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Whole genome sequences of two Trichophyton indotineae clinical isolates from India emerging as threats during therapeutic treatment of dermatophytosis

A Correction to this article was published on 30 October 2021

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Abstract

In the current study, we report the genome sequence of two different clinical isolates from India, Trichophyton indotineae UCMS-IGIB-CI12 and Trichophyton indotineae UCMS-IGIB-CI14. The resulting genome assembly achieved a 143-fold coverage in 824 contigs for T. indotineae UCMS-IGIB-CI12 and a 136-fold coverage in 904 contigs for T. indotineae UCMS-IGIB-CI14. Both the clinical isolates contain a c.1342G>A mutation corresponding to Ala448Thr amino acid substitution in erg1 and exhibit an intermittent drug response to terbinafine. Comparative genomics analysis with available genomes of Trichophyton interdigitale/Trichophyton mentagrophytes species complex revealed a similar genome architecture and identified large number of genes associated with virulence and pathogenicity, namely, lipases, proteases, LysM domain-containing factors, carbon metabolism enzymes and cytochrome P450 enzymes, in all the genomes. An analysis of single amino acid polymorphisms (SAPs) in the protein sequences of subtilisin and lipase enzyme families identified a higher frequency of SAPs in functionally important proteins, Sub3 and Sub6 and their possible use in multilocus phylogenetic analysis of T. interdigitale/T. mentagrophytes species complex. The whole genome sequences of T. indotineae clinical isolates provided in this report will, hence, serve as a key reference point for investigation of clinical strains and emerging drug resistance among dermatophytes originating from different parts of the world.

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Data availability

The sequence of the internal transcribed spacer regions 1–2 of 18S rRNA of the isolates TiCI12 and TiCI14 were deposited in NCBI with Accession numbers MW600527 and MW600653, respectively. The complete annotated genome assemblies of TiCI12 and TICI14 have also been deposited at GenBank and are available under the accession numbers JAATJQ000000000.1 and JAAQVJ000000000.1, respectively.

Code availability

Not applicable.

Change history

Abbreviations

wgs:

Whole genome sequence

cds:

Coding DNA sequences

ITS:

Internal transcribed spacer

TiCI12:

T. indotineae UCMS-IGIB-CI12

TiCI14:

T. indotineae UCMS-IGIB-CI14

MIC:

Minimum inhibitory concentration

AFST:

Antifungal susceptibility test

SNP:

Single nucleotide polymorphism

SAP:

Single amino-acid polymorphism

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Acknowledgements

PK acknowledges Senior Research Fellowship from CSIR. The authors thank Vinod Scaria, S. Ramachandran and Debasis Dash for useful discussions. We thank CSIR-Institute of Genomics and Integrative Biology for providing the infrastructure and central instrument lab facility.

Funding

This work was supported by funding from Department of Biotechnology (DBT), Government of India. (Grant number: BT/PR20790/MED/29/1130/2016).

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Authors and Affiliations

Authors

Contributions

All the authors contributed to this work. PK, SD, SNB and BT conceptualized the work; PK, RT and RP performed the experiments; PK, SD, RT, RP and BT analyzed the data; SD and BT supervised the work; PK and BT wrote the paper. All authors reviewed and approved the manuscript.

Corresponding author

Correspondence to Bhupesh Taneja.

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Conflict of interest

The authors declare that they have no potential conflict of interest.

Ethical approval

This study was approved by the Institutional Human Ethics Committee of UCMS-GTB (IECHR/2016/28/2 dated 27/12/2016) and CSIR-IGIB (CSIR-IGIB/IHEC/2017-18 dated 30/05/2017).

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Kumar, P., Das, S., Tigga, R. et al. Whole genome sequences of two Trichophyton indotineae clinical isolates from India emerging as threats during therapeutic treatment of dermatophytosis. 3 Biotech 11, 402 (2021). https://doi.org/10.1007/s13205-021-02950-1

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  • DOI: https://doi.org/10.1007/s13205-021-02950-1

Keywords

  • Trichophyton spp.
  • Dermatophytes, whole-genome sequencing
  • Phylogenetic analysis