Identification of microbial agents in tissue specimens of ocular and periocular sarcoidosis using a metagenomics approach

Amde Selassie Shifera, Christopher Pockrandt, Natalia Rincon, Yuchen Ge, Jennifer Lu, Ales Varabyou, Anne E. Jedlicka, Karen Sun, Alan L. Scott, Charles Eberhart, Jennifer E. Thorne, Steven L. Salzberg

Research output: Contribution to journalArticlepeer-review


Background: Metagenomic sequencing has the potential to identify a wide range of pathogens in human tissue samples. Sarcoidosis is a complex disorder whose etiology remains unknown and for which a variety of infectious causes have been hypothesized. We sought to conduct metagenomic sequencing on cases of ocular and periocular sarcoidosis, none of them with previously identified infectious causes. Methods: Archival tissue specimens of 16 subjects with biopsies of ocular and periocular tissues that were positive for non-caseating granulomas were used as cases. Four archival tissue specimens that did not demonstrate non-caseating granulomas were also included as controls. Genomic DNA was extracted from tissue sections. DNA libraries were generated from the extracted genomic DNA and the libraries underwent next-generation sequencing. Results: We generated between 4.8 and 20.7 million reads for each of the 16 cases plus four control samples. For eight of the cases, we identified microbial pathogens that were present well above the background, with one potential pathogen identified for seven of the cases and two possible pathogens for one of the cases. Five of the eight cases were associated with bacteria ( Campylobacter concisus, Neisseria elongata, Streptococcus salivarius, Pseudopropionibacterium propionicum, and Paracoccus yeei), two cases with fungi ( Exophiala oligosperma, Lomentospora prolificans and Aspergillus versicolor) and one case with a virus (Mupapillomavirus 1). Interestingly, four of the five bacterial species are also part of the human oral microbiome. Conclusions: Using a metagenomic sequencing we identified possible infectious causes in half of the ocular and periocular sarcoidosis cases analyzed. Our findings support the proposition that sarcoidosis could be an etiologically heterogenous disease. Because these are previously banked samples, direct follow-up in the respective patients is impossible, but these results suggest that sequencing may be a valuable tool in better understanding the etiopathogenesis of sarcoidosis and in diagnosing and treating this disease.

Original languageEnglish (US)
Article number820
StatePublished - 2021


  • Aspergillus versicolor
  • Campylobacter concisus
  • Lomentospora prolificans
  • Metagenomics
  • Mupapillomavirus 1
  • Neisseria elongate
  • Next-generation sequencing
  • Ocular sarcoidosis
  • Orbital sarcoidosis
  • Paracoccus yee; Exophiala oligosperma
  • Pathogen discovery
  • Pseudopropionibacterium propionicum
  • Sarcoidosis
  • Streptococcus salivarius

ASJC Scopus subject areas

  • General Immunology and Microbiology
  • General Pharmacology, Toxicology and Pharmaceutics
  • General Biochemistry, Genetics and Molecular Biology


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