Draft Genome Sequence of an IMP-7-Producing Pseudomonas aeruginosa Bloodstream Infection Isolate from Australia

ABSTRACT

IMP-7 is one of the two IMP-type carbapenemases that in Pseudomonas aeruginosa are not limited to a geographic area, but it has not been previously reported in the Australian setting. We report here the draft genome sequence of an Australian P. aeruginosa bloodstream infection isolate that contains IMP-7.

GENOME ANNOUNCEMENT

Metallo-beta-lactamases comprise the main group of carbapenemases found in Pseudomonas aeruginosa. IMP and VIM types are the most common. These genes are frequently located within class 1 integrons along with other resistance determinants. The association of the integron with a plasmid or a transposon allows transfer between bacteria. IMP-1 (for “active on imipenem”) was the first mobile P. aeruginosa-producing metallo-beta-lactamase discovered in Japan in 1991 (1). More recently, IMP-51 has been identified in Vietnam (2). Most of the IMP types have a defined geographical distribution apart from IMP-1 and IMP-7 (3). IMP-7 has been previously reported in Canada, central and southern Europe, Japan, Malaysia, the Czech Republic, and Saudi Arabia (4–11). This type of IMP in P. aeruginosa has not been previously reported in the Australian setting.

All P. aeruginosa bloodstream infection (BSI) isolates from patients who had blood cultures collected over a 5-year period (1 January 2008 to 31 December 2012) were retrospectively identified from five laboratories that serviced seven central tertiary care hospitals in Brisbane, Australia. Blood cultures were undertaken by the routine diagnostic laboratories using the BD BACTEC (43,003 to 1) blood culture system (BD, North Ryde, Australia) with an incubation period of up to 5 days. Upon detection, each culture-positive blood sample was inoculated onto blood, chocolate, and MacConkey agars and then incubated at 35°C in either 5% CO₂ or aerobic conditions. After overnight incubation, the P. aeruginosa isolates were identified with the VITEK 2 system (bioMérieux Australia Pty. Ltd., Baulkham Hills, Australia). Antimicrobial susceptibility testing was performed by a microdilution method on the VITEK 2 system. The European Committee on Antimicrobial Susceptibility Testing breakpoints or the Clinical Laboratory Standards Institute breakpoints were utilized for interpretation (12, 13). Of the isolates that were available for further study, 24 were resistant to meropenem. To further study the BSI isolates that were carbapenem-resistant, a carbaNP test was performed (14). One isolate had a positive result.

To further study this isolate, its genome was sequenced. Paired-end libraries of whole genomic DNA of the isolate were prepared following the Nextera XT library protocol and sequenced with the Illumina NextSeq500 platform (Illumina, San Diego, CA, USA). The sequence was trimmed in CLC Genomics Workbench version 7.5.1. The sequence was de novo assembled using SPAdes version 3.8.1. Annotation was performed by the NCBI Prokaryotic Genome Annotation Pipeline. The draft genome was 7,097,416 bp long and had 183 contigs (total number of genes: 6,982; coding sequences: 6,913; tRNAs: 62; ncRNAs: 4). Contigs of the draft genome were submitted to the Center for Genomic Epidemiology (http://www.genomicepidemiology.org) to identify the resistance genes of the isolate with the database ResFinder version 2.1 (15). An IMP-7 gene in the isolate was identified.

Accession number(s).

The draft genome sequence is deposited at GenBank under the accession number MWWM00000000.