Evaluation of nationwide analysis surveillance for methicillin-resistant Staphylococcus aureus within Genomic Medicine Sweden.
| Title: | Evaluation of nationwide analysis surveillance for methicillin-resistant Staphylococcus aureus within Genomic Medicine Sweden. |
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| Authors: | Tång Hallbäck E; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.; Region Vstra Gtaland, Sahlgrenska University Hospital, Department of Clinical Microbiology, Gothenburg, Sweden.; Björkman JT; Center for Molecular Diagnostics, Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skne, Lund, Sweden.; Dyrkell F; 1928 Diagnostics, Gothenburg, Sweden.; Welander J; Department of Clinical Microbiology, and Department of Biomedical and Clinical Sciences, Linkping University, Linkping, Sweden.; Fang H; Department of Clinical Microbiology, Medical Diagnostics Karolinska, Karolinska University Hospital, Stockholm, Sweden.; Sylvin I; Bioinformatics Data Center, Core Facilities, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.; Kaden R; Department of Medical Sciences, Clinical Microbiology, Uppsala University, Uppsala, Sweden.; Eilers H; Department of Laboratory Medicine, Clinical Microbiology, Ume University Hospital, Ume, Sweden.; Söderlund Strand A; Clinical Microbiology, Infection Prevention and Control, Office for Medical Services, Region Skne, Lund, Sweden.; Mernelius S; Laboratory Medicine, Jnkping Region County, Jnkping and Department of Clinical and Experimental Medicine, Linkping University, Linkping, Sweden.; Berglind L; Laboratory Medicine, Jnkping Region County, Jnkping, Sweden.; Campillay Lagos A; Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, rebro University, rebro, Sweden.; Engstrand L; Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institute, Solna, Sweden.; Sikora P; Bioinformatics Data Center, Core Facilities, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.; Mölling P; Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, rebro University, rebro, Sweden. |
| Source: | Microbial genomics [Microb Genom] 2025 Jan; Vol. 11 (1). |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: Microbiology Society Country of Publication: England NLM ID: 101671820 Publication Model: Print Cited Medium: Internet ISSN: 2057-5858 (Electronic) Linking ISSN: 20575858 NLM ISO Abbreviation: Microb Genom Subsets: MEDLINE |
| Imprint Name(s): | Publication: Oct. 2015- : [London] : Microbiology Society; Original Publication: [London] : Society for General Microbiology, [2015]- |
| MeSH Terms: | Methicillin-Resistant Staphylococcus aureus*/genetics ; Methicillin-Resistant Staphylococcus aureus*/isolation & purification ; Methicillin-Resistant Staphylococcus aureus*/classification ; Whole Genome Sequencing*/methods ; Staphylococcal Infections*/epidemiology ; Staphylococcal Infections*/microbiology; Sweden/epidemiology ; Multilocus Sequence Typing/methods ; Genomics/methods ; Humans ; Genome, Bacterial ; Polymorphism, Single Nucleotide ; Disease Outbreaks |
| Abstract: | Background. 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.Aim. To evaluate the quality and accuracy of WGS data generated by different laboratories but analysed by joint pipelines to reach a national surveillance approach.Methods. A national methicillin-resistant Staphylococcus aureus (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.Results. 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 |
| References: | Nat Methods. 2022 Jul;19(7):823-826. (PMID: 35789207); One Health Outlook. 2020 Feb 18;2:3. (PMID: 33829127); Lakartidningen. 2021 May 11;118:. (PMID: 33977514); J Clin Microbiol. 2019 May 24;57(6):. (PMID: 30894439); N Engl J Med. 2012 Jun 14;366(24):2267-75. (PMID: 22693998); Front Microbiol. 2018 Mar 20;9:511. (PMID: 29616014); Nat Rev Microbiol. 2019 Sep;17(9):533-545. (PMID: 31209399); Microb Genom. 2020 Apr;6(4):. (PMID: 32228804); Ann Lab Med. 2021 Jan;41(1):25-43. (PMID: 32829577); PLoS One. 2020 Dec 21;15(12):e0244227. (PMID: 33347506); Genome Res. 2018 Sep;28(9):1395-1404. (PMID: 30049790); Microb Genom. 2021 Aug;7(8):. (PMID: 34356004); J Clin Microbiol. 2017 Jun;55(6):1946-1953. (PMID: 28404677); Sci Rep. 2019 Mar 20;9(1):4931. (PMID: 30894568); Swiss Med Wkly. 2018 Dec 15;148:w14693. (PMID: 30552858); Lancet Reg Health West Pac. 2022 Apr 12;23:100446. (PMID: 35465046); Nat Microbiol. 2016 Oct 10;2:16185. (PMID: 27723724); Infect Control Hosp Epidemiol. 2018 Dec;39(12):1412-1418. (PMID: 30282566); Lancet Infect Dis. 2013 Feb;13(2):130-6. (PMID: 23158674); BMJ Open. 2012 Jun 06;2(3):. (PMID: 22674929); Microb Genom. 2018 Mar;4(3):. (PMID: 29543149); Microb Genom. 2023 Feb;9(2):. (PMID: 36752781); J Clin Microbiol. 2014 Jul;52(7):2365-70. (PMID: 24759713); Sci Rep. 2022 Jun 22;12(1):10541. (PMID: 35732699); J Open Source Softw. 2021 Apr 16;6(60):. (PMID: 35360664); Front Microbiol. 2020 Sep 11;11:573972. (PMID: 33013811); Clin Infect Dis. 2017 Aug 15;65(4):644-652. (PMID: 28472416); J Antimicrob Chemother. 2020 May 1;75(5):1117-1122. (PMID: 32025709); PLoS Biol. 2022 Aug 9;20(8):e3001755. (PMID: 35944070); Clin Infect Dis. 2014 Mar;58(5):609-18. (PMID: 24336829) |
| Contributed Indexing: | Keywords: Genomic Medicine Sweden; MRSA; SNP; cgMLST; whole-genome sequencing |
| Entry Date(s): | Date Created: 20250127 Date Completed: 20250504 Latest Revision: 20250524 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC11893271 |
| DOI: | 10.1099/mgen.0.001331 |
| PMID: | 39869391 |
| Database: | MEDLINE |
Journal Article