All (n = 51) sequenced isolates were analyzed with Ridom SeqSphere + software v7.7.5 (Ridom GmbH, Germany) [30 ]. Quality analysis of the sequences was performed with FastQC v0.1.1.7 [31 ] and adapters were removed with Trimmomatic v0.36 [32 ]. Raw reads were assembled with SKESA v2.3.0 using default settings [33 ], and quality trimming was performed with an average quality of ≥ 30 and a window of 20 bases. Remapping and polishing were performed with the BWA-MEM mapping algorithm. Sequencing statistics are presented in Additional file 1 . Acquired AMR genes were identified from assembled genomes with NCBI AMRFinderPlus 3.2.3 [34 ], using 100% alignment and > 90% identity. STs were analyzed by using multilocus sequence types (MLST) [35 ] in Ridom SeqSphere + (Ridom, Munster, Germany). Warwick MLST scheme was chosen for E. coli isolates. E. coli isolates with novel STs were submitted to Enterobase [36 (link)] and K. pneumoniae isolates to Institut Pasteur [37 , 38 ] to assign new STs. Phylogenetic analysis was conducted for all E. coli and K. pneumoniae isolates with core genome multilocus sequence typing (cgMLST) by comparing 2513 and 2365 alleles with pairwise missing values, respectively. A cluster threshold was determined by 10 allelic differences [39 ].
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