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

Leistungen

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

Veröffentlichungen

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

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

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

Autoren: 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
Veröffentlicht in: Gut Microbes, Ausgabe 17, 2025, ISSN 1949-0976
Herausgeber: Informa UK Limited
DOI: 10.1080/19490976.2025.2484385

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

Autoren: 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
Veröffentlicht in: Eurosurveillance, Ausgabe 29, 2024, ISSN 1560-7917
Herausgeber: 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

Autoren: Marie Louise Jespersen, Kamilla Kjærgaard Munk, Sune Fjermedal, Bo Pilgaard, Anne S. Meyer, Frank M. Aarestrup, Saria Otani
Veröffentlicht in: Gut Microbes Reports, Ausgabe 3, 2026, ISSN 2993-3935
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Eurosurveillance, Ausgabe 29, 2024, ISSN 1560-7917
Herausgeber: 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)

Autoren: 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
Veröffentlicht in: Microbial Genomics, Ausgabe 12, 2026, ISSN 2057-5858
Herausgeber: Microbiology Society
DOI: 10.1099/MGEN.0.001813

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

Autoren: Emilie Egholm Bruun Jensen, Néhémie Nzoyikorera, Mirena Ivanova, Pimlapas Leekitcharoenphon, Marie Noelle Uwineza, Idrissa Diawara, Joseph Nyandwi, Frank M. Aarestrup, Saria Otani
Veröffentlicht in: PLOS Neglected Tropical Diseases, Ausgabe 20, 2026, ISSN 1935-2735
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Communications Medicine, Ausgabe 6, 2026, ISSN 2730-664X
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Eurosurveillance, Ausgabe 29, 2024, ISSN 1560-7917
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Communications Medicine, Ausgabe 5, 2025, ISSN 2730-664X
Herausgeber: 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

Autoren: Frank M. Aarestrup, Egon B. Hansen, Happiness H. Kumburu, Tutu Mzee, Saria Otani
Veröffentlicht in: International Journal of Medical Microbiology, Ausgabe 317, 2024, ISSN 1438-4221
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Nature Medicine, 2025, ISSN 1078-8956
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Nature Communications, Ausgabe 16, 2025, ISSN 2041-1723
Herausgeber: 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

Autoren: Fredrick Ogumbo, Latifah Benta, Brian Kimutai, Joseph Mugah, Eddy Johnson, Vanessa Onyonyi, Caroline Dande, Lillian Musila, Steve Wandiga
Veröffentlicht in: American Journal of Epidemiology and Infectious Disease, Ausgabe 12, 2024, ISSN 2333-116X
Herausgeber: 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

Autoren: Malte B Hallgren, Philip T L C Clausen, Frank M Aarestrup
Veröffentlicht in: Biology Methods and Protocols, Ausgabe 9, 2024, ISSN 2396-8923
Herausgeber: Oxford University Press (OUP)
DOI: 10.1093/BIOMETHODS/BPAE057

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

Autoren: 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
Veröffentlicht in: One Health, Ausgabe 23, 2026, ISSN 2352-7714
Herausgeber: Elsevier BV
DOI: 10.1016/J.ONEHLT.2026.101529

Tanzanian goat gut microbiomes adapt to roadside pollutants and environmental stressors

Autoren: Emilie Egholm Bruun Jensen, Marie Louise Jespersen, Christina Aaby Svendsen, Tolbert Sonda, Saria Otani, Frank M. Aarestrup
Veröffentlicht in: Microbiology Spectrum, Ausgabe 14, 2026, ISSN 2165-0497
Herausgeber: American Society for Microbiology
DOI: 10.1128/SPECTRUM.02036-25

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

Autoren: 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
Veröffentlicht in: PLOS One, Ausgabe 21, 2026, ISSN 1932-6203
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Microbiology Spectrum, Ausgabe 13, 2025, ISSN 2165-0497
Herausgeber: 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)

Autoren: 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
Veröffentlicht in: Frontiers in Public Health, 2024, ISSN 2296-2565
Herausgeber: Frontiers
DOI: 10.3389/FPUBH.2024.1298594

Nature Communications

Autoren: 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
Veröffentlicht in: Nature Communications, 2025, ISSN 2041-1723
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Microbiology Spectrum, 2025, ISSN 2165-0497
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Nature Communications, Ausgabe 16, 2025, ISSN 2041-1723
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Microbiology Resource Announcements, Ausgabe 14, 2025, ISSN 2576-098X
Herausgeber: American Society for Microbiology
DOI: 10.1128/MRA.01044-24

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

Autoren: Philip T L C Clausen, Malte B Hallgren, Søren Overballe-Petersen, Vanessa R Marcelino, Henrik Hasman, Frank M Aarestrup
Veröffentlicht in: NAR Genomics and Bioinformatics, Ausgabe 7, 2025, ISSN 2631-9268
Herausgeber: 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

Autoren: 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
Veröffentlicht in: IJID Regions, 2025
Herausgeber: Science Direct
DOI: 10.1016/J.IJREGI.2025.100661

Projektergebnisse

Leistungen

Veröffentlichungen

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