title: Evaluation of applicability of DNA microarray-based characterization of bovine Shiga toxin-producing Escherichia coli isolates using whole genome sequence analysis.
abstract: We assessed the ability of a commercial DNA microarray to characterize bovine Shiga toxin-producing Escherichia coli (STEC) isolates and evaluated the results using in silico hybridization of the microarray probes within whole genome sequencing scaffolds. From a total of 69,954 reactions (393 probes with 178 isolates), 68,706 (98.2%) gave identical results by DNA microarray and in silico probe hybridization. Results were more congruent when detecting the genoserotype (209 differing results from 19,758 in total; 1.1%) or antimicrobial resistance genes (AMRGs; 141 of 26,878; 0.5%) than when detecting virulence-associated genes (VAGs; 876 of 22,072; 4.0%). Owing to the limited coverage of O-antigens by the microarray, only 37.2% of the isolates could be genoserotyped. However, the microarray proved suitable to rapidly screen bovine STEC strains for the occurrence of high numbers of VAGs and AMRGs and is suitable for molecular surveillance workflows.
authors.affiliation: Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany (Barth, Menge, Geue).|Free University Berlin, Institute of Microbiology and Epizootics, Berlin, Germany (Eichhorn, Semmler).|Robert Koch Institute, Berlin, Germany (Semmler).|The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (Pickard).
authors.forename: Stefanie A
authors.initials: SA
authors.lastname: Barth
authors.affiliation: Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany (Barth, Menge, Geue).|Free University Berlin, Institute of Microbiology and Epizootics, Berlin, Germany (Eichhorn, Semmler).|Robert Koch Institute, Berlin, Germany (Semmler).|The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (Pickard).
authors.forename: Christian
authors.initials: C
authors.lastname: Menge
authors.affiliation: Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany (Barth, Menge, Geue).|Free University Berlin, Institute of Microbiology and Epizootics, Berlin, Germany (Eichhorn, Semmler).|Robert Koch Institute, Berlin, Germany (Semmler).|The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (Pickard).
authors.forename: Inga
authors.initials: I
authors.lastname: Eichhorn
authors.affiliation: Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany (Barth, Menge, Geue).|Free University Berlin, Institute of Microbiology and Epizootics, Berlin, Germany (Eichhorn, Semmler).|Robert Koch Institute, Berlin, Germany (Semmler).|The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (Pickard).
authors.forename: Torsten
authors.initials: T
authors.lastname: Semmler
authors.affiliation: Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany (Barth, Menge, Geue).|Free University Berlin, Institute of Microbiology and Epizootics, Berlin, Germany (Eichhorn, Semmler).|Robert Koch Institute, Berlin, Germany (Semmler).|The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (Pickard).
authors.forename: Derek
authors.initials: D
authors.lastname: Pickard
authors.affiliation: Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany (Barth, Menge, Geue).|Free University Berlin, Institute of Microbiology and Epizootics, Berlin, Germany (Eichhorn, Semmler).|Robert Koch Institute, Berlin, Germany (Semmler).|The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (Pickard).
authors.forename: Lutz
authors.initials: L
authors.lastname: Geue
mesh_terms: D000818:Animals; D002417:Cattle / Q000382:microbiology; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000662:veterinary*; D054323:Shiga-Toxigenic Escherichia coli / Q000235:genetics* / Q000302:isolation & purification; D000073336:Whole Genome Sequencing / Q000662:veterinary
keywords: Bovine STEC; DNA microarray; Shiga toxin; in silico hybridization; whole genome sequencing