title: Evaluation of a Method Using Three Genomic Guided Escherichia coli Markers for Phylogenetic Typing of E. coli Isolates of Various Genetic Backgrounds.
abstract: Genotyping and characterization of bacterial isolates are essential steps in the identification and control of antibiotic-resistant bacterial infections. Recently, one novel genotyping method using three genomic guided Escherichia coli markers (GIG-EM), dinG, tonB, and dipeptide permease (DPP), was reported. Because GIG-EM has not been fully evaluated using clinical isolates, we assessed this typing method with 72 E. coli collection of reference (ECOR) environmental E. coli reference strains and 63 E. coli isolates of various genetic backgrounds. In this study, we designated 768 bp of dinG, 745 bp of tonB, and 655 bp of DPP target sequences for use in the typing method. Concatenations of the processed marker sequences were used to draw GIG-EM phylogenetic trees. E. coli isolates with identical sequence types as identified by the conventional multilocus sequence typing (MLST) method were localized to the same branch of the GIG-EM phylogenetic tree. Sixteen clinical E. coli isolates were utilized as test isolates without prior characterization by conventional MLST and phylogenetic grouping before GIG-EM typing. Of these, 14 clinical isolates were assigned to a branch including only isolates of a pandemic clone, E. coli B2-ST131-O25b, and these results were confirmed by conventional typing methods. Our results suggested that the GIG-EM typing method and its application to phylogenetic trees might be useful tools for the molecular characterization and determination of the genetic relationships among E. coli isolates.
authors: Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan.
authors: Kouta
authors: K
authors: Hamamoto
authors: Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Osaka, Japan.
authors: Shuhei
authors: S
authors: Ueda
authors: Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Osaka, Japan Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan.
authors: Yoshimasa
authors: Y
authors: Yamamoto
authors: Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Osaka, Japan hiraii@med.u-ryukyu.ac.jp.
authors: Itaru
authors: I
authors: Hirai
mesh_terms: D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D004926:Escherichia coli / Q000145:classification / Q000235:genetics*; D004927:Escherichia coli Infections / Q000382:microbiology*; D005243:Feces / Q000382:microbiology; D005819:Genetic Markers / Q000235:genetics; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D058889:Molecular Typing / Q000379:methods*; D010802:Phylogeny
chemical_list: D004269:DNA, Bacterial; D005819:Genetic Markers