Skip to main content
SpringerLink
Log in

Molecular Genetics and Genomics of Fungal Infections

  • Chapter
  • First Online:
Book cover Fungal Infections of the Central Nervous System

  • 842 Accesses

Abstract

Fungal infections of central nervous system (CNS) are increasingly encountered in various clinical settings. Any pathogenic fungus is able to produce CNS infection, though only certain groups are neurotropic. The outcome of CNS fungal infections depends on early diagnosis and prompt management. But, the early diagnosis faces stiff challenges due to general considerations of rarity of CNS fungal infection, non-specific clinical symptoms and signs and difficulty in collection of samples for conventional diagnosis. Application of genomic-based molecular techniques is usually rapid and sensitive and may detect the causative agent accurately and help appropriate and prompt antifungal therapy. These techniques can be applied either for detection of nucleic acid in clinical samples or for the accurate identification of fungi isolated from the clinical specimen. Detection of nucleic acid in clinical sample faces the challenge of extraction of nucleic acid, inadequate amount nucleic acid in sample and contamination during test procedure. The current chapter describes the existing knowledge on genomic-based molecular tests for diagnosis and monitoring of CNS fungal diseases.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 179.99
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

Abbreviations

AIDS:

Acquired immunodeficiency syndrome

CDC:

Centers for Disease Control and Prevention

CM:

Cryptococcal meningitis

CNS:

Central nervous system

CSF:

Cerebrospinal fluid

CT:

Computed tomography

EF:

Elongation factor

HIV:

Human immunodeficiency virus

HRCA:

Hyperbranched rolling circle amplification

ISHAM:

International Society for Human and Animal Mycology

ITS:

Internal transcribed spacer

LAMP:

Loop-mediated isothermal amplification

LFA:

Lateral flow assay

ME:

Meningitis/encephalitis

MIC:

Minimal inhibitory concentration

MRI:

Magnetic resonance imaging

PCR:

Polymerase chain reaction

PLB:

Phospholipase B

References

  • de Aguirre L, Hurst SF, Choi JS, Shin JH, Hinrikson HP, Morrison CJ. Rapid differentiation of Aspergillus species from other medically important opportunistic molds and yeasts by PCR-enzyme immunoassay. J Clin Microbiol. 2004;42:3495–504.

    Article  Google Scholar 

  • Alonso R, Pisa D, Fernández-Fernández AM, Rábano A, Carrasco L. Fungal infection in neural tissue of patients with amyotrophic lateral sclerosis. Neurobiol Dis. 2017;108:249–60.

    Article  CAS  Google Scholar 

  • Atkins SD, Clark IM. Fungal molecular diagnostics: a mini review. J Appl Genet. 2004;45:3–15.

    PubMed  Google Scholar 

  • Babady NE, Buckwalter SP, Hall L, Le Febre KM, Binnicker MJ, Wengenack NL. Detection of Blastomyces dermatitidis and Histoplasma capsulatum from culture isolates and clinical specimens by use of real-time PCR. J Clin Microbiol. 2011;49:3204–8.

    Article  CAS  Google Scholar 

  • Badiee P, Alborzi A. Assessment of a real-time PCR method to detect human non-cryptococcal fungal meningitis. Arch Iran Med. 2011;14:381–4.

    CAS  PubMed  Google Scholar 

  • Balajee SA, Gribskov JL, Hanley E, Nickle D, Marr KA. Aspergillus lentulus sp. nov., a new sibling species of A. fumigatus. Eukaryot Cell. 2005;4:625–32.

    Article  CAS  Google Scholar 

  • Barnes RA. Early diagnosis of fungal infection in immunocompromised patients. J Antimicrob Chemother. 2008;61(Suppl 1):i3–6.

    Article  CAS  Google Scholar 

  • Bialek R, Weiss M, Bekure-Nemariam K, Najvar LK, Alberdi MB, Graybill JR, et al. Detection of Cryptococcus neoformans DNA in tissue samples by nested and real-time PCR assays. Clin Diagn Lab Immunol. 2002;9:461–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bialek R, Konrad F, Kern J, Aepinus C, Cecenas L, Gonzalez GM, et al. PCR based identification and discrimination of agents of mucormycosis and aspergillosis in paraffin wax embedded tissue. J Clin Pathol. 2005;58:1180–4.

