Analyses of the Genomes of Chlamydial Isolates from Ruminants and Pigs Support the Adoption of the New Species Chlamydia pecorum

Abstract

Analysis of the genomic DNAs of chlamydial isolates from sheep, cattle, and pigs was performed by Southern blot hybridization and by restriction endonuclease (RE) profiling of DNA amplified by PCR. The hybridization probes were derived from whole genomic DNA, the major outer membrane protein (MOMP) gene, the 16s rRNA gene, and an avian Chlamydia psittaci isolate plasmid. The PCR analysis used targets in the MOMP gene, the 16s rRNA gene, and the 60-kDa cysteine-rich protein gene. Together, the results showed that although there was considerable heterogeneity in the DNA sequence in the MOMP gene region, all the isolates had the same underlying total genomic RE profiles and yielded identical RE profiles for the rRNA and 60-kDa-protein gene regions. Most of the isolates were found to hybridize with the plasmid probe. Comparison of the MOMP sequence of one of the isolates (P787) with that of a known Chlamydia pecorum strain together with the results of the RE analyses allowed the conclusion that the isolates should all be classified within this new species.The genus chlamydia has recently been expanded, largely because of the application of measurements of genomic relatedness to discriminate further the various chlamydial species and types. Currently, there are four species recognized, Chlamydia trachomatis, C. psittaci, C. pneumoniae, and the newest grouping of ruminant strains proposed by Fukushi and Hirai and called C. pecorum (10, 12). Recent multistrain comparisons of the gene sequences of the major outer membrane protein (MOMP) yield phylogenetic trees which support these four species groupings (4, 22,40). However, DNA homology measurements (5, 9) indicate that the species C. trachomatis and C. psittaci could be subdivided further if it is accepted that at least 70% sequence homology is necessary for isolates to be considered as belonging to the same species (20).An important aspect of any taxonomic system is that it should be based on criteria which can easily be applied in a standard fashion by all laboratories and which will allow accurate and rapid identification of isolates. The biological and immunological methods which have been used to identify species and subspecies types of Chlamydia are time-consuming, require considerable skill and experience, and are limited by the problems of generating and standardizing serological reagents. Recently, methods based on identifying variations in DNA sequences, usually through the use of restriction endonuclease (RE) analysis, have been applied to the problem of species and strain identification. When a chlamydia] isolate has been cultured, these methods can be applied either at the whole-genome level (9, 27) or to subgenomic fragments by Southern blotting (11, 18,42). However, a substantial advance has come with the use of the PCR (33), which can be used both to detect the presence of chlamydiae in clinical samples by the amplification of specific chlamydial genes and to identify the chlamydial species and type by analysis of sequence variation in the amplified pro...

Recent advances in the understanding ofChlamydophila pecoruminfections, sixteen years after it was named as the fourth species of the Chlamydiaceae family

“…Some C . pecorum strains do not harbour plasmids (3 out of 11 isolates studied) since they cannot be found by Southern blot analysis [2]. A great number of Chlamydia strains do not have plasmids, suggesting that they are not required for Chlamydial growth.…”

Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes

“…Genetic variation has been reported to occur between C. pecorum strains in ompA , the rrn - nqr F intergenic region, incA , rRNAs, a number of housekeeping genes and the hypothetical protein ORF663 [14–22]. These and other unidentified genomic differences may enable differentiation between strains isolated from asymptomatic or diseased animals.…”

Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms

“…In koalas, Chlamydophila pecorum causes reproductive disease, infertility and urinary tract disease. In other animals, Chlamydophila pecorum has been associated with abortion, conjunctivitis, encephalomyelitis, enteritis, pneumonia and polyarthritis (Anderson et al, 1996;Kaltenboeck et al, 1993). The type strain for Chlamydophila pecorum is E58T (= ATCC VR 62ST).…”

“…Chlamydophila pecorum strains characterized thus far have been limited to mammals, but not to a specific host family: Chlamydophila pecorum has been isolated from ruminants (cattle, sheep and goats) (Denamur et al, 1991;Fukushi & Hirai, 1992), a marsupial (koala) (Girjes et al, 1993;Glassick et al, 1996;M. Jackson et al, 1997) and swine (Anderson et al, 1996;Everett & Andersen, 1997;Kaltenboeck & Storz, 1992). In koalas, Chlamydophila pecorum causes reproductive disease, infertility and urinary tract disease.…”