PCR-based RFLPanalysis ofDNAsequencediversity in thegastric pathogen Helicobacter pylori

DNA sequence diversity among 60 independent isolates ofthegastric pathogen Helicobacterpylori was assessed bytesting forrestriction fragment length polymorphisms (RFLPs) inseveral PCR-amplified gene segments. 18Mboland27Haelll RFLPswerefoundin the2.4kbureA-ureB (urease) segmentfromthe60 strains; thisidentified 44separate groups,witheach group containing one tofourisolates. Withone exception, eachisolate notdistinguished fromthe others byRFLPsinureA-ureB was distinguished by Mboldigestion oftheneighboring 1.7kbureC-ureD segment. The1.5kbflaA(flagellin) gene,whichisnot close touregenecluster, wasalsohighly polymorphic. Incontrast, isolates frominitial andfollowup biopsies yielded identical restriction patterns ineachofthethree casestested. Thepotential ofthis methodfordetecting population heterogeneity was tested bymixing DNAs fromdifferent strains before amplification: thearrays of restriction fragmentsobtained indicated coamplification frombothgenomes ineachofthefive pairwise combinations tested. Theseresults showthat H.pylori isa verydiverse species, thatindicate PCRbasedRFLPtests arealmost assensitive asarbitrary primer PCR(RAPD)tests, andsuggest thatsuchRFLP tests willbeuseful fordirect analysis ofH.pylori in biopsy andgastric juice specimens.