Ann Lab Med.  2024 Jan;44(1):47-55. 10.3343/alm.2024.44.1.47.

Comparative Genomic Analysis of Staphylococcal Cassette Chromosome mec Type V Staphylococcus aureus Strains and Estimation of the Emergence of SCCmec V Clinical Isolates in Korea

• Takahashi T
• Kim H
• Kim HS
• Kim HS
• Song W
• Kim JS

• KMID: 2550222
• DOI: http://doi.org/10.3343/alm.2024.44.1.47

Abstract

Background
Staphylococcal cassette chromosome mec type V (SCCmec V) methicillin-resistant Staphylococcus aureus (MRSA) has been recovered from patients and livestock. Using comparative genomic analyses, we evaluated the phylogenetic emergence of SCCmec V after transmission from overseas donor strains to Korean recipient strains.
Methods
Sixty-three complete MRSA SCCmec V genomes (including six Korean clinical isolates) were used to construct a phylogenetic tree. Single-nucleotide polymorphisms were identified using Snippy, and a maximum-likelihood-based phylogenetic tree was constructed using RAxML. The possible emergence of the most common ancestor was estimated using BactDating. To estimate mecA horizontal gene transfer (HGT) events, Rangerdtl was applied to 818 SCCmec V strains using publicly available whole-genome data.
Results
The phylogenetic tree showed five major clades. German strains formed a major clade; their possible origin was traced to the 1980s. The emergence of Korean SCCmec V clinical isolates was traced to 2000–2010. mecA HGT events in Staphylococcus spp. were identified in seven strains. P7 (Hong Kong outbreak strain) served as the donor strain for two Korean sequence type (ST) 59 strains, whereas the other five recipient strains emerged from different SCCmec V donors.
Conclusions
Most Korean SCCmec V strains may have emerged during 2000–2010. A unique MRSA SCCmec V strain, ST72 (a Korean common type of community-associated MRSA), was also identified. The genomic dynamics of this clone with a zoonotic background should be monitored to accurately understand MRSA evolution.

Keyword

Clades; Comparative genomic analysis; Donor–recipient; Horizontal gene transfer; Korea; Methicillin; One Health; Phylogeny; SCCmec V; Staphylococcus; Whole genome sequence

Figure

• 

  Fig. 1 Circular map of the six Korean complete MRSA SCCmec V strain genomes (including the HL24830 reference strain). A genome map of the constructed MRSA genome was generated using CGView v.2.0.3. The CGView Comparison Tool was used to construct the circular plot of Staphylococcus aureus DNA sequences. COG features for protein-coding genes and locations of protein-coding, transfer RNA, and ribosomal RNA genes are presented on the four outermost concentric rings. Similar regions of MRSA SCCmec V strains are presented on the next six concentric rings. Based on the percent identity determined using the Basic Local Alignment Search Tool between the similar regions, the inside rings of the MRSA genomes appear black (100% identical) to blue (≥88% identical). The black peaks depict GC content, and the innermost green and purple peaks describe positive and negative GC skews, respectively. Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus; COG, clusters of orthologous gene; SCCmec V, staphylococcal cassette chromosome mec type V.

• 

  Fig. 2 Dated phylogenetic tree, including the six Korean MRSA SCCmec V strains and other MRSA SCCmec V strains with complete genomes (N= 57) available from the National Center for Biotechnology Information database. Strain HL24830 appears around 2010 and is situated near strain ER03364.3 from the USA. The six Korean SCCmec V stains may have emerged during 2000–2010. Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus; SCCmec V, staphylococcal cassette chromosome mec type V.

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