Genome Sequence of a Strain of the Human Pathogenic Bacterium Pseudomonas alcaligenes That Caused Bloodstream Infection.

Pseudomonas alcaligenes, a Gram-negative aerobic bacterium, is a rare opportunistic human pathogen. Here, we report the whole-genome sequence of P. alcaligenes strain MRY13-0052, which was isolated from a bloodstream infection in a medical institution in Japan and is resistant to antimicrobial agents, including broad-spectrum cephalosporins and monobactams.

GENOME ANNOUNCEMENT

Pseudomonas alcaligenes is a Gram-negative aerobic rod belonging to the bacterial family Pseudomonadaceae and is a common inhabitant of soil and water. A recent study showed that P. alcaligenes is useful as a microbial inoculant for the biodegradation of toxic polycyclic aromatic hydrocarbons (1). P. alcaligenes has also been known as a rare opportunistic human pathogen (2). Based on 16S rRNA gene sequence analysis, P. alcaligenes was classified in the Pseudomonas aeruginosa group (3). However, little is known about the clinical importance of P. alcaligenes and its virulence factors, mainly because of the difficulties in identifying and distinguishing this bacterium from closely related Pseudomonas species in medical settings.

In this report, we announce the availability of the first draft genome sequence of P. alcaligenes. P. alcaligenes strain MRY13-0052 was recovered from a bloodstream infection in a medical institution in Japan in 2013 and was resistant to broad-spectrum cephalosporins and monobactams. Whole-genome shotgun (WGS) sequencing of strain MRY13-0052 was performed using the Roche 454 pyrosequencing platform (500-bp insert size). The reads were assembled de novo using Newbler Assembler version 2.3 (Roche). The draft genome sequence of MRY13-0052 consists of 237 contigs, yielding a total of 6,876,944 bp with an N50 contig size of 64,175 bp. The mean G+C content was 65.8%. A total of 6,190 coding DNA sequences were identified by the RAST server (http://rast.nmpdr.org) (4). The MRY13-0052 strain carried three class C β-lactamase genes that might confer resistance to β-lactam antibiotics. Any other acquired antimicrobial resistance genes in the WGS data were not detected using a Web-based tool, ResFinder version 1.3 (http://cge.cbs.dtu.dk/services/ResFinder/) (5).

Bacterial pathogens frequently use protein secretions to interact with their hosts. MRY13-0052 contains the type VI secretion system (T6SS) gene cluster and three genes that encode VgrG (valine glycine repeat G) translocator proteins (6). The T6SS, which is conserved among Pseudomonas species (7), delivers effectors into neighboring organisms, including bacteria and mammalian cells, leading to cytotoxicity and cell death in the targets (6). The MRY13-0052 strain furthermore contains a set of genes that encode proteins homologous to P. aeruginosa Tse1 (type VI effector 1) and Tsi1 (type VI immunity 1) (8) (66.9% and 48.8% identities, respectively). On the other hand, MRY13-0052 is devoid of the virulence-associated type III secretion system (T3SS) gene cluster, whereas a T3SS is the major virulence factor in animal and plant pathogenic Pseudomonas species, P. aeruginosa, and Pseudomonas syringae (9, 10). These data suggest that the T6SS might be an important virulence determinant in P. alcaligenes and that P. alcaligenes might partially share the same T6SS-dependent effector and immunity system with P. aeruginosa.

A more detailed report of the virulence phenotype of P. alcaligenes MRY13-0052 will be included in a future publication. A genome-wide comparison of P. alcaligenes with related Pseudomonas species, such as P. aeruginosa, Pseudomonas mendocina, and Pseudomonas pseudoalcaligenes, will facilitate additional comprehensive bioinformatic and phylogenetic analyses, thus expanding our understanding of fatal nosocomial infections caused by these opportunistic human pathogens.

Nucleotide sequence accession numbers.

The WGS projects for P. alcaligenes MRY13-0052 have been deposited at DDBJ/EMBL/GenBank under the accession no. BATO00000000. The version described in this paper is the first version, BATO01000000.