Computational protocol: Mutation of Agr Is Associated with the Adaptation of Staphylococcus aureus to the Host during Chronic Osteomyelitis

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[…] Genomic DNA was extracted from isolates according to a standard protocol (Pitcher et al., ). DNA libraries were prepared using Nextera XT (Illumina, San Diego, CA, USA) and whole genome sequencing was performed using Illumina HiSeq pair-end sequencing with 500 cycles (Instituto Nacional de Tecnología Agropecuaria, Castelar, Buenos Aires, Argentina). FASTQ reads were processed with Trimmomatic (Bolger et al., ) to remove bases from the trailing end that fall below a PHRED score of 30. Short reads were assembled using SPAdes v3.10.1 (Bankevich et al., ). Contigs less than 500 bp and 30X coverage were discarded. Resulting contigs were ordered using Mauve 2.4.0 (Darling et al., ) and strain MRSA252 as reference. The genome was annotated using Prokka 1.12 (Seemann, ). Variant calling was performed using Snippy v3.2 (Seemann, ). The sequences reported in this paper have been deposited in the NCBI Sequence Read Archive under Bioproject number PRJNA414566. […]

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