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Complete genome sequence of the enterotoxigenic Escherichia coli MFDS1016424 isolated from a spicy squid salad
Korean J. Microbiol. 2023;59(1):52-54
Published online March 31, 2023
© 2023 The Microbiological Society of Korea.

Min-Hee Kim1†, Iseul Choi2†, Eunsu Ha2, Woojung Lee1, Eun Sook An1, Seung Hwan Kim1, Jinho Choi2*, and Soon Han Kim1*

1Food Microbiology Division, Ministry of Food and Drug Safety, Osong, Cheongju 28159, Republic of Korea
2Sanigen Co., Ltd, Anyang 14059, Republic of Korea
Correspondence to: *(J. Choi) E-mail:; Tel.: +82-70-5221-1763; Fax: +82-2-573-3134 / (S.H. Kim) E-mail:; Tel.: +82-43-719-4301; Fax: +82-43-719-4300
These authors contributed equally to this work.
Received February 7, 2023; Revised March 23, 2023; Accepted March 23, 2023.
Escherichia coli is an infectious food-borne pathogen that causes major public health problems. This study presents the complete genome sequence of E. coli strain MFDS1016424, isolated from a spicy squid salad sample in 2020 from a school cafeteria in Gyeongju, South Korea. The entire genome sequence of E. coli MFDS1016424 consisted of a 4,837,116 bp chromosome and an 88,935 bp plasmid, with 50.5% and 46.5% G + C content, respectively. Gene prediction revealed that this strain possessed 4,673 coding sequence (CDSs), 88 tRNAs, 22 rRNAs. The several virulence properties were detected including the heat-labile toxins.
Keywords : Escherichia coli, complete genome sequencing, spicy squid salad

Escherichia coli is a Gram-negative bacterium belonging to the family Enterobacteriaceae. Enterotoxigenic E. coli (ETEC) can produce a heat-stable toxin (ST; including two subtypes, STh and STp) and/or heat-labile toxin (LT) (Qadri et al., 2005). ETEC is the most common cause of diarrhea in children, adults, and travelers (Gaastra et al., 1996). This study elucidates the complete genome sequence of an uncommon ETEC strain collected from Gyeongju, South Korea, in 2020.

ETEC MFDS1016424 was detected and isolated from a food poisoning investigation managed by the Ministry of Food and Drug Safety (MFDS, South Korea) after reported food poisoning accidents in Gyeongju, 2020. Strain MFDS1016424 was isolated from a spicy squid salad.

Strain MFDS1016424 was incubated overnight on tryptic soy agar at 37°C. Genomic DNA was extracted using an AccuPrep® Genomic DNA Extraction Kit (Bioneer) following the manufacturer’s instructions. The extracted DNA was quantified using a NanoDrop 2000 UV-visible spectrophotometer (Thermo Fisher Scientific) and a Qubit 3.0 Fluorometer (Thermo Fisher Scientific).

Genome sequencing was performed using two sequencing techniques, Illumina MiSeq and Nanopore. For MiSeq sequencing, library preparation was performed using the Nextera DNA Flex Library Prep kit (Illumina) according to the manufacturer’s instructions. Libraries were sequenced using the MiSeq Reagent Kit v3 (600-cycles) in a MiSeq system using 2 × 300-bp pair-ends. After sequencing, the individual sequence reads were analyzed using FastQC-v.0.11.8. The total number of reads produced was 2,075,252 (total number of bases, 537,350,665; genome coverage, 107.7×; N50, 161,724 bp). For nanopore sequencing, the Oxford Nanopore Rapid Barcoding Kit (Oxford Nanopore Technologies) was used for library construction. Nanopore sequencing data were based on the guppy_barcoder v6.0.1. The total number of reads produced was 155,272 (total number of bases, 625,098,064; genome coverage, 119.9×). Illumina and nanopore sequencing data were processed and de novo assembled with Unicycler v0.4.8, using the Pathosystems Resource Integration Center (PATRIC) v3.6.12 web server; the genome was annotated using RASTtk (Brettin et al., 2015). Virulence-associated genes were predicted using the Virulence Factor Database (VFDB) (Liu et al., 2019) and PATRIC_VF (Snyder et al., 2007). Default parameters were used for all software unless otherwise specified. The complete genome sequence of strain MFDS1016424 was 4,837,116 bp in length with a GC content of 50.5%. A total of 4,673 genes are predicted (Table 1). ETEC are defined as containing a heat-stable toxin (ST) and/or heat-labile toxin (LT). The genome of ETEC MFDS1016424 revealed that the heat-labile toxin subunit A and subunit B were detected in the bacterium’s plasmid. Additionally, the ETEC MFDS1016424 genome contained several genes related to virulence properties, such as biofilm formation (kbaY; OEG87_ 02945, csgB; OEG87_14050, and gatB; OEG87_08325), capsule biosynthesis (etk: OEG87_14325, etp; OEG87_14320), and invasion genes (relA; OEG87_04870, dam; OEG87_01795) (Table 2). This work would be useful for investigating potential possibilities for understanding food-borne pathogens and providing a genetic basis for a more detailed analysis of virulence factors.

