Complete Genome Sequences of Four Mammalian Isolates of Chlamydophila psittaci

Abstract

Chlamydia psittaci is an obligate intracellular zoonotic pathogen primarily of birds, but it is also known to infect a variety of mammalian species. Here we report the genomes of four strains isolated from sheep (C19/98), pigs (01DC11), cattle (02DC15), and humans (08DC60).

GENOME ANNOUNCEMENT

The Gram-negative obligate intracellular bacterial pathogen Chlamydia psittaci targets primarily avian hosts causing psittacosis (parrot's disease). However, infections of a wide variety of mammalian hosts, including cattle and other ruminants, horses, pigs, and humans, have been reported (3, 4, 6). Sequencing of a limited number of genes has suggested an association between different host species and C. psittaci genotypes (5). Here we report the complete genome sequences and annotations of four strains of C. psittaci isolated from sheep, pigs, cattle, and humans.

Ovine C. psittaci strain C19/98 was isolated from afterbirth in 1998, porcine strain 01DC11 was isolated from a conjunctival swab of a pig in 2001, bovine strain 02DC15 was isolated from an aborted calf fetus in 2002 (2), and human strain 08DC60 was isolated from bronchial lavage fluid in 2008. Until 2009, the strains were passaged in Buffalo green monkey kidney cells on a regular basis. Prior to genomic DNA isolation, the strains were proliferated in human HeLa cells (ATCC catalog no. CCL-2) and the amount of host cell components in the host-pathogen suspension was reduced by ultracentrifugation.

The genomes were determined by the whole-genome shotgun strategy using a combination of Roche 454 FLX Titanium pyrosequencing and the Illumina sequencing technology. The average sequencing coverages were 91-fold, 102-fold, 56-fold, and 148-fold for strains C19/98, 01DC11, 02DC15, and 08DC60, respectively. Sections of reduced (<10-fold) coverage were corroborated by subsequent Sanger sequencing. Assembly of the genomes, identification of putative protein-coding genes, and annotation of the genomes were performed as previously described (7).

The genome sequences of the four strains (following the order above) were 1,169,374 bp, 1,172,197 bp, 1,172,182 bp, and 1,172,032 bp in size, and each genome is predicted to encode 978, 975, 978, and 975 putative coding sequences. The distinctly smaller genome size of the ovine isolate (01DC11) is due to the absence of a copy of a chlamydial polymorphic membrane protein that appears to be duplicated in all other C. psittaci genomes. Using the progessiveMauve multiple-genome aligner (1), we found a total of 158 single nucleotide polymorphisms and 72 indels between the strains. Further study of these polymorphisms will help to identify genetic factors that could influence aspects of the pathogenicity and host specificity of C. psittaci.

Nucleotide sequence accession numbers.

The sequences determined in this study have been deposited in the GenBank database under accession numbers CP002804, CP002805, CP002806, and CP002807 for C. psittaci C19/98, 01DC11, 02DC15, and 08DC60, respectively.