Skip to main content
SpringerLink
Log in

MycoSNP: A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris

  • Protocol
  • First Online:
Candida auris

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2517))

Abstract

Candida auris is an urgent public health threat characterized by high drug-resistant rates and rapid spread in healthcare settings worldwide. As part of the C. auris response, molecular surveillance has helped public health officials track the global spread and investigate local outbreaks. Here, we describe whole-genome sequencing analysis methods used for routine C. auris molecular surveillance in the United States; methods include reference selection, reference preparation, quality assessment and control of sequencing reads, read alignment, and single-nucleotide polymorphism calling and filtration. We also describe the newly developed pipeline MycoSNP, a portable workflow for performing whole-genome sequencing analysis of fungal organisms including C. auris.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. U.S. Department of Health and Human Services C (2019) Antibiotic resistance threats in the United States, 2019. CDC. https://www.cdc.gov/drugresistance/pdf/threats-report/2019-ar-threats-report-508.pdf

  2. Meis JF, Chowdhary A (2020) Candida auris—“ten years after”. J Fungi 6:2

    Article  Google Scholar 

  3. Du H, Bing J, Hu T, Ennis CL, Nobile CJ, Huang G (2020) Candida auris: epidemiology, biology, antifungal resistance, and virulence. PLoS Pathog 16:e1008921

    Article  CAS  Google Scholar 

  4. Schelenz S, Hagen F, Rhodes JL, Abdolrasouli A, Chowdhary A, Hall A, Ryan L, Shackleton J, Trimlett R, Meis JF, Armstrong-James D, Fisher MC (2016) First hospital outbreak of the globally emerging Candida auris in a European hospital. Antimicrob Resist Infect Control 5:35. https://doi.org/10.1186/s13756-016-0132-5

    Article  PubMed  PubMed Central  Google Scholar 

  5. Zhai B, Rolling T, Hohl TM (2021) Exploring Candida auris in its habitat. Cell Host Microbe 29(2):150–151. https://doi.org/10.1016/j.chom.2021.01.010

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Welsh RM, Bentz ML, Shams A, Houston H, Lyons A, Rose LJ, Litvintseva AP (2017) Survival, persistence, and isolation of the emerging multidrug-resistant pathogenic yeast Candida auris on a plastic health care surface. J Clin Microbiol 55(10):2996–3005. https://doi.org/10.1128/jcm.00921-17

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Sexton DJ, Welsh RM, Bentz ML, Forsberg K, Jackson B, Berkow EL, Litvintseva AP (2020) Evaluation of nine surface disinfectants against Candida auris using a quantitative disk carrier method: EPA SOP-MB-35. Infect Control Hosp Epidemiol 41(10):1219–1221. https://doi.org/10.1017/ice.2020.278

    Article  PubMed  Google Scholar 

  8. Eyre DW, Sheppard AE, Madder H, Moir I, Moroney R, Quan TP, Griffiths D, George S, Butcher L, Morgan M, Newnham R, Sunderland M, Clarke T, Foster D, Hoffman P, Borman AM, Johnson EM, Moore G, Brown CS, Walker AS, Peto TEA, Crook DW, Jeffery KJM (2018) A Candida auris outbreak and its control in an intensive care setting. N Engl J Med 379(14):1322–1331. https://doi.org/10.1056/NEJMoa1714373

    Article  PubMed  Google Scholar 

  9. Chow NA, Gade L, Tsay SV, Forsberg K, Greenko JA, Southwick KL, Barrett PM, Kerins JL, Lockhart SR, Chiller TM, Litvintseva AP (2018) Multiple introductions and subsequent transmission of multidrug-resistant Candida auris in the USA: a molecular epidemiological survey. Lancet Infect Dis 18(12):1377–1384. https://doi.org/10.1016/s1473-3099(18)30597-8

    Article  PubMed  PubMed Central  Google Scholar 

  10. Chow NA, Muñoz JF, Gade L, Berkow EL, Li X, Welsh RM, Forsberg K, Lockhart SR, Adam R, Alanio A, Alastruey-Izquierdo A, Althawadi S, Araúz AB, Ben-Ami R, Bharat A, Calvo B, Desnos-Ollivier M, Escandón P, Gardam D, Gunturu R, Heath CH, Kurzai O, Martin R, Litvintseva AP, Cuomo CA (2020) Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses. mBio 11(2):e03364–03319. https://doi.org/10.1128/mBio.03364-19

