Recurrent Campylobacter jejuni infections with in vivo selection of resistance to macrolides and carbapenems – assembly dataset

<strong>Dataset</strong> 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. <strong>Genome assembly and annotation</strong> Reads quality control and improvement, species confirmation (using the 8GB database available at https://ccb.jhu.edu/software/kraken/) and <em>de novo</em> 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 <em>de novo</em> 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. <strong>Funding</strong> This work was supported by GenomePT (ref. POCI-01-0145-FEDER-022184) from Fundação para a Ciência e Tecnologia, Portugal.