Draft Genome Sequences of Two IMP-4-Producing Escherichia coli Sequence Type 131 Isolates in Australia

Abstract

We report the draft genome sequences of two unrelated cases of Escherichia coli sequence type 131 (ST131) possessing the carbapenemase gene bla_IMP-4. The E. coli ST131 SN5 isolate also possessed bla_SHV-12 and plasmid-mediated quinolone-resistance genes. Wider dissemination of bla_IMP-4 may occur due to the bla_IMP-4-carrying L/M or HI2 plasmids among E. coli ST131 isolates.

GENOME ANNOUNCEMENT

Carbapenem-resistant Enterobacteriaceae (CRE) are regarded as an urgent antibiotic resistance threat by the Centers for Disease Control and Prevention (CDC). In the United States, the most common CRE strains produce the KPC beta-lactamase (1). Geographic variations in the type of carbapenemase responsible for CRE exist. The dominance of IMP-4-producing Enterobacter cloacae were recently reported in Australia (2). HI2 and L/M plasmids were the two main types of plasmids harboring bla_IMP-4 (2). Escherichia coli sequence type 131 (ST131) has been recognized as a highly successful extraintestinal clone of E. coli causing urinary tract infections and frequently associated with the production of the extended-spectrum beta-lactamase CTX-M-15 (3).

Two carbapenemase-producing E. coli isolates were obtained from patients from two hospitals in Australia. E. coli CR48 and E. coli SN5 were isolated from urine of an elderly woman and from sputum of an elderly man, respectively. Both E. coli isolates were characterized for the genes responsible for the resistance to beta-lactam antibiotics, especially to carbapenems. Initially, both isolates were determined to possess bla_IMP-4 by PCR and classified as E. coli ST131 by repetitive sequence-based PCR (repPCR) (DiversiLab, bioMérieux). The two E. coli isolates were subjected to whole-genome sequencing to characterize the antibiotic resistance and virulence properties of the isolates.

Whole-genomic DNA of E. coli CR48 and SN5 was extracted and prepared using the Nextera XT DNA sample preparation kit and sequenced using the Illumina HiSeq 2000 as previously described (4). De novo assembly was performed using CLC Genomics Workbench version 7.5 (CLC Bio, Denmark). The draft genomes of CR48 and SN5 consisted of 5,184,875 and 5,219,367 bp, respectively. Contigs were initially annotated using RAST (http://rast.nmpdr.org). Sequence typing, antibiotic resistance mechanisms, and plasmid Inc types of E. coli were determined through http://www.genomicepidemiology.org.

The genome data showed that both E. coli isolates were ST131. Both E. coli strains also possessed bla_TEM-1B, sul1, and aac(3)-IId. Additionally, E. coli SN5 possessed bla_SHV-12, bla_OXA-1, qnrA1, and qnrB49. E. coli CR48 possessed L/M and FII. Plasmids HI2, HI2A, FII, I1, Col156, and FIB were determined in SN5. The bla_IMP-4 gene was most likely located on the L/M and HI2 plasmids in CR48 and SN5, respectively.

The annotation through RAST identified type 1 fimbriae fimA-H, virulence determinants relevant for urinary tract adhesion in both isolates (5). Fimbriae related to the protein secretion system were identified: htrE fimbriae cluster, stf fimbriae cluster, and colonization factor antigen I fimbriae (CFA/I fimbriae). In addition, fimbriae usher protein StcC was identified. Further, IncF conjugal transfer pili were identified. The cluster responsible for Curli production or type VIII secretion was identified. There were variations of the siderophore enterobactin, siderophore aerobactin, and other hemin transport systems for iron acquisition in the two isolates.

The bla_IMP-4 genes in CR48 and SN5 were both located in the integron class 1. The genetic context of CR48 was tnpA|intI1|bla_IMP-4|qacG|aacA4|catB3|∆qacE|sul1|ISCR1. Two studies reported the occurrence of IMP-8-producing E. coli ST131 in Taiwan and IMP-4-producing E. coli ST131 in China (6, 7). These cases of IMP-4-producing E. coli ST131 in Australia highlight potential further dissemination of bla_IMP-4 among uropathogenic E. coli.

Nucleotide sequence accession numbers.

This project is registered as BioProject number PRJNA281568 and BioSample numbers SAMN03798494 (E. coli ST131 CR48) and SAMN03491847 (E. coli ST131 SN5). The draft genomes of IMP-4-producing E. coli ST131 CR48 and SN5 have been deposited in GenBank under the accession numbers LFXT00000000 and LFXU00000000, respectively.