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The Chlamydiaceae are a family of obligate intracellular bacteria known for their unique biphasic developmental cycle. Chlamydial are associated with various host organisms, including humans, and have been proposed as emerging pathogens. Genomic studies have significantly enhanced our understanding of chlamydial biology, host adaptation, and evolutionary processes. In this study, we conducted a complete pangenome association analysis (pan-GWAS) using 101 genomes from the Chlamydiaceae family to identify differentially represented genes in Chlamydia and Chlamydophila , revealing their distinct evolutionary strategies for interacting with eukaryotic hosts. Our analysis identified 289 genes with differential abundance between the two clades: 129 showed a strong association with Chlamydia and 160 with Chlamydophila . Most genes in Chlamydia were related to the type III secretion system, while Chlamydophila genes corresponded to various functional categories, including translation, replication, transport, and metabolism. These findings suggest that Chlamydia has developed a high dependence on mammalian cells for replication, facilitated by a complex T3SS for intracellular manipulation. In contrast, the metabolic and functional diversity in Chlamydophila allows it to colonize a broad range of hosts, such as birds, reptiles, amphibians, and mammals, making it a less specialized clade.

Chlamydia abortus is responsible for enzootic abortion (known as ovine enzootic abortion (OEA) and enzootic abortion of ewes (EAE)) in both sheep and goats and has major economic implications for the farming industry worldwide. A virulence-attenuated mutant strain of C. abortus (strain 1B) is currently commercially available as a live attenuated vaccine for immunization of sheep and goats in several European countries. Following an abortion storm in a French flock of 200 ewes that occurred two years after vaccination of 36 replacement ewes with the commercial 1B vaccine strain, the vaginal swabs of 3 vaccinated and 7 unvaccinated aborted ewes and 12 of the 13 dead fetuses were found to be positive for C. abortus by real-time PCR. Genotyping of the samples, using vaccine-specific SNP markers, identified all as positive for the vaccine-type strain. The recent vaccination of this flock with the attenuated commercial vaccine strain, the large number of abortion cases observed in ewes irrespective of vaccination status, the high C. abortus load detected in vaginal swabs or abortion tissues and the identification of specific vaccine-type markers in these samples strongly suggest that the 1B strain has been transmitted from vaccinated to naïve animals, thus mimicking a natural wild-type infection., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Several studies have advanced the idea that the etiology of Alzheimer's disease (AD) could be microbial in origin. In the present study, we tested the possibility that polymicrobial infections exist in tissue from the entorhinal cortex/hippocampus region of patients with AD using immunohistochemistry (confocal laser scanning microscopy) and highly sensitive (nested) PCR. We found no evidence for expression of early (ICP0) or late (ICP5) proteins of herpes simplex virus type 1 (HSV-1) in brain sections. A polyclonal antibody against Borrelia detected structures that appeared not related to spirochetes, but rather to fungi. These structures were not found with a monoclonal antibody. Also, Borrelia DNA was undetectable by nested PCR in the ten patients analyzed. By contrast, two independent Chlamydophila antibodies revealed several structures that resembled fungal cells and hyphae, and prokaryotic cells, but most probably were unrelated to Chlamydophila spp. Finally, several structures that could belong to fungi or prokaryotes were detected using peptidoglycan and Clostridium antibodies, and PCR analysis revealed the presence of several bacteria in frozen brain tissue from AD patients. Thus, our results show that polymicrobial infections consisting of fungi and bacteria can be revealed in brain tissue from AD patients.

