Genome Sequences of Two NDM-1 Metallo-β-Lactamase-Producing Multidrug-Resistant Strains of Klebsiella pneumoniae with a High Degree of Similarity, One of Which Contains Prophage.

We report genome sequences of two NDM-1 metallo-β-lactamase-producing multidrug-resistant Klebsiella pneumoniae isolates of sequence type 147 (ST147) from one hospital. The genomes are highly similar and differ in prophage located in the chromosome of K. pneumoniae KPB-1470/16 and in the additional plasmid-carrying blaOXA-48 gene in K. pneumoniae KPB-417/16.

GENOME ANNOUNCEMENT

Klebsiella pneumoniae carrying New Delhi metallo-β-lactamase (NDM-1) emerging worldwide has raised public health concern. NDM-1 hydrolyzes a wide range of β-lactam antibiotics, including carbapenems, which are the last-resort antibiotics for the treatment of infections caused by resistant bacteria. Nosocomial infections caused by carbapenem-resistant K. pneumoniae are associated with high rates of morbidity and mortality (1, 2). This pathogen was included in the critical level of the “global priority list of antibiotic-resistant bacteria” designed by the World Health Organization (3). The dissemination of NDM-1 is associated with diverse sequence types (STs) of K. pneumoniae, including ST147 (2, 4, 5).

Here, we report the genome sequences of two ST147 K. pneumoniae strains (KPB-1470/16 and KPB-417/16) isolated from endotracheal aspirates of two adult patients in the Moscow neurosurgical intensive care unit (ICU) on 28 March 2016 and 5 September 2016, respectively. The strains were deposited in the State Collection of Pathogenic Microorganisms and Cell Cultures “SCPM-Obolensk” (accession numbers SCPM-O-B-8045 and SCPM-O-B-7954, respectively). Both strains are resistant to amoxicillin-clavulanic acid, ampicillin-sulbactam, cefuroxime, ceftazidime, cefoperazone-sulbactam, cefepime, imipenem, ciprofloxacin, gentamicin, amikacin, and nitrofurantoin.

Genome sequencing was performed using an Illumina MiSeq instrument according to the manufacturer’s instructions. For each genome, reads were assembled de novo using SPAdes v. 3.9.0 (6). The final assemblies had mean coverages of 36× and 43× and consisted of 5,625,359 bp (GC content of 57.0% and 115 contigs) and 5,637,851 bp (GC content of 57.0% and 110 contigs) for KPB-417/16 and KPB-1470/16, respectively.

Draft genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (7). A total of 5,367 and 5,399 protein-coding sequences and 106 and 109 tRNAs were annotated for KPB-417/16 and KPB-1470/16, respectively. Sequences of four plasmid replicon types (IncHIIB, IncFIA, IncFIB, and IncFII) were identified in both genomes by using PlasmidFinder (8). In addition, sequences of IncL/M plasmid were determined in the KPB-417/16 genome. Six different bla genes (blaSHV-11, blaCTX-M-15, blaTEM-1, blaOXA-1, blaOXA-9, and blaNDM-1) that code for extended-spectrum β-lactamase were defined in both genomes using ResFinder (9). An additional blaOXA-48 gene was identified in IncL/M plasmid sequences of K. pneumoniae KPB-417/16. Moreover, genes that determine resistance to aminoglycosides [aadA1, aadA2, armA, aph(3′)-via, and aac(6′)Ib-cr], fluoroquinolones (oqxAB), phosphomycins (fosA), macrolides [msr(E) and mph(E)], phenicols (catB4), sulfonamides (sul1), and trimethoprim (dfrA12) have been identified in chromosome and plasmid sequences of both genomes. Some resistance genes [aac(3)-IIa, qnrS1, and catA2] were determined in plasmid sequences of strain KPB-1470/16 only.

Both strains exhibit a high average nucleotide identity of 99.99% between each other but differ from one another in the plasmid composition mentioned above as well as by the presence of additional prophage sequences located in the chromosome of K. pneumoniae KPB-1470/16. Similar prophage sequences were detected in the genome of K. pneumoniae strain TGH13 (GenBank accession number CP012745) isolated in Greece that belongs to ST147 as well.

According to our knowledge, this is the first report of genome sequences of NDM-1 metallo-β-lactamase-producing strains of K. pneumoniae isolated in Russia. The characteristics of the presented genomes are a step toward a better understanding of the population of clinical multidrug-resistant K. pneumoniae strains.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers NPJW00000000 and NPII00000000 for strains KPB-417/16 and KPB-1470/16, respectively.