Systematic whole-genome sequencing reveals an unexpected diversity among actinomycetoma pathogens and provides insights into their antibacterial susceptibilities

Mycetoma is a neglected tropical chronic granulomatous inflammatory disease of the skin and subcutaneous tissues. More than 70 species with a broad taxonomic diversity have been implicated as agents of mycetoma. Understanding the full range of causative organisms and their antibiotic sensitivity profiles are essential for the appropriate treatment of infections. The present study focuses on the analysis of full genome sequences and antibiotic resistance profiles of actinomycetoma strains from patients seen at the Mycetoma Research Centre in Sudan with a view to developing rapid diagnostic tests. Seventeen pathogenic isolates obtained by surgical biopsies were sequenced using MinION and Illumina methods, and their antibiotic resistance profiles determined. The results highlight an unexpected diversity of actinomycetoma causing pathogens, including three Streptomyces isolates assigned to species not previously associated with human actinomycetoma and one new Streptomyces species. Thus, current approaches for clinical and histopathological classification of mycetoma may need to be updated. The standard treatment for actinomycetoma is a combination of sulfamethoxazole/trimethoprim and amoxicillin/clavulanic acid. Most tested isolates were not susceptible to sulfamethoxazole/trimethoprim or to amoxicillin alone. However, the addition of the β-lactamase inhibitor clavulanic acid to amoxicillin increased susceptibility, particularly for Streptomyces somaliensis and Streptomyces sudanensis. Actinomadura madurae isolates appear to be particularly resistant under laboratory conditions, suggesting that alternative agents, such as amikacin, should be considered for more effective treatment. The results obtained will inform future diagnostic methods for the identification of actinomycetoma and treatment. Author Summary Mycetoma is a common health and medical problem that is endemic in many tropical and subtropical countries and has devastating effects on patients. The destructive nature of late-stage infection means that treatment often requires long term use of antibiotic therapy, massive surgical excisions and amputation. Several different bacterial species have been described as causing this disease but our understanding of the true diversity of mycetoma causing bacteria has been limited by a lack of molecular sequence data. We have now sequenced the genomes of 17 samples isolated from patients at the Mycetoma Research Centre in Sudan, revealing a diverse range of species associated with infection including one new Streptomyces species, and three species with no previous association with human mycetoma. Crucially, all isolates had a high level of resistance against the current first-line antibiotics used to treat actinomycetoma under laboratory conditions. This resistance was strongest in Actinomadura madurae , which was also the most frequently observed species isolated from patients in our study. We hope that these results will aid in the development of future rapid diagnostic tools and the improvement of treatment outcomes.