Draft Genome Sequence of the First Hypermucoviscous Klebsiella quasipneumoniae subsp. quasipneumoniae Isolate from a Bloodstream Infection.

Klebsiella quasipneumoniae is a recently described species, formerly identified as K. pneumoniae phylogroup KpII. Information on pathogenic and virulence potential of this species are lacking. We sequenced the genome of a hypermucoviscous K. quasipneumoniae clinical isolate showing a virulence genes content (allABCDRS, kfuABC, and mrkABCDFHIJ) peculiar to hypervirulent K. pneumoniae strains.

GENOME ANNOUNCEMENT

Klebsiella pneumoniae is a major human pathogen causing hospital- and community-acquired infections (1, 2). The latter also include invasive infections characterized by pyogenic liver abscesses with possible dissemination to distant sites (3). The majority of strains causing these infections exhibit a “hypermucoviscous” phenotype which is considered a distinctive virulence factor (3, 4). Recent taxonomic studies have demonstrated that strains formerly classified in K. pneumoniae phylogroups KpII and KpIII actually belong to two new sister species, namely, Klebsiella quasipneumoniae and Klebsiella variicola, respectively (5, 6). The former species includes in turn two subspecies, K. quasipneumoniae subsp. quasipneumoniae and K. quasipneumoniae subsp. similipneumoniae (5).

Sequencing of the first genome of a K. variicola showing a hypermucoviscous phenotype has recently been announced (7).

In this report, we announce the first draft genome sequence of the K. quasipneumoniae subsp. quasipneumoniae strain (FI_HV_2014), characterized by a hypermucoviscous phenotype. The strain was isolated from a Peruvian patient hospitalized in Italy with biliary tract and bloodstream infection. To the best of our knowledge, this is the first reported hypermucoviscous strain of K. quasipneumoniae subsp. quasipneumoniae.

FI_HV_2014 genomic DNA was subjected to whole-genome sequencing with the MiSeq platform (Illumina Inc., San Diego, CA), using a 2×250-paired-end approach. In total 2,781,628 reads were obtained, with an average coverage of 84× and an estimated genome size of 5,335,587 bp. Reads were assembled using A5-miseq software (8) into 107 contigs and 84 scaffolds (N50 contig sizes of 316,178 bp). Scaffolds annotated using the NCBI Prokaryotic Genome Annotation Pipeline (release 2013) contained 4,799 coding sequences (CDS). The average GC content of the chromosome was about 55%. The species identification was deduced from the presence and nature of the chromosomal blaOKP-type beta-lactamase, characteristic of K. quasipneumoniae subsp. quasipneumoniae (9), and confirmed by fusA, gapA, gyrA, leuS, and rpoB gene analysis (5). The predicted DNA-DNA hybridization (DDH), estimated using the GGDC 2.0 software (10), between FI_HV_2014 and type strains of K. quasipneumoniae subsp. quasipneumoniae (01A030, accession no. CCDF00000000), K. quasipneumoniae subsp. similipneumoniae (07A044, accession no. CBZR000000000), K. variicola (342, accession no. CP000964) and K. pneumoniae subsp. pneumoniae (DSM 30104, accession no. AJJI00000000) were 93.6%, 72.1%, 52.3%, and 53.7%, respectively.

A screening for (putative) virulence genes present in the BIGSdb-Kp database (http://bigsdb.web.pasteur.fr/perl/bigsdb/bigsdb.pl?db=pubmlst_klebsiella_seqdef_public&page=downloadAlleles), performed using the BLASTn tool, revealed (i) an allABCDRS operon (11), responsible for the allantoin anaerobic assimilation, linked with arcC, fdrA, gcl, glxKR, ybbWY, ylbEF, KP1_1364, KP_1371, and hyi genes in the same contig (accession no. AB115590); (ii) the kfuABC system (12), responsible for ferric iron uptake, and (iii) the mannose-resistant Klebsiella-like (type III) fimbriae cluster, mrkABCDFHIJ (13). Interestingly, the allantoin operon was not present in the genome of the K. quasipneumoniae subsp. quasipneumoniae type strain, suggesting recent horizontal acquisition by FI_HV_2014. The strain possessed a new capsular wzi allele (not present in the BIGSdb database). Notably, the rmpA and rmpA2 genes, previously associated with the hypermucoviscous phenotype in K. pneumoniae strains (4), were not found in the genome of FI_HV_2014, suggesting the presence of a different capsular regulation mechanism.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LGAL00000000. The version described in this paper is version LGAL01000000.