Ndayisenga, Bas B. Oude Munnink, Marion P.G. Koopmans, Pacifique Ndishimye
Publicado en: One Health, Edición 23, 2026, ISSN 2352-7714
Editor: Elsevier BV
DOI: 10.1016/J.ONEHLT.2026.101529

Tanzanian goat gut microbiomes adapt to roadside pollutants and environmental stressors

Autores: Emilie Egholm Bruun Jensen, Marie Louise Jespersen, Christina Aaby Svendsen, Tolbert Sonda, Saria Otani, Frank M. Aarestrup
Publicado en: Microbiology Spectrum, Edición 14, 2026, ISSN 2165-0497
Editor: American Society for Microbiology
DOI: 10.1128/SPECTRUM.02036-25

Whole-genome sequencing reveals a previously unrecognized measles virus cluster in Burundi

Autores: Néhémie Nzoyikorera, David F. Nieuwenhuijse, Leonard Schuele, Cassien Nduwimana, Armstrong Ndihokubwayo, Théogène Ihorimbere, Denis Niyomwungere, Hayley Cassidy, Marjan Boter, Celestin Nibogora, Richard Molenkamp, Alexis Niyomwungere, Dionis Nizigiyimana, Marie Noelle Uwineza, Idrissa Diawara, Saria Otani, Rogier Bodewes, Frank M. Aarestrup, Marion Koopmans, Joseph Nyandwi, Bas B. Oude Munnink
Publicado en: PLOS One, Edición 21, 2026, ISSN 1932-6203
Editor: Public Library of Science (PLoS)
DOI: 10.1371/JOURNAL.PONE.0351691

Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC

Autores: Leonard Schuele, Leandre Murhula Masirika, Hayley Cassidy, Philip T. L. C. Clausen, Luca M. Zaeck, Marjan Boter, Pacifique Ndishimye, Jean Claude Udahemuka, Rory D. de Vries, Saria Otani, Richard Molenkamp, David F. Nieuwenhuijse, Justin Bengehya Mbiribindi, Freddy Belesi Siangoli, Marion Koopmans, Frank M. Aarestrup, Bas B. Oude Munnink
Publicado en: Microbiology Spectrum, Edición 13, 2025, ISSN 2165-0497
Editor: American Society for Microbiology
DOI: 10.1128/SPECTRUM.00512-25

Rift Valley Fever outbreaks in the East African Community: insights from ProMed data (2010–2024)

Autores: Pacifique Ndishimye; Pacifique Ndishimye; Pacifique Ndishimye; Therese Umuhoza; Therese Umuhoza; Therese Umuhoza; Brigitte Umutoni; Brigitte Umutoni; Fathiah Zakham; Fathiah Zakham; Matin Ndayambaje; Matin Ndayambaje; Benjamin Hewins; Methode Ngabo Gasana; Ali Toloue Ostadgavahi; Gustavo Sganzerla; Fabrice Ndayisenga; David Kelvin; Jean Claude Udahemuka; Jean Claude Udahemuka; Jean Claude Udahemuka
Publicado en: Frontiers in Public Health, 2024, ISSN 2296-2565
Editor: Frontiers
DOI: 10.3389/FPUBH.2024.1298594

Nature Communications

Autores: Leandre Murhula Masirika; Luca M. Zaeck; Pacifique Ndishimye; Jean Claude Udahemuka; Saria Otani; Frank M. Aarestrup; Leonard Schuele; Babs E. Verstrepen; Scott Jones; Ashley Otter; Corine H. GeurtsvanKessel; Jean Pierre Musabyimana; Justin Bengehya Mbiribindi; Jules Minega Ndoli; Bas B. Oude Munnink; Freddy Siangoli Belesi; Marion P. G. Koopmans; Rory D. de Vries
Publicado en: Nature Communications, 2025, ISSN 2041-1723
Editor: Spring Nature
DOI: 10.1038/S41467-025-62064-7

Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC

Autores: Leonard Schuele; Leandre Murhula Masirika; Hayley Cassidy; Philip T. L. C. Clausen; Luca M. Zaeck; Marjan Boter; Pacifique Ndishimye; Jean Claude Udahemuka; Rory D. de Vries; Saria Otani; Richard Molenkamp; David F. Nieuwenhuijse; Justin Bengehya Mbiribindi; Freddy Belesi Siangoli; Marion Koopmans; Frank M. Aarestrup; Bas B. Oude Munnink
Publicado en: Microbiology Spectrum, 2025, ISSN 2165-0497
Editor: ASM Journals
DOI: 10.1128/SPECTRUM.00512-25

Serological evidence of clade Ib Mpox transmission by sex workers and within household in South Kivu, DRC

Autores: Leandre Murhula Masirika, Luca M. Zaeck, Pacifique Ndishimye, Jean Claude Udahemuka, Saria Otani, Frank M. Aarestrup, Leonard Schuele, Babs E. Verstrepen, Scott Jones, Ashley Otter, Corine H. GeurtsvanKessel, Jean Pierre Musabyimana, Justin Bengehya Mbiribindi, Jules Minega Ndoli, Bas B. Oude Munnink, Freddy Siangoli Belesi, Marion P. G. Koopmans, Rory D. de Vries
Publicado en: Nature Communications, Edición 16, 2025, ISSN 2041-1723
Editor: Springer Science and Business Media LLC
DOI: 10.1038/S41467-025-62064-7

Draft genomic sequences of <i>Vibrio cholerae</i> strains linked to the cholera outbreak in Kamituga, South Kivu, DRC

Autores: Pimlapas Leekitcharoenphon, Pacifique Ndishimye, Saria Otani, Frederik Duus Møller, Leonard Schuele, Bas B. Oude Munnink, Jean Claude Udahemuka, Freddy Belesi Siangoli, Justin Bengehya Mbiribindi, Marion Koopmans, Frank M. Aarestrup, Leandre Murhula Masirika
Publicado en: Microbiology Resource Announcements, Edición 14, 2025, ISSN 2576-098X
Editor: American Society for Microbiology
DOI: 10.1128/MRA.01044-24

Assembly-free typing of Nanopore and Illumina data through proximity scoring with KMA

Autores: Philip T L C Clausen, Malte B Hallgren, Søren Overballe-Petersen, Vanessa R Marcelino, Henrik Hasman, Frank M Aarestrup
Publicado en: NAR Genomics and Bioinformatics, Edición 7, 2025, ISSN 2631-9268
Editor: Oxford University Press (OUP)
DOI: 10.1093/NARGAB/LQAF116

Trends and seasonal variation in gastrointestinal infections in Tanzania: Analysis of 5-year DHIS2 data toward implementing the sampling cycles and metagenomic analyses

Autores: Gerald Phares Mwing’a; Patrick A. Kimu; Melkiory Beti; Mariana Shayo; Davis Kuchaka; Zaina Mchome; Masoud Mahundi; Claud Kumalija; Calvin Sindato; Tolbert Sonda; Paul E. Kazyoba
Publicado en: IJID Regions, 2025
Editor: Science Direct
DOI: 10.1016/J.IJREGI.2025.100661

Resultados de proyectos

Resultado final

Publicaciones

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