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Fungal pathogens cause a wide rangeof diseases ranging from mild, superficialinfections to severe, life-threatening infections.The medical importance of fungi has beenshown to be significantly increased, particularlyin settings involving immunocompromisedpatients (1,2). Some fungal pathogens havebeen reported to be implicated in presumedoutbreaks. Among medically-important fungiwhich have been implicated in severe fungalinfectionsincludeCandida, Cryptococcus,andanumberoffilamentousfungisuchasAspergillus,Scedosporium, Penicillium, and Fusarium (1).Manyof these fungal infectionsresulted inpooroutcome despite administration of antifungalagents.Therefore,inordertoimproveoutcomes,early interventions including preventativemeasuresarewarranted.Epidemiologicalstudiestounderstand the courseandevolutionof theseorganisms in clinical settings require accuratespeciesidentificationandgenotyping. Fungal genotyping is defined as geneticanalysis of fungi (below species level) whichis performed to determine strain specificfingerprints.Genotypingwillgeneratemolecularmarkerswhichenablecomparisonamongstrainsand study their genetic relatedness. In therecent years, a number ofmolecular techniqueshave been applied for strain typing of fungalpathogens (2). Methods which have been usedforfungalgenotypingincludemultilocusenzymeelectrophoresis (MLEE), random amplificationof polymorphic DNA (RAPD), pulse field gelelectrophoresis (PFGE), restriction fragmentlengthpolymorphism(RFLP)analysis,amplified

Editorial Fungal Genotyping – Current Clinical Application

Azian Harun

Sub-Editor (Laboratory Base), Malaysian Journal of Medical Sciences, Universiti Sains Malaysia Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia

1Malays J Med Sci. Nov-Dec 2014; 21(6): 1-2

Abstract Theemergenceoffungalspeciesasopportunisticpathogenshaswarrantedfurtherstudiesontheirpathogenicity,epidemiology,andtransmissibility.Fungalgenotypinghasbeenemployedtostudythegeneticrelatednesswithintheorganism,inordertoobtainanswerstoepidemiologicalquestions(suchasinoutbreakconfirmation)aswellastoprovidebasisfortheimprovementforpatients care.Various fungal genotypingmethodshavebeenpreviouslypublished,which canbechosendependingontheintendeduseandthecapabilityofindividuallaboratory.

Keywords:fungi, genotyping, epidemiology

Submitted:19Oct2014Accepted:20Oct2014

fragment-lengthpolymorphism(AFLP)analysis,variablenumberofshorttandemrepeats(VNTR)and DNA sequence-based method such asmultilocussequencetyping(MLST)(2,3). Inmedicalmycology,genotypingtechniquesare employed to study the population dynamicsand transmissibility of fungal pathogens inboth clinical and environmental settings. Manyopportunistic fungal pathogens are ubiquitousin nature and may pose as a significant threatto susceptible patients. Therefore, using datagenerated from genotyping methods, therelationship between isolates from environmentandpatientscanbeanalysed,whichsubsequentlyenables determination of environmental sourceofinfection.Similarly,inthepresenceofaclusteroffungalinfections(presumedoutbreak),theuseof an accurate genotyping technique is crucialto prove or disprove outbreak situation. Moreimportantly,analysisofgenotypingdataenablesestablishmentofpatient-to-patient transmissionandtheindexpatientservingasthesourceoftheoutbreakcanbeidentified.Suchexerciseiscrucialin an outbreak management, in which promptand effective employment of infection controlmeasuresismandatory(2,3). Genotyping also enables furtherunderstandingofhowafungalpathogenbehavesinaparticularpatienthost.Multipleisolationsofan organismmay occur in a single patient hostoveraparticulartimeframe.Inmanyinstances,the organism can either be present as transientcolonisationoraspersistent colonisation,whicheventually may result in a genuine invasiveinfection. Genotyping enables differentiation

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Malays J Med Sci. Nov-Dec 2014; 21(6): 1-2

of these strains and the genotype associatedwith potential infection can be determined. Inaddition,associated factors leading topersistentcolonisationandinfectioncanbeevaluated(3). Fungal genotyping techniques differ intheir discriminatory power, which consequentlyaffect theirapplicability indifferentiating fungalstrains (2). Gel-based methods such as PFGE,RAPD, andAFLP have been frequently applied.Although thesemethods offermoderate to highdiscriminatory power, their interpretations andanalysesareoftendifficultandsubjectedtoperson-to-person variability (operator-dependent).VNTR and MLST, on the other hand, provideeasierinterpretationduetotheirunambiguouslygenerated data, which enables interlaboratorycomparisonwith high reproducibility.However,thesemethodsaregenerallymorecostlythantheformer methods (2,3). Therefore, each medicallaboratorymustidentifyitsneedsandcapabilitiesbeforechoosingthemostappropriategenotypingmethodsforitsclinicaluse. Genotyping databases have been developedforanumberof fungal species.Thesedatabasesare publically accessible through specificwebsitese.g.www.mlst.net.AvailabilityofMLSTdatabaseforCandida albicansandCryptococcus neoformansusingstandardconsensus-generatedprotocolspromotessharingofdataandenhancesglobalcollaborationamongresearchersinmedicalmycology.

Correspondence

DrAzianHarunMBBS (Malaya), M.Path (Microbiology) (USM), PhD(Sydney)MalaysianJournalofMedicalSciencesUniversitiSainsMalaysiaHealthCampus16150KubangKerianKelantan,MalaysiaTel:+609-7676972Fax:+609-7672359Email:azian@usm.my

Reference

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2. HarunA,PerdomoH,GilgadoF,ChenSCA,CanoJ,GuarroJ,etal.GenotypingofScedosporiumspecies:areviewofmolecularapproaches. Med Mycol. 2009;47:406–414.

3. Vanhee LME, Nelis HJ, Coenye T. What can belearned from genotyping of fungi? Med Mycol.2010;48(Suppl1):S60–S69.doi:10.3109/13693786.2010.484816.