Dataset This dataset comprises the genome assemblies of the first isolate collected from each clinical case (A1 and B1), together with the respective annotation. File “Cje_metadata.xlsx” contains the genome assembly statistics for each isolate, including the European Nucleotide Archive (ENA) accession numbers, genotyping and antibiotic resistance profiles. The directory “Assemblies/” contains the genome assembly (.fasta and .gbk formats) of each isolate presented in the metadata file. Genome assembly and annotation Reads quality control and improvement, species confirmation (using the 8GB database available at https://ccb.jhu.edu/software/kraken/) and de novo assembly were performed using the INNUca v4.2.2 pipeline (https://github.com/B-UMMI/INNUca). Briefly, after reads’ quality analysis using FastQC v0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and cleaning with Trimmomatic v0.38 (http://www.usadellab.org/cms/?page=trimmomatic), genomes were de novo assembled with SPAdes 3.14.0 (http://bioinf.spbau.ru/spades) with a mean depth of coverage above 160x, and subsequently improved using Pilon v1.23. Multi-Locus Sequence Typing (MLST) was performed using mlst v2.18.1 software (https://github.com/tseemann/mlst). Genome annotation was performed with RAST server v2.0 (http://rast.nmpdr.org/). The raw sequence reads of each isolate were deposited at ENA under the study accession numbers PRJEB42628 and PRJNA505131. Funding This work was supported by GenomePT (ref. POCI-01-0145-FEDER-022184) from Fundação para a Ciência e Tecnologia, Portugal.