title: Meta-analysis of pulsed-field gel electrophoresis fingerprints based on a constructed Salmonella database.
abstract: A database was constructed consisting of 45,923 Salmonella pulsed-field gel electrophoresis (PFGE) patterns. The patterns, randomly selected from all submissions to CDC PulseNet during 2005 to 2010, included the 20 most frequent serotypes and 12 less frequent serotypes. Meta-analysis was applied to all of the PFGE patterns in the database. In the range of 20 to 1100 kb, serotype Enteritidis averaged the fewest bands at 12 bands and Paratyphi A the most with 19, with most serotypes in the 13-15 range among the 32 serptypes. The 10 most frequent bands for each of the 32 serotypes were sorted and distinguished, and the results were in concordance with those from distance matrix and two-way hierarchical cluster analyses of the patterns in the database. The hierarchical cluster analysis divided the 32 serotypes into three major groups according to dissimilarity measures, and revealed for the first time the similarities among the PFGE patterns of serotype Saintpaul to serotypes Typhimurium, Typhimurium var. 5-, and I 4,[5],12:i:-; of serotype Hadar to serotype Infantis; and of serotype Muenchen to serotype Newport. The results of the meta-analysis indicated that the pattern similarities/dissimilarities determined the serotype discrimination of PFGE method, and that the possible PFGE markers may have utility for serotype identification. The presence of distinct, serotype specific patterns may provide useful information to aid in the distribution of serotypes in the population and potentially reduce the need for laborious analyses, such as traditional serotyping.
authors.affiliation: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, United States of America. wen.zou@fda.hhs.gov
authors.forename: Wen
authors.initials: W
authors.lastname: Zou
authors.forename: Hung-Chia
authors.initials: HC
authors.lastname: Chen
authors.forename: Kelley B
authors.initials: KB
authors.lastname: Hise
authors.forename: Hailin
authors.initials: H
authors.lastname: Tang
authors.forename: Steven L
authors.initials: SL
authors.lastname: Foley
authors.forename: Joe
authors.initials: J
authors.lastname: Meehan
authors.forename: Wei-Jiun
authors.initials: WJ
authors.lastname: Lin
authors.forename: Rajesh
authors.initials: R
authors.lastname: Nayak
authors.forename: Joshua
authors.initials: J
authors.lastname: Xu
authors.forename: Hong
authors.initials: H
authors.lastname: Fang
authors.forename: James J
authors.initials: JJ
authors.lastname: Chen
mesh_terms: D016208:Databases, Factual; D016521:Electrophoresis, Gel, Pulsed-Field / Q000379:methods*; D012475:Salmonella / Q000145:classification / Q000378:metabolism*; D012703:Serotyping / Q000379:methods*