Draft Genome Sequence of an NDM-5-Producing Klebsiella pneumoniae Sequence Type 14 Strain of Serotype K2

Abstract

We report here the draft genome sequence of uropathogenic Klebsiella pneumoniae sequence type 14 strain of serotype K2 possessing bla_NDM-5, isolated from a 65-year-old male in China without a history of travel abroad.

GENOME ANNOUNCEMENT

Klebsiella pneumoniae is a major human pathogen causing hospital- and community-acquired infections (1, 2). The spread of NDM producers is now considered an endemic threat in K. pneumoniae and represents an important source of multidrug resistance around the world. K. pneumoniae sequence type 14 (ST14) has previously been described as a host lineage for the NDM-1 enzyme (3). Further, Serotype K2 has been described in one previous publication as frequently linked to ST14 (4).

Here, we report the unscaffolded whole-genome shotgun sequence of K. pneumoniae strain NUHL24835 recovered from a urine sample from a 65-year-old female patient hospitalized in the teaching hospital of Nanchang University, China, in 2015. The strain belongs to ST14 with a K2 capsular serotype and shows multiple resistances to clinically used antibiotics, including all β-lactams (ertapenem, meropenem, and imipenem showed MICs of >32 µg/ml), fluoroquinolones, aminoglycosides (except for amikacin), sulfonamides, and macrolides. It was susceptible to colistin and tigecycline.

The genomic DNA from K. pneumoniae NUHL24835 was sequenced by next-generation sequencing using an Illumina HiSeq 2000 instrument with a 2 × 151-bp paired-end approach. The draft genome of K. pneumoniae NUHL24835 comprises 5,387,996 bp, with a G+C content of approximately 58.53%. The protein-coding regions were predicted by Glimmer version 3.02 (http://www.cbcb.umd.edu/software/glimmer). In total, 5,191coding genes were identified, for a total length of 4,804,392 bp and 86.56% coverage of the genome. Eighty-four tRNA genes and 24 rRNA genes have putative functions assigned on the basis of the annotation.

The contigs were initially annotated using RAST (http://rast.nmpdr.org). A BLAST analysis and manual annotation utilized previously reannotated reference sequences and IS Finder (https://www-is.biotoul.fr). The MLST, ResFinder, and PlasmidFinder (http://www.genomicepidemiology.org) databases were used to characterize sequence typing, antibiotic resistance mechanisms, and the plasmid Inc types, respectively, of K. pneumoniae NUHL24835. ST14, plasmid Inc types of IncFII and IncX3, and the genes bla_NDM-5, bla_CTX-M-15, bla_TEM-1, qnrS1, aadA5, sul1, and dfrA17 were identified. This finding is consistent with previously reported experimental results (5). A comparative analysis of the genome from our isolate with published K. pneumoniae genomes will be reported in the future.

A screening for (putative) virulence genes present in the BIGSdb-Kp database (http://bigsdb.web.pasteur.fr/klebsiella/klebsiella.html), performed using the BLASTn tool, revealed (i) the kfuABC system (6), which is responsible for ferric iron uptake, and (ii) the mannose-resistant Klebsiella-like (type III) fimbriae cluster mrkABCDFHIJ (7). Interestingly, the allantoin operon was not present in the genome of the K. quasipneumoniae subsp. quasipneumoniae type strain, suggesting recent horizontal acquisition by K. pneumoniae NUHL24835. The strain possessed a capsular wzi-2/K2 allele. Notably, the rmpA gene, previously associated with the hypermucoviscous phenotype in K. pneumoniae strains (8), was found in the genome of K. pneumoniae NUHL24835, suggesting the presence of a different capsular regulation mechanism. The identified virulence determinants may have contributed to the infection and/or colonization of K. pneumoniae NUHL24835 in the urinary tract.

Nucleotide sequence accession number.

The whole-genome shotgun project of K. pneumoniae NUHL24835 has been deposited at GenBank under the accession number CP014004.