Many studies have aimed to set up boundaries for the classification and definition of prokaryotic genus and species classification; however, studies that focused on genus-level genomic differences for existing taxonomy systems are limited. Recently, a novel method was described for prokaryotic genus delineation using the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance (Qin et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196: :2210-5). Here, we extended the POCP analysis of the order Chlamydiales and pairwise compared all currently recognized species and candidate species of the family Chlamydiaceae as well as some species from other families. Using the taxonomy advised by the International Committee on Systematics of Prokaryotes, subcommittee on the taxonomy of the Chlamydiae, POCP analysis revealed that all pairwise comparisons of species from different families resulted in values lower than 50%, the proposed threshold for genus boundary. In contrast, all interspecies pairwise comparisons of species from the single genus within the family Chlamydiaceae resulted in POCP values higher than 70%. We conclude that the recommended genus classification of the family Chlamydiaceae is rational and that POCP analyses can provide a robust genomic index for the taxonomy of members of the order Chlamydiales in terms of genus demarcation., (© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Chlamydiae induce a range of pathological syndromes in small ruminants. Abortion is the most common clinical expression of the infection that causes important economic losses and presents a risk to human health, particularly in pregnant women. The present paper gives an overview of chlamydial infections in sheep and goats, focusing specifically on abortion and on recent data brought by cellular and genomic approaches regarding genotyping, virulence of strains, epidemiology, diagnosis, pathogenesis and control of the disease., (Copyright © 2015 Elsevier B.V. All rights reserved.)

The family Chlamydiaceae (order Chlamydiales, phylum Chlamydiae) comprises important, obligate intracellular bacterial pathogens of humans and animals. Subdivision of the family into the two genera Chlamydia and Chlamydophila has been discussed controversially during the past decade. Here, we have revisited the current classification in the light of recent genomic data and in the context of the unique biological properties of these microorganisms. We conclude that neither generally used 16S rRNA sequence identity cut-off values nor parameters based on genomic similarity consistently separate the two genera. Notably, no easily recognizable phenotype such as host preference or tissue tropism is available that would support a subdivision. In addition, the genus Chlamydophila is currently not well accepted and not used by a majority of research groups in the field. Therefore, we propose the classification of all 11 currently recognized Chlamydiaceae species in a single genus, the genus Chlamydia. Finally, we provide emended descriptions of the family Chlamydiaceae, the genus Chlamydia, as well as the species Chlamydia abortus, Chlamydia caviae and Chlamydia felis., (Copyright © 2015 Elsevier GmbH. All rights reserved.)

Chlamydiosis, caused by Chlamydiaceae, is a zoonotic disease found in humans and several species of animals, including reptiles and amphibians. Although chlamydiosis in saltwater crocodiles has been previously reported in South Africa and Papua New Guinea, the reported strains have not been identified or confirmed. Therefore, the main aim of this study was to sequence and characterize Chamydiaceae isolated from Siamese crocodiles. Results showed the 16S ribosomal (r) RNA and the 16S/23S rRNA gene of the crocodile isolates were closely related to the genus Chlamydophila with matched identity greater than 98%. The phylogenetic tree constructed from the 16S/23S rRNA gene showed the crocodile cluster diverges far from Cp. caviae with a 100% bootstrap value. The tree based on the ompA gene loci distinguished the crocodile strains into genotypes I, II, and III. The present study is the first report on Chlamydophila detected in Siamese crocodiles that is genetically distinct from the known species of Chlamydiaceae.

Toxoplasma gondii and Chlamydophila abortus are the 2 most common infectious causes of ovine abortion worldwide. These obligate intracellular pathogens are associated with severe placentitis leading to abortion or stillbirth in pregnant ewes, and resulting in significant economic losses. The objectives of the current study were the development, validation, and application of a duplex real-time polymerase chain reaction (PCR) assay capable of quantifying the burden of infection by T. gondii and C. abortus in material submitted for diagnostic purposes. The validation was carried out using samples from ewes experimentally infected with these organisms. Based on the numbers of genome copies detected, an arbitrary cutoff level was established to correlate with significant pathological changes sufficient to give rise to abortion. When the PCR assay was applied to samples from 66 Irish farms with naturally occurring outbreaks of ovine abortion, toxoplasmosis and enzootic abortion of ewes (EAE) accounted for 14% and 20% of the farms, respectively, while on 6% of the farms, there was evidence of dual infection. When standard diagnostic techniques including histopathological examination, serological analysis, chlamydial antigen detection, and bacteriological culture, were used on samples from the same farms, toxoplasmosis was diagnosed in 17% of farms, and EAE in 12%; dual infection was diagnosed on 3% of the farms. In general, good agreement was found between the PCR and the standard methods. The duplex real-time PCR assay developed in this study has proved to be a very sensitive and rapid tool that might provide a valuable addition to the methods currently available for routine diagnosis of ovine abortions.

