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Forty-four VAP loci were analyzed for discriminatory power among 79<jats:italic>E. coli<\/jats:italic>O157:H7 strains of 13 phage types (PT). Twenty-three loci were found to maximize resolution among strains, generating 54 separate fingerprints, each of which contained strains of unique PT. Strains from the three previously identified major<jats:italic>E. coli<\/jats:italic>O157:H7 lineages, LSPA6-LI, LSPA6-LI\/II, and LSPA6-LII, formed distinct branches on a dendrogram obtained by hierarchical clustering of comparative genomic fingerprinting (CGF) data. By contrast, pulsed-field gel electrophoresis (PFGE) typing generated 52 XbaI digestion profiles that were not unique to PT and did not cluster according to O157:H7 lineage. Our analysis identified a subpopulation comprised of 25 strains from a closed herd of cattle, all of which were of PT87 and formed a cluster distinct from all other<jats:italic>E. coli<\/jats:italic>O157:H7 strains examined. CGF found five related but unique fingerprints among the highly clonal herd strains, with two dominant subtypes characterized by a shift from the presence of locus fprn33 to its absence. CGF had equal resolution to PFGE typing but with greater specificity, generating fingerprints that were unique among phenotypically related<jats:italic>E. coli<\/jats:italic>O157:H7 lineages and PT. As a comparative genomics typing method that is amenable for use in high-throughput platforms, CGF may be a valuable tool in outbreak investigations and strain characterization.<\/jats:p>","DOI":"10.1128\/aem.00985-08","type":"journal-article","created":{"date-parts":[[2008,9,13]],"date-time":"2008-09-13T00:44:55Z","timestamp":1221266695000},"page":"6606-6615","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":28,"title":["Rapid Determination of<i>Escherichia coli<\/i>O157:H7 Lineage Types and Molecular Subtypes by Using Comparative Genomic Fingerprinting"],"prefix":"10.1128","volume":"74","author":[{"given":"Chad","family":"Laing","sequence":"first","affiliation":[{"name":"Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Lethbridge, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Crystal","family":"Pegg","sequence":"additional","affiliation":[{"name":"Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Lethbridge, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Davis","family":"Yawney","sequence":"additional","affiliation":[{"name":"Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Lethbridge, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kim","family":"Ziebell","sequence":"additional","affiliation":[{"name":"Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina","family":"Steele","sequence":"additional","affiliation":[{"name":"Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roger","family":"Johnson","sequence":"additional","affiliation":[{"name":"Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James E.","family":"Thomas","sequence":"additional","affiliation":[{"name":"Faculty of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduardo N.","family":"Taboada","sequence":"additional","affiliation":[{"name":"Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Lethbridge, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongxiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Lethbridge, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor P. 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