Mhmoud, N. A. | bioRxiv Science

bioRxiv2022

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 {beta}-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 SummaryMycetoma 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.

genomics↗

bioRxiv2018

The Accuracy of Histopathological and Cytopathological Techniques in the Identification of the Mycetoma Causative Agents

Mycetoma is a devastating neglected tropical disease, caused by various fungal and bacterial pathogens. Correct diagnosis to the species level is mandatory for proper treatment. In endemic areas, various diagnostic tests and techniques are in use to achieve that, and that includes grain culture, surgical biopsy histopathological examination, fine needle aspiration cytological (FNAC) examination and in certain centres molecular diagnosis such as PCR.\n\nIn this retrospective study, the sensitivity, specificity and diagnostic accuracy of grain culture, surgical biopsy histopathological examination and FNAC to identify the mycetoma causative organisms were determined. The histopathological examination appeared to have better sensitivity and specificity.\n\nThe histological examination results were correct in 714 (97.5%) out of 750 patients infected with Madurella mycetomatis, in 133 (93.6%) out of 142 patients infected with Streptomyces somaliensis, in 53 (74.6%) out of 71 patients infected with Actinomadura madurae and in 12 (75%) out of 16 patients infected with Actinomadura pelletierii.\n\nFNAC results were correct in 604 (80.5%) out of 750 patients with Madurella mycetomatis eumycetoma, in 50 (37.5%) out of 133 Streptomyces somaliensis patients, 43 (60.5%) out of 71 Actinomadura madurae patients and 11 (68.7%) out of 16 Actinomadura pelletierii. The mean time required to obtain the FNAC result was one day, and for the histopathological examinations results it was 3.5 days, and for grain, it was a mean of 16 days.\n\nIn conclusion, histopathological examination and FNAC are more practical techniques for rapid species identification than grain culture in many endemic regions.\n\nAuthor summaryIn mycetoma endemic regions, the medical and health settings are commonly suboptimal, and only a few diagnostic tests and techniques are available. That had badly affected the patients proper diagnosis and management and thus the late presentation of patients with advanced disease. In this retrospective study, the experience of the MRC on the common in use diagnostic tests in the period between 1991 and 2018 is presented.\n\nIn this study, the sensitivity, specificity rates and diagnostic accuracy of grain culture, surgical biopsy histopathological examination and FNAC to identify the mycetoma causative organisms were determined. The histopathological examination appeared to have better sensitivity and specificity. Furthermore, the grain culture identification needs high experience, it is the tedious procedure, and cross-contamination is common hence misdiagnosis is frequent. It can be concluded that histopathological examination and FNAC are more practical techniques for rapid species identification than grain culture in many endemic regions with poor diagnostic setting.

microbiology↗