Volume 32, Number 9—September 2026
Research
Dual PCR–Sanger Sequencing Assay for Simultaneous sqle-Based Identification and Resistance Detection in Trichophyton Species
, Karin M. Jørgensen, Karen Marie Thyssen Astvad, and Maiken Cavling Arendrup
Table 1
MICs determined using the EUCAST E.Def 11.0 reference method for dermatophytes in study of dual PCR–Sanger sequencing assay for simultaneous sqle-based identification and resistance detection in Trichophyton species†
| Species | SQLE amino acid alteration (intrinsic SNPs) | Terbinafine MIC, mg/L |
No. isolates | |
|---|---|---|---|---|
| Modal MIC‡ | Range | |||
| T. indotineae, n = 105 |
WT | ND | 0.03–0.06 | 3 |
| L393F | ND | >4 | 1 | |
| L393S | ND | 0.5–1 | 3 | |
| F397L | >4 | 2–>4 | 63 | |
| F397L/Y414H | ND | >4 | 1 | |
| F397L/A448T | ND | 4–>4 | 6 | |
| Q408L | 2 | 1–4 | 20 | |
| F415C | ND | 1 | 1 | |
| F415L | ND | 0.5 | 1 | |
| A448T |
ND |
0.03–0.125 |
6 |
|
| T. interdigitale, n = 26 |
WT | 0.008/0.016 | <0.004-0.06 | 21 |
| L393F | ND | >4 | 1 | |
| L393S | ND | 0.25–1 | 3 | |
| F415L |
ND |
0.25 |
1 |
|
| T. mentagrophytes ITS genotype DK-I, n = 1§ |
WT (SNPs: N276¶, F419 and T454) |
ND |
0.06 |
1 |
| T. mentagrophytes ITS genotype DK-II, n = 4§ |
WT (SNPs: N276¶, F419 and P454) |
ND |
0.008–0.06 |
4 |
| T. mentagrophytes ITS genotype III, n = 2§ |
WT (SNPs: N276¶, F419 and T454) |
ND |
0.016–0.03 |
2 |
| T. mentagrophytes ITS genotype III*, n = 9§ |
WT (SNPs: N276¶, F419 and T454) |
ND |
0.008–0.03 |
9 |
| T. mentagrophytes ITS genotype IV, n = 1§ |
WT (SNPs: K276¶, L419 and T454) |
ND |
0.03 |
1 |
| T. mentagrophytes ITS genotype VII, n = 2§ |
WT (SNPs: N276¶, F419 and T454) |
ND |
0.016–0.03 |
2 |
| T. rubrum, n = 285 |
WT | 0.016 | <0.004–0.06 | 143 |
| Y110C¶ | ND | 0.008 | 1 | |
| I121M¶ | ND | 0.03 | 1 | |
| I121M¶/F415S | ND | 0.5 | 1 | |
| L335F¶/F415S | ND | 2 | 1 | |
| L393del | ND | 4 | 2 | |
| L393F | ND | >4 | 7 | |
| L393F/Y394del | ND | >4 | 2 | |
| L393S | 0.5 | 0.25–2 | 15 | |
| S395_I396insS | ND | 0.5 | 3 | |
| F397I | 1 | 0.25–1 | 11 | |
| F397L | 4 | 1->4 | 78 | |
| Y414H | ND | 0.03–0.06 | 2 | |
| F415L | ND | 0.125 | 1 | |
| F415S | ND | 0.125–1 | 3 | |
| H440Y | ND | 0.016–0.125 | 9 | |
| A448T | ND | 0.03 | 1 | |
| A448V | ND | 0.004 | 1 | |
| L451P | ND | 0.125 | 1 | |
| C476Y |
ND |
0.016–0.03 |
2 |
|
| T. soudanense, n = 2§ |
WT |
ND |
<0.004–0.008 |
2 |
| T. tonsurans, n = 16§ |
WT |
0.016 |
0.008–0.06 |
16 |
| T. violaceum, n = 24§ |
WT |
0.03 |
0.004–0.125 |
24 |
| T. equinum, n = 1§ |
WT |
ND |
0.03 |
1 |
| T. simii, n = 1§ |
WT |
ND |
<0.004 |
1 |
| T. erinacei, n = 2§# |
WT |
ND |
Not tested |
2 |
| T. concentricum, n = 1§# |
WT |
ND |
Not tested |
1 |
| T. europaeum, n = 1§ |
WT |
ND |
0.03 |
1 |
| T. benhamiae var. benhamiae/var. luteum, n = 10§ | WT | ND | 0.004–0.06 | 10 |
†EUCAST tentative epidemiological cutoff values for terbinafine (0.125 mg/L for T. indotineae and 0.03 mg/L for T. rubrum) were used to classify isolates as wild-type or non–wild-type. Underlined SQLE alterations are associated with terbinafine MICs above the corresponding tentative epidemiological cutoff values. An expanded version of this table appears in the Appendix. DK-I, unassigned I; DK-II, unassigned II; EUCAST, European Committee on Antimicrobial Susceptibility Testing; ITS, internal transcribed spacer; ND, not determined; SNP, single-nucleotide polymorphism; SQLE, squalene epoxidase; WT, wild-type. ‡Modal MIC is reported only for distributions comprising >10 isolates. Bimodal distributions are reported as both modal MICs. §Indicates that all isolates of the indicated species were wild-type. DK-I and DK-II denote novel ITS genotypes identified in this study. ¶Indicates that the codon is not covered by sequencing of the short sqle fragment (spanning amino acids H376–V483). #EUCAST susceptibility testing was not performed.