    Article  Google Scholar 

  11. Lockhart SR, Etienne KA, Vallabhaneni S, Farooqi J, Chowdhary A, Govender NP, Colombo AL, Calvo B, Cuomo CA, Desjardins CA, Berkow EL, Castanheira M, Magobo RE, Jabeen K, Asghar RJ, Meis JF, Jackson B, Chiller T, Litvintseva AP (2017) Simultaneous emergence of multidrug-resistant Candida auris on 3 continents confirmed by whole-genome sequencing and epidemiological analyses. Clin Infect Dis 64(2):134–140. https://doi.org/10.1093/cid/ciw691

    Article  PubMed  CAS  Google Scholar 

  12. Bakker HC, Switt AI, Cummings CA, Hoelzer K, Degoricija L, Rodriguez-Rivera LD, Wright EM, Fang R, Davis M, Root T, Schoonmaker-Bopp D, Musser KA, Villamil E, Waechter H, Kornstein L, Furtado MR, Wiedmann M (2011) A whole-genome single nucleotide polymorphism-based approach to trace and identify outbreaks linked to a common Salmonella enterica subsp. enterica serovar Montevideo pulsed-field gel electrophoresis type. Appl Environ Microbiol 77(24):8648–8655. https://doi.org/10.1128/aem.06538-11

    Article  PubMed  Google Scholar 

  13. Uelze L, Grützke J, Borowiak M, Hammerl JA, Juraschek K, Deneke C, Tausch SH, Malorny B (2020) Typing methods based on whole genome sequencing data. One Health Outlook 2(1):3. https://doi.org/10.1186/s42522-020-0010-1

    Article  PubMed  PubMed Central  Google Scholar 

  14. Muñoz JF, Welsh RM, Shea T, Batra D, Gade L, Howard D, Rowe LA, Meis JF, Litvintseva AP, Cuomo CA (2021) Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in Candida auris. Genetics 218(1):iyab029. https://doi.org/10.1093/genetics/iyab029

    Article  PubMed  PubMed Central  Google Scholar 

  15. Muñoz JF, Gade L, Chow NA, Loparev VN, Juieng P, Berkow EL, Farrer RA, Litvintseva AP, Cuomo CA (2018) Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species. Nat Commun 9(1):5346. https://doi.org/10.1038/s41467-018-07779-6

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  16. Walter KS, Colijn C, Cohen T, Mathema B, Liu Q, Bowers J, Engelthaler DM, Narechania A, Lemmer D, Croda J, Andrews JR (2020) Genomic variant-identification methods may alter mycobacterium tuberculosis transmission inferences. Microbial. Genomics 6:mgen000418. https://doi.org/10.1099/mgen.0.000418

    Article  CAS  Google Scholar 

  17. Ambaraghassi G, Dufresne PJ, Dufresne SF, Vallières É, Muñoz JF, Cuomo CA, Berkow EL, Lockhart SR, Luong M-L (2019) Identification of Candida auris by use of the updated Vitek 2 yeast identification system, version 8.01: a multilaboratory evaluation study. J Clin Microbiol 57(11):e00884–e00819. https://doi.org/10.1128/jcm.00884-19

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  18. Wöstemeyer J, Kreibich A (2002) Repetitive DNA elements in fungi (Mycota): impact on genomic architecture and evolution. Curr Genet 41(4):189–198. https://doi.org/10.1007/s00294-002-0306-y

    Article  PubMed  CAS  Google Scholar 

  19. Treangen TJ, Salzberg SL (2011) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 13(1):36–46. https://doi.org/10.1038/nrg3117

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Frith MC, Hamada M, Horton P (2010) Parameters for accurate genome alignment. BMC Bioinform 11(1):80. https://doi.org/10.1186/1471-2105-11-80

    Article  CAS  Google Scholar 

  21. Tarailo-Graovac M, Chen N (2009) Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinform. Chapter 4: Unit 4.10. https://doi.org/10.1002/0471250953.bi0410s25

  22. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6):841–842. https://doi.org/10.1093/bioinformatics/btq033

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Delcher AL, Salzberg SL, Phillippy AM (2003) Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinform. Chapter 10: Unit 10.13. https://doi.org/10.1002/0471250953.bi1003s00

  24. Jo H, Koh G (2015) Faster single-end alignment generation utilizing multi-thread for BWA. Biomed Mater Eng 26(Suppl 1):S1791–S1796. https://doi.org/10.3233/bme-151480

    Article  PubMed  Google Scholar 

  25. Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997

    Google Scholar 

  26. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43(5):491–498. https://doi.org/10.1038/ng.806

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  27. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297–1303. https://doi.org/10.1101/gr.107524.110

