Several different molecular typingmethodshavebeenused in industrial
contamination analysis.Mostof themare basedon the physical characterization
of molecules suchas proteins or DNA. There are differences betweenthe
molecular typingmethods,which the user should be awareof. A goodmolecular
typing methodshouldhavea highdiscriminatorypower in orderto recognize
differentsubtypesof a wide rangeof species(typeability)and it should be
reproducible. Furthermoreit should be rapidand economical. However, these
characteristics are not usuallyall met in a singletypingmethodand the user has
to evaluatewhichcharacteristics are most important.
DNAmacrorestrictionanalysisby pulsedfieldgel electrophoresis (PFGE)
typing is considered to be a feasiblemethodfor subtyping many different
microorganisms.Thismethod has a veryhigh discriminatory power,good
typeabilityand reproducibility(Broschet al., 1996).The methodis basedon the
cutting of chromosomal DNAinto large fragmentswithrare cutting restriction
endonucleases. Thefragments are run in a pulsed-field gel electrophoresis
allowing separationof largefragments (Schwartz and Cantor,1984).PFGE
typing has beensuccessfullyusedin contaminationanalysis of e.g.Listeria
monocytogenes,Yersinia enterocolitica,EscherichiacoliO157and lacticacid
bacteria (Bjo»rkrothet al., 1996,1998;Autioet al., 1999; Fredriksson-Ahomaaet
al., 2000;Lahtiet al., 2002).
Ribotypingshows a goodtypeability,but the discriminatory power is not as
highas in PFGEtyping(Swaminathanet al., 1996;Aarnisaloet al., 2003). An
advantage of the methodis that it can be automatedand largeamountsof
isolates can be typed in a shorttime.The methodis basedon the restriction of
DNA, followed by gel electrophoresisof obtained fragments. A subset of
fragmentsis visualized by hybridizingwitha labelledribosomal RNA(Stullet
al., 1988).Ribotyping has beenusedin severalcontamination analysis studies
(Bjo»rkrothand Korkeala, 1996;Aarnisaloet al., 2003).
Other molecular typing methods used in contamination analysis are
multilocus enzyme electrophoresis (MEE) typing, restriction endonuclease
analysis (REA)and randomamplificationof polymorphicDNA(RAPD). MEE
is basedon the separationof the solublemetabolic enzymesin a gel electro-
phoresis, and the methodshowsgoodtypeability,but poordiscriminatorypower
(Caugantet al., 1996).In REAchromosomalDNAis cut withfrequently cutting
restrictionendonucleases.REAhas a highdiscriminatorypower,but mayresult
in numerousfragments, whichcomplicatesthe interpretation(Gerner-Smidtet
al., 1996).RAPD is a PCR-basedtypingmethod(Williamset al., 1990),which
shows a highdiscriminatorypower(Boerlinet al., 1995).However, obtaining
reproducibleresults is problematic (Wernarset al., 1996),whichlimitsthe use
of the methodin contamination analysis. Recently, amplifiedfragmentlength
polymorphism(AFLP) typing(FonnesbechVogelet al., 2001; Autioet al.,
2003;Keto-Timonenet al., 2003)has beenusedin contaminationanalysis.
AFLPis a PCR-based typingmethodwitha discriminatorypowersimilarto
PFGE(FonnesbechVogelet al., 2001;Keto-Timonenet al., 2003).
542 Handbookof hygiene controlin the foodindustry