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Complete genome of the multidrug-resistant Escherichia coli strain KBN10P04869 isolated from a patient with acute myeloid leukemia
Korean J. Microbiol 2018;54(4):442-444
Published online December 31, 2018
© 2018 The Microbiological Society of Korea.

Yu Kyung Kim1, Won Kil Lee1, and Kyung Eun Song1,2,*

1Department of Clinical Pathology, School of Medicine, Kyungpook National University, Daegu 41566, Republic of Korea,
2Department of Laboratory Medicine, Kyungpook National University Medical Center, Daegu 41566, Republic of Korea
Correspondence to: E-mail: kesong@knu.ac.kr; Tel.: +82-53-200-2831; Fax: +82-53-200-3309
Received August 8, 2018; Revised September 10, 2018; Accepted September 17, 2018.
Abstract

Recently, we isolated a multidrug-resistant Escherichia coli strain KBN10P04869 from a patient with acute myeloid leukemia. We report the complete genome of this strain which consists of 5,104,264 bp with 4,457 protein-coding genes, 88 tRNAs, and 22 rRNAs, and the co-occurrence of multidrug-resistant genes including blaCMY-2, blaTEM-1, blaCTX-M-15, blaNDM-5, and blaOXA-18.

Keywords : Escherichia coli, carbapenem, multidrug-resistance
Body
!#italic#!#Escherichia coli is a Gram-negative, facultatively anaerobic, rod-shaped bacterium; clinically, it is one of the major causative pathogens of urinary tract infection, intra-abdominal infection, and primary bacteremia (Javaloyas et al., 2002). In the last two decades, there have been great concern regarding multidrug-resistant (MDR) E. coli, due to its increased incidence and its resistance to a broad range of β-lactams and other groups of antimicrobial agents (Rodríguez-Baño et al., 2006).

We isolated an antibiotic-resistant E. coli strain KBN10P04689, which caused bacteremia from the bloodstream of an acute myeloid leukemia patient. Antibiotics susceptibility testing with VITEK2 (bioMérieux) showed that the strain was resistant to carbapenem, non-extended spectrum cephalosporin, extended-spectrum cephalosporin, cephamycin, fluoroquinolones, folate pathway inhibitors, monobactams, and penicillins.

To investigate the genomic potential of the drug-resistant E. coli strain KBN10P04689 extensively, the strain was cultured at 37°C on blood agar. Then, genomic DNA was extracted using the i-genomic BYF Mini Kit (iNtRON Biotechnology). Genome sequencing was performed using PacBio RS II single-molecule real-time (SMRT) sequencing technology (Pacific Biosciences). A standard PacBio library with an average of 20-kb inserts were prepared and sequenced, yielding an average genome coverage of >179.2X. De novo assembly of the 101,776 reads with an average of 15,304 nucleotides (total 1,557,581,797 bp) was conducted using the hierarchical genome-assembly process (HGAP) pipeline of SMRT Analysis v2.3.0 (Chin et al., 2013).

The genome consists of one circular chromosome (4,840,855 bp with 50.57% G + C content) and three circular plasmids, pKBN10P04689A (107,229 bp with 51.69% G + C content), pKBN10P04689B (104,701 bp with 46.96% G + C content) and pKBN10P04689C (51,479 bp with 46.37% G + C content) (Table 1).

General features ofE. colistrain KBN10P04869 complete genome

 AttributeChromosomepKBN10P04869ApKBN10P04869BpKBN10P04869C
Assembly size (bp)4,840,855107,229104,70151,479
Contigs1111
GC content (%)50.5751.6946.9646.37
DNA coding region (%)84%68%82%79%
Predicted ORFs4211919461
rRNA22
tRNA853
Genes assigned to COGs3,558602125
Genes with Pfam domains3,820742434
Genes with signal peptides416426
Genes with transmembrane helices1,03211810

