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

Deliverables

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

Publications

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

Author(s): David T.S. Hayman, Marion P.G. Koopmans, Andrew A. Cunningham, Salome A. Bukachi, Leandre Murhula Masirika, Wanda Markotter, Thomas C. Mettenleiter
Published in: One Health, Issue 20, 2026, ISSN 2352-7714
Publisher: Elsevier BV
DOI: 10.1016/J.ONEHLT.2025.101059

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

Author(s): 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
Published in: Gut Microbes, Issue 17, 2025, ISSN 1949-0976
Publisher: Informa UK Limited
DOI: 10.1080/19490976.2025.2484385

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

Author(s): 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
Published in: Eurosurveillance, Issue 29, 2024, ISSN 1560-7917
Publisher: 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

Author(s): Marie Louise Jespersen, Kamilla Kjærgaard Munk, Sune Fjermedal, Bo Pilgaard, Anne S. Meyer, Frank M. Aarestrup, Saria Otani
Published in: Gut Microbes Reports, Issue 3, 2026, ISSN 2993-3935
Publisher: 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

Author(s): 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
Published in: Eurosurveillance, Issue 29, 2024, ISSN 1560-7917
Publisher: 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)

Author(s): 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
Published in: Microbial Genomics, Issue 12, 2026, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/MGEN.0.001813

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

Author(s): Emilie Egholm Bruun Jensen, Néhémie Nzoyikorera, Mirena Ivanova, Pimlapas Leekitcharoenphon, Marie Noelle Uwineza, Idrissa Diawara, Joseph Nyandwi, Frank M. Aarestrup, Saria Otani
Published in: PLOS Neglected Tropical Diseases, Issue 20, 2026, ISSN 1935-2735
Publisher: 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

Author(s): 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
Published in: Communications Medicine, Issue 6, 2026, ISSN 2730-664X
Publisher: 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

Author(s): 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
Published in: Eurosurveillance, Issue 29, 2024, ISSN 1560-7917
Publisher: 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

Author(s): 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
Published in: Communications Medicine, Issue 5, 2025, ISSN 2730-664X
Publisher: 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

Author(s): Frank M. Aarestrup, Egon B. Hansen, Happiness H. Kumburu, Tutu Mzee, Saria Otani
Published in: International Journal of Medical Microbiology, Issue 317, 2024, ISSN 1438-4221
Publisher: 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

Author(s): 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
Published in: Nature Medicine, 2025, ISSN 1078-8956
Publisher: 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

Author(s): 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
Published in: Nature Communications, Issue 16, 2025, ISSN 2041-1723
Publisher: 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

Author(s): Fredrick Ogumbo, Latifah Benta, Brian Kimutai, Joseph Mugah, Eddy Johnson, Vanessa Onyonyi, Caroline Dande, Lillian Musila, Steve Wandiga
Published in: American Journal of Epidemiology and Infectious Disease, Issue 12, 2024, ISSN 2333-116X
Publisher: 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

Author(s): Malte B Hallgren, Philip T L C Clausen, Frank M Aarestrup
Published in: Biology Methods and Protocols, Issue 9, 2024, ISSN 2396-8923
Publisher: Oxford University Press (OUP)
DOI: 10.1093/BIOMETHODS/BPAE057

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

Author(s): 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
Published in: One Health, Issue 23, 2026, ISSN 2352-7714
Publisher: Elsevier BV
DOI: 10.1016/J.ONEHLT.2026.101529

Tanzanian goat gut microbiomes adapt to roadside pollutants and environmental stressors

Author(s): Emilie Egholm Bruun Jensen, Marie Louise Jespersen, Christina Aaby Svendsen, Tolbert Sonda, Saria Otani, Frank M. Aarestrup
Published in: Microbiology Spectrum, Issue 14, 2026, ISSN 2165-0497
Publisher: American Society for Microbiology
DOI: 10.1128/SPECTRUM.02036-25

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

Author(s): 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
Published in: PLOS One, Issue 21, 2026, ISSN 1932-6203
Publisher: 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

Author(s): 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
Published in: Microbiology Spectrum, Issue 13, 2025, ISSN 2165-0497
Publisher: 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)

Author(s): 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
Published in: Frontiers in Public Health, 2024, ISSN 2296-2565
Publisher: Frontiers
DOI: 10.3389/FPUBH.2024.1298594

Nature Communications

Author(s): 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
Published in: Nature Communications, 2025, ISSN 2041-1723
Publisher: 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

Author(s): 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
Published in: Microbiology Spectrum, 2025, ISSN 2165-0497
Publisher: 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

Author(s): 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
Published in: Nature Communications, Issue 16, 2025, ISSN 2041-1723
Publisher: 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

Author(s): 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
Published in: Microbiology Resource Announcements, Issue 14, 2025, ISSN 2576-098X
Publisher: American Society for Microbiology
DOI: 10.1128/MRA.01044-24

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

Author(s): Philip T L C Clausen, Malte B Hallgren, Søren Overballe-Petersen, Vanessa R Marcelino, Henrik Hasman, Frank M Aarestrup
Published in: NAR Genomics and Bioinformatics, Issue 7, 2025, ISSN 2631-9268
Publisher: 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

Author(s): 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
Published in: IJID Regions, 2025
Publisher: Science Direct
DOI: 10.1016/J.IJREGI.2025.100661

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Deliverables

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