Microbiological Examination of Extraintestinal Tissues

Microbiological examination was performed as described previously [36 (link)]. Briefly, swabs taken from extraintestinal tissues at necropsy were cultured on Columbia colistin-nalidixic acid (CNA) agar (Oxoid GmbH, Wesel, Germany) for 24 h at 37 °C under microaerophilic conditions. Colonies of an EC-typical morphology (small, grey, mucoid colonies with slight alpha-haemolysis) were subcultured and identified as EC via oxidase and catalase testing, Gram staining, and, in case of doubt, by 16S rRNA partial gene sequencing (Microsynth AG, Lindau, Germany [37 (link)–39 (link)]). DNA was isolated from swabs taken from the jejunum, ileum, and caecum (InnuPrep DNA Mini Kit, Analytik Jena AG, Jena, Germany), and EC-specific real-time PCR was performed exactly as published previously [36 (link)].