{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:49:34Z","timestamp":1787010574936,"version":"build-2736575974"},"reference-count":32,"publisher":"Microbiology Society","issue":"1","license":[{"start":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T00:00:00Z","timestamp":1737936000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001858","name":"VINNOVA","doi-asserted-by":"crossref","award":["2021-03660"],"award-info":[{"award-number":["2021-03660"]}],"id":[{"id":"10.13039\/501100001858","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,27]]},"abstract":"<jats:p>\n                    <jats:bold>Background.<\/jats:bold>\n                    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.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Aim.<\/jats:bold>\n                    To evaluate the quality and accuracy of WGS data generated by different laboratories but analysed by joint pipelines to reach a national surveillance approach.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Methods.<\/jats:bold>\n                    A national methicillin-resistant\n                    <jats:italic>Staphylococcus aureus<\/jats:italic>\n                    (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.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Results.<\/jats:bold>\n                    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 &lt;10 allele differences for core genome multilocus sequence typing (cgMLST) and &lt;20 genetic differences for SNP analysis in a pairwise comparison.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Conclusions.<\/jats:bold>\n                    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.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001331","type":"journal-article","created":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T11:16:56Z","timestamp":1737976616000},"source":"Crossref","is-referenced-by-count":1,"title":["Evaluation of nationwide analysis surveillance for methicillin-resistant Staphylococcus aureus within Genomic Medicine Sweden"],"prefix":"10.1099","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0787-8786","authenticated-orcid":false,"given":"Erika","family":"T\u00e5ng Hallb\u00e4ck","sequence":"first","affiliation":[{"name":"Region Vstra Gtaland, Sahlgrenska University Hospital, Department of Clinical Microbiology, Gothenburg, Sweden"},{"name":"Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonas T.","family":"Bj\u00f6rkman","sequence":"additional","affiliation":[{"name":"Center for Molecular Diagnostics, Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skne, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fredrik","family":"Dyrkell","sequence":"additional","affiliation":[{"name":"1928 Diagnostics, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenny","family":"Welander","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, and Department of Biomedical and Clinical Sciences, Linkping University, Linkping, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Fang","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Medical Diagnostics Karolinska, Karolinska University Hospital, Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isak","family":"Sylvin","sequence":"additional","affiliation":[{"name":"Bioinformatics Data Center, Core Facilities, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ren","family":"Kaden","sequence":"additional","affiliation":[{"name":"Department of Medical Sciences, Clinical Microbiology, Uppsala University, Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hinnerk","family":"Eilers","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Clinical Microbiology, Ume University Hospital, Ume, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"S\u00f6derlund Strand","sequence":"additional","affiliation":[{"name":"Clinical Microbiology, Infection Prevention and Control, Office for Medical Services, Region Skne, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Mernelius","sequence":"additional","affiliation":[{"name":"Laboratory Medicine, Jnkping Region County, Jnkping and Department of Clinical and Experimental Medicine, Linkping University, Linkping, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda","family":"Berglind","sequence":"additional","affiliation":[{"name":"Laboratory Medicine, Jnkping Region County, Jnkping, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amaya","family":"Campillay Lagos","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, rebro University, rebro, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars","family":"Engstrand","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institute, Solna, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Per","family":"Sikora","sequence":"additional","affiliation":[{"name":"Bioinformatics Data Center, Core Facilities, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paula","family":"M\u00f6lling","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, rebro University, rebro, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","volume-title":"ECDC. 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