Genome-Based Analysis of spp. Isolates from Animals and Food Products in Germany, 2013-2017.

The increase in infections with multidrug-resistant and virulent () strains poses a serious threat to public health. However, environmental reservoirs and routes of transmission for spp. that cause infections in humans and in livestock animals are not well understood. In this study, we aimed to analyze the distribution of antibiotic resistance genes and important virulence determinants (, , , , ) among 94 spp. isolates from different animal and food sources isolated between 2013 and 2017 in Germany. Antibiotic susceptibility testing was performed, and the genomes were sequenced by Illumina and Nanopore technology. Genetic relationships were assessed by conducting core genome multilocus sequence typing (cgMLST). was used to predict resistance and virulence genes; was used to derive the capsule types. The results revealed that 72 isolates (76.6%) belonged to the complex. Within this complex, 44 known sequence types (STs), 18 new STs, and 38 capsule types were identified. Extended-spectrum beta-lactamase (ESBL) genes were detected in 16 isolates (17.0%) and colistin resistance in one (1.1%) isolate. Virulence genes were found in 22 isolates. Overall, nine (9.6%) and 18 (19.1%) isolates possessed the genes and , respectively. Notably, aerobactin ( lineage 3) was only detected in isolates from domestic pigs and wild boars. This study provides a snapshot of the genetic diversity of spp. in animals and food products in Germany. The siderophore aerobactin was found to be more prevalent in strains isolated from pigs than other sources. Further investigations are needed to evaluate if pigs constitute a reservoir for lineage 3.