Detection of multiple mycetoma pathogens using fungal metabarcoding analysis of soil DNA in an endemic area of Sudan

Environmental detection of eumycetoma pathogens using multiplex real-time PCR for soil DNA in Sennar State, Sudan

BACKGROUND

Mycetoma is a chronic disease affecting the skin and subcutaneous tissue endemic in the tropical and subtropical regions. Several bacteria and fungi can cause mycetoma, but fungal mycetoma (eumycetoma) is challenging because the treatment requires a combination of a long-term antifungal agent and surgery. Although the transmission route has not yet been elucidated, infection from the soil is a leading hypothesis. However, there are few soil investigation studies, and the geographical distribution of mycetoma pathogens is not well documented. Here, we used multiplex real-time PCR technology to identify three fungal species from soil samples.

METHODS

In total, 64 DNA samples were extracted from soil collected in seven villages in an endemic area in Sennar State, Sudan, in 2019. Primers and fluorescent probes specifically targeting the ribosomal DNA of Madurella mycetomatis, Falciformispora senegalensis, and F. tompkinsii were designed.

RESULTS

Multiplex real-time PCR was performed and identified the major pathogen, M. mycetomatis that existed in most sites (95%). In addition, two other pathogens were identified from some sites. This is the first report on the use of this technique for identifying the eumycetoma causative microorganisms.

CONCLUSIONS

This study demonstrated that soil DNA investigation can elucidate the risk area of mycetoma-causative agents. The results will contribute to the design of prevention measures, and further large-scale studies may be effective in understanding the natural habitats of mycetoma pathogens.

Mycetoma and the environment

Mycetoma is a chronic, incapacitating, destructive inflammatory disease with many serious damaging impacts. Currently, there is no control or prevention program as many of its epidemiological characteristics, such as the causative organisms' ecological niche, natural habitat, primary reservoir, transmission mode, geographical distribution, incidence, and prevalence, remain unclear. This may be due to a lack of research interest, as mycetoma is still a neglected disease and the scarcity of accurate molecular diagnostic techniques in disease-endemic regions for accurate causative microorganisms identification and mapping. With this background, this study set out to address this knowledge gap by considering the mycetoma environmental occurrence predictors. The medical literature obtained data showed a close association between mycetoma occurrence and its environment. The causative microorganisms are available in the environment in active or dormant forms. Animal dung may be a natural niche and reservoir for these organisms, and thorns may facilitate the subcutaneous inoculation. Some environmental factors, such as the soil type and consistency, temperature, water sources, aridity index, and thorny trees, may be risk factors. The population in endemic areas socioeconomic, hygiene, and health education status are contributory factors for mycetoma. The individual's genetic and immunological backgrounds may determine the disease's susceptibility and resistance. Environmental conditions and personal hygiene improvement are mandatory to reduce disease occurrence. Mycetoma spatial mapping can detect disease cluster areas and then develop public health strategies for early case detection and management to reduce the disease burden. More research interests and facilities are needed to understand disease pathogenesis and appropriate patient management better.

The Fungal, Nutritional, and Metabolomic Diagnostics of the Oil Palm Elaeis guineensis Affected by Bud Rot Disease in Esmeraldas, Ecuador

The oil palm Elaeis guineensis represents one of the most important crops in Ecuador. Considering that bud rot disease is deadly in Ecuador, more attention has been given to identifying possible causes for palm debility from this disease. We studied the involvement of fungi and nutrients in triggering bud rot disease in E. guineensis. Special emphasis was given to the molecules synthesized by the plant to protect against this devastating disease. Techniques like Diagnosis and Recommendation Integrated System (DRIS) and metagenomic analysis were used to understand the possible implications of biotic and abiotic factors in the development of bud rot disease in oil palm in Ecuador. Liquid chromatography-mass spectrometry (LC-MS) analysis was used to identify the phenolic protection barrier of the palm facing the disease. Our results indicate that fungi from Ascomyceta phylum were found in the tested samples. The species directly involved are different in soil compared with plants. The results indicate a deficiency of chemical elements, such as Ca, Mn, Mg, and Fe, which are responsible for palm debility from bud rot disease. More than 30 compounds with protective roles were identified in the leaves of symptomatic plants from the first stage of the infection.

The First Case of Fusarium falciforme Eumycetoma in Sudan and an Extensive Literature Review about Treatment Worldwide

Eumycetoma is an infectious disease caused by various fungal pathogens. The disease is characterised by black and pale-yellowish grain discharge. In this communication, we report a case of eumycetoma with a pale grain foot-eumycetoma caused by Fusarium falciforme. The patient presented at the outpatient clinic of the Mycetoma Research Centre in Sudan. The causative agent was initially misidentified as Aspergillus nidulans based on its seemingly similar histopathological appearance. However, sequencing the internally transcribed spacer region of the extracted grain confirmed infection with Fusarium falciforme. Although the patient received Itraconazole and underwent surgical excision, the disease was recurrent. To our knowledge, this is the first report on Fusarium falciforme causing eumycetoma in Sudan, indicating the expansion of the geographical distribution of this pathogen. This calls for raising the awareness of healthcare providers and improving the diagnostic and surveillance systems in at-risk areas to improve the case management and reduce the threat of further spread. Considering the potential impacts of F. falciforme infection including threatening the global health, food security, and ecosystem balance, as well as loss of biodiversity and negative socioeconomic changes in endemic countries, we recommend the implementation of an integrated transdisciplinary One Health strategy for the prevention and control of emerging infectious diseases including F. falciforme.