Infection of koalas by Chlamydophila pecorum is very common and causes significant morbidity, infertility and mortality. Fundamental to management of the disease is an understanding of the importance of multi-serotype infection or pathogen virulence in pathogenesis; these may need consideration in plans involving koala movement, vaccination, or disease risk assessment. Here we describe diversity of ompA VD1-3, and ORF663 hypothetical gene tandem repeat regions, in a single population of koalas with diverse disease outcomes. We PCR amplified and sequenced 72 partial ompA segments and amplified 25 tandem repeat segments (ORF663 hypothetical gene) from C. pecorum obtained from 62 koalas. Although several ompA genotypes were identified nationally, only one ompA genotype existed within the population studied, indicating that severe chlamydial disease occurs commonly in free-ranging koalas in the absence of infection by multiple MOMP serotypes of C. pecorum. In contrast, variation in tandem repeats within the ORF663 hypothetical gene was very high, approaching the entire range reported for pathogenic and non-pathogenic C. pecorum of European ruminants; providing an impetus for further investigation of this as a potential virulence trait., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Bacteria belonging to the family Chlamydiaceae cause a broad spectrum of diseases in a wide range of hosts, including humans, other mammals and birds. However, very little is known about chlamydial infections in birds in our region. In the present study, we examined 28 clinically normal birds in illegal captivity that were confiscated in the province of C6rdoba, Argentina. The objective was to detect Chlamydophila spp. in cloacal swabs by genetic analysis of the ompA gene. Nested-PCR of the ompA gene identified five samples as Chlamydophila pecorum and the sequence analysis demonstrated the presence of the ompA gene of C. pecorum in these birds. On the other hand, Chlamydophila psittaci was not detected. These birds could be either asymptomatic reservoirs or subclinical carriers of C. pecorum. This is the first report of the detection of C. pecorum in Argentina.

The aim of this study was to investigate the epidemiology of chlamydiosis in free-ranging asymptomatic and diarrhoeic sheep and goats in Egypt. Faecal swabs were examined for the presence of Chlamydiae by culture in Vero cells and chick embryos, and staining with Giménez, direct fluorescein-conjugated monoclonal antibodies, and immunoperoxidase. Specific chlamydial DNA was identified by amplification of the omp2 gene. The asymptomatic goats were 50% positive for the presence of the omp2 gene of the family Chlamydiaceae, and all isolates were Chlamydophila psittaci. The percentage of diseased goats in which Chlamydiaceae were identified was 16.2%, and all were positive for Cp. psittaci. Of the asymptomatic sheep, 6.7% were positive for the omp2 gene of the family Chlamydiaceae, and again all were positive for Cp. psittaci. In contrast, 42.9% of the samples that were collected from the diseased sheep were positive for Chlamydiaceae, of which 25.7% were Cp. psittaci and 4.8% Cp. pecorum.

Infections caused by members of the Chlamydiaceae family have long been underestimated due to the requirement of special laboratory facilities for the detection of this group of intracellular pathogens. Furthermore, new studies of this group of intracellular pathogens have revealed that host specificity of different species is not as clear as recently believed. As most members of the genus Chlamydophila have shown to be transmissible from animals to humans, sensitive and fast detection methods are required. In this study, SYBR green-based real-time assays were developed that detect all members of Chlamydiaceae and differentiate the most prevalent veterinary Chlamydophila species: Cp. psittaci, Cp. abortus, Cp. felis, and Cp. caviae. By adding bovine serum albumin to the master mixes, target DNA could be detected directly in crude lysates of enzymatically digested conjunctival or pharyngeal swabs or tissue specimens from heart, liver, and spleen without further purification. The assays were evaluated on veterinary specimens where all samples were screened using a family-specific PCR, and positive samples were further tested using species-specific PCRs. Cp. psittaci was detected in 47 birds, Cp. felis was found in 10 cats, Cp. caviae was found in one guinea pig, and Cp. abortus was detected in one sheep. The screening assay appeared more sensitive than traditional microscopical examination of stained tissue smears. By combining a fast, robust, and cost-effective method for sample preparation with a highly sensitive family-specific PCR, we were able to screen for Chlamydiaceae in veterinary specimens and confirm the species in positive samples with additional PCR assays.

