Barcoding of Medical Fungi

The ISHAM working group on "Barcoding medical Fungi" had its successful first meeting at TIMM 5 in Valencia on the 3. October 2011 with more than 40 people attending the special session. The symposium followed on a - Meet the expert session: Molecular identification by barcoding - in the morning of the same day in which Teun Boekhout (CBS) and Arun Balajee (CDC) gave an introduction to DNA barcoding.and the molecular methods which may take advantage of the barcodes fro fungal identification . The afternoon session focused more specifically on DNA barcoding of pathogenic fungi contained 5 talks reaching from the basics of DNA barcoding, the advances made till today, to the use of sequencing in a mycology reference laboratory, the usefulness of the currently used genetic loci and the future of sequence independent identification using MALDI-TOF. The abstracts and the pdf files of all 5 talks are place on the ISHAM website under the Barcoding of Medical fungi heading. The present researchers concluded that the next step for DNA barcoding of pathogenic fungi would be the establishment of a unified ITS sequence database using BioloMICS as a basis. The next meeting of the ISHAM working group on "Barcoding of medical Fungi" will be organized at the ISHAM meeting in Berlin in 2012, which wil be organizzed by Wieland Meyer and Sybren de Hoog. If you are interested to actively participate in this working group pease contact either Wieland Meyer (w.meyer@usyd.edu.au) or Sybren de Hoog (de.hoog@cbs.knaw.nl).

 

Established

  •   January 2010

 

Founding Coordinators

  • A/Prof. Wieland Meyer (University of Sydney, Australia)
  • Prof. Sybren de Hoog (CBS-KNAW, The Netherlands)
  • Dr. Arun Balajee (CDC, USA)

 

Current Coordinators

  • A/Prof. Wieland Meyer
    Molecular Mycology Research Laboratory, CIDM,                  
    ICPMR, University of Sydney, Sydney
    Medical School-Westmead Hospital, Darcy Road, Westmead, NSW, 2145, Australia,
    P:         +61-2-98456895
    F:         +61-2-98915317
    e-mail: w.meyer@usyd.edu.au
  • Prof. Sybren de Hoog
    CBS-KNAW Fungal Biodiversity Center,
    3508 AD Utrecht, The Netherlands,
    P:         +31-30-2122663
    F:         +31-30-2512097
    e-mail: s.hoog@cbs.knaw.nl

 

 

Members

The working group is open to everybody who is interested on molecular identification of pathogenic fungi. For membership please contact either Wieland Meyer (w.meyer@usyd.edu.au) or Sybren de Hoog  (s.hoog@cbs.knaw).

