Comparison of Three Molecular Subtyping Methods among O157 and Non-O157 Shiga Toxin-Producing Escherichia coli Isolates from Japanese Cattle. 2018

Hiromi Nakamura, and Atsushi Iguchi, and Tomofumi Maehara, and Kyohei Fujiwara, and Atsushi Fujiwara, and Jun Ogasawara
Microbiology Section, Osaka Institute of Public Health.

To determine the infection source, route, and extent of an outbreak, it is important to subtype Shiga toxin-producing Escherichia coli (STEC) isolates belonging to the same serotype for clustering into clonally related groups. In this study, we compared 3 molecular subtyping methods-multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and multiple-locus variable-number of tandem repeat analysis (MLVA)-using O157 and non-O157 STEC isolates from Japanese beef cattle. A total of 73 STEC isolates belonging to 9 O-serogroups were analyzed. By means of 3 molecular subtyping methods, the strains were subdivided into 9 MLST sequence types (STs), 23 PFGE types, and 26 MLVA types. The STEC classification by O-serogrouping and MLST was almost identical. Furthermore, PFGE and MLVA could systematically classify STEC isolates of the same serotypes and STs. MLVA and PFGE were found to be highly efficient subtyping methods after O-serogrouping for the classification of not only O157 but also non-O157 STEC isolates in an outbreak investigation.

UI MeSH Term Description Entries
D007564 Japan A country in eastern Asia, island chain between the North Pacific Ocean and the Sea of Japan, east of the Korean Peninsula. The capital is Tokyo. Bonin Islands
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D002417 Cattle Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor. Beef Cow,Bos grunniens,Bos indicus,Bos indicus Cattle,Bos taurus,Cow,Cow, Domestic,Dairy Cow,Holstein Cow,Indicine Cattle,Taurine Cattle,Taurus Cattle,Yak,Zebu,Beef Cows,Bos indicus Cattles,Cattle, Bos indicus,Cattle, Indicine,Cattle, Taurine,Cattle, Taurus,Cattles, Bos indicus,Cattles, Indicine,Cattles, Taurine,Cattles, Taurus,Cow, Beef,Cow, Dairy,Cow, Holstein,Cows,Dairy Cows,Domestic Cow,Domestic Cows,Indicine Cattles,Taurine Cattles,Taurus Cattles,Yaks,Zebus
D002418 Cattle Diseases Diseases of domestic cattle of the genus Bos. It includes diseases of cows, yaks, and zebus. Bovine Diseases,Bovine Disease,Cattle Disease,Disease, Bovine,Disease, Cattle,Diseases, Bovine,Diseases, Cattle
D004927 Escherichia coli Infections Infections with bacteria of the species ESCHERICHIA COLI. E coli Infections,E. coli Infection,Infections, E coli,Infections, Escherichia coli,E coli Infection,E. coli Infections,Escherichia coli Infection,Infection, E coli,Infection, E. coli,Infection, Escherichia coli
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D016521 Electrophoresis, Gel, Pulsed-Field Gel electrophoresis in which the direction of the electric field is changed periodically. This technique is similar to other electrophoretic methods normally used to separate double-stranded DNA molecules ranging in size up to tens of thousands of base-pairs. However, by alternating the electric field direction one is able to separate DNA molecules up to several million base-pairs in length. Electrophoresis, Gel, Pulsed-Field Gradient,Gel Electrophoresis, Pulsed-Field,Contour-Clamped Homogeneous-Field Gel Electrophoresis,Electrophoresis, Gel, Pulsed Field,Electrophoresis, Pulsed Field Gel,Field Inversion Gel Electrophoresis,Orthogonal Field Alternation Gel Electrophoresis,Orthogonal-Field Alternation-Gel Electrophoresis,Pulsed Field Gradient Gel Electrophoresis,Pulsed-Field Gel Electrophoresis,Pulsed-Field Gradient Gel Electrophoresis,Alternation-Gel Electrophoresis, Orthogonal-Field,Contour Clamped Homogeneous Field Gel Electrophoresis,Electrophoresis, Orthogonal-Field Alternation-Gel,Electrophoresis, Pulsed-Field Gel,Gel Electrophoresis, Pulsed Field,Pulsed Field Gel Electrophoresis
D054323 Shiga-Toxigenic Escherichia coli Strains of ESCHERICHIA COLI with the ability to produce at least one or more of at least two antigenically distinct, usually bacteriophage-mediated cytotoxins: SHIGA TOXIN 1 and SHIGA TOXIN 2. These bacteria can cause severe disease in humans including bloody DIARRHEA and HEMOLYTIC UREMIC SYNDROME. E coli, Verotoxigenic,Escherichia coli, Verotoxigenic,STEC,Verotoxigenic Escherichia coli,Shiga Toxigenic E. coli,Shiga Toxigenic Escherichia coli,Shiga Toxin-Producing Escherichia coli,VTEC,Vero Cytotoxin-Producing Escherichia coli,Verotoxigenic E. coli,Verotoxin-Producing Escherichia coli
D058885 Multilocus Sequence Typing Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level. Multilocus Sequence Analysis,Analyses, Multilocus Sequence,Analysis, Multilocus Sequence,Multilocus Sequence Analyses,Sequence Analyses, Multilocus,Sequence Analysis, Multilocus,Sequence Typing, Multilocus,Typing, Multilocus Sequence
D058889 Molecular Typing Using MOLECULAR BIOLOGY techniques, such as DNA SEQUENCE ANALYSIS; PULSED-FIELD GEL ELECTROPHORESIS; and DNA FINGERPRINTING, to identify, classify, and compare organisms and their subtypes. Typing, Molecular

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