The complete ITS2 barcoding region for Strongylus vulgaris and Strongylus edentatus

Gastrointestinal nematode parasites are of major concern for horses, where Strongylus vulgaris is considered the most pathogenic among the Strongylus species. Diagnosis of S. vulgaris infections can be determined with next generation sequencing techniques, which are inherently dependent on reference sequences. The best marker for parasitic nematodes is internal transcribed spacer 2 (ITS2) and we provide the first complete ITS2 sequences from five morphologically identified S. vulgaris and additional sequences from two S. edentatus. These sequences have high similarity to already published partial sequences and amplicon sequence variants (ASV) based on next generation sequencing (NGS). The ITS2 sequences from S. vulgaris matched available partial ITS2 sequences and the full ASVs, whereas the S. edentatus sequence matched another complete sequence. We also compare Sanger sequencing and NGS methods and conclude that the ITS2 variation is better represented with NGS methods. Based on this, we recommend that further sequencing of morphologically identified specimens of various species should be performed with NGS cover the intraspecific variation in the ITS2.

Automated summary

Gastrointestinal nematode parasites, especially Strongylus vulgaris, pose a significant threat to horses. Next generation sequencing techniques can accurately diagnose S. vulgaris infections, and the internal transcribed spacer 2 (ITS2) is the best marker for parasitic nematodes. We have provided complete ITS2 sequences for S. vulgaris and S. edentatus, which show high similarity to previously published sequences and amplicon sequence variants (ASV) based on next generation sequencing (NGS). Comparison of Sanger sequencing and NGS methods suggests that NGS is more effective in capturing ITS2 variation. We recommend further NGS sequencing of morphologically identified specimens to cover intraspecific ITS2 variation.