Different types of antibiotic-resistant genes encoding enzymes for structure-altering or inactivating antibiotics and modifying target sites, and encoding the enzymes resistant to inhibitors of a metabolic pathway (trimethoprim-sulfamethoxazole) were found in the chromosome, pKBN10P04689A and pKBN10P04689C. The chromosome harbors two antibiotic-resistant genes, blaCMY-2 (YKEC1_2769) and arnA (YKEC1_1480). In the plasmid pKBN10P04689A, the genes related to gentamicin resistance (aac(3)-IIb/YKEC1_4558), penicillin and cefazolin resistance (blaTEM-1/YKEC1_4537 and YKEC1_4562), extended-spectrum cephalosporin resistance (blaCTX-M-15/YKEC1_4533) and folate pathway inhibitor resistance (dfrA12/ YKEC1_4578, sul1/ YKEC1_4570 and YKEC1_4581, sul2 /YKEC1_4546) were identified. In addition, the plasmid contains blaNDM-5 (YKEC1_4575), which has been reported to confer resistance against piperacillin-tazobactam and carbapenem, extended-spectrum cephalosporins, and blaNDM-5 or its variant, which has recently spread to a large extent (Hawkey and Jones, 2009). Besides, the genes involved in erythromycin, chloramphenicol and tetracycline resistance (mphA/YKEC1_4553, catB3/YKEC1_4533, and tetB/YKEC1_4586) were detected. The plasmid pKBN10P04689C harbors genes that confer resistance to amoxicillin-clavulanic acid (blaOXA-181/YKEC1_4795) and resistance to fluoroquinolones, including ciprofloxacin (qnrS1/YKEC1_4788). Although the aac(6’)-Ib-cr gene (YKEC1_4527), which encodes a bifunctional protein to catalyze the acetylation of fluoroquinolones as well as aminoglycosides such as amikacin and gentamicin, was detected in pKBN10P04869A, the strain shows susceptibility against amikacin, as observed after an antimicrobial test (Table 2).

Results of antimicrobial test and resistant genes

 AntibioticsSusceptibility (MIC)Antimicrobial resistant genes

 Genes (Locus_tag)Position
AmikacinS (8)acc(6’)-Ib-cr (YKEC1_4527)pKBN10P04869A

GentamicinR (≥32)aac(6’)-Ib-cr (YKEC1_4527)pKBN10P04869A
aac(3)-IIb (YKEC1_4558)

Piperacillin-tazobactamR (≥128)bla TEM-1 (YKEC1_4537, YKEC1_4562)pKBN10P04869A
bla OXA-181 (YKEC1_4795)pKBN10P04869C
bla NDM-5 (YKEC1_4575)pKBN10P04869A

ErtapenemR (≥8)bla NDM-5 (YKEC1_4575)pKBN10P04869A

ImipenemR (≥16)bla NDM-5 (YKEC1_4575)pKBN10P04869A

CefazolinR (≥64)bla TEM-1 (YKEC1_4537, YKEC1_4562)pKBN10P04869A

CefotaximeR (≥64)bla CTX-M-15 (YKEC1_4533)pKBN10P04869A

CeftazidimeR (≥64)bla CTX-M-15 (YKEC1_4533)pKBN10P04869A
bla NDM-5 (YKEC1_4575)

CefepimeR (≥64)bla NDM-5 (YKEC1_4575)pKBN10P04869A
bla OXA-181 (YKEC1_4795)pKBN10P04869C

CefoxitinR (≥64)bla CMY-2 (YKEC1_2769)Chromosome
bla NDM-5 (YKEC1_4575)pKBN10P04869A

CiprofloxacinR (≥4)aac(6’)-Ib-cr (YKEC1_4527)pKBN10P04869A
qnrS1 (YKEC1_4788)pKBN10P04869C

Trimethoprim/ sulfamethoxazoleR (≥320)dfrA12 (YKEC1_4578)pKBN10P04869A
sul1 (YKEC1_4570, YKEC1_4581)
sul2 (YKEC1_4546)

TigecyclineS (≤0.5)--

AztreonamR (≥64)bla CMY-2 (YKEC1_2769)Chromosome

AmpicillinR (≥32)bla TEM-1 (YKEC1_4537, YKEC1_4562)pKBN10P04869A

Amoxicillin-clavulanic acidR (≥32)bla OXA-181 (YKEC1_4795)pKBN10P04869C

ChloramphenicolNDcatB3 (YKEC1_4533)pKBN10P04869A

ColistinNDarnA (YKEC1_1480)Chromosome

TetracyclineNDtetB (YKEC1_4586)pKBN10P04869A

ND: not determined


The complete genome sequence of the E. coli strain KBN10P04869 has been deposited at DDBJ/EMBL/GenBank under the accession numbers CP026473 (chromosome), CP026474 (pKBN10P04869A), CP026475 (pKBN10P04869B), and CP026476 (pKBN10P04869C). This strain is available from the Kyungpook National University Hospital Culture Collection for Pathogens.

적 요

저자들은 최근 급성골수성백혈병 환자로부터 다제내성대장균 균주 KBN10P04869를 분리했다. 균주는 4,457개의 단백질 코딩 유전자, 88개의 운반 RNA, 22개의 리보솜 RNA를 포함하는 5,104,264 염기쌍으로 구성되고, blaCMY-2, blaTEM-1, blaCTX-M-15, blaNDM-5, blaOXA-18를 포함한 다제내성유전자를 가지고 있다. 저자들은 이 균주의 총유전체를 보고하는 바이다.

Conflict of Interest

No potential conflicts of interest relevant to this article are reported.

Acknowledgements

This research was supported by Kyungpook National University Research Fund, 2017.

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