Objective: To determine the presence of chlamydial species including recently described chlamydial agents as well as the human pathogen Chlamydophila pneumoniae in feline conjunctivitis., Animal Studied: Twenty five cats without and 49 cats with conjunctivitis were tested for chlamydia using a Chlamydiaceae real time (RT) PCR (targeting the 23S rRNA gene sequence), a Chlamydiales PCR (targeting the 16S rRNA gene sequence), and cell culture. The PCR products of all positive samples were sequenced and subsequently analyzed using a basic local alignment search tool search., Results: Chlamydiaceae RT PCR and subsequent sequence analyses identified C. pneumoniae in five cats in the conjunctivitis group. The presence of Chlamydophila felis was shown in two cats with conjunctivitis. Chlamydiae related to uncultured members of Chlamydiales were detected in three conjunctivitis cases and in one cat without clinical symptoms., Conclusion: This study detects for the first time, the known human pathogen C. pneumoniae in feline conjunctivitis cases using Chlamydiaceae RT PCR and sequence analyses., (© 2011 American College of Veterinary Ophthalmologists.)

This study used PCR-RFLP to investigate the genetic variability of pmp-encoding genes from fifty-two Chlamydophila abortus (C. abortus) strains originating from abortion cases from various geographical regions and host species. Six primer pairs were used to PCR-amplify DNA fragments encoding eighteen pmps. PCR products were digested using four restriction endonucleases and Bayesian methodologies were used to compare RFLP profiles and assign strains to a RFLP genotype. Strains could be assigned to 2 genotypes in the region encoding pmp18D, 3 genotypes in the regions encoding pmp1A-pmp2B, pmp3E-pmp6H and pmp11G-pmp15G, 4 genotypes in the region encoding pmp7G-pmp10G and 5 genotypes in the region encoding pmp16G-pmp17G. In all regions, the majority of strains (88.4-96.1%) had the same genotype as the reference strain S26/3. No correlation could be made between genotype, host species or geographical origin except for the two variant Greek strains, LLG and POS, which formed a discrete genotype in all pmp-encoding regions except pmp18D. Relative rates of evolution calculated for each pmp-encoding gene locus suggest that differing selective pressures and functional constraints may exist on C. abortus polymorphic membrane proteins. These findings suggest that although intraspecies heterogeneity of pmp-encoding genes in C. abortus is low, the sequence heterogeneity should be an important consideration when using pmps as the basis for novel diagnostics or vaccine development., (Copyright © 2011 Elsevier B.V. All rights reserved.)

PCR amplification and nucleotide sequencing of the ompA gene of Chlamydia trachomatis were used to determine the prevalence and distribution of genotypes in 51 urine and urethral specimens from Greek male patients with urethritis, that were positive by the COBAS Amplicor test. A single C. trachomatis serovar was identified in 43 of the 51 amplified samples. Serovars F and E were the most prevalent (both 12, 28%), followed by D (9, 21%), G (4, 9%), B and K (both 2, 5%) and H and J (both 1, 2%). Over one third of the samples bared a variant ompA genotype that had been previously identified in other areas worldwide. Two results in this study, both observed for the first time, were of particular interest. First, the emergence of the unique variant genotype D/Ep6 (X77364.2) identified in 3 urethral samples. Second, the ompA genotype OCLH196 of the animal pathogen Chlamydophila abortus as well as a 23S rRNA gene fragment of this species detected by the assay ArrayTube™ was found in 7 urethral samples. The implications resulting from this observation for the health of the general population are discussed., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Chlamydophila abortus is a common cause of ruminant abortion. Here we report the genome sequence of strain LLG, which differs genotypically and phenotypically from the wild-type strain S26/3. Genome sequencing revealed differences between LLG and S26/3 to occur in pseudogene content, in transmembrane head/inc family proteins, and in biotin biosynthesis genes.

