Whole-Genome Sequence of the Human Pathogen Legionella pneumophila Serogroup 12 Strain 570-CO-H

Abstract

We present the genomic sequence of the human pathogen Legionella pneumophila serogroup 12 strain 570-CO-H (ATCC 43290), a clinical isolate from the Colorado Department of Health, Denver, CO. This is the first example of a genome sequence of L. pneumophila from a serogroup other than serogroup 1. We highlight the similarities and differences relative to six genome sequences that have been reported for serogroup 1 strains.

GENOME ANNOUNCEMENT

The Gram-negative gammaproteobacterium Legionella pneumophila is an opportunistic human pathogen that causes Legionnaires' disease, an acute pneumonia acquired from aerosolized contaminated fresh water. Currently only the genomes of L. pneumophila serogroup 1 strains—130b (10), Alcoy (4), Corby (7), Lens (1), Paris (1), Philadelphia 1 (2)—have been reported. Whole-genome analysis revealed a highly plastic genome and a large repertoire of effector proteins, which may be a consequence of the ability of legionellae to grow within a wide range of phylogenetically diverse protozoan hosts and human macrophages (6).

The L. pneumophila serogroup 12 strain 570-CO-H (ATCC 43290), whose genome was sequenced here, is a clinical isolate from the Colorado Department of Health, Denver, CO (human isolate 570-CO-H) (11). For whole-genome sequencing of strain 570-CO-H, short-insert and long-insert shotgun libraries were generated from 5 μg of genomic DNA using standard Illumina protocols. A total of 7,061,382 (416-fold coverage) and 3,023,590 (178-fold coverage) reads for each library were generated using an Illumina DNA analyzer and de novo assembled into 892 contigs larger than 900 bp with Geneious software. Contigs generated from both libraries were further analyzed and assembled into one scaffold with Geneious.

Open reading frames predicted by Glimmer 3 (5) were annotated by BLAST searches against the GenBank nonredundant nucleotide and protein databases. tRNA genes were identified with the tRNAscanSE program (9), and RNA genes were identified by a BLAST search. Gene names and protein products were assigned based on significant homology to known genes found by BLAST and homology searches against previously sequenced genomes of L. pneumophila strains. Mauve (3) was used to compare the genome of 570-CO-H with the other sequenced L. pneumophila genomes (strains Alcoy, Corby, Lens, Paris, Philadelphia, and 130b).

The complete genome of L. pneumophila strain 570-CO-H consists of a single circular chromosome of approximately 3.36 Mb with an average G+C content of 38.2%. The genome sequence is predicted to contain 3 rRNA operons, 43 tRNA genes, and 2,942 putative coding sequences, of which 837 are for hypothetical proteins (28%). Whole-genome comparative analysis showed that the genome of 570-CO-H is highly syntenic with those of the six sequenced L. pneumophila serogroup 1 strains, although duplications, deletions, and translocations of gene clusters were detected. Genes encoding all the structural components of the type I secretion system (T1SS), the T2SS, and the Icm/Dot T4BSS were found in syntenic positions. However, the gene cluster encoding the Lvh T4ASS was not present in the 570-CO-H genome. Of the proven 275 Icm/Dot translocated effectors (8), 274 were identified in the 570-CO-H genome. The proposed core set of 220 effector genes common to all six sequenced serogroup 1 strains (8) was also present in the 570-CO-H genome. A total of 117 genes encoding eukaryotic-type proteins present in other L. pneumophila strains were also identified. Major differences from other L. pneumophila genomes include a particular 46-kb cluster of genes encoding proteins involved in lipopolysaccharide biosynthesis and a cluster of seven hypothetical proteins that are not present in other L. pneumophila genomes.

Nucleotide sequence accession number.

The L. pneumophila serogroup 12 strain 570-CO-H whole-genome sequence has been deposited at GenBank under accession number CP003192.