Non-typhoidal Salmonella enterica serovar Typhimurium is the primary causative agent of acute foodborne diseases in humans worldwide (Wang et al., 2019). At food production or distribution stage, Salmonella serovars originating from food animals such as swine and poultry have been identified (Yuan et al., 2018). Recently, plasmids larger than 200 kb carrying antimicrobial resistance genes have been spreading in food-borne Salmonella (Lin et al., 2015). A rectal swab specimen from a 5-week-old piglet in Korea was used to isolate S. Typhimurium strain Z01323SSL0063. Cultivation of Salmonella followed the Food Code provided by the Ministry of Food and Drug Safety (Korea). Rappaport-Vassiliadis Salmonella Enrichment broth (Difco) was employed to suspend the fecal swab and cultivation was performed under aerobic conditions at 42°C for 48 h. Rambach agar (CHROMagar) was used to obtain a single colony from the culture. After cultivation at 37°C for 24 h, single violet colonies were streaked onto MacConkey agar (Difco) to verify the genus. Genomic DNA was extracted from the strain Z01323SSL0063 using a DNasey Blood and Tissue kit (QIAGEN). The genome sequencing was conducted in Macrogen Inc. and our laboratory. Two next-generation sequencing (NGS) platforms were used to obtain the complete genome of the Z01323SSL0063 strain. HiSeq X (Illumina) was used for short-read sequencing (Macrogen Inc.), and a MinION sequencer equipped with a Flow Cell R10 Version (Oxford Nanopore Technologies) was employed for long-read sequencing. The NGS results included 10,384,690 short-reads and 590,995 long-reads, respectively. Trimmomatic (v.0.39) (Chen et al., 2020) was used to trim the adapter/primer and low-quality sequences from the generated short-read raw data. In contrast, the obtained long-read raw sequences were trimmed for low-quality with Filtlong (v.0.2.0) and adapter sequence with Porechop (v.0.2.4) (Chen et al., 2020). Unicycler (v.0.4.9b) and Pilon (v.1.21) (Chen et al., 2020) were used for hybrid de novo assembly and polishing. Protein coding sequences were classified into cluster of orthologous genes (COGs)

functional categories using COGclassifier v.1.0.5 (https://github.com/moshi4/COGclassifier). The web-based analysis for potential virulence factors and antimicrobial resistance genes in the genome was conducted at the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) (Olson et al., 2023). The complete genome of the strain Z01323SSL0063 contained one circular chromosome (4,972,243 bp, 52.2% guanine-cytosine [GC] content) along with three plasmids designated as pZ1323SSL0063-1 (228,305 bp, 47.2% GC content), pZ1323SSL0063-2 (100,887 bp, 47.6% GC content), and pZ1323SSL0063-3 (4,473 bp, 53.8% GC content) (Table 1 and Fig. 1). In the genome, 5,389 protein coding sequences (CDSs) and 111 non-coding genes (22 rRNA and 89 tRNA) were identified. A total of 3,940 annotated proteins were assigned to the COGs database for functional categorization. The five most abundant COG categories were carbohydrate transport and metabolism (category K, 415 genes, 10.6%), amino acid transport and metabolism (category E, 354 genes, 9.0%), transcription (category K, 315 genes, 8.0%), cell wall/membrane/envelop biogenesis (category M, 304 genes, 7.7%), and energy production and conversion (category G, 285 genes, 7.2%) (Fig. 2). The plasmid pZ1323SSL0063-1 of the strain harbored multi-drug resistance genes; bla_CTX-M-65 (cefotaxime), bla_TEM-76 (ampicillin), bla_OXA-10 (cephalosporin and β-lactamase inhibitor combinations), aph(6)-Id (streptomycin), aph(3’)-Ia (kanamycin), aph(3’)-Ib (kanamycin), aadA (streptomycin and spectinomycin), aadA22 (streptomycin and spectinomycin), aac(3)-IV (apramycin), aph(4)-Ia (hygromycin B), arr2 (rifampicin), dfrA14 (trimethoprim), qnrS1 (quinolone), linG (lincosamide), tetC (tetracycline), and floR (phenicols).

Table 1

Genome features of Salmonella enterica serovar Typhimurium strain Z01323SSL0063

Properties	Chromosome		Plasmids
	Z1323SSL0063		pZ1323SSL0063-1	pZ1323SSL0063-2	pZ1323SSL0063-3
Accession no.	CP133183		CP133184	CP133185	CP133186
Genome size (bp)	4,972,243		228,305	100,887	4,473
GC content (%)	52.2		47.2	47.6	53.8
No. of CDSs	4,972		294	119	4
rRNA genes	22		ND	ND	ND
tRNA genes	86		ND	3	ND

ND, not detected.

Fig. 1. The genome of Salmonella Typhimurium strain Z01323SSL0063. CDS-FWD, forward strand coding sequences; CDS-REV, reverse strand coding sequences; AMR, antimicrobial resistance; VF, virulence factor; GC, guanine (G) and cytosine (C).

Fig. 2. COG (Cluster of Orthologous Group) functional categories of predicted protein coding sequences in the genome of Salmonella Typhimurium strain Z01323SSL0063.

Nucleotide sequence and strain accession numbers

The strain is available at the Korean Collection for Type Cultures (KCTC) under deposition number BP1918528. The genome of strain Z01323SSL0063 has been deposited in GenBank/EMBL/DDBJ under the accession numbers, CP133183 (chromosome), CP133184 (plasmid-1), CP133185 (plasmid-2), and CP133186 (plasmid-3), respectively.

다제내성 Salmonella Typhimurium Z01323SSL0063 균주는 돼지 분변으로부터 분리되었다. Z01323SSL0063 균주의 유전체는 긴 염기서열과 짧은 염기서열을 혼합 조립하여 결정되었다. 유전체는 4,972,243 bp 크기(52.2% GC 비율)의 염색체 1개와 228,305 bp 크기(47.2% GC 비율)의 pZ1323SSL0063-1, 100,887 bp 크기(47.6% GC 비율)의 pZ1323SSL0063-2, 4,473 bp 크기(53.8% GC 비율)의 pZ1323SSL0063-3으로 구성된 플라스미드 3개로 분석되었다. 이 유전체에는 5,266개의 단백질 암호화 염기서열, 22개의 rRNA 유전자, 89개의 tRNA 유전자가 포함되어 있었다. Z01323SSL0063 균주의 ampicillin, cefotaxime, streptomycin, kanamycin, fluoroquinolone, rifampin, chloramphenicol, lincosamide, trimethoprim, tetracycline에 대한 내성은 플라스미드 pZ1323SSL0063-1에 존재하는 항생제 내성유전자들로부터 기인되었다.

This study was supported by grants of Korea Disease Control and Prevention Agency (2022-ER2103-01 and 2024-ER2103-00) and Ministry of Food and Drug Safety (23194MFDS012).

Jong-Chan Chae is Editor of KJM. He was not involved in the review process of this article. Also, authors have no conflicts of interest to report.