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Genome of Escherichia coli KCTC 72668 isolated from rectum of companion dog
Korean J. Microbiol. 2019;55(4):436-437
Published online December 31, 2019
© 2019 The Microbiological Society of Korea.

Kishor Sureshbhai Patil1, Haeseong Lee1, Hyeonbin Kim1, Seung Je Lee2, and Jong-Chan Chae1*

1Division of Biotechnology, Jeonbuk National University, Iksan 54596, Republic of Korea
2Jeonbuk Institute for Food-Bioindustry, Jeonju 54810, Republic of Korea
Correspondence to: *E-mail: chae@jbnu.ac.kr;
Tel.: +82-63-850-0840; Fax: +82-63-850-0834
Received October 24, 2019; Accepted November 15, 2019.
Abstract

Escherichia coli KCTC 72668 was isolated from rectum of companion dog. The draft genome of strain KCTC 72668 comprised of 5,215,239 bp with a G + C content of 50.7% which contained 5,688 predicted coding DNA sequences (CDS), 87 tRNA genes, and 22 rRNA genes. And the genome harbored two antibiotic resistance genes, ampC and bacA, corresponding to resistances against beta-lactam and bacitracin.

Keywords : Escherichia coli, companion dog, genome
Body

Companion animals such as dogs are treated with various antimicrobial agents and share the same habitats with humans allowing the chance to disseminate microorganisms between them (Tamang et al., 2012). Therefore, bacteria isolated from companion animals are recently attracting concerns in a view of public health including antibiotic resistance issue (Weese, 2008).

The genus Escherichia contains seven species Escherichia coli, Escherichia albertii, Escherichia blattae, Escherichia fergusonii, Escherichia hermanii, and Escherichia vulneris (Gaastra et al., 2014). E. coli is usually a commensal bacterium of humans and animals (Tadesse etal., 2012). It has been known as an opportunistic pathogen in different diseases (Sharma etal., 2017). E. coli is also one of the most frequently isolated bacterial pathogens in companion animal practice (Cummings etal., 2015). Whole-genome sequencing is considered essential in the epidemiological surveillance of antibiotic resistant strains circulating in different hosts to decipher their resistome and transmission dynamics. We describe the genome sequence of E. coli KCTC 72668 isolated from rectum of companion dog.

The strain was recovered from rectal swab after enrichment on CHROMagar Orientation (CHROMagar) at 30ºC for 2 days under aerobic condition. A purified isolate was identified as E. coli by average nucleotide identity (ANI) analysis and deposited in Korean Collection for Type Cultures (KCTC) under 72668 of deposit number. Although 16S rRNA gene sequence of the strain showed the highest similarity (%) with Escherichia fergusonii, the genome exhibited the closest similarity (98.09%) with E. coli ATCC 11775 and thus the isolate was finally identified as E. coli.

Genomic DNA of KCTC 72668 strain was extracted from cells which were grown aerobically at 30ºC for 20 h in blood agar medium. We constructed libraries and sequenced using MinION (Oxford Nanopore), respectively. For a MinION sequencing library, genomic DNA was processed by using ligation sequencing kit (SQK-LSK109, Oxford Nanopore). The libraries were sequenced with the MinION Mk1 sequencer (Oxford Nanopore) using MinION flow cell with R9 chemistry. Determined sequencing reads with about 211 fold coverage were assembled using Flye assembler (v.2.6). De novo assembly generated one contig of 5,215,239 bp with a G + C content of 50.7%. Genome annotation was performed using the Prokaryotic Genome Annotation Pipeline 2.0 (PGAP) (Tatusova et al., 2016), which predicted a total of 5,688 coding DNA sequences (CDS), 87 tRNA genes, and 22 rRNA genes as described in Table 1.

Genome features of Escherichia coli KCTC 72668

FeatureValue
Genome size5,215,239 bp
G + C content50.7%
Contig1
Coding DNA sequence5,688
tRNA genes87
rRNA genes (5S, 16S, 23S)22 (8, 7, 7)
ncRNAs6

The draft genome analysis revealed the presence of two antibiotic resistance genes, namely, ampC and bacA responsible for resistances against beta-lactam and bacitracin. Additionally, the genes for multiple antibiotic resistance protein (marA, marB, marR) and transferase family protein (murA) were also detected.

Nucleotide sequence accession number

The genome sequence of Escherichia coli KCTC 72668 has been deposited in NCBI GenBank under accession no. CP 045140.

적 요

반려견의 직장으로부터 Escherichia coli KCTC 72668을 분리하였다. 결정된 KCTC 72668 균주의 유전체는 50.7%의 G + C 함량을 가진 5,215,239 bp의 크기로 구성되어 있었으며 5,688개의 암호화 유전자와 87개의 tRNA, 22개의 rRNA 유전자가 존재하였다. 그리고 유전체에서 베타 락탐 항생제와 바시트라신 내성과 관련된 ampCbacA 유전자가 검출되었다.

Acknowledgements

This study was supported by the Korea Ministry of Environment (MOE) as The Environmental Health Action Program under Project No. 2016001350005 and Jeonbuk National University.

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December 2019, 55 (4)