    Article  CAS  Google Scholar 

  • Binnicker MJ, Popa AS, Catania J, Alexov M, Tsaras G, Lloyd F, et al. Meningeal coccidioidomycosis diagnosed by real-time polymerase chain reaction analysis of cerebrospinal fluid. Mycopathologia. 2011;171:285–9.

    Article  Google Scholar 

  • Buitrago MJ, Bernal-Martínez L, Castelli MV, Rodríguez-Tudela JL, Cuenca-Estrella M. Histoplasmosis and paracoccidioidomycosis in a non-endemic area: a review of cases and diagnosis. J Travel Med. 2011;18:26–33.

    Article  Google Scholar 

  • Centers for Disease Control and Prevention (CDC). Multistate fungal meningitis outbreak – interim guidance for treatment. MMWR Morb Mortal Wkly Rep. 2012;61:842.

    Google Scholar 

  • Chew KL, Lee CK, Cross GB, Lum LHW, Yan B, Jureen R. Culture-confirmed cryptococcal meningitis not detected by Cryptococcus PCR on the Biofire meningitis/encephalitis panel®. Clin Microbiol Infect. 2018;24(7):791–2.

    Article  CAS  Google Scholar 

  • Demogines A, Fouch S, Everhart K, Leber A, Barney T, Daly JA, et al. Multi-center clinical evaluation of a multiplex meningitis/encephalitis PCR panel for simultaneous detection of bacteria, yeast, and viruses in cerebrospinal fluid specimens. J Clin Microbiol. 2015;54:2251–61.

    Google Scholar 

  • Elsayed S, Fitzgerald V, Massey V, Hussain Z. Evaluation of the Candigen enzyme-linked immunosorbent assay for quantitative detection of Candida species antigen. Arch Pathol Lab Med. 2001;125:344–6.

    CAS  PubMed  Google Scholar 

  • Farina C, Perin S, Andreoni S, Conte M, Fazii P, Lombardi G, et al. Evaluation of the peptide nucleic acid fluorescence in situ hybridisation technology for yeast identification directly from positive blood cultures: an Italian experience. Mycoses. 2012;55:388–92.

    Article  Google Scholar 

  • Frías-De-León MG, Ramírez-Bárcenas JA, Rodríguez-Arellanes G, Velasco-Castrejón O, Taylor ML, Reyes-Montes M d R. Usefulness of molecular markers in the diagnosis of occupational and recreational histoplasmosis outbreaks. Folia Microbiol (Praha). 2017;62:111–6.

    Article  Google Scholar 

  • Gade L, Scheel CM, Pham CD, Lindsley MD, Iqbal N, Cleveland AA, et al. Detection of fungal DNA in human body fluids and tissues during a multistate outbreak of fungal meningitis and other infections. Eukaryot Cell. 2013;12:677–83.

    Article  CAS  Google Scholar 

  • Gade L, Grgurich DE, Kerkering TM, Brandt ME, Litvintseva AP. Utility of real-time PCR for detection of exserohilum rostratum in body and tissue fluids during the multistate outbreak of fungal meningitis and other infections. J Clin Microbiol. 2015;53:618–25.

    Article  CAS  Google Scholar 

  • Gunaratne PS, Wijeyaratne CN, Seneviratne HR. Aspergillus meningitis in Sri Lanka – a post-tsunami effect? N Engl J Med. 2007;356:754–6.

    Article  CAS  Google Scholar 

  • Hanson KE. The first fully automated molecular diagnostic panel for meningitis and encephalitis: how well does it perform, and when should it be used? J Clin Microbiol. 2016;54:2222–4.

    Article  Google Scholar 

  • de Hoog GS, Nishikaku AS, Fernandez-Zeppenfeldt G, Padín-González C, Burger E, Badali H, et al. Molecular analysis and pathogenicity of the Cladophialophora carrionii complex, with the description of a novel species. Stud Mycol. 2007;58:219–34.

    Article  Google Scholar 

  • Hummel M, Spiess B, Kentouche K, Niggemann S, Böhm C, Reuter S, et al. Detection of Aspergillus DNA in cerebrospinal fluid from patients with cerebral aspergillosis by a nested PCR assay. J Clin Microbiol. 2006;44:3989–93.

    Article  CAS  Google Scholar 

  • Kami M, Ogawa S, Kanda Y, Tanaka Y, Machida U, Matsumura T, et al. Early diagnosis of central nervous system aspergillosis using polymerase chain reaction, latex agglutination test, and enzyme-linked immunosorbent assay. Br J Haematol. 1999a;106:536–7.

    Article  CAS  Google Scholar 

  • Kami M, Shirouzu I, Mitani K, Ogawa S, Matsumura T, Kanda Y, et al. Early diagnosis of central nervous system aspergillosis with combination use of cerebral diffusion-weighted echo-planar magnetic resonance image and polymerase chain reaction of cerebrospinal fluid. Intern Med. 1999b;38:45–8.

    Article  CAS  Google Scholar 

  • Kaocharoen S, Wang B, Tsui KM, Trilles L, Kong F, Meyer W. Hyperbranched rolling circle amplification as a rapid and sensitive method for species identification within the Cryptococcus species complex. Electrophoresis. 2008;29:3183–91.

    CAS  PubMed  Google Scholar 

  • Khot PD, Fredricks DN. PCR-based diagnosis of human fungal infections. Expert Rev Anti Infect Ther. 2009;7:1201–21.

    Article  CAS  Google Scholar 

  • Klingspor L, Jalal S. Molecular detection and identification of Candida and Aspergillus spp. from clinical samples using real-time PCR. Clin Microbiol Infect. 2006;12:745–53.

    Article  CAS  Google Scholar 

  • Komatsu H, Fujisawa T, Inui A, Horiuchi K, Hashizume H, Sogo T, et al. Molecular diagnosis of cerebral aspergillosis by sequence analysis with panfungal polymerase chain reaction. J Pediatr Hematol Oncol. 2004;26:40–4.

    Article  Google Scholar 

  • Landlinger C, Preuner S, Willinger B, Haberpursch B, Racil Z, Mayer J, et al. Species-specific identification of a wide range of clinically relevant fungal pathogens by use of Luminex xMAP technology. J Clin Microbiol. 2009;47:1063–73.

    Article  CAS  Google Scholar 

  • Lass-Flörl C, Mutschlechner W, Aigner M, Grif K, Marth C, Girschikofsky M, et al. Utility of PCR in diagnosis of invasive fungal infections: real-life data from a multicenter study. J Clin Microbiol. 2013;51:863–8.

    Article  Google Scholar 

  • Leeflang MM, Debets-Ossenkopp YJ, Visser CE, Scholten RJ, Hooft L, Bijlmer HA, et al. Galactomannan detection for invasive aspergillosis in immunocompromised patients. Cochrane Database Syst Rev. 2008;(4):CD007394.

    Google Scholar 

  • Liesman RM, Strasburg AP, Heitman AK, Theel ES, Patel R, Binnicker MJ. Evaluation of a commercial multiplex molecular panel for diagnosis of infectious meningitis and encephalitis. J Clin Microbiol. 2018;56:1–27.

    Article  Google Scholar 

  • López LF, Muñoz CO, Cáceres DH, Tobón ÁM, Loparev V, Clay O, et al. Standardization and validation of real time PCR assays for the diagnosis of histoplasmosis using three molecular targets in an animal model. PLoS One. 2017;12:e0190311.

    Article  Google Scholar 

  • Mandviwala T, Shinde R, Kalra A, Sobel JD, Akins RA. High-throughput identification and quantification of Candida species using high resolution derivative melt analysis of panfungal amplicons. J Mol Diagn. 2010;12:91–101.

    Article  CAS  Google Scholar 

  • Martins M d A, Brighente KBS, de Matos TA, Vidal JE, de Hipólito DDC, Pereira-Chioccola VL. Molecular diagnosis of cryptococcal meningitis in cerebrospinal fluid: comparison of primer sets for Cryptococcus neoformans and Cryptococcus gattii species complex. Braz J Infect Dis. 2015;19:62–7.

    Article  Google Scholar 

  • Mitchell M, Dizon D, Libke R, Peterson M, Slater D, Dhillon A. Development of a real-time PCR assay for identification of Coccidioides immitis by use of the BD Max system. J Clin Microbiol. 2015;53:926–9. https://doi.org/10.1128/JCM.02731-14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McCarthy MW, Walsh TJ. Molecular diagnosis of invasive mycoses of the central nervous system. Expert Rev Mol Diagn. 2017;17:129–39.

    Article  CAS  Google Scholar 

  • Moling O, Lass-Floerl C, Verweij PE, Porte M, Boiron P, Prugger M, et al. Case reports. Chronic and acute Aspergillus meningitis – Falldarstellungen. Chronische und akute Aspergillus-Meningitis. Mycoses. 2002;45:504–11.

    CAS  PubMed  Google Scholar 

  • Chen M, Zhou J, Li J, Li M, Sun J, Fang WJ, Al-Hatmi AMS, Xu J, Boekhout T, Liao WQ, Pan WH. Evaluation of five conventional and molecular approaches for diagnosis of cryptococcal meningitis in non-HIV-infected patients. Mycoses. 2016;59(8):494–502. https://doi.org/10.1111/myc.12497.

    Article  CAS  PubMed  Google Scholar 

  • O’Donnell K, Sutton DA, Rinaldi MG, Sarver BAJ, Balajee SA, Schroers H-J, et al. Internet-accessible DNA sequence database for identifying fusaria from human and animal infections. J Clin Microbiol. 2010;48:3708–18.

    Article  Google Scholar 

  • Pappas PG, Rex JH, Sobel JD, Filler SG, Dismukes WE, Walsh TJ, et al. Guidelines for treatment of candidiasis. Clin Infect Dis. 2004;38:161–89.

    Article  Google Scholar 

  • Paschoal RC, Hirata MH, Hirata RC, Melhem MDSC, Dias ALT, Paula CR. Neurocryptococcosis: diagnosis by PCR method. Rev Inst Med Trop Sao Paulo. 2004;46:203–7.

    Article  Google Scholar 

  • Preuner S, Lion T. Towards molecular diagnostics of invasive fungal infections. Expert Rev Mol Diagn. 2009;9:397–401.

    Article  Google Scholar 

  • Qishui O, Ling J, Ni L, Bin Y, Wen L. Comparison of real-time florescence quantitative PCR measurements of VAD1 mRNA with three conventional methods in diagnosis and follow-up treatment of Cryptococcus neoformans infection. Mycoses. 2012;55:326–32.

    Article  Google Scholar 

  • Ralph ED, Hussain Z. Chronic meningitis caused by Candida albicans in a liver transplant recipient: usefulness of the polymerase chain reaction for diagnosis and for monitoring treatment. Clin Infect Dis. 1996;23:191–2.

    Article  CAS  Google Scholar 

  • Rappelli P, Are R, Casu G, Fiori PL, Cappuccinelli P, Aceti A. Development of a nested PCR for detection of Cryptococcus neoformans cerebrospinal fluid. J Clin Microbiol. 1998;36:3438–40.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Reinwald M, Buchheidt D, Hummel M, Duerken M, Bertz H, Schwerdtfeger R, et al. Diagnostic performance of an Aspergillus-specific nested PCR assay in cerebrospinal fluid samples of immunocompromised patients for detection of central nervous system Aspergillosis. PLoS One. 2013;8:1–6.

    Article  Google Scholar 

  • Rhein J, Bahr NC, Hemmert AC, Cloud JL, Bellamkonda S, Oswald C, et al. Diagnostic performance of a multiplex PCR assay for meningitis in an HIV-infected population in Uganda. Diagn Microbiol Infect Dis. 2016;84:268–73.

    Article  CAS  Google Scholar 

  • Saha DC, Xess I, Biswas A, Bhowmik DM, Padma MV. Detection of Cryptococcus by conventional, serological and molecular methods. J Med Microbiol. 2009;58:1098–105. https://doi.org/10.1099/jmm.0.007328-0.

    Article  CAS  PubMed  Google Scholar 

  • Shamim MS, Enam SA, Ali R, Anwar S. Craniocerebral aspergillosis: a review of advances in diagnosis and management. J Pak Med Assoc. 2010;60:573–9.

    PubMed  Google Scholar 

  • Simoneau E, Kelly M, Labbe AC, Roy J, Laverdière M. What is the clinical significance of positive blood cultures with Aspergillus sp in hematopoietic stem cell transplant recipients? A 23 year experience. Bone Marrow Transplant. 2005;35:303–6.

    Article  CAS  Google Scholar 

  • Tavares ER, Azevedo CS, Panagio LA, Pelisson M, Pinge-Filho P, Venancio EJ, et al. Accurate and sensitive real-time PCR assays using intergenic spacer 1 region to differentiate Cryptococcus gattii sensu lato and Cryptococcus neoformans sensu lato. Med Mycol. 2016;54:89–96.

    CAS  PubMed  Google Scholar 

  • Trilles L, Meyer W, Wanke B, Guarro J, Lazéra M. Correlation of antifungal susceptibility and molecular type within the Cryptococcus neoformans/C. gattii species complex. Med Mycol. 2012;50:328–32.

    Article  Google Scholar 

  • Trilles L, Wang B, Firacative C, Lazéra MDS, Wanke B, Meyer W. Identification of the major molecular types of Cryptococcus neoformans and C. gattii by Hyperbranched rolling circle amplification. PLoS One. 2014;9:e94648.

    Article  Google Scholar 

  • Valero C, De L, Cruz-Villar L, Zaragoza Ó, Buitrago MJ. New panfungal real-time PCR assay for diagnosis of invasive fungal infections. J Clin Microbiol. 2016;54:2910–8.

    Article  CAS  Google Scholar 

  • Veron V, Simon S, Blanchet D, Aznar C. Real-time polymerase chain reaction detection of Cryptococcus neoformans and Cryptococcus gattii in human samples. Diagn Microbiol Infect Dis. 2009;65:69–72.

    Article  CAS  Google Scholar 

  • Verweij PE, Brinkman K, Kremer HPH, Kullberg B, Meis JFGM. Aspergillus meningitis: diagnosis by non-culture-based microbiological methods and management Aspergillus meningitis: diagnosis by non-culture-based microbiological methods and management. J Clin Microbiol. 1999;37:1186–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Vucicevic D, Blair JE, Binnicker MJ, McCullough AE, Kusne S, Vikram HR, et al. The utility of Coccidioides polymerase chain reaction testing in the clinical setting. Mycopathologia. 2010;170:345–51.

    Article  CAS  Google Scholar 

  • White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Shinsky JJ, White TJ, editors. PCR protocols: a guide to methods and applications. New York: Academic Press Inc.; 1990.

    Google Scholar 

  • Zaman K, Rudramurthy SM, Das A, Panda N, Honnavar P, Kaur H, et al. Molecular diagnosis of rhino-orbito-cerebral mucormycosis from fresh tissue samples. J Med Microbiol. 2017;66:1124–9.

    Article  CAS  Google Scholar 

  • Zhao Y, Petraitiene R, Walsh TJ, Perlin DS. A real-time PCR assay for rapid detection and quantification of Exserohilum rostratum, a causative pathogen of fungal meningitis associated with injection of contaminated methylprednisolone. J Clin Microbiol. 2013;51:1034–6.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India

    Shivaprakash M. Rudramurthy & Arunaloke Chakrabarti

  2. Center of Advance Research in Medical Mycology, WHO Collaborating Center for Reference and Research of Fungi of Medical Importance, National Culture Collection of Pathogenic Fungi, Chandigarh, India

    Arunaloke Chakrabarti

Authors
  1. Shivaprakash M. Rudramurthy
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Arunaloke Chakrabarti
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Neurosurgery, Aydın Adnan Menderes University, School of Medicine, Aydın, Turkey

    Mehmet Turgut

  2. Department of Pathology, Basavatarakam Indo-American Hospital & Research Institute, Hyderabad, Telangana, India

    Sundaram Challa

  3. Department of Neurosurgery, Avicenne Military Hospital, Mohammed V University in Rabat, Marrakech, Morocco

    Ali Akhaddar

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Rudramurthy, S.M., Chakrabarti, A. (2019). Molecular Genetics and Genomics of Fungal Infections. In: Turgut, M., Challa, S., Akhaddar, A. (eds) Fungal Infections of the Central Nervous System. Springer, Cham. https://doi.org/10.1007/978-3-030-06088-6_7

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-06088-6_7

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-06087-9

  • Online ISBN: 978-3-030-06088-6

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation