دورية أكاديمية
أعرض في EDS

SaLTy: a novel Staphylococcus aureus Lineage Typer.

التفاصيل البيبلوغرافية
العنوان: SaLTy: a novel Staphylococcus aureus Lineage Typer.
المؤلفون: Cheney L; School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia., Payne M; School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia., Kaur S; School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia., Lan R; School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia.
المصدر: Microbial genomics [Microb Genom] 2024 May; Vol. 10 (5).
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: 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
أسماء مطبوعة: Publication: Oct. 2015- : [London] : Microbiology Society
Original Publication: [London] : Society for General Microbiology, [2015]-
مواضيع طبية MeSH: Staphylococcus aureus*/genetics , Staphylococcus aureus*/classification , Staphylococcus aureus*/isolation & purification , Phylogeny* , Staphylococcal Infections*/microbiology, Humans ; Genome, Bacterial ; Methicillin-Resistant Staphylococcus aureus/genetics ; Methicillin-Resistant Staphylococcus aureus/classification ; Methicillin-Resistant Staphylococcus aureus/isolation & purification ; Alleles
مستخلص: Staphylococcus aureus asymptomatically colonises 30 % of humans but can also cause a range of diseases, which can be fatal. In 2017 S . aureus was associated with 20 000 deaths in the USA alone. Dividing S. aureus isolates into smaller sub-groups can reveal the emergence of distinct sub-populations with varying potential to cause infections. Despite multiple molecular typing methods categorising such sub-groups, they do not take full advantage of S. aureus genome sequences when describing the fundamental population structure of the species. In this study, we developed Staphylococcus aureus Lineage Typing (SaLTy), which rapidly divides the species into 61 phylogenetically congruent lineages. Alleles of three core genes were identified that uniquely define the 61 lineages and were used for SaLTy typing. SaLTy was validated on 5000 genomes and 99.12 % (4956/5000) of isolates were assigned the correct lineage. We compared SaLTy lineages to previously calculated clonal complexes (CCs) from BIGSdb ( n =21 173). SALTy improves on CCs by grouping isolates congruently with phylogenetic structure. SaLTy lineages were further used to describe the carriage of Staphylococcal chromosomal cassette containing mecA (SCC mec ) which is carried by methicillin-resistant S. aureus (MRSA). Most lineages had isolates lacking SCC mec and the four largest lineages varied in SCC mec over time. Classifying isolates into SaLTy lineages, which were further SCC mec typed, allowed SaLTy to describe high-level MRSA epidemiology. We provide SaLTy as a simple typing method that defines phylogenetic lineages (https://github.com/LanLab/SaLTy). SaLTy is highly accurate and can quickly analyse large amounts of S. aureus genome data. SaLTy will aid the characterisation of S. aureus populations and ongoing surveillance of sub-groups that threaten human health.
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فهرسة مساهمة: Keywords: Staphylococcus aureus; genomic surveillance; genomic typing; microbial genomics; population structure
تواريخ الأحداث: Date Created: 20240513 Date Completed: 20240513 Latest Revision: 20240613
رمز التحديث: 20240613
مُعرف محوري في PubMed: PMC11165655
DOI: 10.1099/mgen.0.001250
PMID: 38739116
قاعدة البيانات: MEDLINE
الوصف
تدمد:2057-5858
DOI:10.1099/mgen.0.001250