Mycetoma management and clinical outcomes: the Mycetoma Research Center experience

BACKGROUND

Mycetoma is a chronic granulomatous inflammatory disease that affects the cutaneous and subcutaneous tissues, leading to gruesome complications if not treated early. As a neglected disease, it has received scant attention in developing curable drugs. Mycetoma treatment is still based on expert opinions in the absence of guidelines.

METHODS

This descriptive, cross-sectional, hospital-based study aimed to determine and assess the disease treatment outcomes observed at Mycetoma Research Center, Sudan.

RESULTS

In this study, 75% of patients had eumycetoma, all of whom were treated with itraconazole and 37.4% underwent surgical excision, while 25% of the patients had actinomycetoma, 99.2% of whom were treated with a combination of cotrimoxazole and amoxicillin-clavulanate. The cure rate was 12.7% and 14.3% for patients with eumycetoma and actinomycetoma, respectively. Only 6.1% of eumycetoma patients underwent amputation. Remarkably, no patient with actinomycetoma underwent an amputation. Small lesions (OR=10.09, p<0.001) and good follow-up (OR=6.81, p=0.002) were positive predictors of complete cure. In terms of amputation, history of surgical recurrence at presentation (OR=3.67, p=0.020) and presence of grains (OR=7.13, p=0.012) were positive predictors, whereas small lesions were negative predictors (OR=0.06, p=0.009).

CONCLUSIONS

Treatment of mycetoma was suboptimal, with a low cure rate despite a long treatment duration. Complete cure has a significant association with small lesions and good follow-up.

Eumycetoma Caused by Madurella pseudomycetomatis in a Captive Tiger (Panthera tigris)

A captive-kept adult male tiger presented with a large cutaneous and subcutaneous mass on the thigh with a fistula. During sedation, multiple nodules were detected and samples for a histopathological exam were collected. Histologically, granulomatous panniculitis and dermatitis were seen around dense aggregates of pigmented fungal hyphae, and a diagnosis of phaeohyphomycosis was made; considering the clinical features, it was classified as a eumycotic mycetoma. This is a rarely reported subcutaneous fungal infection in humans and animals, caused by dematiaceous fungi. Clinically, it is characterized by tumefaction, fistulous sinus tracts, and the formation of macroscopically visible grains. In the literature, only a few infections in wild felids have been reported. In this case, Fontana-Masson staining better showed pigmentation and panfungal PCR and sequencing identified Madurella pseudomyectomatis (OP623507) as the causative agent. Systemic therapy with oral administration of itraconazole was planned, but the patient died during the first period of treatment. The animal was not submitted for post-mortem examination. Visceral dissemination of the agent cannot be excluded. To the authors' knowledge, this is the first report of eumycotic mycetoma by Madurella pseudomycetomatis in a captive tiger.

Epidemiologic Aspects of Mycetoma in Africa

Mycetoma is a chronic, disabling infection caused by fungi or actinomycetes that affects the disadvantaged rural populations of arid tropical regions. The identification of etiological agents is long, difficult, and often imprecise or unsuccessful. Recently developed molecular methods can be used to identify causal agents at the species level. However, diagnosis can only be implemented in specialized laboratories. For these reasons, the distribution of causal agents in endemic African countries remains approximate. It is known that the pathogenic organisms of mycetoma are present in the environment, introduced as a result of injuries or trauma. There are still unknowns concerning the natural habitats of agents and the mode of infection. A potential association between mycetoma and acacia was uncovered in Sudan, allowing the elaboration of a risk map of the country. A new hypothesis for the mode of contamination involves the intervention of an intermediate host. The first surveys in Sudanese endemic villages gave a higher prevalence than the previous estimates, indicating that the prevalence of mycetoma in endemic African countries has previously been underestimated.

Mycetoma, chromoblastomycosis and other deep fungal infections: diagnostic and treatment approach

PURPOSE OF REVIEW

to review recent advances in the epidemiology, diagnosis, and treatment of deep fungal infections.

RECENT FINDINGS

Mycetoma and chromoblastomycosis are the only deep fungal infections incorporated in the list of neglected tropical diseases. These infections start in the skin but progress to deep tissues if not recognized early. A wide array of fungal pathogens are the causative agents. Molecular methods allow for early and accurate identification of the pathogens, but are unfortunately not available in endemic areas. Treatment options are mostly based upon clinical experience rather than on well-designed clinical trials.

SUMMARY

Deep fungal infections of the skin and soft tissues are rare conditions of wide world distribution but mostly reported from tropical countries. Urgent need for affordable and easily accessible molecular methods and well-conducted studies to allow for accurate diagnosis and to provide evidence to guide proper therapy are urgently needed.