Draft Genome Sequence of Klebsiella pneumoniae Strain KP-1

Abstract

Klebsiella pneumoniae is ubiquitous in the environment and is a member of a three-species biofilm model. We compared the genome sequence of an environmental isolate, K. pneumoniae strain KP-1, to those of two clinical strains (NTUH-K2044 and MGH 78578). KP-1 possesses strain-specific prophage sequences that distinguish it from the clinical strains.

GENOME ANNOUNCEMENT

Klebsiella pneumoniae is ubiquitous in the environment, where it is involved in nitrogen fixation (1). It also causes bovine mastitis (2) and nosocomial infections in humans (3). It coexists with Pseudomonas aeruginosa and Pseudomonas protegens in metalworking fluids and the gut of the silk moth Bombyx mori (4, 5). A reproducible, mixed-species biofilm model comprising K. pneumoniae KP-1, P. aeruginosa PAO1, and P. protegens Pf-5 was thus developed to study bacterial interspecies interactions and their effects on biofilm development and fitness (6). While the complete genome sequences of PAO1 and Pf-5 were available to facilitate “omics” studies such as transcriptomics, KP-1 is a newly isolated environmental isolate, and its genome has not been sequenced previously.

The strain was shotgun sequenced on a 454 GS-FLX sequencing platform (Roche, Basel, Switzerland) and an Illumina MiSeq benchtop sequencer (Illumina, CA, USA). The reads from both platforms were trimmed, and de novo assembly was performed using Newbler v2.6 (Roche). With 1,673,246 and 1,840,620 reads from the 454 GS-FLX and MiSeq sequencing platforms, respectively, 24 contigs with a total length of 5,131,085 bp and an average GC content of 57.6% were assembled. The open reading frames (ORFs) were predicted using Glimmer v3.02 (7) and annotated by performing BLASTX analysis (E value <10^-3, >80% identity) against the nonredundant protein sequence database of the National Center for Biotechnology Information. The tRNAs were predicted using tRNAscan-SE v1.3.1 (8), while rRNA sequences were identified by RNAmmer v1.2 (9). A total of 4,587 ORFs were annotated in addition to 73 tRNAs, five 5S rRNAs, and one 23S rRNA. Genomic comparisons to two clinical isolates, K. pneumoniae strain NTUH-K2044 (GenBank accession number AP006725) and strain MGH 78578 (GenBank accession number CP000647), by mGenomeSubtractor v1.3 (H value <0.42) (10) showed that KP-1 possesses several strain-specific genes that encode phage-related proteins such as tail proteins, capsid proteins, terminases, and integrases. Differences between the prophage sequences of strain NTUH-K2044 and strain MGH 78578 were previously reported and suggested to be markers that could be used to distinguish the various lineages of K. pneumoniae (11). The present study further suggests that prophage sequences could be the ideal evolutionary markers for identifying the different lineages of K. pneumoniae.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession number AVNZ00000000. The version described in this paper is version AVNZ01000000.