Metagenomic analysis – Mycetoma

Metagenomic analysis – Mycetoma

Metagenomic analysis of Environmental samples from Mycetoma endemic area in Sudan

 

Sahar Mubarak Bakhiet 1 , Abdalla Ahmed3  , Najwa A. Mhmoud 2, Emmanuel Edwar Siddig 2 Lamis Yahia Mohamed 4 , Ahmed Mudawi Musa 1, Ahmed Hassan Fahal 2

1 Institute of Endemic Diseases, University of Khartoum, Sudan.

2 The Mycetoma Research Centre, University of Khartoum, Khartoum, Sudan

3 Umm Al-Qura University, MAKKAH, Saudi Arabia

4 Faculty of Pharmacy-University of Khartoum

 

Background: Mycetoma is a unique neglected tropical disease caused by a considerable number of microorganisms of fungal or bacterial origins and characterized by devastating deformities, disabilities and high morbidity. Studies to date suggest a soil-borne or thorn-prick-mediated origin of mycetoma infections suggesting an environmental role in the disease transmission.

Study objective: To identify and characterize the different Madurella species communities from soils, thorns, water and other environmental samples collected from Sennar State, Sudan using ITS rRNA genes sequencing.

Methods: This cross sectional study was conducted at Eastern Sennar Governate , Sudan in 2016. A total of 105 environmental specimens were collected form mycetoma endemic villages. Environmental samples were including soil, thorns, animal dung and others. DNA was extracted from all environmental samples and pooled into 18 pools according to the similarity of ecological niches. The Internal Transcribed Spacer 2 of the ribosomal DNA were enriched by PCR for sequencing and the libraries were sequenced using Illumina MiSeq. The sequence reads were checked for quality using FastQC and directly mapped to a database containing reference ITS2 sequences of Madurella mycetomatis, Madurella pseudomycetomatis, Madurella tropicana and Madurella fahalii. Additionally, the sequence reads from different samples’ pools were denovo assembled using SeqMan NGen and the assembled contigs were used for BLAST search in Unite Database.

Results: Madurella mycetomatis was found in 6 environmental samples’ pools. In these 6 positive samples, Madurella pseudomycetomatis or/and Madurella tropicana were also detected. Madurella fahalii was found in only one pool co-existing with all other Madurella species. Madurella mycetomatis and Madurella fahalii were co-detected in two different contigs in the assembled reads from only one samples’ pool. Conclusion: Madurella mycetomatis was found to be more common than other Madurella species in this highly endemic area. The use of direct mapping of raw sequence reads is more sensitive in the detection of Madurella species in metagenomics environmental specimens.

 

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