{ "abstract": "Mycetoma is a neglected tropical disease characterized by mutilating tumorous lesions in the subcutaneous tissue. The causative agents are found embedded in granules called grains. Mycetoma is either caused by bacteria (actinomycetoma) or fungi (eumycetoma). To initiate the appropriate treatment, it is important to identify the causative agent rapidly and molecular identification for eumycetoma revolutionized the time to identification. For actinomycetoma this was not possible yet. Here we developed a multiplex qPCR identification scheme for the most common causative agents of actinomycetoma in Africa. Whole genome sequencing was used to identify species-specific gene families for Actinomadura madurae, Actinomadura pelletieri, Streptomyces somaliensis and Streptomyces sudanensis. qPCR primers and probes were developed on these species and validated against DNA isolated from mycetoma strains and grains. Each probe was unique with no cross-reactivity with other tested species. The limit of detection ranged from 0.000013 to 0.00067 ng bacterial DNA. When the qPCRs were validated against 28 grain samples, all fungal grains remained negative and 11 out of 12 Actinomadura grains were correctly identified. This resulted in a sensitivity of 85.7% for the A. pelletieri probe and a specificity of 100%. For the A. madurae probe, a sensitivity and specificity of 100% was obtained. The actinomycetoma qPCR developed in this study can be used to identify the most common causative agents of actinomycetoma in Africa. Author summary: Mycetoma is a devastating disease with large tumorous lesions. It can be caused by fungi and bacteria. Most laboratories use either histology and/or culturing to identify the causative agents, but these procedures can take up to six weeks till a positive identification is obtained. Recently we demonstrated that qPCR can be used directly on mycetoma grains and can be used to discriminate actinomycetoma from eumycetoma within 2 hours. Furthermore, for actinomycetoma identification to the genus level can be achieved with this qPCR. However, if a species identification was needed there were no qPCR assays available to achieve this. Therefore, in this project we aimed to develop qPCR methods to identify the most common causative agents of actinomycetoma in Africa. Instead of using classical barcode genes, we searched the genomes of Actinomadura madurae, Actinomadura pelletieri, Streptomyces somaliensis and Streptomyces sudanensis to find conserved unique genes for each lineage. qPCRs were designed on these genes and validated against a large cohort of fungal and bacterial mycetoma causative agents. No cross reaction was observed. Next, we also validated these qPCRs against the mycetoma grains. In these clinical samples a sensitivity of 85.7% and a specificity of 100% was achieved. The next step is to validate this qPCR identification scheme throughout different mycetoma endemic regions in Africa and beyond.", "abstract_shown": true, "affiliations": [ "Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom", "ErasmusMC, Department of Medical Microbiology and Infectious Diseases, Rotterdam, The Netherlands", "Mycetoma Research Centre, University of Khartoum, Khartoum, Sudan", "The Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan", "Faculty of Medical laboratory Sciences, University of Khartoum, Khartoum, Sudan", "Centre de Recherche sur les maladies Tropicales Négligées, UFR Sciences de la Santé, Université Gaston Berger, Saint-Louis, Senegal", "Department of medical microbiology and parasitology, faculty of Medical Laboratory sciences, University of Dongola, Dongola, Sudan", "Sydney Institute for Infectious Diseases, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia" ], "article_type": "Research Article", "arxiv": null, "author_total": 14, "authors": [ { "affs": [ 0 ], "name": "Andrew K. Watson" }, { "affs": [ 1 ], "name": "Sahar Bakhiet" }, { "affs": [ 2 ], "name": "Emmanuel E. Siddig" }, { "affs": [ 3 ], "name": "Carole Pab Minlekib" }, { "affs": [ 4 ], "name": "Rihab Mohammed" }, { "affs": [ 5 ], "name": "Willemien Zandijk" }, { "affs": [ 6 ], "name": "Mickey Konings" }, { "affs": [ 7 ], "name": "Ahmed H. Fahal" }, { "name": "Maguette Faye" }, { "name": "Katarzyna Mickiewicz" }, { "name": "Fatehmeh Mazraati Tajabadi" }, { "name": "Doudou Sow" }, { "name": "Jeffrey Errington" }, { "name": "Wendy W. J. van de Sande" } ], "bibtex": "https://research.draconitic.com/paper/5n2e1pdakak4t.bib", "cited_by": 0, "doi": "10.1371/journal.pntd.0014710", "fulltext_url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014710", "id": "5n2e1pdakak4t", "issns": [ "1935-2735" ], "landing_url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014710", "language": null, "licence": "CC-BY-4.0", "licence_label": "CC BY 4.0", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "2726|Actinomycetales infections and treatment" ], [ "plos", "/Biology and life sciences/Genetics/Genomics" ], [ "plos", "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Fungal pathogens/Actinomadura" ], [ "plos", "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Fungal pathogens/Streptomyces" ], [ "plos", "/Biology and life sciences/Molecular biology/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction" ], [ "plos", "/Biology and life sciences/Molecular biology/Molecular biology techniques/Biomolecular isolation/DNA isolation" ], [ "plos", "/Biology and life sciences/Mycology/Fungal pathogens/Actinomadura" ], [ "plos", "/Biology and life sciences/Mycology/Fungal pathogens/Streptomyces" ], [ "plos", "/Biology and life sciences/Organisms/Eukaryota/Fungi/Rice blast fungus" ], [ "plos", "/Biology and life sciences/Plant science/Plant pathology/Plant pathogens/Plant fungal pathogens/Rice blast fungus" ], [ "plos", "/Medicine and health sciences/Medical conditions/Infectious diseases/Fungal diseases/Mycetoma" ], [ "plos", "/Medicine and health sciences/Medical conditions/Tropical diseases/Neglected tropical diseases/Mycetoma" ], [ "plos", "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Fungal pathogens/Actinomadura" ], [ "plos", "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Fungal pathogens/Streptomyces" ], [ "plos", "/Research and analysis methods/Electrophoretic techniques/Gel electrophoresis" ], [ "plos", "/Research and analysis methods/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction" ], [ "plos", "/Research and analysis methods/Molecular biology techniques/Biomolecular isolation/DNA isolation" ] ], "openalex": "W7211963329", "pdf_url": "https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0014710&type=printable", "pmcid": null, "pmid": null, "published": "2026-09-08", "publisher": "Public Library of Science", "ris": "https://research.draconitic.com/paper/5n2e1pdakak4t.ris", "sources": [ { "first_seen": "2026-10-30T12:17:56Z", "native_id": "10.1371/journal.pntd.0014710", "source": "plos", "url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014710" } ], "subjects": [ { "field": "biochemistry", "origin": "plos:molecular biology", "subfield": "molecular-biology" }, { "field": "biology", "origin": "plos:microbiology", "subfield": "microbiology" } ], "title": "A qPCR identification scheme to detect the most common causative agents of actinomycetoma in Africa", "title_text": "A qPCR identification scheme to detect the most common causative agents of actinomycetoma in Africa", "type": "peer-reviewed", "updated_at": "2026-10-30T12:17:56Z", "url": "https://research.draconitic.com/paper/5n2e1pdakak4t", "venue": "PLOS Neglected Tropical Diseases", "versions": [] }