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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2024; 52(1): 97-98

https://doi.org/10.48022/mbl.2312.12009

Received: December 28, 2023; Revised: February 22, 2024; Accepted: March 7, 2024

Whole Genome Sequencing of a Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Strain SA492 Isolated from a Patient in Korean

Ji Heon Park, Gi Yong Lee, Ji Hyun Lim, and Soo-Jin Yang*

Department of Veterinary Microbiology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea

Correspondence to :
Soo-Jin Yang,        soojinjj@snu.ac.kr

Methicillin-resistant Staphylococcus aureus (MRSA) represents antimicrobial-resistant bacteria that can cause a wide range of illnesses both in humans and animals. Multidrug resistance phenotype is common, especially in healthcare-associated (HA) MRSA strains. Currently, one of the most prevalent HA-MRSA clonal lineages in Korean hospitals is sequence type (ST) 5 carrying staphylococcal cassette chromosome mec type II (ST5-SCCmec II). Here, we report the complete genome sequence of an ST5 HA-MRSA strain (SA492) originated from a patient in Korea.

Keywords: Staphylococcus aureus, HA-MRSA, sequence type 5

Staphylococcus aureus is an opportunistic human and animal pathogen capable of causing a wide spectrum of clinical and subclinical disease [1, 2]. One of the most significant healthcare-associated (HA) MRSA lineages in Korea is sequence type (ST) 5 carrying staphylococcal cassette chromosome mec type II (ST5-SCCmec II) [3]. Here, we report the complete genome sequence of an ST5-SCCmec II strain, SA492, isolated from a tertiary hospital in Korea.

HA-MRSA SA492, a clinical bloodstream isolate, was kindly provided from the Asian Bacterial Bank of Asia Foundation for Infectious Disease in Korea [4]. Genomic DNA was extracted using a Genenmed Kit (Seoul, Korea). Whole genome sequence data were generated by hybrid sequencing using Oxford Nanopore MinION (Oxford Nanopore Technologies, UK) and Illumina iSeq platforms (Illumina, USA). Basecalling of Nanopore data and removal of low-quality data were performed with Guppy v3.1.5. and NanoFilt v2.8.0 (remove Q score < 7 with minimum length 1,000), respectively. Adapters and low-quality reads for Illumina data were eliminated by Trimmomatic v0.39 (remove Q score < 20). De novo assembly of Nanopore and Illumina data was carried out with Unicycler v0.4.8. software. Rapid Annotation using Prokka v1.14.6 and Subsystem Technology (RAST) v.2.0 were used to annotate the complete sequence of SA492 strain.

The resulting genome was 2,856,680 bp in length with 90× genome coverages, which were comprised of one large circular chromosome (32.91% G+C content) with no plasmid. The complete genome sequence of SA492 was submitted to the GenBank sequence database and accession number of CP101314 has been assigned. The average nucleotide identity (ANI) value obtained by comparing the sequence data to previously published sequences of the ST5 HA-MRSA NCCP14562 strain was 99.80% [5].

In silico genotype analysis was conducted using Center for Genomic Epidemiology (CGE) software for SCCmec, multilocus sequence type (MLST), agr, and spa types. SA492 strain was identified as ST5-SCCmec II with agr II and spa type t2460 (Table 1). Genetic factors for antimicrobial resistance and pathogenicity were identified by integrative data from BLAST search and ResFinder (https://cge.food.dtu.dk/services/ResFinder/) of CGE. ResFinder analysis revealed three ARGs correspond to the resistance phenotypes to b-lactams, erythromycin, and tetracycline: mecA, ant(9)-Ia, erm(A), and tet(M). Moreover, virulence genes encoding aureolysin (aur), serine protease (splA and splB), gamma-hemolysin complements (hlgABC), leukocidin E and D (lukED), toxic shock syndrome toxin-1 (tst1), and staphylococcal enterotoxins (sec, seg, sei, sel, sem, sen, seo, and seu) were identified in the SA492 genome.

Table 1 . Comparison of genetic characteristics of SA492 and NCCP14562 strains.

StrainSA492NCCP14562
Genome size (bp)2,856,6802,910,941
G+C content (%)32.932.9
Coverage9021-22
MLSTST5ST5
SCCmec typeIIII
spa typet2460t002
agr typeIIII
ARGsant(9)-la , erm(A), mecA, tet(M)ant(9)-la , erm(A), mecA, tet(M)
Virulence genesgamma hemolysin (hlgA, hlgB, hlgC)gamma hemolysin (hlgA, hlgB, hlgC)
LukED (lukD, lukE)LukED (lukD, lukE)
auraur
serine protease (splA, splB)serine protease (splA, splB)
SEs (sec, seg, sei, sel, sem, sen, seo, seu)SEs (sec, seg, sei, sel, sem, sen, seo, seu)
tst1tst1
GenBank accession no.CP101314CP013953.1
Referencein this study[5]

This study was supported by Ministry of Food and Drug Safety (Project No. 23194MFDS012).

The authors have no financial conflicts of interest to declare.

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