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 Brasília (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 Brasília, 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 Brasília 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. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement A.M.N was funded by FAP-DF awards 0193.001048/2015-0193.001561/2017 and the CNPq grant 437484/2018-1. B.M.B. was supported by NIH/NIAID award R21AI28536. D.R.M. was supported by NIH/NIGMS award R01GM121750. M.M.T was supported by CNPq/UNIVERSAL award 43460/2018-2. M.S.S.F was supported by FAP-DF/PRONEX award 193.001.533/2016. S.A.P. was supported by FAPERJ, grant number E-26/202.737/2019. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Human studies were previously approved by the Ethics Committee of the Faculty of Medicine, University of Brasília (protocol CAAE: 873718.0.00005558). Animal observations and tests were previously approved by the University of Brasília Ethics Committee on the Use of Animals (CEUA-UnB), protocol: 66716/2016. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The data presented in this manuscript is either available on public databases, such as GenBank, or is available upon request to the authors.