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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2023; 51(3): 293-295

Received: August 16, 2023; Revised: September 11, 2023; Accepted: September 20, 2023

Complete Genome Sequence of an optrA-positive Linezolid-resistant Staphylococcus rostri Strain PJFA-333 Isolated from a Pig in Korea

Gi Yong Lee 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,

Linezolid, the first oxazolidinone introduced into human clinical use, has become a last resort antibiotic in treatment of serious infections caused by Gram-positive pathogens, including methicillin-resistant staphylococci and vancomycin-resistant enterococci. Although oxazolidinones are strictly prohibited for use in food-producing animals, occurrence of linezolid-resistant staphylococci has recently been reported in livestock farms in Korea. Here, we report the complete genome sequence of an optrA-positive linezolid-resistant Staphylococcus rostri strain PJFA-333 isolated from a pig farm in Korea.

Keywords: Staphylococcus rostri, linezolid resistance, optrA

Emergence of linezolid resistance in Staphylococcus spp. isolated from livestock farms has become a significant threat to public health [1]. Linezolid resistance in staphylococci has frequently been associated with acquisition of the transferable oxazolidinone gene, cfr [2]. Recently, a novel oxazolidinone-phenicol resistance gene, optrA, has also been detected in enterococcal and staphylococcal isolates of humans and animals [3]. In the current report, we present the complete genome sequencing results of an optrA-positive linezolid-resistant Staphylococcus rostri PJFA-333 strain isolated from a pig in Korea.

A linezolid-resistant S. rostri PJFA-333 strain was isolated from a nasal swab sample obtained from a finishig pig in Jeolla-do, Korea. For whole-genome sequencing analysis, genomic DNA sample of the PJFA-333 strain was prepared using the Wizard Genomic DNA Kit (Promega, USA) according to the manufacture’s recommendation. Genome sequence libraries were constructed by a combination of Illumina iSeq (Illumina, USA) and Oxford Nanopore MinION (Oxford Nanopore Technologies, UK) sequencing platforms. Trimmed and filtered high-quality reads of Nanopore and Illumina sequence data were assembled de novo using the Unicycler v.0.5.0 software. The assembled PJFA-333 genome revealed a genome size of 2,390,967 bp (G+C content of 38.4%), which contained seven contigs. The seven contigs were comprised of a single large chromosome of 2,337,213 bp and six plasmids (Table 1). The complete sequence was annotated using Rapid Annotation using Subsystem Technology (RAST) v.2.0 [4] and Prokka v.1.14.6 [5]. The sequence of a 16S rRNA gene extracted from the genome showed 100% sequence similarity to a S. rostri strain ARI 262T (GenBank Accession No. FM242137). Genomic comparison with a previsouly published sequences of S. rostri strain DSM 21968 (GenBank Accession No. GCA_002902145.1) resulted in 99.8% average nucleotide identity (ANI) value calculated by OrthoANIu algorithm [6]. Analysis of antimicrobial resistance genes in PJFA-333 strains was carried out using ResFinder ( of Center for Genomic Epidemiology and BLAST search. Standard antimicrobial susceptibility tests [7] of PJFA-333 strain revealed resistance phenotypes to chloramphenicol, clindamycin, linezolid, and tetracycline. BLAST anaylsis of the genome also identified various antimicrobial resistance genes [mecA, vga(A)V, bleO, ant(9)-la, cfr, optrA, fexA, and tet(M)]. The two oxazolidinone resistance genes, cfr and optrA, were located on a 36-kb plasmid pSR7-1 and 8 kb-plasmid pSR7-2, respectively. Moreover, the florfenicol resistance gene, fexA, was co-localized with cfr on the pSR7-1.

Table 1 . Genetic characteristics of the linezolid-resistant S. rostri PJFA-333 strain.

Genetic featuresPJFA-333
Antimicrobial resistanceaCHL-CLI-LZD-TET
Genome size2,390,967 bp
GC content38.4%
No. of contigs (bp, G+C contet, and CDS)7
Chromosome2,337,213 bp; 38.5%; 2,239
PlasmidspSR7-1 (36,227 bp; 32.8%; 40)
pSR7-2 (8,025 bp; 32.4%; 9)
pSR7-3 (4,047 bp; 29.1%; 4)
pSR7-4 (2,706 bp; 27.2%; 3)
pSR7-5 (1,491 bp; 32.9%; 2)
pSR7-6 (1,258 bp; 33.8%; 2)
No. of RNAs76 (tRNA, 57 ; and rRNA, 19)
Antimicrobial resistance genes (location)mecA (chrb); tet(M) (chr); vga(A)V (chr); cfr (pSR7-1); fexA (pSR7-1); bleO (pSR7-2); ant(9)-la (pSR7-2); optrA (pSR7-2)
GenBank accession numbersCP113107 (Chr)
pSR7-1 (CP113108), pSR7-2 (CP113109), pSR7-3 (CP113110), pSR7-4 (CP113111), pSR7-5 (CP113112), pSR7-6 (CP113113)

aCHL, chloramphenicol; CLI, clindamycin; LZD, linezolid; and TET, tetracycline

CDS, coding sequence; chr, chromosome

The complete genome sequences of the PJFA-333 strain (CP113107) and the six plasmids (CP113108 - CP113113) have been deposited in the GenBank sequence database.

This study was supported by grants from Research of Korea Centers for Disease Control and Prevention (2020ER540500) and Ministry of Food and Drug Safety (23194MFDS012).

The authors have no financial conflicts of interest to declare.

  1. Lee GY, Kim GB, Yang SJ. 2022. Co-occurrence of cfr-mediated linezolid-resistance in ST398 LA-MRSA and non-aureus staphylococci isolated from a pig farm. Vet. Microbiol. 266: 109336.
    Pubmed CrossRef
  2. Schwarz S, Werckenthin C, Kehrenberg C. 2000. Identification of a plasmid-borne chloramphenicol-florfenicol resistance gene in Staphylococcus sciuri. Antimicrob. Agents Chemother. 44: 2530-2533.
    Pubmed KoreaMed CrossRef
  3. Wang Y, Lv Y, Cai J, Schwarz S, Cui L, Hu Z, et al. 2015. A novel gene, optrA, that confers transferable resistance to oxazolidinones and phenicols and its presence in Enterococcus faecalis and Enterococcus faecium of human and animal origin. J. Antimicrob. Chemother. 70: 2182-2190.
    Pubmed CrossRef
  4. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42: D206-214.
    Pubmed KoreaMed CrossRef
  5. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30: 2068-2069.
    Pubmed CrossRef
  6. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110: 1281-1286.
    Pubmed CrossRef
  7. Clinical, Laboratory Standards Institute (CLSI). 2022. Performance Standards for Antimicrobial Susceptibility Testing M100 32th edition.

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