Fig.1

Overview of the bacterial isolates in the study. During a prospective observational study of community-onset severe sepsis and septic shock in adults conducted at Skaraborg Hospital, Sweden Ljungstrom [8] approximately 1,800 bacterial isolates were recovered. Definite species identification of the collected isolates was performed by MALDI-TOF MS, identifying 272 bacterial isolates as S. aureus. Five isolates could not be recovered after freezing. In all, 267 isolates were prepared for DNA extraction and WGS. The output FASTQ pair-ended (PE) files for three of the isolates were excluded from the dataset after quality control of the raw data and the remaining 264 S. aureus were used as input into the bioinformatic analysis in the in-house pipeline and 1928 platform. During the benchmarking of species identification (step 1) nine FASTQ files did not pass the quality control levels in the 1928 platform. Only when benchmarking species identification, the depth/coverage was lowered to 11-29X. During the benchmarking of antibiotic sensitivity, virulence genes and ST (step 2) output from 255 isolates identified as S. aureus both phenotypically and genotypically were included