Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis

• DOI: 10.1186/s12879-022-07977-0
• Publication Date: 2023-01-20T16:05:48Z
• Authors: Mahnaz Irani Shem...; Diana Tilevik; Andreas Tilevik; Sanja Jurcevic; Dimitrios Arnellos; Helena Enroth; Anna-Karin Pernestig
• Keywords: Medical microbiology; Parasitology; Benchmarking; Mycology

Abstract Background The rapidly growing area of sequencing technologies, and more specifically bacterial whole-genome sequencing, could offer applications in clinical microbiology, including species identification bacteria, prediction genetic antibiotic susceptibility virulence genes simultaneously. To accomplish the aforementioned points, commercial cloud-based platform, 1928 platform (1928 Diagnostics, Gothenburg, Sweden) was benchmarked against an in-house developed bioinformatic pipeline as well to reference methods laboratory. Methods Whole-genome data retrieved from 264 Staphylococcus aureus isolates using Illumina HiSeq X next-generation technology used. S. were collected during a prospective observational study community-onset severe sepsis septic shock adults at Skaraborg Hospital, western region Sweden. characterized according accredited laboratory i.e., by MALDI-TOF MS analysis phenotypic testing (AST) following EUCAST guidelines. Concordance between tools, concordance tools assessed calculating percent agreement. Results There overall high agreement predicted genotypic AST results, 98.0% (989/1006, 95% CI 97.3–99.0). Nevertheless, delivered results with lower very major error rates but somewhat higher compared pipeline. differences processing times minutes versus hours, where faster. Furthermore, workflows showed 99.4% (1267/1275, 98.7–99.7) gene characteristics 97.9% (231/236, 95.0–99.2%) predicting sequence types (ST) isolates. Conclusions Altogether, benchmarking disclosed that both are able deliver accuracy aiding diagnostics infections caused . It also illustrates need international on quality control metrics facilitate standardization analytical approaches for based predictions.