Abstract
Chlamydia psittaci is a highly prevalent avian pathogen and the cause of a potentially lethal zoonosis, causing life-threatening pneumonia in humans. We report the genome sequences of C. psittaci 6BC, the prototype strain of the species, and C. psittaci Cal10, a widely used laboratory strain.
GENOME ANNOUNCEMENT
The obligate intracellular pathogen Chlamydia psittaci causes zoonotic psittacosis or ornithosis, a severe and sometimes fatal respiratory disease of humans that is acquired from infected birds. C. psittaci is found in bird populations worldwide, with sporadic epidemic outbreaks (1). Infection in birds is often asymptomatic, with transmission to humans reported regularly, particularly in individuals with a high exposure risk, such as veterinarians and other animal handlers (4). C. psittaci is a U.S. CDC category B bioterrorism agent due to the ease of respiratory dissemination and associated morbidity and mortality rates (5). Notably, a 1930 Maryland outbreak of psittacosis, linked to the 1929-1930 psittacosis pandemic, directly led to the founding of the National Institutes of Health (7, 9).
We sequenced the type strain C. psittaci 6BC, isolated from a parrot during the 1929-1930 psittacosis pandemic (3). Isolates of C. psittaci 6BC have been shown to be genetically variable (10)—we sequenced a genetic variant of C. psittaci with lower virulence. We also sequenced C. psittaci Cal10, originally termed the meningopneumonitis virus, which was isolated from ferrets inoculated with throat washings from humans with an influenza-like respiratory infection (8).
The finished genome of C. psittaci 6BC was determined using the whole-genome shotgun method (11). Gaps were closed using a combination of primer walking, generation and sequencing of transposon-tagged libraries of large-insert clones, and multiplex PCR (11). Gene identification and annotation were performed as previously described (11). Functional assignment, identification of membrane-spanning domains, determination of paralogous gene families, and identification of regions of unusual nucleotide composition were performed as previously described (11). The C. psittaci Cal10 draft genome was determined using Titanium pyrosequencing on a 454 GS FLX and assembled using Celera Assembler with C. psittaci 6BC as the reference. The C. psittaci Cal10 draft genome consists of 3 ordered contigs (160-fold coverage). C. psittaci 6BC annotation was mapped to Cal10 using a pipeline based on the Mummer 3.1 package (6).
The C. psittaci 6BC genome is 1,171,667 bp, containing 1,016 putative coding sequences (CDSs). The C. psittaci Cal10 draft genome is 1,169,283 bp, containing 982 CDSs. Both strains possess the conserved C. psittaci plasmid (8 CDSs, 7,553 bp). C. psittaci 6BC and Cal10 both possess a single full-length copy of the cytotoxin ortholog within the chlamydial plasticity zone (PZ). The virulence-associated membrane attack complex/perforin gene, truncated in or absent from all other chlamydial genomes except koala strain C. pneumoniae LPCoLN (11), is also located in the PZ in two copies, one full length and one truncated.
The C. psittaci 6BC and Cal10 chromosomes are essentially identical, with 119 intragenic (48 nonsynonymous, 30 synonymous, and 41 insertion/deletion) single-nucleotide polymorphisms (SNPs) and 31 intergenic SNPs identified. SNP accumulation (“hot spots”) occurs in four regions; one hot spot maps to the chlamydial PZ within the C. psittaci cytotoxin ortholog, two other hotspots are found within distinct pmpG clusters, and the fourth centers on a CDS predicted to encode phosphatidylinositol-4-phosphate 5-kinase, a lipid-modifying enzyme involved in actin remodeling that has been shown to be instrumental in chlamydial entry into the host cell (2).
Nucleotide sequence accession numbers.
Genome and plasmid sequences have been deposited at GenBank under accession numbers CP002586 (C. psittaci 6BC chromosome), CP002587 (C. psittaci 6BC plasmid), and AEZD00000000 (C. psittaci Cal10 draft chromosome and plasmid).
Acknowledgments
This work was supported by NIAID 1R01AI051472.
Footnotes
Published ahead of print on 27 May 2011.
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