Evaluation of nationwide analysis surveillance for methicillin-resistant within Genomic Medicine Sweden.
Erika T��ng Hallb��ck, Jonas T Bj��rkman, Fredrik Dyrkell, Jenny Welander, Hong Fang, Isak Sylvin, Ren Kaden, Hinnerk Eilers, Anna S��derlund Strand, Sara Mernelius, Linda Berglind, Amaya Campillay Lagos, Lars Engstrand, Per Sikora, Paula M��lling
Author Information
Erika T��ng Hallb��ck: Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
Jonas T Bj��rkman: Center for Molecular Diagnostics, Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skne, Lund, Sweden.
Fredrik Dyrkell: 1928 Diagnostics, Gothenburg, Sweden.
Jenny Welander: Department of Clinical Microbiology, and Department of Biomedical and Clinical Sciences, Linkping University, Linkping, Sweden.
Hong Fang: Department of Clinical Microbiology, Medical Diagnostics Karolinska, Karolinska University Hospital, Stockholm, Sweden.
Isak Sylvin: Bioinformatics Data Center, Core Facilities, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
Ren Kaden: Department of Medical Sciences, Clinical Microbiology, Uppsala University, Uppsala, Sweden.
Hinnerk Eilers: Department of Laboratory Medicine, Clinical Microbiology, Ume University Hospital, Ume, Sweden.
Anna S��derlund Strand: Clinical Microbiology, Infection Prevention and Control, Office for Medical Services, Region Skne, Lund, Sweden.
Sara Mernelius: Laboratory Medicine, Jnkping Region County, Jnkping and Department of Clinical and Experimental Medicine, Linkping University, Linkping, Sweden.
Linda Berglind: Laboratory Medicine, Jnkping Region County, Jnkping, Sweden.
Amaya Campillay Lagos: Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, rebro University, rebro, Sweden.
Lars Engstrand: Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institute, Solna, Sweden.
Per Sikora: Bioinformatics Data Center, Core Facilities, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
Paula M��lling: Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, rebro University, rebro, Sweden.
National epidemiological investigations of microbial infections greatly benefit from the increased information gained by whole-genome sequencing (WGS) in combination with standardized approaches for data sharing and analysis. To evaluate the quality and accuracy of WGS data generated by different laboratories but analysed by joint pipelines to reach a national surveillance approach. A national methicillin-resistant (MRSA) collection of 20 strains was distributed to nine participating laboratories that performed in-house procedures for WGS. Raw data were shared and analysed by three pipelines: 1928 Diagnostics, JASEN (GMS pipeline) and CLC-Genomics Workbench. The outcomes were compared according to quality, correct strain identification and genetic distances. One isolate contained intraspecies contamination and was excluded from further analysis. The mean sequencing depth varied between sites and technologies. However, all analysis methods identified 12 strains that belonged to one of five outbreak clusters. The cut-off definition was set to <10 allele differences for core genome multilocus sequence typing (cgMLST) and <20 genetic differences for SNP analysis in a pairwise comparison. MRSA isolates, which are whole genome sequenced by different laboratories and analysed using the same bioinformatic pipelines, yielded comparable results for outbreak clustering for both cgMLST and SNP, using the 1928 analysis pipeline. In this study, JASEN was best suited to analyse Illumina data and CLC to analyse within respective technology. In the future, real-time sharing of data and harmonized analysis within the Genomic Medicine Sweden consortium will further facilitate investigations of outbreaks and transmission routes.
