Draft Genome Sequence of a Hospital-Associated Clone of Klebsiella pneumoniae ST340/CC258 Coproducing RmtG and KPC-2 Isolated from a Pediatric Patient.

We report here the draft genome sequence of a Klebsiella pneumoniae strain 1194/11, belonging to the hospital-associated sequence type 340 (ST340; clonal complex CC258), isolated from a catheter tip culture from a pediatric patient. The multidrug-resistant strain coproduced the 16S rRNA methyltransferase rRNA RmtG and β-lactamases KPC-2 and CTX-M-15.

GENOME ANNOUNCEMENT

Klebsiella pneumoniae is a leading cause of nosocomial infection. In this regard, clinical strains exhibiting a multidrug-resistant (MDR) profile have been associated with the persistence of clonally related sequence types (STs), clustered in high-risk complexes (1). In this regard, most KPC-2-producing K. pneumoniae strains belong to the clonal complex 258 (CC258), which includes ST11, ST258, ST340, and ST437 (1). In Brazil, strains of K. pneumoniae ST340 coproducing KPC-2 and CTX-M-15 have been found in clinical settings and aquatic ecosystems (2–4). Here, we present the draft genome sequence of an MDR ST340 K. pneumoniae strain coproducing the 16S rRNA methyltransferase rRNA RmtG and β-lactamases KPC-2 and CTX-M-15.

K. pneumoniae strain 1194/11 was isolated in 2011 from a catheter tip culture from a pediatric patient admitted to a children’s hospital in São Paulo, southern Brazil (5). The strain was collected at the Instituto Adolfo Lutz (IAL), which serves as a state reference laboratory and receives multidrug-resistant Gram-negative pathogens on an ongoing basis. The isolate belonged to ST340/CC258 and displayed resistance to gentamicin, tobramycin, amikacin, arbekacin, neomycin, apramycin, ceftazidime, cefotaxime, cefepime, ertapenem, and meropenem (5).

The genomic DNA of K. pneumoniae strain 1194/11 was sequenced using an Illumina MiSeq sequencing platform, which produced 1,824,432 paired-end reads at 100× total coverage. De novo assembly was performed using the A5-MiSeq pipeline (6), and the assembled contigs were annotated using NCBI Prokaryotic Genome Annotation Pipeline version 3.2. In total, there were 5,643 protein-coding genes, 123 RNA-coding genes (81 tRNAs, 27 rRNAs, and 15 noncoding RNAs [ncRNAs]), and 108 pseudogenes, with a G+C content of 56.7% and estimated 5,702,010-bp genome size.

The resistome of K. pneumoniae strain 1194/11 was analyzed using ResFinder 2.1 (7), identifying aac(3)-IId, rmtG, and aadA2 aminoglycoside resistance genes; blaCTX-M-15, blaSHV-11, blaKPC-2, and blaTEM-1B β-lactam resistance genes; the sul1 sulfonamide resistance gene; the tet(D) gene (conferring resistance to tetracycline); trimethoprim resistance genes dfrA12 and dfrA25; the fosfomycin resistance fosA-like gene, and plasmid-mediated quinolone resistance (PMQR) genes oqxA, oqxB, and qnrB2.

Accession number(s).

The genome sequence of Klebsiella pneumoniae 1194/11 has been deposited in the GenBank database under the accession number LYZC00000000.