Draft Genome Sequence of Chromobacterium haemolyticum Causing Human Bacteremia Infection in Japan

Abstract

Chromobacterium haemolyticum is a Gram-negative bacterium displaying remarkable hemolysis against human and sheep erythrocytes. In addition, C. haemolyticum infects humans, in which the infection mechanism remains unknown. We report here the draft genome sequence of C. haemolyticum strain T124, isolated from a young patient with sepsis in Japan.

GENOME ANNOUNCEMENT

Chromobacterium haemolyticum is a Gram-negative bacterium that has a remarkable ability to lyse human and sheep erythrocytes (1). The genus Chromobacterium consists of seven species, including C. violaceum and C. haemolyticum. C. violaceum is an environmental bacterium living especially in tropical regions and has also been recognized as a pathogenic bacterium. Although rare, an infection with C. violaceum progresses rapidly to various organs, especially the lungs, liver, and spleen, and thus is a life-threatening sepsis having highly mortality rates (2, 3). The genome sequence of C. violaceum revealed the presence of potential virulence genes, especially three gene clusters encoding two type III secretion systems (T3SSs) (4, 5). The T3SS is a common virulence determinant in various Gram-negative pathogenic bacteria by injecting bacterial toxins, called effectors, into the host cell directly. We previously showed that a T3SS encoded by Chromobacterium pathogenicity island 1 and 1a (Cpi-1/-1a) is a major virulence determinant (6) and that an effector CopE secreted from the Cpi-1/1a–encoded secretion machinery plays a critical role in host cell invasion and systemic infection in mice (7). Recently, clinical evidence for invasive infection with C. haemolyticum has been reported in Japan (8). At present, infection mechanisms by the human pathogen C. haemolyticum remain completely unknown. Here, we briefly announce the draft genome sequence of one clinical isolate of C. haemolyticum strain T124, which will provide novel insight into and a better understanding of infections with this bacterium.

The whole genome of C. haemolyticum T124 was sequenced using a combined Illumina HiSeq 2000 and Roche GS-FLX approach. Reads obtained from sequencing by Illumina HiSeq were assembled using Velvet. Furthermore, reads obtained from sequencing by Roche GS-FLX were combined with the passed Illumina reads and then were assembled using the Genome Sequencer de novo assembler. The hybrid data yielded 72 large contigs (≥500 bp each) with N₅₀ contig sizes of 189,800 bp, with an average length of 70,602 bp and a largest length of 745,057 bp. The resulting genome sequence of C. haemolyticum T124 is 5,110,775 bp with 161-fold coverage and has a G+C content of 62.8%. Annotation by the Rapid Annotations using Subsystems Technology (RAST) sever revealed 4,557 coding genes, 73 tRNA genes, and 8 copies of the rRNA genes. In addition, RAST showed that the closest neighbor is C. violaceum ATCC 12472 (4).

Similar to C. violaceum ATCC 12472, C. haemolyticum T124 contains the virulence-associated type III secretion gene cluster. ATCC 12472 has two distinct T3SSs encoded by Cpi-1/-1a and -2, respectively, whereas T124 lacks the Cpi-2-like second T3SS. These data suggest that a major virulence determinant of C. haemolyticum T124 might be the Cpi-1/-1a–like T3SS. The genome sequence reported here will aid in future studies of C. haemolyticum to understand the fatal infection mechanism and to develop efficient antimicrobial therapy against the life-threatening sepsis.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JRFR00000000. The version described in this paper is version JRFR01000000.