Infection can initiate symptoms of mental illness. It has been shown previously that Chlamydophila DNA is present six times more often in the blood of patients with schizophrenia than in the blood of control individuals. Monocytes, the main targets of Chlamydiaceae infection, are microglia precursors. We identified Chlamydiaceae infection using blinded brain DNA samples derived from the frontal cortex. Using PCR and sequence analysis, we found Chlamydophila DNA to be four times greater in patients with schizophrenia than in controls (schizophrenia: N=34, microbial DNA frequency 23.5%; controls: N=35, microbial DNA frequency 5.7%; P=0.045, OR=5.08). Persistent Chlamydophila-infected microglia or neuronal cells may impair neuronal circuits and thus be a mechanism for causing psychiatric illness in these patients., (Copyright © 2011 Elsevier B.V. All rights reserved.)

The evolutionary relationships among known Chlamydophila abortus variant strains including the LLG and POS, previously identified as being highly distinct, were investigated based on rRNA secondary structure information. PCR-amplified overlapping fragments of the 16S, 16S-23S intergenic spacer (IS), and 23S domain I rRNAs were subjected to cloning and sequencing. Secondary structure analysis revealed the presence of transitional single nucleotide variations (SNVs), two of which occurred in loops, while seven in stem regions that did not result in compensatory substitutions. Notably, only two SNVs, in 16S and 23S, occurred within evolutionary variable regions. Maximum likelihood and Bayesian phylogeny reconstructions revealed that C. abortus strains could be regarded as representing two distinct lineages, one including the "classical" C. abortus strains and the other the "LLG/POS variant", with the type strain B577(T) possibly representing an intermediate of the two lineages. The two C. abortus lineages shared three unique (apomorphic) characters in the 23S domain I and 16S-23S IS, but interestingly lacked synapomorphies in the 16S rRNA. The two lineages could be distinguished on the basis of eight positions; four of these comprised residues that appeared to be signature or unique for the "classical" lineage, while three were unique for the "LLG/POS variant". The U277 (E. coli numbering) signature character, corresponding to a highly conserved residue of the 16S molecule, and the unique G681 residue, conserved in a functionally strategic region also of 16S, are the most pronounced attributes (autapomorphies) of the "classical" and the "LLG/POS variant" lineages, respectively. Both lineages were found to be descendants of a common ancestor with the Prk/Daruma C. psittaci variant. Compared with the "classical", the "LLG/POS variant" lineage has retained more ancestral features. The current rRNA secondary structure-based analysis and phylogenetic inference reveal new insights into how these two C. abortus lineages have differentiated during their evolution.

The presence of a plasmid in the Chlamydiaceae is both species and strain specific. Knowledge of the prevalence of the plasmid in different Chlamydia species is important for future studies aiming to investigate the role of the plasmid in chlamydial biology and disease. Although strains of Chlamydophila felis with or without the plasmid have been identified, only a small number of laboratory-adapted strains have been analysed and the prevalence of the plasmid in field isolates has not been determined. This study aimed to determine the prevalence of the plasmid in C. felis-positive conjunctival and oropharyngeal clinical samples submitted for routine diagnosis of C. felis by real-time (Q)PCR. DNA extracts from four laboratory-adapted strains were also analysed. QPCR assays targeting regions of C. felis plasmid genes pCF01, pCF02 and pCF03 were developed for the detection of plasmid DNA. QPCR analysis of DNA extracts from C. felis-positive clinical samples found evidence of plasmid DNA in 591 of 595 samples representing 561 of 564 (99.5%) clinical cases. Plasmid DNA was also detected by QPCR in laboratory-adapted strains 1497V, K2487 and K2490, but not strain 905. We conclude that the plasmid is highly conserved in C. felis, and plasmid-deficient strains represent a rare but important population for future studies of chlamydial plasmid function., (Copyright © 2010 Elsevier B.V. All rights reserved.)

