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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2023; 51(4): 542-544

https://doi.org/10.48022/mbl.2311.11008

Received: November 10, 2023; Revised: November 25, 2023; Accepted: November 30, 2023

Complete Genome of Methicillin-Resistant Staphylococcus pseudintermedius Z0118SP0130 Isolated from a Companion Dog

Haeseong Lee, Jae-Young Oh, and Jong-Chan Chae*

Division of Biotechnology, Jeonbuk National University, Iksan 54596, Republic of Korea

Correspondence to :
Jong-Chan Chae,       chae@jbnu.ac.kr

Abstract

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Methicillin-resistant Staphylococcus pseudintermedius Z0118SP0130 was isolated from eye specimen of a companion dog in South Korea. The complete genome of Z0118SP0130 consisted of a 2,663,277 bp chromosome and there was no plasmid. The strain was identified as the sequence type 45 and contained a mecA gene which comprised of staphylococcal cassette chromosome mec type Vb (5C2&5). Antimicrobial resistance to erythromycin, clindamycin, quinupristin-dalfopristin, trimethoprim-sulfamethoxazole, mupirocin, oxacillin, streptomycin, and gentamicin was observed in the strain.

Keywords: Staphylococcus pseudintermedius, companion dog, complete genome

Body

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Staphylococci is a normal flora in the skin of humans and other mammals. Among them, Staphylococcus pseudintermedius is a bacterium found in mucous membranes and skin of many mammals including companion animals [1]. The potential of animal disease caused by S. pseudintermedius was recently recognized because it was identified as S. intermedius until taxonomic assignment of the name was proposed [2]. The species exhibits phenotypic features similar to coagulase-positive S. intermedius and cause opportunistic infections in body tissues such as pyoderma and wound infections [1]. Although S. pseudintermedius was generally reported to be sensitive against antibiotics belonging to beta-lactam class in the past, methicillin-resistant S. pseudintermedius (MRSP) has been emerged and contains a mecA gene responsible for production of an altered penicillin binding protein organizing staphylococcal chromosomal cassette (SCCmec) [3]. MRSP infection has not only been increased in animals but also its animal-to-human transmission has been occurred causing public health problem [4, 5].

S. pseudintermedius Z0118SP0130 (KCTC 43165) was isolated from eye specimen of a companion dog and identified as sequence type 45. A sample swap was inoculated in CHROMagar Orientation (CHROMagar, France) and incubated at 30℃ for 48 h under aerobic condition. A single colony was isolated and identified as S. pseudintermedius by 16S rRNA gene comparison which showed 100% similarity to one of S. pseudintermedius strain 21-3929 (GenBank accession No. CP128234.1).

Antibiotic susceptibility testing was performed according to the Kirby-Bauer method. Twelve antibiotic discs (oxacillin, erythromycin, clindamycin, quinupristin/dalfopristin, trimethoprim/sulfamethoxazole, streptomycin, gentamicin, mupirocin, vancomycin, teicoplanin, linezolid, tigecycline) (Oxoid, UK) were placed on the Mueller Hinton agar (BD Difco, USA) medium using the disc dispenser (Oxoid) which was inoculated with the bacterial suspension diluted in saline solution. After incubating at 37℃ for 18 h, the disc zone diameter was measured with the SCAN 4000 equipment (Interscience, USA). Antibiotic resistance was determined according to the criteria of the Clinical and. Laboratory Standards Institute guidelines. The Z0118SP0130 strain was resistant to oxacillin, erythromycin, clindamycin, quinupristin-dalfopristin, trimethoprim-sulfamethoxazole, streptomycin, gentamicin, and mupirocin.

Genomic DNA of strain Z0118SP0130 was extracted with QIAamp DNA mini kit (Qiagen, Germany) from cells which were grown aerobically at 37℃ for 24 h in blood agar medium. Whole genome sequencing was conducted at Macrogen Inc. (Republic of Korea) using Pac-Bio RSII (PacBio, USA) and HiSeq X ten (Illumina, USA) platforms. The determined subreads exhibited about 217-fold coverage and only one contig of 2,663,277 bp was generated from them by assembly using Unicycler v0.4.8 [6]. Prokka v1.11 [7] was used for gene annotation which subsequently found 2,454 protein coding sequences (CDSs), 60 tRNA genes, and 19 rRNA genes as described in Table 1. The GC content of the genome was 37.50%. The circular genomic map was generated with genome circular viewer in PATRIC server (Fig. 1) [8]. The genomic distances between strain Z0118SP0130 and the related strains were measured with the online Average Nucleotide Identity calculator (CJ Bioscience, Republic of Korea). The values were 99.24% with S. pseudintermedius strain 21-3929 (GenBank accession No. CP128234.1) and 99.42% with S. pseudintermedius strain LMG 22219 (GenBank accession No. GCA_001792775.2).

Table 1 . Genome features of Staphylococcus pseudintermedius Z0118SP0130.

FeaturesValue
GenBank accession No.CP060700.1
No. of contigs1
Length (bp)2,663,277
G+C content (%)37.50
No. of CDSs2,454
No. of rRNA (5S, 16S, 23S) genes7, 6, 6
No. of tRNA genes60
No. of ncRNA genes4

CDSs, protein coding sequences
Figure 1.The genome of strain Z0118SP0130 generated using genome circular viewer in PATRIC server. Each color represents CDS (green and purple), AMR genes (red), GC contents (pink), genome size (blue), and non-coding sequences (cyan).

Investigation on antibiotic resistant genes in the genome was performed using the Comprehensive Antibiotic Resistance Database (CARD) v3.2.8 [9] and found the β-lactam antibiotics resistance genes (mecA, blaZ), tetracycline resistance gene (tetM), trimethoprim resistance gene (dfrG), streptogramin resistance gene (vatE), lincosamide resistance gene (lmrB), mupirocin resistance gene (ileS), erythromycin resistance gene (ermB), and aminoglycoside resistance genes [aad(6) and aac(6’)-Ie-aph(2’’)-Ia]. This was consistent with the result of antimicrobial susceptibility test.

A SCCmec responsible for methicillin resistance was found in the genome. The structure was closely similar to the SCCmec type Vb (5C2&5) identified in Staphylococcus aureus which consisted of insertion sequences IS431 and two ccrC1, cassette chromosome recombinase genes, on both sides of mecA gene (Fig. 2) [10].

Figure 2.The genetic structure of staphylococcal cassette chromosome mec (SCCmec). Staphylococcus pseudintermedius Z0118SP0130 had a similar structure to SCCmec V(5C2&5)b.

Nucleotide Sequence Accession Number

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The genome sequence of Staphylococcus pseudintermedius Z0118SP0130 has been deposited in NCBI GenBank under accession CP060700.1. The strain was deposited in KCTC under deposition number 43165.

Acknowledgments

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This work was supported by grants of Korea Disease Control and Prevention Agency (2022-ER2103-00) and Ministry of Food and Drug Safety (23194MFDS012).

Conflict of Interest

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The authors have no financial conflicts of interest to declare.

References

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