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Hybrid genome assembly and annotation of multidrug-resistant Staphylococcus aureus genotype ST672-SCCmec type IVd

Jiffy John1, Lekshmi Narendrakumar2, Sabu Thomas2

  • 1Bioinformatics Laboratory, Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India; Manipal Academy of Higher Education (MAHE), Manipal, India.

Journal of Global Antimicrobial Resistance
|January 28, 2023
PubMed
Abstract

Insights

We sequenced the complete genome of multidrug-resistant Staphylococcus aureus S145, revealing its Staphylococcal Cassette Chromosome mec (SCCmec) IVd (2B) subtype. This provides a reference for understanding resistance mechanisms in this important pathogen.

Area of Science:

  • Microbiology
  • Genomics
  • Molecular Biology

Background:

  • Multidrug-resistant Staphylococcus aureus poses a significant threat, with mobile genetic elements like Staphylococcal Cassette Chromosome mec (SCCmec) mediating resistance.
  • SCCmec type IV is prevalent in hospital and community-associated methicillin-resistant S. aureus, but complete genome sequences for subtypes like IVd (2B) are lacking.

Purpose of the Study:

  • To report the complete genome sequence of a multidrug-resistant Staphylococcus aureus isolate, S. aureus S145, belonging to the SCCmec IVd (2B) subtype.
  • To provide a reference genome for comparative genomic analysis of SCCmec IVd strains.

Main Methods:

  • Phenotypic and genotypic characterization of S. aureus S145.
  • Whole-genome sequencing using a hybrid-genome approach.
  • Detection and comparison of antibiotic resistance genes with existing S. aureus genomes.

Main Results:

  • A complete genome sequence of S. aureus S145 (2.7 Mbp, 32.8% GC content) with 2,548 protein-coding regions, 79 virulence factors, and 90 antibiotic resistance genes was obtained.
  • The isolate harbors a ~17-kb SCCmec IVd (2B) element encoding mecA, mecR1, ccrA2B2, and CG002.
  • A ~30-kb multidrug-resistant plasmid containing three clusters of antibiotic resistance genes (penicillin, aminoglycoside-streptothricin, macrolides) was identified, with genetic organization similar to USA300 S. aureus.

Conclusions:

  • The complete genome sequence of S. aureus SCCmec IVd (2B) is now available.
  • This genome serves as a valuable reference for future comparative genomic studies of S. aureus strains.
Keywords:
Hybrid genome assemblyMultidrug-resistant plasmidST672-SCCmec-IVd (2B)Staphylococcus aureusVirulence factors

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