Chlamydophila abortus, the agent of ovine enzootic abortion (OEA), is a major cause of lamb mortality worldwide. Disease can be controlled through the use of vaccines based on the 1B temperature-sensitive mutant strain of C. abortus. This study investigated suspected OEA cases across Scotland for the presence of the 1B strain by analysis of recently identified unique point mutations (9). Thirty-five cases were C. abortus-positive and 14 came from vaccinated flocks. Analysis of single nucleotide polymorphisms by PCR-RFLP and sequence analysis revealed the presence of point mutations consistent with the presence of the 1B vaccine strain in 5 of these 14 samples. Quantitative real-time PCR revealed comparable numbers of genome copies of the 1B strain in infected placentas to those present following wild-type infection. This study is the first to demonstrate the presence of the 1B vaccine strain in the placentas of OEA cases and suggests a probable causal role in the disease., (Copyright 2010 Elsevier Ltd. All rights reserved.)

Comparative genomic analysis of a wild-type strain of the ovine pathogen Chlamydophila abortus and its nitrosoguanidine-induced, temperature-sensitive and virulence-attenuated live vaccine derivative identified point mutations unique to the mutant (Burall et al. [1]). Here, we evaluate the capacity of some of these mutations to either create or eliminate restriction sites using the wild-type strain C. abortus S26/3 as a reference. Three of eight genomic sites with confirmed point mutations (CAB153, CAB636 and CAB648) were retained for analysis as each resulted in the loss of a restriction site in the genome sequence of the vaccine strain. PCR-restriction fragment length polymorphism analysis using restriction enzymes chosen to specifically target the three genomic sites was then applied to a large number of C. abortus field isolates and reference strains. Our results indicate that the three mutations are uniquely present in the vaccine strain, and as such provide easy-to-use markers for the differential identification of the vaccine strain and wild-type isolates., (Copyright 2010 Elsevier Ltd. All rights reserved.)

Chlamydophila pecorum strains are commonly found in the intestine and vaginal mucus of asymptomatic ruminants and may therefore induce a positive serological response when the animals are tested for C. abortus. They have also been associated with different pathological diseases in ruminants, swine and koala. The aim of this study was to identify specific C. pecorum immunodominant antigens which could be used in ELISA tests allowing to distinguish between animals infected with C. pecorum and those infected with other chlamydial species. A gene encoding 35-kDa inclusion membrane protein incA of C. pecorum was isolated by immunoscreening of the C. pecorum DNA library using ovine anti-C. pecorum antibodies. The recombinant IncA protein did not react with a murine serum directed against C. abortus but did react with a specific monoclonal antibody of C. pecorum and toward several ovine serum samples obtained after experimental infection with different C. pecorum strains. This protein could be a good candidate for specific diagnosis of C. pecorum infection., ((c) 2009 Elsevier B.V. All rights reserved.)

At a stud farm of Trakehner horses, all 33 foals of a birth cohort developed conjunctivitis and serous to muco-purulent rhinitis, and 7 older horses showed recurrent signs of conjunctivitis. Examination of nasal and conjunctival swabs by bacterial and cell culture, as well as real-time PCR, ArrayTube microarray analysis and DNA sequencing led to the identification of Chlamydophila (C.) caviae (first description in horses) and Streptococcus (S.) equi subsp. zooepidemicus. We presume a synergistic effect associated with these two agents by hypothesising that primary lesions were set by C. caviae and subsequently aggravated by Streptococcus equi subsp. zooepidemicus. Indications supporting this assumption include (i) the conjunctivitis caused by mono-infection with C. caviae, (ii) recurrent clinical symptoms in the affected animals, and (iii) the absence of a sustained clinical effect of antibiotic therapy with trimethoprim-sulfonamide, enrofloxacin and amoxicillin. The detection of C. caviae in horses raises questions about the significance and natural host range of this agent., (Copyright 2009 Elsevier B.V. All rights reserved.)

