Seqsphere v 4

The assembled genomes were uploaded in the FASTA format to the Center for Genomic Epidemiology (CGE) multi-locus sequence typing (MLST) finder website (version 1.7) to identify the sequence types (STs) of the isolates [15 (link)]. The presence of antibiotic-resistant genes was determined by uploading the assembled genomes in FASTA format to ResFinder 2.1 [16 (link)] from the CGE server. The virulence genes were identified using the Basic Local Alignment Search Tool of the NCBI or European Nucleotide Archive database with the CLC Genomics Workbench v10.0.1 (CLC bio A/S, Aarhus, Denmark) tool (see the complete list of virulence genes in Supplementary Data S1 and S2). The serotypes of K. pneumoniae and E. coli isolates were predicted using the Kaptive web tool [17 (link)] and SerotypeFinder tool, respectively [18 (link)]. To determine the phylogenetic characteristics, the sequences were uploaded into SeqSphere v.4.1.9 (Ridom, Munster, Germany) and genotyped using a gene-by-gene typing approach with a 2358-gene core-genome MLST (cgMLST) scheme. The plasmid replicon types were identified by uploading the genome sequences of the isolate to the PlasmidFinder v.2.0.1 [19 (link)] webtool. The plasmids in the isolates were reconstructed using the MOB-suite tool [20 (link)].

The virulence genes were identified by blasting them against known virulence reference genes (see Data sheet S3) downloaded from the NCBI or ENA database into the CLC Genomics Workbench v10.0.1 (Qiagen, CLC bio A/S, Aarhus, Denmark). In total, 64 virulence genes were investigated and the predictive virulence score was determined using the number of genes found in each isolate. Predictive virulence genes scores were also used to characterize the isolates as ExPEC or UPEC as described by Johnson et al. (2015 (link)). The virotype of the ST131 isolates was defined as described by Dahbi et al. (2014 (link)). Phylogenetic groups were defined as described by Clermont et al. (2013 (link)). To determine the phylogenetic relationship the isolates were uploaded into SeqSphere v.4.1.9 (Ridom, Munster, Germany) and a gene-by-gene typing approach using a 2764-genes core genome (cg) MLST scheme was used as previously described (Ferdous et al., 2016 (link)).