RESEARCH ARTICLE

Complete chromosome and plasmid sequences of Staphylococcus aureus strain JDFM SA01, isolated from a milk filter in Korean dairy farm

Sangdon Ryu1https://orcid.org/0000-0001-5338-8385, Donghyun Shin2https://orcid.org/0000-0002-0819-0553, Jaeyoung Heo3https://orcid.org/0000-0002-9721-8043, Seong-Yeop Jeong4https://orcid.org/0000-0001-8995-9901, Do-Youn Jeong4https://orcid.org/0000-0003-4105-1624, Bohyun Yun1https://orcid.org/0000-0001-6723-5849, Minkyoung Kang5https://orcid.org/0000-0002-2366-7970, Younghoon Kim6,#,*https://orcid.org/0000-0001-6769-0657, Sangnam Oh5,#,*https://orcid.org/0000-0002-2428-412X
Author Information & Copyright
1Department of Animal Science and Institute of Milk Genomics, Jeonbuk National University, Jeonju 54896, Korea
2The Animal Molecular Genetics and Breeding Center, Jeonbuk National University, Jeonju 54896, Korea
3International Agricultural Development and Cooperation Center, Jeonbuk National University, Jeouju 54896, Korea
4Microbial Institute for Fermentation Industry, Sunchang 56048, Korea
5Department of Functional Food and Biotechnology, Jeonju University, Jeonju 55069, Korea
6Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea

#These authors contributed equally to this work.

*Corresponding author: Younghoon Kim, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea. Tel: +82-2-880-4808, E-mail: ykeys2584@snu.ac.kr
*Corresponding author: Sangnam Oh, Department of Functional Food and Biotechnology, Jeonju University, Jeonju 55069, Korea. Tel: +82-63-220-3109, E-mail:osangnam@jj.ac.kr

© Copyright 2020 Korean Society of Animal Science and Technology. This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Received: Mar 18, 2020; Revised: Mar 19, 2020; Accepted: Mar 19, 2020

Published Online: May 31, 2020

Abstract

Staphylococcus aureus is a significant pathogen that can source a variety of illness worldwide. In this announcement, we report here the complete genome sequence of S. aureus strain JDFM SA01, isolated from a milk filter collected from Korean dairy farm. The final complete genome assembly consists of one circular chromosome (2,748,925 bp) with an overall GC content of 32.9% and one circular plasmid sequence (24,655 bp) with a GC content of 28.7%.

Keywords: Staphylococcus aureus strain JDFM SA01; Dairy farm; Whole genome sequencing

Staphylococcus aureus is a Gram-positive bacteria that is detected in the environment and also existing in normal human microbiome [1]. In addition, this bacterium is a representative bacterial human pathogen and contaminated with food through purulent wounds of humans and animals. Particularly, methicillin-resistant S. aureus (MRSA) has appeared as a significant issue, with important anxieties about public health because they can spread easily through healthy carriers and increase the likelihood of infection by expressing a number of toxic factors, cell wall-related adecines and secreted exoproteins [2]. Therefore, monitoring of S. aureus in a dairy environment with high sensitivity is very important for ensuring milk quality and food safety [3].

Table 1. Genome features of Staphylococcus aureus strain JDFM SA01
Name Length (bp) GC (%) Depth CDSs tRNA rRNA
Chromosome 2,748,925 32.9 408 2,520 61 19
Plasmid 24,655 28.7 323 29 0 0
Total 2,773,580 32.84 407 2,549 61 19

CDSs, coding DNA sequences.

Download Excel Table
jast-62-3-423-g1
Fig. 1. Circular chromosome and plasmid maps of Staphylococcus aureus strain JDFM SA01. Marked characteristics are shown from outside to the center; coding DNA sequences (CDSs) on forward strand, CDS on reverse strand, tRNA, rRNA, GC content and GC skew. (A) Chromosome, (B) Plasmid.
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In the present study, S. aureus strain JDFM SA01 was isolated from a milk filter in Korean dairy farm (Jeollabuk-do; sampled during May 2017 to May 2018). The sample was added to 10% NaCl-added Tryptic Soy Broth (TSB) and incubated at 37°C for 24 h. The enrichment culture was inoculated onto Baird Parker (Oxoid) agar and cultured at 37°C for 24 h [4]. After incubation, a single colony, designated S. aureus strain JDFM SA01, was selected and routinely maintained on tryptic soy broth at 37°C for sequencing. Total genomic DNA was extracted using the PureHelixTM GenomicDNA prep kit (Nanohelix, Korea), according to the manufacturer’s instructions.

The whole genome of S. aureus strain JDFM SA01 was sequenced by using the Pacbio RS II (Pacific Biosciences, USA) / Illumina HiSeq (151 × 2 bp paired-end sequencing) platforms at Macrogen (Seoul, Korea). Library preparation for Illumina and PacBio sequencing was performed using the NEBNext Ultra DNA library prep kit for Illumina (NE, USA) and the PacBio DNA template prep kit 1.0 (Pacific Biosciences, USA), respectively, according to the manufacturers’ instructions. A total number of 179,260 reads with a mean subread length of 8,498 bases (N50, 12,066 bases) were obtained with PacBio sequencing, and 10,257,096 paired-end reads totaling 1,548,821,496 bp were obtained with Illumina sequencing. De novo assembly was carried out using the Hierarchical Genome Assembly Process v3.0 (HGAP3) with default options within SMRT Portal v2.3.0 software [1]. During the preassembly step, filtering and assembly were performed using preAssembler Filter v1 (minimum subread length, 500 bp; minimum polymerase read quality, 0.80; minimum polymerase read length, 100 bp) and preAssembler v2 (Minimum seed read length, 6,000 bp; number of seed read chunks, 6; alignment candidates per chunk, 10; total alignment candidates, 24; minimum coverage for correction, 6). The read quality was confirmed by aligning shorter reads on longer reads applying Basic Local Alignment with Successive Refinement v1 (BLASR) [5] and correcting errors using Pilon version 1.16 [6]. The chromosome and plasmid annotation performed using rapid prokaryotic genome annotation (Prokka) v1.12b [7].

The complete genome sequence of S. aureus strain JDFM SA01 consists of one circular chromosome (2,748,925 bp) with an overall GC content of 32.9% and one circular plasmid sequence (24,655 bp) with a GC content of 28.7%. A total of 2,549 predicted genes were identified on the genome, including 19 rRNA, 61 tRNA, and 2,520 coding DNA sequences (CDSs) from chromosome, while 29 CDSs were identified on the plasmid. The genomic information of S. aureus JDFM SA01 could be applied to develop new sanitation strategy for safe and high-quality dairy products.

Competing interests

No potential conflict of interest relevant to this article was reported.

Funding sources

This research was supported by the High Value-Added Food Technology Development Program of the Korean Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry, and Fisheries (iPET), the Ministry for Food, Agriculture, Forestry, and Fisheries of the Korea (318090-03-1-WT011) and Microbial Institute for Fermentation Industry (MIFI) through Establishment of Integrated Biobank for Agriculture, Food and Livestock Microbiome Project, funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA) (MIFI2020KMBB01).

Acknowledgements

Not applicable.

Availability of data and material

The complete genome sequences have been deposited in GenBank under the accession numbers CP032821 and CP032822 for the S. aureus strain JDFM SA01 chromosome and plasmid, respectively. The BioProject accession number is PRJNA491802, and the BioSample accession numbers are SAMN10147904 for S. aureus strain JDFM SA01.

Authors’ contributions

Conceptualization: Ryu S, Kim Y, Oh S.

Data curation: Ryu S, Shin D, Kim Y, Oh S.

Formal analysis: Ryu S, Shin D, Kim Y, Oh S.

Methodology: Ryu S, Kim Y, Oh S.

Software: Ryu S, Shin D, Kim Y, Oh S.

Validation: Ryu S, Kim Y, Oh S.

Investigation: Kim Y, Oh S.

Writing - original draft: Ryu S, Shin D, Heo J, Jeong SY, Jeong DY, Yun B, Kang M, Kim Y, Oh S.

Writing - review & editing: Ryu S, Shin D, Heo J, Jeong SY, Jeong DY, Yun B, Kang M, Kim Y, Oh S.

Ethics approval and consent to participate

This manuscript does not require IRB/IACUC approval.

REFERENCES

1.

Chu J, Vila-Farres X, Inoyama D, Ternei M, Cohen LJ, Gordon EA, et al. Discovery of MRSA active antibiotics using primary sequence from the human microbiome. Nat Chem Biol. 2016; 12:1004-6

2.

Rodvold KA, McConeghy KW. Methicillin-resistant staphylococcus aureus therapy: past, present, and future. Clin Infect Dis. 2014; 58:S20-7

3.

Yang Q, Zhang Y, Li S, Lu X, Yuan Y, Zhang W. Saltatory rolling circle amplification for sensitive visual detection of Staphylococcus aureus in milk. J Dairy Sci. 2019; 102:9702-10

4.

Lee JH, Song KY, Hyeon JY, Hwang IG, Kwak HS, Han JA, et al. Comparison of standard culture method and real-time PCR assay for detection of Staphylococcus aureus in processed and unprocessed foods. Food Sci Anim Resour. 2010; 30:410-8

5.

Chaisson MJ, Tesler G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics. 2012; 13:238

6.

Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLOS ONE. 2014; 9:e112963

7.

Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014; 30:2068-9

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