A novel Sporothrix brasiliensis genomic variant in Midwestern Brazil: evidence for an older and wider sporotrichosis outbreak

Sporotrichosis is a subcutaneous infection caused by fungi from the genus Sporothrix. The disease is transmitted by inoculation of infective particles found in plant-contaminated material or diseased animals, characterizing the classic sapronotic and emerging zoonotic transmission, respectively. Since 1998, Brazil has experienced a zoonotic sporotrichosis epidemic due to S. brasiliensis, centered in the state of Rio de Janeiro. Our observation of feline sporotrichosis cases in Brasilia (Midwestern Brazil), around 900 km away from Rio de Janeiro, led us to question whether the epidemic caused by S. brasiliensis has spread from the epicenter in Rio de Janeiro, emerged independently in the two locations, or whether the disease has been present and unrecognized in Midwestern Brazil. A retrospective analysis of 91 human and 4 animal cases from Brasilia, ranging from 1993 to 2018, suggests the occurrence of both sapronotic and zoonotic transmission. Molecular typing identified S. schenckii as the agent in two animals and all seven human patients from which we were able to recover clinical isolates. However, in two animals, the disease was caused by S. brasiliensis. Whole-genome sequence typing of seven S. brasiliensis strains suggests that isolates from Brasilia are genetically distinct from those obtained at the epicenter of the outbreak in Rio de Janeiro, both in phylogenomic and population genomic analyses. The two S. brasiliensis populations seem to have separated 2.24 - 3.09 million years ago, indicating independent outbreaks or that the zoonotic S. brasiliensis outbreak might have started earlier and be spread wider in South America than previously recognized.