Fig. 2

A Comparison of SSU5 prophage features with known C. sakazakii phage-plasmid class members: Four known and two new plasmid sequences from this study were compared using PROKSEE with the annotations of the Salmonella prophage SSU5. The inner circle represents the sequence clockwise and the scale marks indicate positions of annotated genes. GenBank annotations of the reference phage-plasmid SSU5 (CDS in Black colored ring, arranged outside ring), pCS1 (Green), pCsa767a (purple), pCsaC757b (Tan), pCsaC105731a (Red), pGK1025B_1 (Teal) and pH322_1 (Mauve) were downloaded as GFF files for analysis using the default configuration on the PROKSEE server. Across the circular genomes, selected genes or regions of interest are shown as follows: Missing regions identified by the BLAST analysis on the CGView server’s PROKSEE software are shown as ‘gaps’ (white color) on each of the circular genomes. These plasmids contained a near-complete SSU5 phage. A BLAST analysis of 630 + WGS assemblies of Cronobacter revealed varied coverage of the phage sequences in many plasmids (See Additional file 3: Table S3). The analysis was carried out on the PROKSEE Server from the Stothard Research Group (University of Alberta, CA) that uses BLAST analysis to illustrate conserved and missing genomic sequences (available online: https://beta.proksee.ca/tools). B Mauve alignment of SSU5 illustrates variations in lengths of the phage-sequences in Cronobacter plasmids: Plasmids from C. sakazakii and C. muytjensii were compared using the Mauve progressive alignment tool (http://darlinglab.org/mauve/user-guide/progressivemauve.html, [27, 28]) implemented on Geneious suite 12. pCS1 from C. sakazakii NCTC 8155 was seen to be the largest plasmid with almost 110 kb when compared to pCmuyZ38_1 from C. muytjensii JZ38 and the two new plasmids from this study. A detailed analysis of these plasmids, and their inclusion in plasmid-finding pipelines, would enable the identification of SSU5-like sequences from the growing number of Cronobacter WGS datasets