Genome features of ETEC MFDS1016424
Genomic features Value
Contig 2 (1 chromosome and 1 plasmid)
Genome size (bp) 4,837,116
Plasmid size (bp) 88,935
GC contents (%) 50.5
Total number of CDSs 4,673
tRNA genes 88
rRNA genes 22

Genes related to virulence properties of ETEC MFDS1016424
Classification Gene(s) Predicted function Reference
Biofilm formation kbaY Ketose–bis–phosphate aldolase, tagatose–bisphosphate aldolase; part of aga cluster for K1 transport Berlyn et al. (1998)
csgB Curlin nucleator protein, homology with major curlin Berlyn et al. (1998)
gatB Galactitol-specific enzyme IIB of PTS Berlyn et al. (1998)
Capsule biosynthesis etk An inner membrane protein that catalyses tyrosine autophosphorylation and phosphorylation of a synthetic co-polymer poly (Glu:Tyr) Ilan et al. (1999)
etp Phosphotyrosine–protein phosphatase and involved in capsule formation Vincent et al. (2000)
Invasion relA Required for ppGpp synthesis during stringent response to amino acid starvation; ATP:GTP 3′-pyrophosphotransferase Berlyn et al. (1998)
dam DNA adenine methylase Berlyn et al. (1998)

Nucleotide sequence and strain accession numbers

Nucleotide sequence accession numbers. The complete genome sequence of Escherichia coli MFDS1016424 has been deposited at the NCBI GenBank database under the accession numbers CP106924 (chromosome, MFDS1016424), CP106925 (plasmid, pMFDS1016424). The strain has been deposited in the Korean Culture Collection for foodborne Pathogens under the strain number MFDS1016424.

적 요

대장균은 주요 공중 보건 문제를 일으키는 전염성 식품 매개 병원균 중 하나이다. 본 연구에서는 2020년 경주에 있는 한 고등학교 교내 식당에서 일어난 식중독 사고의 원인 식품으로 추정되는 오징어 진미 야채 초무침으로부터 분리된 Escherichia coli (MFDS1016424)의 유전체 분석을 수행하였다. Escherichia coli MFDS1016424는 4,837,116 bp 길이의 chromosome 과 88,935 bp 길이의 plasmid 로 구성되어 있으며, 각각의 G + C contents는 50.5%와 46.5%로 확인되었다. 유전자 예측 결과, 4,673개의 CDS, 88개의 tRNA, 22개의 rRNA를 가지고 있는 것으로 확인되었다. 또한, 이열성 독소를 포함한 병원성 유전자들이 확인되었다.


This research was financially supported by the Ministry of Food and Drug Safety, Republic of Korea (20161MFDS030, 21162MFDS027).

Conflict of Interest

There are no conflicts of interest to declare.

  1. Berlyn MK. 1998. Linkage map of Escherichia coli K-12, edition 10: the traditional map. Microbiol. Mol. Biol. Rev. 62, 814-984.
    Pubmed KoreaMed CrossRef
  2. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, and Pusch GDPusch GD, et al. 2015. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci. Rep. 5, 8365.
    Pubmed KoreaMed CrossRef
  3. Gaastra W and Svennerholm AM. 1996. Colonization factors of human enterotoxigenic Escherichia coli (ETEC). Trends Microbiol. 4, 444-452.
    Pubmed CrossRef
  4. Ilan O, Bloch Y, Frankel G, Ullrich H, Geider K, and Rosenshine I. 1999. Protein tyrosine kinases in bacterial pathogens are associated with virulence and production of exopolysaccharide. EMBO J. 18, 3241-3248.
    Pubmed KoreaMed CrossRef
  5. Liu B, Zheng D, Jin Q, Chen L, and Yang J. 2019. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res. 47, D687-D692.
    Pubmed KoreaMed CrossRef
  6. Qadri F, Svennerholm AM, Faruque AS, and Sack RB. 2005. Enterotoxigenic Escherichia coli in developing countries: epidemiology, microbiology, clinical features, treatment, and prevention. Clin. Microbiol. Rev. 18, 465-483.
    Pubmed KoreaMed CrossRef
  7. Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, and Yoo HYoo H, et al. 2007. PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res. 35, D401-D406.
    Pubmed KoreaMed CrossRef
  8. Vincent C, Duclos B, Grangeasse C, Vaganay E, Riberty M, Cozzone AJ, and Doublet P. 2000. Relationship between exopolysaccharide production and protein-tyrosine phosphorylation in Gram-negative bacteria. J. Mol. Biol. 304, 311-321.
    Pubmed CrossRef

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