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079. https://doi.org/10.1093/bioinformatics/btp352

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Institute B Picard Toolkit: Repository. http://broadinstitute.github.io/picard/

  30. Sedlar K, Skutkova H, Vitek M, Provaznik I (2016) Set of rules for genomic signal downsampling. Comput Biol Med 69:308–314. https://doi.org/10.1016/j.compbiomed.2015.05.022

    Article  PubMed  CAS  Google Scholar 

  31. SEQTK Tookit: Repository. https://github.com/lh3/seqtk

  32. Kircher M, Heyn P, Kelso J (2011) Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics 12(1):382. https://doi.org/10.1186/1471-2164-12-382

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Pont-Kingdon G, Gedge F, Wooderchak-Donahue W, Schrijver I, Weck KE, Kant JA, Oglesbee D, Bayrak-Toydemir P, Lyon E (2012) Design and analytical validation of clinical DNA sequencing assays. Arch Pathol Lab Med 136(1):41–46. https://doi.org/10.5858/arpa.2010-0623-OA

    Article  PubMed  CAS  Google Scholar 

  34. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred II. Error probabilities. Genome Res 8(3):186–194

    Article  CAS  Google Scholar 

  35. Simon A (2010) FastQC: a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

  36. Lo C-C, Chain PSG (2014) Rapid evaluation and quality control of next generation sequencing data with FaQCs. BMC Bioinform 15(1):366. https://doi.org/10.1186/s12859-014-0366-2

    Article  Google Scholar 

  37. Hansen KD, Brenner SE, Dudoit S (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 38(12):e131. https://doi.org/10.1093/nar/gkq224

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  38. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ (2008) A large genome center's improvements to the Illumina sequencing system. Nat Methods 5(12):1005–1010. https://doi.org/10.1038/nmeth.1270

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ (2009) Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 6(4):291–295. https://doi.org/10.1038/nmeth.1311

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  40. Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, Altaf-Ul-Amin M, Ogasawara N, Kanaya S (2011) Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res 39(13):e90. https://doi.org/10.1093/nar/gkr344

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Cheng AY, Teo YY, Ong RT (2014) Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals. Bioinformatics 30(12):1707–1713. https://doi.org/10.1093/bioinformatics/btu067

    Article  PubMed  CAS  Google Scholar 

  42. Ye H, Meehan J, Tong W, Hong H (2015) Alignment of short reads: a crucial step for application of next-generation sequencing data in precision medicine. Pharmaceutics 7(4):523–541. https://doi.org/10.3390/pharmaceutics7040523

    Article  PubMed  PubMed Central  Google Scholar 

  43. Bravo Ruiz G, Ross ZK, Holmes E, Schelenz S, Gow NAR, Lorenz A (2019) Rapid and extensive karyotype diversification in haploid clinical Candida auris isolates. Curr Genet 65(5):1217–1228. https://doi.org/10.1007/s00294-019-00976-w

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. GATK. Hard-filtering germline short variants https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants

  45. Welsh RM, Misas E, Forsberg K, Lyman M, Chow NA (2021) Candida auris whole-genome sequence benchmark dataset for phylogenomic pipelines. J Fungi (Basel) 7:214. https://doi.org/10.3390/jof7030214

    Article  Google Scholar 

  46. Argimón S, Abudahab K, Goater RJE, Fedosejev A, Bhai J, Glasner C, Feil EJ, Holden MTG, Yeats CA, Grundmann H, Spratt BG, Aanensen DM (2016) Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom 2(11):e000093. https://doi.org/10.1099/mgen.0.000093

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA

    Ujwal R. Bagal, Rory M. Welsh, Elizabeth Misas, Lalitha Gade, Anastasia P. Litvintseva & Nancy A. Chow

  2. Centers for Disease Control and Prevention, Atlanta, GA, USA

    John Phan

  3. IHRC, Inc., Atlanta, GA, USA

    Darlene Wagner

  4. Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Christina A. Cuomo

Authors
  1. Ujwal R. Bagal
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. John Phan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rory M. Welsh
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Elizabeth Misas
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Darlene Wagner
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Lalitha Gade
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Anastasia P. Litvintseva
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Christina A. Cuomo
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Nancy A. Chow
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nancy A. Chow .

Editor information

Editors and Affiliations

  1. Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, UK

    Alexander Lorenz

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Bagal, U.R. et al. (2022). MycoSNP: A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris. In: Lorenz, A. (eds) Candida auris. Methods in Molecular Biology, vol 2517. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2417-3_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2417-3_17

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2416-6

  • Online ISBN: 978-1-0716-2417-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation