Skip to main content
SpringerLink
Log in

Molecular Characterization of Medically Important Fungi: Current Research and Future Prospects

  • Chapter
  • First Online:
Recent Trends in Mycological Research

Part of the book series: Fungal Biology ((FUNGBIO))

  • 683 Accesses

Abstract

Fungi have raised serious problems for human health as invasive fungal pathogens. These fungal infections are the possible reason of increased death and morbidity rates in immune-compromised patients. In this regard, early diagnosis and characterization of the invasive fungal species is of utmost importance. Currently employed fungal identification and diagnostic techniques, for example, microscopy, biochemical tests, histopathology, culture based and staining procedures, due to low sensitivity and time consumption are not ideal. To surmount this hurdle, molecular tools such as PCR, hybridization methods, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and nano-diagnostic approaches have gained considerable attention by researchers since they allow rapid detection and identification of invasive fungal pathogens.

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
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
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

References

  • Agrios G (2004) Plant pathology, 5th edn. Elsevier, Academic Press

    Google Scholar 

  • Ajello L (1986) Hyalohyphomycosis and phaeohyphomycosis: two global disease entities of public health importance. Eu J Epidemiol 2:243–251

    Article  CAS  Google Scholar 

  • Alanio A, Bretagne S (2014) Difficulties with molecular diagnostic tests for mould and yeast infections: where do we stand? Clin Microbiol Infect 20:36–41

    Article  CAS  PubMed  Google Scholar 

  • Alanio A, Desnos-Ollivier M, Garcia-Hermoso D, Bretagne S (2017) Investigating clinical issues by genotyping of medically important fungi: why and how? Clin Microbiol Rev 30:671–707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Almeida F, Rodrigues ML, Coelho C (2019) The still underestimated problem of fungal diseases worldwide. Front Microbiol 10:214

    Article  PubMed  PubMed Central  Google Scholar 

  • Arantes TD, Theodoro RC, Teixeira MDM, Bagagli E (2017) Use of fluorescent oligonucleotide probes for differentiation between Paracoccidioides brasiliensis and Paracoccidioides lutzii in yeast and mycelial phase. Mem I Oswaldo Cruz 112:140–145

    Article  CAS  Google Scholar 

  • Arias M, Santiago L, Vidal-García M, Redrado S, Lanuza P, Comas L et al (2018) Preparations for invasion: modulation of host lung immunity during pulmonary aspergillosis by gliotoxin and other fungal secondary metabolites. Fron Immunol 9:2549

    Article  CAS  Google Scholar 

  • Arvanitis M, Anagnostou T, Fuchs BB, Caliendo AM, Mylonakis E (2014) Molecular and nonmolecular diagnostic methods for invasive fungal infections. Clin Microbiol Rev 27:490–526

    Article  PubMed  PubMed Central  Google Scholar 

  • Badiee P, Kordbacheh P, Alborzi A, Malekhoseini S, Zeini F, Mirhendi H et al (2007) Prospective screening in liver transplant recipients by panfungal PCR-ELISAfor early diagnosis of invasive fungal infections. Liver Transpl 13:1011–1016

    Article  PubMed  Google Scholar 

  • Balajee SA, Gribskov JL, Hanley E, Nickle D, Marr KA (2005) Aspergillus lentulus sp. Nov., a new sibling species of A. fumigatus. Eukaryot Cell 4:625–632

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boles DJ, Benton JL, Siew GJ, Levy MH, Thwar PK, Sandahl MA et al (2011) Droplet-based pyrosequencing using digital microfluidics. Anal Chem 83:8439–8447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bouchara JP, Mignon B, Chaturvedi V (2017) Dermatophytes and dermatophytoses: a thematic overview of state of the art, and the directions for future research and developments. Mycopathologia 182:1–4

    Article  CAS  PubMed  Google Scholar 

  • Bougnoux ME, Brun S, Zahar JR (2018) Healthcare-associated fungal outbreaks: new and uncommon species, new molecular tools for investigation and prevention. Antimicrob Resist Infect Control 7:45

    Article  PubMed  PubMed Central  Google Scholar 

  • Boyce KJ, Andrianopoulos A (2015) Fungal dimorphism: the switch from hyphae to yeast is a specialized morphogenetic adaptation allowing colonization of a host. FEMS Microbiol Rev 39:797–811

    Article  CAS  PubMed  Google Scholar 

  • Brunke S, Mogavero S, Kasper L, Hube B (2016) Virulence factors in fungal pathogens of man. Curr Opin Microbiol 32:89–95

    Article  CAS  PubMed  Google Scholar 

  • Buchan BW, Ledeboer NA (2014) Emerging technologies for the clinical microbiology laboratory. Clin Microbiol Rev 27:783–822

    Article  PubMed  PubMed Central  Google Scholar 

  • Bunn TW, Sikarwar AS (2016) Diagnostics: conventional versus modern methods. J Am Med Pharm Sci 8:1–7

    Google Scholar 

  • Casadevall A, Coelho C, Cordero RJ, Dragotakes Q, Jung E, Vij R et al (2019) The capsule of Cryptococcus neoformans. Vir 10:822–831

    CAS  Google Scholar 

  • Chae HS, Jang GE, Kim NH, Son HR, Lee JH, Kim SH et al (2012) Classification of Cryptococcus neoformans and yeast-like fungus isolates from pigeon droppings by colony phenotyping and ITS genotyping and their seasonal variations in Korea. Avi Dis 56:58–64

    Article  CAS  Google Scholar 

  • Chalupová J, Raus M, Sedlářová M, Šebela M (2014) Identification of fungal microorganisms by MALDI-TOF mass spectrometry. Biotechnol Adv 32:230–241

    Article  PubMed  CAS  Google Scholar 

  • Chandra J, Kuhn DM, Mukherjee PK, Hoyer LL, McCormick T, Ghannoum MA (2001) Biofilm formation by the fungal pathogen Candida albicans: development, architecture, and drug resistance. J Bacterial 183:5385–5394

    Article  CAS  Google Scholar 

  • Chiaro TR, Soto R, Stephens WZ, Kubinak JL, Petersen C, Gogokhia L et al (2017) A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice. Sci Transl Med 9:e9044

    Article  CAS  Google Scholar 

  • Choi S, Tripathi A, Singh D (2014) Smart nanomaterials for biomedics. J Biomed Nanotechnol 10:3162–3188

    Article  CAS  PubMed  Google Scholar 

  • Chuku A (2018) Effective diagnostic techniques in the identification of medically important fungi: a developing world perspective. Ann Res Rev Biol 28:1–9

    Article  Google Scholar 

  • Clancy CJ, Nguyen MH (2013) Finding the “missing 50%” of invasive candidiasis: how nonculture diagnostics will improve understanding of disease spectrum and transform patient care. Clin Infect Dis 56:1284–1292

    Article  PubMed  Google Scholar 

  • Cuenca-Estrella M, Bassetti M, Lass-Flörl C, Ráčil Z, Richardson M, Rogers TR (2011) Detection and investigation of invasive mould disease. J Antimicrob Chemother 66:15–24

    Article  CAS  Google Scholar 

  • Davari M, van Diepeningen AD, Babai-Ahari A, Arzanlou M, Najafzadeh MJ, van der Lee TA et al (2012) Rapid identification of Fusarium graminearum species complex using Rolling Circle Amplification (RCA). J Microbiol Meth 89:63–70

    Article  CAS  Google Scholar 

  • Davis DA (2009) How human pathogenic fungi sense and adapt to pH: the link to virulence. Curr Opin Microbiol 12:365–370

    Article  CAS  PubMed  Google Scholar 

  • De Heer K, Van Der Schee MP, Zwinderman K, Van Den Berk IA, Visser CE, Van Oers R et al (2013) Electronic nose technology for detection of invasive pulmonary aspergillosis in prolonged chemotherapy-induced neutropenia: a proof-of-principle study. J Clin Microbiol 51:1490–1495

    Article  PubMed  PubMed Central  Google Scholar 

  • De Lucca AJ (2007) Harmful fungi in both agriculture and medicine. Rev Iberoam Micol 24:3

    PubMed  Google Scholar 

  • Dhama K, Chakraborty S, Verma AK, Tiwari R, Barathidasan R, Kumar A, l. (2013) Fungal/mycotic diseases of poultry-diagnosis, treatment and control: a review. Pak J Biol Sci 16:1626–1640

    Article  PubMed  Google Scholar 

  • Dolatabadi S, De Hoog GS, Meis JF, Walther G (2014) Species boundaries and nomenclature of Rhizopus arrhizus (syn. R. oryzae). Mycoses 57:108–127

    Article  CAS  PubMed  Google Scholar 

  • Duong TA (1996) Infection due to Penicillium marneffei, an emerging pathogen: review of 155 reported cases. Clin Infect Dis 23:125–130

    Article  CAS  PubMed  Google Scholar 

  • Ellepola AN, Morrison CJ (2005) Laboratory diagnosis of invasive candidiasis. J Microbiol 43:65–84

    PubMed  Google Scholar 

  • Fakruddin M, Mannan KSB, Chowdhury A, Mazumdar RM, Hossain MN, Islam S et al (2013) Nucleic acid amplification: alternative methods of polymerase chain reaction. J Pharm Bioallied Sci 5:245

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fraser VJ, Jones M, Dunkel J, Storfer S, Medoff G, Dunagan WC (1992) Candidemia in a tertiary care hospital: epidemiology, risk factors, and predictors of mortality. Clin Infect Dis 15:414–421

    Article  CAS  PubMed  Google Scholar 

  • Gabaldón T (2019) Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev 43:517–547

    Article  PubMed  PubMed Central  Google Scholar 

  • Galgiani J (2010) Coccidioides species. In: WJH MB (ed) Mandell, Douglas and Bennett’s principles and practice of infectious diseases. Churchill Livingstone, Elsevier, pp 3333–3344. https://doi.org/10.1016/B978-1-4557-4801-3.00267-8

    Chapter  Google Scholar 

  • García MI, Rodríguez M-BJL (2013) Identification of fungal clinical isolates by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Rev Esp Quim 26:193–197

    Google Scholar 

  • Gauthier GM, Keller NP (2013) Crossover fungal pathogens: the biology and pathogenesis of fungi capable of crossing kingdoms to infect plants and humans. Fungal Genet Biol 61:146–157

    Article  CAS  PubMed  Google Scholar 

  • Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A et al (2010) Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PloS Pathog 6:1

    Article  CAS  Google Scholar 

  • Guruceaga X, Ezpeleta G, Mayayo E, Sueiro-Olivares M, Abad-Diaz-De-Cerio A, Aguirre Urízar JM et al (2018) A possible role for fumagillin in cellular damage during host infection by Aspergillus fumigatus. Vir 9:1548–1561

    CAS  Google Scholar 

  • Hage CA, Carmona EM, Epelbaum O, Evans SE, Gabe LM, Haydour Q, l. (2019) Microbiological laboratory testing in the diagnosis of fungal infections in pulmonary and critical care practice. An official American Thoracic Society clinical practice guideline. Am J Resp Crit Care Med 200:535–550

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hamill RJ (2013) Amphotericin B formulations: a comparative review of efficacy and toxicity. Drugs 73:919–934

    Article  CAS  PubMed  Google Scholar 

  • Hanage WP (2014) Microbiology: microbiome science needs a healthy dose of scepticism. Nat News 512:247

    Article  CAS  Google Scholar 

  • Hawksworth DL, Lücking R (2017) Fungal diversity revisited: 2.2 to 3.8 million species. In: Heitman J, Howlett JB, Crous WP, Stukenbrock HE, James YT (eds) Gow RAN the fungal kingdom. ASM Press, pp 79–95. https://doi.org/10.1128/9781555819583.ch4

  • Hoarau G, Mukherjee PK, Gower-Rousseau C, Hager C, Chandra J, Retuerto MA et al (2016) Bacteriome and mycobiome interactions underscore microbial dysbiosis in familial Crohn’s disease. Mbio 7:e01250–e01216

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Holt SL, Drew RH (2011) Echinocandins: addressing outstanding questions surrounding treatment of invasive fungal infections. Am J Health Syst Pharm 68:1207–2220

    Article  CAS  PubMed  Google Scholar 

  • Iyalla C (2017) A review of the virulence factors of pathogenic fungi. Afr J Clin Exp Micro 18:53–58

    Article  Google Scholar 

  • Juvvadi PR, Lee SC, Heitman J, Steinbach WJ (2017) Calcineurin in fungal virulence and drug resistance: prospects for harnessing targeted inhibition of calcineurin for an antifungal therapeutic approach. Vir 8:186–197

    CAS  Google Scholar 

  • Kaplan E, Iikit M, de Hoog GS (2018) Comparison of the rolling circle amplification and ligase-dependent reaction methods for the identification of opportunistic Exophiala species. Med Mycol 56:759–769

    Article  CAS  PubMed  Google Scholar 

  • Karkowska-Kuleta J, Rapala-Kozik M, Kozik A (2009) Fungi pathogenic to humans: molecular bases of virulence of Candida albicans, Cryptococcus neoformans and Aspergillus fumigatus. Acta Biochim Pol 56:2

    Article  Google Scholar 

  • Keikha M (2018) LAMP method as one of the best candidates for replacing with PCR method. Malays J Med Sci 25:121–123

    PubMed  PubMed Central  Google Scholar 

  • Kempf VA, Trebesius K, Autenrieth IB (2000) Fluorescent in situ hybridization allows rapid identification of microorganisms in blood cultures. J Clin Microbiol 38:830–838

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kidd SE, Chen SCA, Meye W, Halliday CL (2020) A new age in molecular diagnostics for invasive fungal disease: are we ready? Front Microbiol 10:2903

    Article  PubMed  PubMed Central  Google Scholar 

  • Kipyegon KE, Musyoki SK, Kariuki SM (2017) Detection of Histoplasma Capsulatum in domestic chicken droppings in Olenguruone, Nakuru County. Eu Sci J 13:15

    Google Scholar 

  • Klein BS, Tebbets B (2007) Dimorphism and virulence in fungi. Curr Opini Microbiol 10:314–319

    Article  CAS  Google Scholar 

  • Kontoyiannis DP, Sumoza D, Tarrand J, Bodey GP, Storey R, Raad II (2000) Significance of aspergillemia in patients with cancer: a 10-year study. Clin Infect Dis 31:188–189

    Article  CAS  PubMed  Google Scholar 

  • Kozel TR, Wickes B (2014) Fungal diagnostics. Cold Spring Harb Perspect Med 4:a019299

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lackner M, De Hoog GS, Verweij PE, Najafzadeh MJ, Curfs-Breuker I, Klaassen CH et al (2012) Species-specific antifungal susceptibility patterns of Scedosporium and Pseudallescheria species. Antimicrob Agents Chemother 56:2635–2642

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lasker BA (2006) Nucleotide sequence-based analysis for determining the molecular epidemiology of Penicillium marneffei. J Clin Microbiol 44:3145–3153

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lau A, Chen S, Sleiman S, Sorrell T (2009) Current status and future perspectives on molecular and serological methods in diagnostic mycology. Future Microbiol 4:1185–1222

    Article  CAS  PubMed  Google Scholar 

  • Lesho EP (2016) How next-generation sequencing might not transform infectious disease practice. Clin Infect Dis 62:1052–1053

    Article  PubMed  Google Scholar 

  • Lim W, Eadie K, Konings M, Rijnders B, Fahal AH, Oliver JD et al (2020) Madurella mycetomatis, the main causative agent of eumycetoma, is highly susceptible to olorofim. J Antimicrob Chemother 75:936–941

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lindsley Mark D (2016) Serological and molecular diagnosis of fungal infections. In: Detrick B, Schmitz LJ, Hamilton GR (eds) Manual of molecular and clinical laboratory immunology. American Society of Microbiology Press, Washington DC, pp 503–534. https://doi.org/10.1128/9781555818722.ch55

    Chapter  Google Scholar 

  • Loeffler J, Hebart H, Cox P, Flues N, Schumacher U, Einsele H (2001) Nucleic acid sequence-based amplification of aspergillus RNA in blood samples. J Clin Microbiol 39:1626–1629

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lyberopoulou A, Efstathopoulos EP, Gazouli M (2016) Nanotechnology-based rapid diagnostic tests. In: Saxena KS (ed) Proof and concepts in rapid diagnostic tests and technologies. InTech, Croatia, pp 89–106. https://doi.org/10.5772/63908

    Chapter  Google Scholar 

  • Mahadevan A, Susarla SK (2019) Cryptococcosis. In: Turgut M, Challa S, Akhaddar A (eds) Fungal infections of the central nervous system. Springer, Cham, pp 167–185. https://doi.org/10.1007/978-3-030-06088-6_12

    Chapter  Google Scholar 

  • Malhotra S, Sharma S, Bhatia NJK, Kumar P, Bhatia NK, Patil V et al (2014) Recent diagnostic techniques in mycology. J Med Microbiol Diagn 3:1

    Google Scholar 

  • Martins JF, Castilho ML, Cardoso MA, Carreiro AP, Martin AA, Raniero L (2012) Identification of Paracoccidioides brasiliensis by gold nanoprobes, Biomedical vibrational spectroscopy V: advances in research and industry, vol 8219. International Society for Optics and Photonics

    Google Scholar 

  • Medici NP, Del Poeta M (2015) New insights on the development of fungal vaccines: from immunity to recent challenges. Mem Inst Oswaldo Cruz 110:966–973

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mercer DK, Stewart CS (2019) Keratin hydrolysis by dermatophytes. Med Mycol 57:13–22

    Article  CAS  PubMed  Google Scholar 

  • Miceli MH, Díaz JA, Lee SA (2011) Emerging opportunistic yeast infections. Lancet Infect Dis 11:142–151

    Article  PubMed  Google Scholar 

  • Mohanta TK, Bae H (2015) The diversity of fungal genome. Biol Proced Online 17:8

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Monod M (2019) Antifungal resistance in dermatophytes: emerging problem and challenge for the medical community. J Mycol Med 29:283

    Article  CAS  PubMed  Google Scholar 

  • Montone KT, Litzky LA, Feldman MD, Peterman H, Mathis B, Baliff J et al (2010) In situ hybridization for Coccidioides immitis 5.8 S ribosomal RNA sequences in formalin-fixed, paraffin-embedded pulmonary specimens using a locked nucleic acid probe: a rapid means for identification in tissue sections. Diagn Mol Pathol 19:99–104

    Article  CAS  PubMed  Google Scholar 

  • Montone KT, LiVolsi VA, Lanza DC, Kennedy DW, Palmer J, Chiu AG et al (2011) In situ hybridization for specific fungal organisms in acute invasive fungal rhinosinusitis. Am J Clin Pathol 135:190–199

    Article  PubMed  Google Scholar 

  • Mor V, Farnoud AM, Singh A, Rella A, Tanno H, Ishii K et al (2016) Glucosylceramide administration as a vaccination strategy in mouse models of cryptococcosis. PLoS One 11:4

    Article  CAS  Google Scholar 

  • Moter A, Göbel UB (2000) Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Meth 41:85–112

    Article  CAS  Google Scholar 

  • Moyes DL, Wilson D, Richardson JP, Mogavero S, Tang SX, Wernecke J et al (2016) Candidalysin is a fungal peptide toxin critical for mucosal infection. Nats 532:64–68

    Article  CAS  Google Scholar 

  • Naglik JR, Challacombe SJ, Hube B (2003) Candida albicans secreted aspartyl proteinases in virulence and pathogenesis. Microbiol Mol Biol Rev 67:400–428

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nett JE, Andes DR (2016) Antifungal agents: spectrum of activity, pharmacology, and clinical indications. Infect Dis Clin 30:51–83

    Article  Google Scholar 

  • Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larsson KH, Kõljalg U (2006) Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS One 1:e59

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Noguchi H, Iwase T, Omagari D, Asano M, Nakamura R, Ueki K et al (2017) Rapid detection of Candida albicans in oral exfoliative cytology samples by loop-mediated isothermal amplification. J Oral Sci 59:541–547

    Article  PubMed  Google Scholar 

  • Orsi CF, Gennari W, Venturelli C, La Regina A, Pecorari M, Righi E et al (2012) Performance of 2 commercial real-time polymerase chain reaction assays for the detection of Aspergillus and Pneumocystis DNA in bronchoalveolar lavage fluid samples from critical care patients. Diagn Microbiol Infect Dis 73:138–143

    Article  CAS  PubMed  Google Scholar 

  • Ostrosky-Zeichner L (2012) Invasive mycoses: diagnostic challenges. Am J Med 125:14–24

    Article  Google Scholar 

  • Ostrosky-Zeichner L, Pappas PG (2006) Invasive candidiasis in the intensive care unit. Crit Care Med 34:857–863

    Article  PubMed  Google Scholar 

  • Özenci V, Patel R, Ullberg M, Strålin K (2018) Demise of polymerase chain reaction/electrospray ionization-mass spectrometry as an infectious diseases diagnostic tool. Clin Infect Dis 66:452–455

    Article  PubMed  CAS  Google Scholar 

  • Panda A, Ghosh AK, Mirdha BR, Xess I, Paul S, Samantaray JC et al (2015) MALDI-TOF mass spectrometry for rapid identification of clinical fungal isolates based on ribosomal protein biomarkers. J Microbiol Meth 109:93–105

    Article  CAS  Google Scholar 

  • Pappas PG, Kauffman CA, Andes DR, Clancy CJ, Marr KA, Ostrosky-Zeichner L et al (2016) Clinical practice guideline for the management of candidiasis: 2016 update by the Infectious Diseases Society of America. Clin Infect Dis 62:1–50

    Article  Google Scholar 

  • Parida M, Sannarangaiah S, Dash PK, Rao PVL, Morita K (2008) Loop mediated isothermal amplification (LAMP): a new generation of innovative gene amplification technique; perspectives in clinical diagnosis of infectious diseases. Rev Med Virol 18:407–421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Patel R (2019) A moldy application of MALDI: MALDI-ToF mass spectrometry for fungal identification. J Fungi 5:4

    Article  CAS  Google Scholar 

  • Patil RT, Sangwan J, Juyal D, Lathwal S (2013) Meningitis due to Cryptococcus gatti in an immunocompetent patient. J Clin Diagnos Res 7:2274

    Google Scholar 

  • Perlin DS, Wiederhold NP (2017) Culture-independent molecular methods for detection of antifungal resistance mechanisms and fungal identification. J Infect Dis 216:458–465

    Article  CAS  Google Scholar 

  • Peyton LR, Gallagher S, Hashemzadeh M (2015) Triazole antifungals: a review. Drugs 51:705–718

    CAS  Google Scholar 

  • Philpott CC (2006) Iron uptake in fungi: a system for every source. BBA-Mol Cell Res 1763:636–645

    CAS  Google Scholar 

  • Posteraro B, De Carolis E, Vella A, Sanguinetti M (2013) MALDI-TOF mass spectrometry in the clinical mycology laboratory: identification of fungi and beyond. Expert Rev Proteom 10:151–164

    Article  CAS  Google Scholar 

  • Pradhan A, Herrero-de-Dios C, Belmonte R, Budge S, Garcia AL, Kolmogorova A et al (2017) Elevated catalase expression in a fungal pathogen is a double-edged sword of iron. PLoS Pathol 13:1006405

    Article  CAS  Google Scholar 

  • Prakash PY, Irinyi L, Halliday C, Chen S, Robert V, Meyer W (2017) Online databases for taxonomy and identification of pathogenic fungi and proposal for a cloud-based dynamic data network platform. J Clin Microbiol 55:1011–1024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Procop GW (2007) Molecular diagnostics for the detection and characterization of microbial pathogens. Clin Infect Dis 45:99–111

    Article  CAS  Google Scholar 

  • Radhakrishnan N, Panigrahi AK, Balasubramanium A, Das M, Prajna NV (2019) Colonization of therapeutic contact lens by dematiaceous fungi. Contact Lens Anterio 42:470–472

    Article  Google Scholar 

  • Ramage G, Rajendran R, Gutierrez-Correa M, Jones B, Williams C (2011) Aspergillus biofilms: clinical and industrial significance. FEMS Microbiol Lett 324:89–97

    Article  CAS  PubMed  Google Scholar 

  • Rappleye CA, Goldman WE (2006) Defining virulence genes in the dimorphic fungi. Annu Rev Microbiol 60:281–303

    Article  CAS  PubMed  Google Scholar 

  • Rementeria A, López-Molina N, Ludwig A, Vivanco AB, Bikandi J, Pontón J et al (2005) Genes and molecules involved in Aspergillus fumigatus virulence. Rev Iberoam Micol 22:1–23

    Article  PubMed  Google Scholar 

  • Revankar SG (2007) Dematiaceous fungi. Mycoses 50:91–101

    Article  PubMed  Google Scholar 

  • Richardson M (2009) The ecology of the Zygomycetes and its impact on environmental exposure. Clin Microbiol Infect 15:2–9

    Article  PubMed  Google Scholar 

  • Rigby S, Procop GW, Haase G, Wilson D, Hal G, Kurtzman C et al (2002) Fluorescence in situ hybridization with peptide nucleic acid probes for rapid identification of Candida albicans directly from blood culture bottles. J Clin Microbiol 40:2182–2186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roilides E, Kontoyiannis DP, Walsh TJ (2012) Host defenses against zygomycetes. Clin Infect Dis 54:61–66

    Article  Google Scholar 

  • Rychert J, Slechta ES, Barker AP, Miranda E, Babady NE, Tang YW et al (2018) Multicenter evaluation of the Vitek MS v3. 0 system for the identification of filamentous fungi. J Clin Microbiol 56:e01353–e01317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Safavieh M, Coarsey C, Esiobu N, Memic A, Vyas JM, Shafiee H et al (2017) Advances in Candida detection platforms for clinical and point-of-care applications. Crit Rev Biotechnol 37:441–458

    Article  CAS  PubMed  Google Scholar 

  • Sahu MC, Padhy RN (2014) Bayesian evaluation of two conventional diagnostic methods for pathogenic fungal infections. J Acute Med 4:109–119

    Article  Google Scholar 

  • Salcedo DT, Powers-Fletcher MV (2020) Updates in laboratory diagnostics for invasive fungal infections. J Clin Microbiol 58:e01487–e01419

    Google Scholar 

  • San-Blas G, San-Blas F, Mackenzie DW (1984) Molecular aspects of fungal dimorphism. CRC Crit Rev Microbiol 11:101–127

    Article  CAS  Google Scholar 

  • Saubolle MA, McKellar PP, Sussland D (2007) Epidemiologic, clinical, and diagnostic aspects of coccidioidomycosis. J Clin Microbiol 45:26–30

    Article  CAS  PubMed  Google Scholar 

  • Schell WA, Benton JL, Smith PB, Poore M, Rouse JL, Boles DJ et al (2012) Evaluation of a digital microfluidic real-time PCR platform to detect DNA of Candida albicans in blood. Eur J Clin Microbiol Infect Dis 31:2237–2245

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schuler B, Meyer G, Peña D, Mullins OC, Gross L (2015) Unraveling the molecular structures of asphaltenes by atomic force microscopy. J Am Chem Soc 137:9870–9876

    Article  CAS  PubMed  Google Scholar 

  • Scorzoni L, de Paula e Silva AC, Marcos CM, Assato PA, de Melo WC, de Oliveira HC et al (2017) Antifungal therapy: new advances in the understanding and treatment of mycosis. Fron Microbiol 8:36

    Google Scholar 

  • Seipke RF, Kaltenpoth M, Hutchings MI (2012) Streptomyces as symbionts: an emerging and widespread theme? FEMS Microbiol Rev 36:862–876

    Article  CAS  PubMed  Google Scholar 

  • Seyedmousavi S, Bosco SDM, De Hoog S, Ebel F, Elad D, Gomes RR et al (2018) Fungal infections in animals: a patchwork of different situations. Medical Mycol J 56:S165–S187

    Article  Google Scholar 

  • Shahid SK (2016) Newer patents in antimycotic therapy. Pharm Pat Anal 5:115–134

    Article  CAS  PubMed  Google Scholar 

  • Sharma KK (2016) Fungal genome sequencing: basic biology to biotechnology. Crit Rev Biotechnol 36:743–759

    Article  CAS  PubMed  Google Scholar 

  • Sibley CD, Peirano G, Church DL (2012) Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. Infect Genet Evol 12:505–521

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Simner PJ, Uhl JR, Hall L, Weber MM, Walchak RC, Buckwalter S, Wengenack NL (2013) Broad-range direct detection and identification of fungi by use of the PLEX-ID PCR-electrospray ionization mass spectrometry (ESI-MS) system. J Clin Microbiol 51:1699–1706

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singhal N, Kumar M, Kanaujia PK, Virdi JS (2015) MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 6:791

    Article  PubMed  PubMed Central  Google Scholar 

  • Smith ML, Bruhn JN, Anderson JB (1992) The fungus Armillaria bulbosa is among the largest and oldest living organisms. Nats 356:428–431

    Article  Google Scholar 

  • Sojinrin T, Conde J, Liu K, Curtin J, Byrne HJ, Cui D et al (2017) Plasmonic gold nanoparticles for detection of fungi and human cutaneous fungal infections. Anal Bioanal Chem 409:4647–4658

    Article  CAS  PubMed  Google Scholar 

  • Soler-Hurtado MM, Sandoval-Sierra JV, Machordom A, Diéguez-Uribeondo J (2016) Aspergillus sydowii and other potential fungal pathogens in gorgonian octocorals of the Ecuadorian Pacific. PLoS One 11:e0165992

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Soliman H, El-Matbouli M (2005) An inexpensive and rapid diagnostic method of Koi Herpesvirus (KHV) infection by loop-mediated isothermal amplification. Virol J 2:83

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sugawara Y, Nakase K, Nakamura A, Ohishi K, Sugimoto Y, Fujieda A et al (2013) Clinical utility of a pan fungal polymerase chain reaction assay for invasive fungal diseases in patients with haematologic disorders. Eur J Haematol 90:331–339

    Article  CAS  PubMed  Google Scholar 

  • Sugui JA, Peterson SW, Figat A, Hansen B, Samson RA, Mellado E et al (2014) Genetic relatedness versus biological compatibility between Aspergillus fumigatus and related species. J Clin Microbiol 52:3707–3721

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sun J, Najafzadeh MJ, Zhang J, Vicente VA, Xi L, De Hoog GS (2011) Molecular identification of Penicillium marneffei using rolling circle amplification. Mycoses 54:e751–e759

    Article  CAS  PubMed  Google Scholar 

  • Tekaia F, Latge JP (2005) Aspergillus fumigatus: saprophyte or pathogen? Curr Opin Microbiol 8:385–392

    Article  CAS  PubMed  Google Scholar 

  • Teles F, Seixas J (2015) The future of novel diagnostics in medical mycology. J Med Microbiol 64:315–322

    Article  CAS  PubMed  Google Scholar 

  • Tîlmaciu CM, Morris MC (2015) Carbon nanotube biosensors. Front Chem 3:59

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tobón AM, Agudelo CA, Rosero DS, Ochoa JE, De Bedout C, Zuluaga A et al (2005) Disseminated histoplasmosis: a comparative study between patients with acquired immunodeficiency syndrome and non-human immunodeficiency virus–infected individuals. Am J Trop Med Hyg 73:576–582

    Article  PubMed  Google Scholar 

  • Trilles L, Wang B, Firacative C, dos Santos LM, Wanke B, Meyer W (2014) Identification of the major molecular types of Cryptococcus neoformans and C. gattii by hyperbranched rolling circle amplification. PLoS One 9:–4

    Google Scholar 

  • Valdez M, Moosavi L, Heidari A (2019) Concomitant central nervous system toxoplasmosis and seronegative disseminated coccidioidomycosis in a newly diagnosed acquired immune deficiency syndrome patient. J Investig Med High Impact Case Rep 7:2324709619869372

    PubMed  PubMed Central  Google Scholar 

  • Valones MAA, Guimarães RL, Brandão LAC, Souza PRED, Carvalho ADAT, Crovela S (2009) Principles and applications of polymerase chain reaction in medical diagnostic fields: a review. Braz J Microbiol 40:1–11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Varga J, Houbraken J, Van Der Le HA, Verweij PE, Samson RA (2008) Aspergillus calidoustus sp. nov., causative agent of human infections previously assigned to Aspergillus ustus. Eukaryot Cell 7:630–638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vecchiarelli A, Pericolini E, Gabrielli E, Pietrella D (2012) New approaches in the development of a vaccine for mucosal candidiasis: progress and challenges. Fron Microbiol 3:294

    Google Scholar 

  • Villamizar RA, Maroto A, Rius FX (2009) Improved detection of Candida albicans with carbon nanotube field-effect transistors. Sensor Actuat B Chem 136:451–457

    Article  CAS  Google Scholar 

  • Walsh TJ, Petraitis V, Petraitiene R, Field-Ridley A, Sutton D, Ghannoum M et al (2003) Experimental pulmonary aspergillosis due to Aspergillus terreus: pathogenesis and treatment of an emerging fungal pathogen resistant to amphotericin B. J Infect Dis 188:305–319

    Article  CAS  PubMed  Google Scholar 

  • Weitzman I, Summerbell RC (1995) The dermatophytes. Clin Microbiol Rev 8:240–259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wibawa T, Aman AT (2015) Virulence of Candida albicans isolated from HIV infected and non infected individuals. Spring Plus 4:408

    Article  Google Scholar 

  • Wickes BL, Wiederhold NP (2018) Molecular diagnostics in medical mycology. Nat Commun 9:1–13

    Article  CAS  Google Scholar 

  • Wieser A, Schneider L, Jung J, Schubert S (2012) MALDI-TOF MS in microbiological diagnostics identification of microorganisms and beyond. App Microbiol Biot 93:965–974

    Article  CAS  Google Scholar 

  • Wolk DM, Clark AE (2018) Matrix-assisted laser desorption time of flight mass spectrometry. Clin Lab Med 38:471–486

    Article  PubMed  Google Scholar 

  • Wong EH, Revankar SG (2016) Dematiaceous molds. Infect Dis Clin 30:165–178

    Article  Google Scholar 

  • Woo PC, Zhen H, Cai JJ, Yu J, Lau SK, Wang J et al (2003) The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts. FEBS Lett 555:469–477

    Article  CAS  PubMed  Google Scholar 

  • Yoo JH, Choi SM, Lee DG, Park SH, Choi JH, Kwon EY et al (2007) Comparison of the real-time nucleic acid sequence-based amplification (RTi-NASBA) with conventional NASBA, and galactomannan assay for the diagnosis of invasive aspergillosis. J Korean Med Sci 22:672–676

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoo SM, Kang T, Kang H, Lee H, Kang M, Lee SY et al (2011) Combining a nanowire SERRS sensor and a target recycling reaction for ultrasensitive and multiplex identification of pathogenic fungi. Small 7:3371–3376

    Article  CAS  PubMed  Google Scholar 

  • Zhang SX, O’donnell K, Sutton DA (2015) Fusarium and other opportunistic hyaline fungi. In: Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (eds) Manual of clinical microbiology. American Society of Microbiology Press, Washington, DC, pp 2057–2086. https://doi.org/10.1128/9781555817381.ch120

    Chapter  Google Scholar 

  • Zhao Y, Paderu P, Railkar R, Douglas C, Iannone R, Shire N et al (2016) Blood Aspergillus RNA is a promising alternative biomarker for invasive aspergillosis. Sabouraudia 54:801–807

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan

    Amber Malik, Tehsin Fatma, Wajeeha Shamsi, Haris Ahmed Khan, Alvina Gul & Muhammad Faraz Bhatti

  2. Crop Diseases Research Institute (CDRI), National Agricultural Research Centre (NARC), Islamabad, Pakistan

    Atif Jamal

Authors
  1. Amber Malik
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tehsin Fatma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wajeeha Shamsi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Haris Ahmed Khan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Alvina Gul
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Atif Jamal
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Muhammad Faraz Bhatti
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Muhammad Faraz Bhatti .

Editor information

Editors and Affiliations

  1. Department of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh, India

    Ajar Nath Yadav

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Malik, A. et al. (2021). Molecular Characterization of Medically Important Fungi: Current Research and Future Prospects. In: Yadav, A.N. (eds) Recent Trends in Mycological Research. Fungal Biology. Springer, Cham. https://doi.org/10.1007/978-3-030-60659-6_15

Download citation

Publish with us

Policies and ethics

Search

Navigation