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J Glob Antimicrob Resist. 2018 Dec 12;16:120-122. doi: 10.1016/j.jgar.2018.11.024. [Epub ahead of print]

Draft genome sequence of an Escherichia coli ST410 isolate co-harbouring blaCTX-M-15, blaCMY-42, blaOXA-1, aac(3)-IIa and aac(6')-Ib-cr genes with gyrA and parC mutations isolated from a paediatric patient in Poland.

Author information

1
Department of Bacteriology and Biocontamination Control, National Institute of Public Health-National Institute of Hygiene, 24 Chocimska Str., 00-791 Warsaw, Poland. Electronic address: mrzeczkowska@pzh.gov.pl.
2
Department of Bacteriology and Biocontamination Control, National Institute of Public Health-National Institute of Hygiene, 24 Chocimska Str., 00-791 Warsaw, Poland.
3
Department of Clinical Microbiology and Immunology, The Children's Memorial Health Institute, Warsaw, Poland.

Abstract

OBJECTIVES:

Escherichia coli is one of the major causative agents of nosocomial infections. Here we report the first draft genome sequence of an E. coli strain (no. 158) isolated in Poland carrying blaCTX-M-15, blaCMY-42, blaOXA-1, aac(3)-IIa and aac(6')-Ib-cr genes together with mutations in the gyrA and parC genes.

METHODS:

Total DNA was sequenced using an Illumina NextSeq 500 platform. The draft genome of E. coli strain 158 was assembled using SPAdes 3.9 assembler. Contigs were annotated using the Prokka v.1.12 algorithm. Species confirmation, multilocus sequence typing (MLST), serotyping, molecular virulence and resistance traits, and plasmid replicons were analysed using appropriate bioinformatics tools available at the Centre for Genomic Epidemiology website. Additional in silico analyses were also conducted.

RESULT:

The genome size was estimated at 4883487bp, with 4601 predicted coding sequences. The presence of blaCTX-M-15, blaCMY-42, blaOXA-1, aac(3)-IIa and aac(6')-Ib-cr genes was detected in addition to other antimicrobial resistance genes as well as mutations in the gyrA (Ser83Leu and Asp87Asn) and parC (Ser80Ile) genes. The investigated strain E. coli 158 belongs to ST410.

CONCLUSION:

To our knowledge, this is the first draft genome of an E. coli strain co-harbouring blaCTX-M-15, blaCMY-42, blaOXA-1, aac(3)-IIa and aac(6')-Ib-cr genes with mutations in gyrA and parC reported in Poland. The reported genome sequence contains valuable information on genetic features of antimicrobial resistance mechanisms of E. coli in Poland.

KEYWORDS:

CMY-42; CTX-M-15; Escherichia coli; ST410; Whole-genome sequencing; aac(6′)-Ib-cr

PMID:
30553112
DOI:
10.1016/j.jgar.2018.11.024

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