Comparative gene expression analysis in closely related dermatophytes reveals secondary metabolism as a candidate driver of virulence

Dermatophytes are important fungal skin pathogens affecting humans and animals worldwide. Although several virulence factors have been identified using genomic, proteomic, and transcriptomic approaches, their roles remain incompletely understood. In this study, we applied a comparative approach using four closely related taxa within the <i>Trichophyton benhamiae</i> complex, which differ in infectivity despite sharing common hosts. We focused on the emerging zoonotic pathogen <i>T.benhamiae</i> var. <i>luteum</i>, currently responsible for epidemic outbreaks in Europe, and compared it to its less infective relatives. A set of 16 candidate genes, informed by preliminary transcriptomic screening, was assessed via RT-qPCR across 12 strains grown <i>in vitro</i> (Sabouraud dextrose broth) and <i>ex vivo</i> (murine skin explants). Genes associated with secondary metabolism were consistently upregulated under <i>ex vivo</i> conditions, particularly in <i>T.benhamiae</i> var. <i>luteum</i>. While two of the biosynthetic gene clusters examined are linked to known metabolites, others remain uncharacterized. These findings reveal key gene expression differences that may explain the enhanced infectivity of emerging strains and underscore the potential role of secondary metabolites in dermatophyte virulence. They also highlight the need for improved genome annotation in <i>T.benhamiae</i> to better understand the molecular basis of pathogenesis.IMPORTANCE<i>Trichophyton benhamiae</i> var. <i>luteum</i> is an emerging fungal pathogen responsible for a rising number of skin infections transmitted from guinea pigs to humans, especially in Europe. We investigated why this pathogen spreads more effectively than its close relatives, which infect the same hosts but are less epidemic. Using a laboratory model that mimics skin infection, we found that genes involved in producing fungal compounds-called secondary metabolites, some of which act as toxins-are more active in this pathogen. These compounds may help the fungus suppress the host immune response and establish infection. Our findings shed light on how fungal pathogens adapt to their hosts and highlight gene pathways that could be targeted in future diagnostics or treatments. Understanding these mechanisms is key to managing emerging fungal threats in both animals and humans.