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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2024; 52(3): 325-327

https://doi.org/10.48022/mbl.2406.06004

Received: June 9, 2024; Revised: July 12, 2024; Accepted: July 15, 2024

Complete Genome Sequence of an ESBL-producing Salmonella Infantis Strain IJCS5-22 that Harbors blaCTX-M-65 Isolated from Retail Chicken Meat in Korea

Yeon A Kim1 and Kun Taek Park1,2*

1Department of Digital Anti-aging and Healthcare, Inje University, Gimhae 50834, Republic of Korea
2Department of Biological Sciences, Inje University, Gimhae 50834, Republic of Korea

Correspondence to :
Kun Taek Park,      ktpark@inje.ac.kr

Abstract

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We report the complete genome sequence of an extended-spectrum beta-lactamase-producing Salmonella enterica subsp. enterica Serovar Infantis strain IJCS5-22 that harbors blaCTX-M-65, which was isolated from whole chicken meat purchased from a retail market in South Korea. The assembled IJCS5-22 genome comprised a 4,727,133 bp circular chromosome and a 318,349 bp plasmid that encoded several antimicrobial resistance genes, including blaCTX-M-65, with 52.27% and 50.39% GC contents, respectively.

Keywords: Salmonella enterica Infantis, blaCTX-M-65, extended spectrum beta-lactamase, retail chicken meat

Body

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Salmonella is a major gastroenteritis causing (e.g., salmonellosis) food-borne pathogen in humans that has a significant impact on public health [1]. Salmonella infections are associated with consumption of contaminated foods, particularly poultry products [2, 3]. While third-generation cephalosporins and fluoroquinolones have been used to effectively treat salmonellosis, the emergence of antibiotic-resistant Salmonella, including extended-spectrum beta-lactamase (ESBL)-producing Salmonella in recent years, has become a major concern worldwide [4, 5]. Salmonella enterica subsp. enterica serovar Infantis is one of the most common serovars causing human salmonellosis worldwide. The emergence of S. Infantis harboring blaCTX-M-65 in the mega plasmid, named as plasmid of emerging S. Infantis (pESI), is associated with ESBL-producing phenotypes [6−8]. We report the complete genome sequence of the ESBL-producing S. Infantis strain IJCS5-22, which was isolated from whole chicken meat purchased from a retail market in South Korea following the Food Code isolation protocol [9]. Antimicrobial susceptibility test was performed against 16 antimicrobials using the SentititreTM KRNV6F kit (Thermo Fisher Scientific, USA). Minimum inhibitory concentration was determined by the Clinical and Laboratory Standards Institute criteria [10]. The genomic DNA of the strain was extracted using Nucleo Spin® Microbial DNA mini kit (Macherey-Nagel, Germany). Genome sequencing of the IJCS5-22 strain was performed by Illumina NextSeq and Nanopore sequencing techniques. Library preparation was performed using the TruSeq Nano DNA Prep Kit (Illumina, USA) as per the manufacturer’s instructions for NextSeq sequencing. Libraries were sequenced using NextSeq P1 600 cycles in a NextSeq2000 system using 2x 300bp pair-ends, and individual sequence reads were analyzed using FastQC (v.0.11.8). A library was constructed using a ligation sequencing kit (Oxford Nanopore Technologies, UK), and sequencing data were based on the guppy (v.4.2.2) for nanopore sequencing. All sequencing data were processed for de novo genome assembly using Unicycler (v.0.5.0) and annotated with Prokka (v.1.14.6). The serotype and sequence type (ST) of IJCS5-22 were confirmed using MLST (v.2.23.0) and Seqsero2 (v.1.2.1). Virulence factor Database (VFDB, http://www.mgc.ac.cn/cgi-bin/VFs/v5/main.cgi) was used for the detection of virulence genes. Antimicrobial resistance genes (ARGs) were identified using NCBI AMRFinderPlus (v.3.11.26). The complete genome of the IJCS5-22 strain was found to comprise one circular chromosome (4,727,133 bp, 52.27% guanine-cytosine [GC] content) and one plasmid, designated as pIJCS5-22 (318,349 bp, 50.39% GC content) (Table 1). The complete genome of the strain IJCS5-22 encoded 4,725 protein-coding sequences (CDSs) and 108 non-coding genes (22 rRNA and 86 tRNA genes). Further, the IJCS5-22 strain was identified as ST32, and the predicted serotype was S. Infantis (antigenic formula: 7:r:1,5). Comparative genomic analysis of publicly available sequences of S. Infantis was conducted using FastANI (v.1.3.3). The average nucleotide identity (ANI) value of the chromosome of IJCS5-22 in comparisons with the sequence data of S. Infantis strain Z1323CSL0002 (GenBank accession No. CP148836.1) was calculated to be 99.99%. A total of 158 virulence genes were detected in IJCS5-22 (Supplementary material). Most of the virulence genes were located in the chromosome, whereas 12 yersiniabactin genes (irp1, irp2, fyuA/psn, fyuA, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX) were present in the plasmid pIJCS5-22. Several ARGs related to aminoglycoside (aadA1, aph(4)-Ia, aac(3)-Iva, aph(3')-Ia), beta-lactams (blaCTX-M-65), sulfonamide (sul1), tetracycline (tet(A)), phenicol (floR), trimethoprim (dfrA14) and the point gyrA mutation (D87Y) were identified in IJCS5-22, and these genotypes were corresponding to the observed resistance phenotype (Table 1) [8]. While most ARGs were present in plasmids, mdsB, mdsA, and gyrA point mutations were detected in the IJCS5-22 chromosome. The complete genome sequence of S. Infantis strain IJCS5-22 was deposited in the NCBI GenBank sequence database under the accession numbers, CP157394.1 (chromosome) and CP157395.1 (plasmid).

Table 1 . Genomic features of S. Infantis strain IJCS5-22.

Genome featuresValue
Number of contigs2
Chromosome size (bp)4,727,133 (Chromosome), 318,349 (Plasmid)
GC contents (%)52.27 (Chromosome), 50.39 (Plasmid)
Coding genes (CDSs)4,403 (Chromosome), 322 (Plasmid)
Transfer RNAs (tRNAs)86 (Chromosome)
Ribosomal RNAs (rRNAs)22 (Chromosome)
MLSTaST32b
Antimicrobial resistance phenotypescAMP-CHL-CTX-FIS-GEN-NAL-STRSXT- TET
Antimicrobial resistance genesmdsB, mdsA, gyrA_D87Y, aadA1, sul1, tet(A), blaCTX-M-65, floR, aph(4)-Ia, aac(3)-Iva, dfrA14, aph(3')-Ia

aMLST, multilocus sequence typing.

bST, sequence type.

cAMP, ampicillin; CHL, chloramphenicol; CTX, cefotaxime; FIS, sulfisoxazole; GEN, gentamicin; NAL, nalidixic acid; STR, streptomycin; SXT, trimethoprim/sulfamethoxazole; TET, tetracycline.

Acknowledgments

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This study was supported by a grant from the Ministry of Food and Drug Safety (22192MFDS021) of the Republic of Korea.

Conflict of Interest

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The authors have no financial conflicts of interest to declare.

References

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