  • A/Prof. Wieland Meyer (General human pathogenic fungi ITS database, University of Sydney) (Australia)
    e-mail: w.meyer@usyd.edu.au
  • Prof. Sydren de Hoog (General human pathogenic fungi ITS database, CBS) (The Netherlands)
    e-mail: s.hoog@cbs.knaw.nl
  • Dr. Arun Balajee (General human pathogenic fungi ITS database, CDC) (USA)
    e-mail: fir3@CDC.GOV
  • Prof. Aristea Velegraki (General human pathogenic fungi ITS database, University of Athens) (Greece)
    e-mail: aveleg@med.uoa.gr
  • Dr. Kerry O'Donnell (Fusarium database) (USA)
    e-mail: Kerry.ODonnell@ARS.USDA.GOV
  • Dr. Michaela Lackner (Scedosporium database) (Austria)
    ela.youngisham@googlemail.com
  • Dr. Heide-Marie Daniel (Yeast database) (Belgium)
    heide-marie.daniel@uclouvain.be
  • Dr. Vincent Robert (BioloMIXC software) (Belgium/The Netherlands)
    v.robert@cbs.knaw.nl
  • Dr. Grit Walther (extensive unpublished database of medical filamentous basidiomycetes) (Germany)
    grit_walther44@yahoo.de
  • Dr. Yvonne Gräser (Dermatophyte database) (Germany)
    yvonne.graeser@charite.de
  • Dr. Kerstin Voigt (Zygomycetes, database) (Germany)
    Kerstin.Voigt@uni-jena.de
  • Dr. Janos Varga (Penicillium/Aspergillus dataabse) (Hungary)
    jvarga@bio.u-szeged.hu
  • Prof. Christian P. Kubicek (Trichoderma database) (Austria)
    ckubicek@mail.zserv.tuwien.ac.at
  • Dr. Irina S. Druzhinina (Trichoderma database) (Austria)
    e-mail: druzhini@mail.zserv.tuwien.ac.at
  • Dr. Michael Arabatzis (General human pathogenic fungi ITS database, University of Athens/Thessaloniki) (Greece)
    marabatz@med.uoa.gr
  • Dr. Conrad Schoch (Genbank) (USA)
    schoch2@ncbi.nlm.nih.gov
  • Dr. Dea Garcia-Hermoso (ITS sequence database of the French National Reference Center for Mycoses and Antifungals) (France)
    dea.garcia-hermoso@pasteur.fr
  • Dr. Rosely Zancope-Olivera (Brazil)
    rosely.zancope@ipec.fiocruz.br
  • Frederic Grenouillet (France)
    fgrenouillet@chu-besancon.fr
  • Dr. Stephane Bretagne (France)
    bretagne@univ-paris12.fr
  • Dr. Martina Lengerova (Czek Republique)
    mlengerova@scznam.cz
  • Dr. Gilles Nevez (France)
    gilles.nevez@chu-brest.fr
  • Dr. Deanna Sutton (USA)
    suttonf@uthscsa.eduMALDI_TOF
  • Dr. Annette Fothergill (USA)
    fothergill@uthscsa.edu
  • Dr. Juliette Guitard
    gulietteguitard@gmail.com
  • Dr. Montarop Sudhadham
    sudhadham@yahoo.com
  • Dr. Svetlana Jgnatyeva (Russia)
    jgn0452@mail.ru
  • Dr. Rebecca Gorton (UK)
    rebecca.gorton@nhs.net
  • Dr. M. Javad Najahzadch
    jjavadi2000@yahoo.com
  • Dr. Hamid Badali
    badali@yahoo.com
  • Dr. Christophe Hennequin (France)
    christoph.hennequin@upmc.fr
  • Dr. Rungmei Sk Marak
    rungmei@gmail.com
  • Kathrien Lagrou (Belgium)
    katrien.lagrou@uzleuven.be
  • Dr. Ana Alastruey-Izquierdo (Spain)
    anaalastruey@gmail.com
  • Dr. Mary E. Brandt (USA)
    mbb4@cdc.gov

     

 

 

Objectives

The objectives of the working group are:
(1) to establish a medical barcode database as part of BOLD by incorporating the different already existing fungal group specific databases,

(2) to extend the number of quality controlled ITS sequences to cover all medical important fungi over the next 3 years,

(3) to incorporate this sequences into BOLD, and

(4) to achieve a special status as quality controlled reference sequences for those sequences within Genbank.

Fungal Infections are stately increasing due to the increasing number of immunocompromised patients, more and more fungal are encountered to cause human infections and the number of antifungal resistant species is increasing in parallel. In view of these facts it is of utmost importance to correctly identify fungal disease agents. With the advancement of molecular biology a large number of DNA based identification techniques have been developed, with DNA sequencing having emerged as the gold standard for fungal identification, using mainly the ITS1 and 2 region of the rDNA gene cluster. However, any sequence base identification only works if there is a reference sequence database of the respective genetic locus being used available. Traditionally GenBank was and is used as such a reference database. The major problem with GenBank is that it is user driven and as such contains a large number of incorrect sequences. An additional problem with GenBank is, that only a very small % of fungi are currently represented. To overcome this problems a number of research groups have developed their own quality controlled genus specific databases, such as Fusarium spp. (FUSARIUM-ID v. 1.0 (16); http://fusarium.cbio.psu. edu/index.html), or for medical fungi the CBS Fungal Biodiversity Centre (http://www.cbs. knaw.nl/databases/) and the University of Sydney  (http://www.mycologylab.org). To allow for a standardized sequence based identification of all forms of life on earth an international initiative to Barcode all living organism is currently underway. The general aim of this initiative is to select a unique DNA sequence as a barcode of the species in question. Originally COX1 was suggested to fulfil this role. However, COX1 is not suitable for the identification of fungi. That is why, the International Subcommission on Fungal Barcoding has proposed the ITS region as the prime fungal barcode or the default region for species identification (http://www.allfungi.com/its-barcode.php.). However, there are currently very few fungal ITS sequences in the Barcode of Life Database (BOLD), and no medical important fungi at all. The objectives of the newly established working group are: (1) to establish a medical barcode database as part of BOLD by incorporating the different already existing fungal group specific databases,(2) to extend the number of quality controlled ITS sequences to cover all medical important fungi over the next 3 years, (3) to incorporate this sequences into BOLD, and (4) to achieve a special status as quality controlled reference sequences for those sequences within Genbank.