Polymerase Chain Reaction (PCR),can be used for molecular typing of the causative agents. Different techniques are in use and that include restriction endonuclease analyses (REA), random amplified polymorphic DNA (RAPD) and amplification fragment length polymorphism (AFLP).
For M. mycetomatis, a species-specific PCR procedure was developed. This PCR-RFLP analysis showed strict homogeneity between M. mycetomatis isolates and can be used to identify the causative agent in clinical material and also from soil and thorn samples.
Although results with RAPD are variable, REA and AFLP were able to differentiate between M. mycetomatis isolates from different countries, or even within a country.
Certain AFLP types were associated with the origin of the strain or the size of the lesion.
For eumycetoma, various molecular techniques have been used to identify causative agents and all of them are based on the identification of the internal transcribed spacer (ITS). In order to identify all fungal mycetoma causative agents, the ITS regions are usually amplified with pan-fungal primers and sequenced. Identification is based on comparing the resulting sequence with sequences previously submitted to Genbank.
Using this approach, multiple studies have shown that a number of causal agents for eumycetoma are underspeciated, as exemplified by the identification of three new Madurella species;Madurella fahalii, Madurella pseudomycetomatis and Madurella tropicana, and Pleurostomophoraochracea.
All of these tests are expensive, are not field friendly, nor are they available in endemic areas.