Diagnostic Allele-Specific PCR for the Identification of Candida auris Clades
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sequence Analysis for Species- and Clade-Specific Allele Selection
2.2. Strains and Media
2.3. DNA Extraction
2.4. PCR and Sequencing
2.5. Allele-Specific Primer Design
2.6. AS-PCR
3. Results
3.1. C. auris Identification
3.2. C. auris Clade Identification
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Name | NCBI Accession Nr. | Strain | Size (bp) |
---|---|---|---|
Candida auris | NR_154998.1 | CBS 10913 | 342 |
Candida haemulonii | JX459664.1 | CBS 6590 | 479 |
Candida haemulonii var. vulnera | JX459687.1 | CNMCL7256 | 322 |
Candida pseudohaemulonii | EU881972.1 | C4368 | 327 |
Candida duobushaemulonii | JX459667.1 | CBS 7799 | 487 |
Candida albicans | NR_125332.1 | CBS 562 | 462 |
Candida tropicalis | NR_111250.1 | CBS 94 | 454 |
Candida lusitaniae | NR_130677.1 | CBS 6936 | 307 |
Candida glabrata | NR_130691.1 | NRRL Y-65 | 655 |
Candida dubliniensis | NR_119386.1 | CBS 7987 | 460 |
Candida parapsilosis | NR_130673.1 | ATCC 22019 | 461 |
Candida orthopsilosis | NR_130661.1 | ATCC 96139 | 436 |
Candida metapsilosis | NR_165186.1 | CBS 10907 | 472 |
Candida sake | NR_151807.1 | CBS 159 | 432 |
Candida inconspicua | NR_111116.1 | CBS 180 | 379 |
Candida castellii | NR_154958.1 | CBS 4332 | 628 |
Candida bracarensis | NR_136973.1 | CBS 10154 | 704 |
Candida pararugosa | MF797780.1 | S200 | 324 |
Candida guilliermondii (Meyerozyma guillermondii) | NR_111247.1 | CBS 2030 | 532 |
Candida krusei (Pichia kudriavzevii) | NR_131315.1 | ATCC 6258 | 435 |
Candida famata (Debaryomyces hansenii) | NR_120016.1 | JCM 1990 | 580 |
Candida kefyr (Kluyveromyces marxianus) | NR_111251.1 | CBS 712 | 628 |
Candida norvegensis (Pichia norvegensis) | MH396411.1 | URM 7762 | 434 |
Lodderomyces elongisporus | NR_111593.1 | ATCC 11503 | 496 |
Yarrowia lipolytica | NR_111212.1 | CBS 6124 | 285 |
Nakaseomyces delphensis | NR_167682.1 | CBS 2170 | 709 |
Nakaseomyces bacillisporus | NR_138202.1 | NRRL Y-17846 | 662 |
Kodameae ohmeri | NR_121464.1 | CBS 5367 | 348 |
Diutina catenulata | NR_077200.1 | CBS 565 | 343 |
Rhodotorula mucilaginosa (R. rubra) | NR_073296.1 | CBS 316 | 557 |
Rhodotorula glutinis | MH665424.1 | R.g0726 | 582 |
Saccharomyces cerevisiae | NR_111007.1 | CBS 1171 | 613 |
Nr. | Strain Name | Origin | Clade | Typing Reference |
---|---|---|---|---|
1 | B11244 | Venezuela | IV | [2,13,17] |
2 | B11245 | Venezuela | IV | |
3 | B11221 | South Africa | III | [2,3,13,17] |
4 | B11222 | South Africa | III | |
5 | CDC_390 | India | I | |
6 | - | Colombia | IV | |
7 | B11098 | Pakistan | I | |
8 | B11203 | India | I | |
9 | - | India | I | |
10 | - | India | I | |
11 | - | India | I | |
12 | - | India | I | |
13 | VPCI 714/P/14 | India | I | |
14 | B8441 | Pakistan | I | [2,3,13,17] |
15 | 317052804 | Oman | I | |
16 | VPCI 514/P/14 | India | I | |
17 | VPCI 1133/P/13 | India | I | |
18 | B11109 | India | I | |
19 | VPCI 1131/P/13 | India | I | |
20 | OS299 | Belgium | I | |
21 | MRU224 | South Africa | III | |
22 | IFRC2087/B18474 | Iran | V | [12,17] |
23 | B11220 | Japan | II | [2,3,13,17] |
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Primer Name | Sequence | Use (Ta) | Target | Reference |
---|---|---|---|---|
ITS1 | TCCGTAGGTGAACCTGCGG | Sequencing (59) AS-PCR (68 or 78) 1 | Fungi | [47] |
ITS4 | TCCTCCGCTTATTGATATGC | Sequencing (60) | Fungi | [47] |
ITS_Cau_R | TTTGTGAATGCAACGCCATCG | AS-PCR (78) | C. auris | This study |
ITS_CauCII_R | GAGATCCGTTGTTGAAAGTTTTCTTTATA | AS-PCR (68) | Clade II | This study |
RHA1_CauCIII/V_F | TTGCGGTTGAAATGGGTGCT | AS-PCR (68) | Clade III/V | This study |
RHA1_CauCIII/V_R | TGGCATGTTTCCGGCTTAGA | AS-PCR (68) | Clade III/V | This study |
ITS_CauCIV/V_R | AGATCCGTTGTTGAAAGTTTTATGTTCTG | AS-PCR (68) | Clade IV/V | This study |
ITS_CauCV_R | AAGAGATCCGTTGTTGAAAGTTTCCTA | AS-PCR (68) | Clade V | This study |
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Carolus, H.; Jacobs, S.; Lobo Romero, C.; Deparis, Q.; Cuomo, C.A.; Meis, J.F.; Van Dijck, P. Diagnostic Allele-Specific PCR for the Identification of Candida auris Clades. J. Fungi 2021, 7, 754. https://doi.org/10.3390/jof7090754
Carolus H, Jacobs S, Lobo Romero C, Deparis Q, Cuomo CA, Meis JF, Van Dijck P. Diagnostic Allele-Specific PCR for the Identification of Candida auris Clades. Journal of Fungi. 2021; 7(9):754. https://doi.org/10.3390/jof7090754
Chicago/Turabian StyleCarolus, Hans, Stef Jacobs, Celia Lobo Romero, Quinten Deparis, Christina A. Cuomo, Jacques F. Meis, and Patrick Van Dijck. 2021. "Diagnostic Allele-Specific PCR for the Identification of Candida auris Clades" Journal of Fungi 7, no. 9: 754. https://doi.org/10.3390/jof7090754