Genome-Based Bacterial Typing and Analysis

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)].