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Targeted long-read sequencing analysis and antifungal susceptibility profiles of Sporothrix schenckii isolates from Thailand

Summary

This research examined a fungal infection called sporotrichosis found in Thailand, particularly in cats and humans. Scientists used advanced DNA sequencing technology to accurately identify which species of the fungus caused the infections and understand how they are related to each other. They also tested how well common antifungal medications work against these fungi, finding that some strains have become resistant to itraconazole, the main drug used to treat sporotrichosis.

Background

Sporothrix spp. are dimorphic fungi causing sporotrichosis ranging from local skin infections to systemic infections. Species identification requires molecular techniques as morphological similarity makes microscopy insufficient. The calmodulin gene offers higher resolution for phylogenetic classification compared to the ITS region.

Objective

This study evaluated the ability of long-read nanopore sequencing of calmodulin and ITS regions to identify species level and allow phylogenetic analysis of Sporothrix strains isolated from humans and felines in Thailand. The study also assessed antifungal susceptibility profiles of these isolates.

Results

ONT sequencing of calmodulin consistently classified all 26 isolates as S. schenckii sensu stricto with 99-100% identity, while ITS showed lower discriminatory power. Phylogenetic analysis revealed all isolates clustered in subclade I with other Southeast Asian isolates, distinct from three other S. schenckii subclades associated with different geographic locations. Antifungal susceptibility testing showed 8 out of 26 isolates (31%) had elevated itraconazole MICs (>2 µg/mL).

Conclusion

ONT sequencing of the calmodulin gene allows accurate species identification and phylogenetic analysis of S. schenckii sensu stricto isolates from Thailand. The presence of elevated itraconazole MICs in 31% of isolates highlights growing concern about antifungal resistance. Nanopore-generated sequences achieve taxonomic resolutions comparable to Sanger sequencing, supporting its utility for improved diagnostic accuracy and epidemiological understanding of sporotrichosis.
  • Published in:PLoS Neglected Tropical Diseases,
  • Study Type:Observational Study,
  • Source: 10.1371/journal.pntd.0013253, PMID: 40587582
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