Genomics and metagenomics of Madurella mycetomatis, a causative agent of black grain mycetoma in Sudan

Abstract

Madurella mycetomatis is one of the main causative agents of mycetoma, a debilitating neglected tropical disease. Improved understanding of the genomic diversity of the fungal and bacterial causes of mycetoma is essential to advances in diagnosis and treatment. Here, we describe a high-quality genome assembly of M. mycetomatis and results of the whole genome sequence analysis of 26 isolates from Sudan. We demonstrate evidence of at least seven genetically diverse lineages and extreme clonality among isolates within these lineages. We also performed shotgun metagenomic analysis of DNA extracted from mycetoma grains and showed that M. mycetomatis reads were detected in all sequenced samples with the average of 11,317 reads (s.d. +/- 21,269) per sample. In addition, 10 (12%) of the 81 tested grain samples contained bacterial reads including Streptococcus sp., Staphylococcus sp. and others.

Fig 1

A. States of origin of mycetoma patients in this study. Map outline was reprinted from GADM database under a CC BY license, with permission from Global Administrative Areas (www.gadm.org), original copyright 2018. B. Phylogenetic relationship among isolates of M. mycetomatis visualized my maximum likelihood method, the colors correspond to states on the map. Isolates from patients residing in village A or B are marked with arrows. The phylogenetic tree is not shown in scale.

Fig 2. Counts of M. mycetomatis-related reads versus all combined bacterial clade reads.

Grain samples are plotted along the x-axis in order of increasing M. mycetomatis content. Greater abundance of bacterial reads versus M. mycetomatis reads is apparent for the grain samples, Myc_125, Myc_69, and Myc_70.

Fig 3. Mycetoma grain samples with top 10 highest bacterial count.

In grain samples, Myc_125, Myc_69, and Myc_70, bacterial reads exceeded M. mycetomatis reads, while the latter predominated in the other seven samples shown. Bacterial reads are subdivided into genera where ‘Various soil clades’ include Rhodospirillales, Rhizobiales, and Actinobacteria.