3.3. Bioinformatics Analysis, Characterization and Visualization of the WGS Data

To determine the most prevalent qnrS1 plasmid type, a reference database comprising all available closed qnr-plasmid genomes of the Genbank database was developed. Raw reads of all individual isolates were aligned to the genomes of the qnr-plasmid database using plasmidID v1.6.5 (https://github.com/BU-ISCIII/plasmidID, accessed on 17 April 2021) to identify the matching reference based on the closest relationship. Further analysis and SNP difference prediction between the estimated reference and the actual investigated plasmid was performed using snippysnake (https://gitlab.com/bfr_bioinformatics/snippySnake, accessed on 17 April 2021).

Visualisation of DNA alignments was done with BRIG [53]. Investigation of similar plasmids was conducted through blast searches [54]. Determination of the multi-locus sequence types (MLST) and the identification of genes involved in antimicrobial resistance development was conducted using the bakcharak pipeline [52]. Annotation of genomes was operated with the annotation tool prokka (v1.14.5) [55]. Phylogenetic relationship of the plasmids was determined with Clustal Omega alignment (v1.2.4) [56] and visualised with iTOL (v6) [57]. Mapping of the corresponding sequences was conducted through visualisation and analysation of the bed-file in geneious (v2020.2.2) [58]. To determine the conjugational transfer of the respective plasmids, we further screened for MOB and MPF components with the mob-suite-tool [59].