title: Molecular Subtyping of Shiga Toxin-Producing Escherichia coli Using a Commercial Repetitive Sequence-Based PCR Assay.
abstract: PCR-based typing methods, such as repetitive sequence-based PCR (rep-PCR), may facilitate the identification of Shiga toxin-producing Escherichia coli (STEC) by serving as screening methods to reduce the number of isolates to be processed for further confirmation. In this study, we used a commercial rep-PCR typing system to generate DNA fingerprint profiles for STEC O157 (n = 60) and non-O157 (n = 91) isolates from human, food, and animal samples and then compared the results with those obtained from pulsed-field gel electrophoresis (PFGE). Fifteen serogroups were analyzed using the Kullback Leibler or extended Jaccard statistical method, and the unweighted pair group method of averages algorithm was used to create dendrograms. Among the 151 STEC isolates tested, all were typeable by rep-PCR. Among the non-O157 isolates, rep-PCR clustered 79 (88.8%) of 89 isolates according to serogroup status, with peak differences ranging from 1 (96.4% similarity) to 12 (58.7% similarity). The genetic relatedness of the non-O157 serogroups mirrored the branching of distinct clonal groups elucidated by other investigators. Although the discriminatory power of rep-PCR (Simpson's index of diversity [SID] = 0.954) for the O157 isolates was less than that of PFGE (SID = 0.993), rep-PCR was able to identify 29 pattern types, suggesting that this method can be used for strain typing, although not to the same level as PFGE. Similar results were obtained from analysis of the non-O157 isolates. With rep-PCR, we assigned non-O157 isolates to 46 pattern types with a SID of 0.977. By PFGE, non-O157 STEC strains were divided into 77 pattern types with a SID of 0.996. Together, these results indicate the ability of the rep-PCR typing system to distinguish between and within O157 and non-O157 STEC groups. Rapid PCR-based typing methods could be invaluable tools for use in outbreak investigations by excluding unrelated STEC isolates within 24 h.
authors.affiliation: U.S. Food and Drug Administration, Office of Regulatory Affairs, San Francisco District Laboratory, Alameda, California 94502, USA. kimberly.anderson@fda.hhs.gov.
authors.forename: Kimberly M
authors.initials: KM
authors.lastname: Anderson
authors.affiliation: U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland 20708, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: Abbott
authors.affiliation: U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland 20708, USA.
authors.forename: Shaohua
authors.initials: S
authors.lastname: Zhao
authors.affiliation: U.S. Food and Drug Administration, Office of Regulatory Affairs, San Francisco District Laboratory, Alameda, California 94502, USA.
authors.forename: Eileen
authors.initials: E
authors.lastname: Liu
authors.affiliation: U.S. Food and Drug Administration, Office of Regulatory Affairs, Office of Regulatory Science, Rockville, Maryland 20857, USA.
authors.forename: Sunee
authors.initials: S
authors.lastname: Himathongkham
mesh_terms: D000818:Animals; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000235:genetics; D004927:Escherichia coli Infections / Q000382:microbiology*; D005516:Food Microbiology; D006801:Humans; D058889:Molecular Typing; D016133:Polymerase Chain Reaction / Q000191:economics / Q000295:instrumentation / Q000379:methods*; D011933:Reagent Kits, Diagnostic; D012091:Repetitive Sequences, Nucleic Acid; D054323:Shiga-Toxigenic Escherichia coli / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D004269:DNA, Bacterial; D011933:Reagent Kits, Diagnostic