Open AccessRapid Determination ofEscherichia coliO157:H7 Lineage Types and Molecular Subtypes by Using Comparative Genomic Fingerprinting
Author(s) -
Chad R. Laing,
Crystal Pegg,
Davis Yawney,
Kim Ziebell,
M. William Steele,
Roger P. Johnson,
James E. Thomas,
Eduardo N. Taboada,
Yongxiang Zhang,
Victor P. J. Gan
Publication year - 2008
Publication title -
applied and environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.552
H-Index - 324
eISSN - 1070-6291
pISSN - 0099-2240
DOI - 10.1128/aem.00985-08
Subject(s) - biology , typing , dendrogram , escherichia coli , genetics , locus (genetics) , pulsed field gel electrophoresis , dna profiling , lineage (genetic) , computational biology , gene , genotype , genetic diversity , population , dna , demography , sociology
In this study, variably absent or present (VAP) regions discovered through comparative genomics experiments were targeted for the development of a rapid, PCR-based method to subtype and fingerprintEscherichia coli O157:H7. Forty-four VAP loci were analyzed for discriminatory power among 79E. coli 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 majorE. coli 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 otherE. coli 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 relatedE. coli 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.