Genome Sequence of Chlamydia suis MD56, Isolated from the Conjunctiva of a Weaned Piglet.

Chlamydia suis is a natural pathogen of pigs (Sus scrofa) and causes conjunctivitis, pneumonia, enteritis, and various reproductive disorders that adversely impact this economically important animal. Here, we report the first C. suis genome, that of C. suis MD56, isolated from a conjunctival swab of a weaned piglet.

GENOME ANNOUNCEMENT

Members of the genus Chlamydia are obligate intracellular bacterial pathogens responsible for a variety of diseases in both humans and animals (1). Chlamydia suis infects pigs (Sus scrofa) and is associated with porcine conjunctivitis, rhinitis, pneumonia, enteritis, pericarditis, polyarthritis, polyserositis, various reproductive disorders, and inferior semen quality (2). C. suis infections appear to be common in both wild and domesticated pig herds and often occur in mixed infections with Chlamydia abortus and Chlamydia pecorum (2).

We sequenced C. suis MD56, originally isolated in 2009 from a weaned piglet (Udine, Friuli-Venezia Giulia, Italy) with conjunctivitis. A draft MD56 genome sequence was determined using Illumina sequencing chemistry on an Illumina GAII instrument, producing 3,136,872 total reads. These reads were assembled into a draft genome using Velvet (version 1.1) (3). The MD56 draft genome consists of 47 contigs, representing 160× coverage. Gene identification and annotation were performed as previously described (4). Functional assignment, identification of membrane-spanning domains, determination of paralogous gene families, and identification of regions of unusual nucleotide composition were also performed as previously described (4). The MD56 genome is 1,074,340 bp and contains 933 coding sequences (CDSs). To our knowledge, this is the first C. suis genome to be reported. One assembled contig exhibits high homology to the conserved 7.5-kb chlamydial plasmid.

The chlamydial plasticity zone (PZ) is a region at the replication terminus of the chromosome that encapsulates much of the observed interspecies chlamydial variation (5, 6). This heterogeneous region includes putative chlamydial virulence factors that may play a role in host tropism or niche specificity (7). The C. suis plasticity zone is similar to the Chlamydia trachomatis and Chlamydia muridarum PZs in both relative size and gene organization. C. suis possesses two copies of the chlamydial cytotoxin ortholog, whereas C. muridarum has three copies and C. trachomatis has only gene decay fragments. Both C. suis and C. trachomatis have the trpBA operon at the 3′ end of the PZ and lack the guaBA operon found in the same location in C. muridarum.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. AYKJ00000000. The version described in this paper is the first version, AYKJ01000000.