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

Author: mycolabadmin
6/30/2025
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Summary

Researchers in Thailand studied a fungal infection called sporotrichosis caused by Sporothrix schenckii, which infects both cats and humans. Using advanced DNA sequencing technology from Oxford Nanopore, they identified and classified 26 fungal samples and tested how well common antifungal medications worked against them. They found that calmodulin gene sequencing was better than the standard ITS test for identifying the fungus species, and that about one-third of the samples showed reduced sensitivity to the main treatment drug, itraconazole.

Background

Sporothrix species are dimorphic fungi causing sporotrichosis that can range from localized skin infections to systemic disease in immunocompromised individuals. Species identification within the Sporothrix clinical clade requires molecular techniques as microscopy is insufficient. The calmodulin gene offers higher phylogenetic resolution than the ITS region for Sporothrix species classification.

Objective

This study evaluated the ability of Oxford Nanopore Technology (ONT) long-read sequencing of calmodulin and ITS regions to identify Sporothrix species level and enable phylogenetic analysis of isolates from humans and felines in Thailand. The study also assessed antifungal susceptibility profiles and compared two bioinformatic clustering methods for improving sequence accuracy.

Results

ONT calmodulin sequencing identified all 26 isolates as S. schenckii sensu stricto with 99-100% identity, whereas ITS showed lower discriminatory power with some isolates identified as other Sporothrix species. Phylogenetic analysis revealed all isolates clustered in a specific S. schenckii sensu stricto subclade associated with Southeast Asia. Eight of 26 isolates (31%) exhibited elevated itraconazole MICs (>2 µg/mL) above tentative epidemiological cutoff values.

Conclusion

ONT sequencing of the calmodulin gene allows accurate species identification and phylogenetic analysis of S. schenckii sensu stricto isolates from Thailand, with better resolution than ITS sequencing. The findings demonstrate high concordance between ONT consensus sequences and Sanger sequencing for phylogenetic classification. The increasing prevalence of elevated itraconazole MICs in Thai isolates emphasizes the need for ongoing antifungal susceptibility surveillance.

Published in:PLoS Neglected Tropical Diseases,
Study Type:Molecular epidemiology and antifungal susceptibility study,
Source: PMID: 40587582, DOI: 10.1371/journal.pntd.0013253