Shiga toxin-producing Escherichia coli (STEC) isolated from fecal samples of African dromedary camels

Baschera, Melinda; Cernela, Nicole; Stevens, Marc J.A.; Liljander, Anne; Jores, Jörg; Corman, Victor Max; Nüesch-Inderbinen, Magdalena; Stephan, Roger

To assess the genetic relatedness of the isolates, core genome multilocus sequence typing (cgMLST) was carried out using Ridom Seq-Sphere Software (version 4.1.9, available at http://www.ridom.de/ seqsphere/cgmlst/). The MLST schemes "Warwick" and "Pasteur" were used for MLST-typing, and the Enterobase Escherichia/Shigella v1 scheme (http://enterobase.warwick.ac.uk) for cgMLST typing. Assembled genomes were blasted against the reference database using standard settings and the option "ignore missing values pairwise" and "Discard genomes with > 3% missing genes" were used for typing. Trees were visualised using the minimal spanning tree option in seqsphere. 2.6. Antibiotic resistance profiles Antimicrobial susceptibility testing was performed using the diskdiffusion method and the antibiotics ampicillin (AM), amoxicillin-clavulanic acid (AMC), cefazolin (CZ), cefotaxime (CTX), cefepime (FEP), nalidixic acid (NA), ciprofloxacin (CIP), gentamicin (GM), kanamycin (K), streptomycin (S), sulfamethoxazole/trimethoprim (SXT), fosfomycin (FOS), azithromycin (AZM), nitrofurantoin (F/M), chloramphenicol (C) and tetracycline (T) (Becton Dickinson, Heidelberg, Germany). Results were interpreted according to Clinical and Laboratory Standards Institute (CLSI) performance standards [28] .