Plasmids have been detected in the majority of strains in the genus Chlamydia and in many Chlamydophila species. Previous studies showed that FP Pring and FP Cello Chlamydophila felis strains have an extrachromosomial plasmid, whereas the FP Baker strain does not. Azuma et al. recently sequenced the entire genomic DNA sequence of the Japanese Cp. felis strain Fe/C-56 and described a 7,552 base pair circular plasmid. In the present study a highly conserved plasmid gene was detected in 11 Italian Cp. felis isolates, showing 100% nucleotide identity with the plasmid gene of Fe/C-56 Cp. felis strain.

In 2000, chlamydial strains OK133 and OK135 were isolated from 2 female patients with cervicitis. These strains were unresponsive to commercially available PCR and LCR test kits for the diagnosis of Chlamydia trachomatis infection, and their phenotypic characteristics were very similar. The OK135 nucleotide sequence in MOMP-VD2 gene closely resembled that of Chlamydophila caviae GPIC. A similar strain was isolated in 2003 from a male patient OKM2 with urethritis, from which the strain SC10-6 was cloned by the plaque purification method. The nucleotide sequence of the entire MOMP gene of SC10-6 was exactly the same as that of OK135. Thus, the strains OK135 and SC10-6, together with OK133, have been called C. caviae-like Chlamydia. We designed primers for nested PCR assay, the product of which showed a single-band 311-bp fragment, to detect C. caviae-like Chlamydia. Of swab specimens obtained from 202 patients from 2003 to 2006 (119 male and 83 female patients), 18 specimens (8.9%) from 14 male and 4 female patients were positive, suggesting that C. caviae-like Chlamydia infection is rather common. Thus far, it has not been determined whether C. caviae-like Chlamydia is pathogenic for humans.

Background: Reproductive disorders associated with chlamydial infection have been reported worldwide in cattle and there are indications of potential venereal transmission., Methods: Semen samples from 21 dairy bulls and cauda epididymidis tissue samples from 43 beef bulls were analysed for chlamydial agent by real-time polymerase chain reaction (PCR) including an internal amplification control (mimic). Additionally, presence of antibodies against Chlamydophila (Cp.) abortus among the bulls was investigated with the commercial Pourquier ELISA Cp. abortus serum verification kit., Results: No chlamydial agent was detected by PCR in either the semen samples or in the tissue samples. Additionally, no antibodies against Cp. abortus were detected., Conclusions: The results suggest that Cp. abortus is very rare, or absent in Swedish bulls and thus the risk for venereal transmission of chlamydial infection through their semen is low. However, because Chlamydophila spp. infection rates seem to differ throughout the world, it is essential to clarify the relative importance of transmission of the infection through semen on cattle fertility.

Chlamydophila psittaci and Chlamydophila abortus are the causative agents of avian chlamydiosis (psittacosis) and ovine enzootic abortion, respectively. Both pathogens are known to possess zoonotic potential. Due to their close genetic relatedness, direct and rapid species identification is difficult. In the present study, new real-time PCR assays are reported for both species. The tests are based on highly specific probes targeting the ompA gene region and were conducted as duplex PCRs including an internal amplification control. The Cp. psittaci assay successfully passed a proficiency test at national level. Examination of field samples revealed Cp. psittaci as the dominating species in birds, but also Cp. abortus in a few psittacines. Real-time PCR assays for species-specific detection of Cp. psittaci and Cp. abortus are suited for routine diagnosis, which renders them important tools for the recognition of outbreaks of psittacosis and ovine enzootic abortion.

Chlamydophila (C.) abortus is the causative agent of ovine enzootic abortion with zoonotic potential whose epidemiology has been held back because of the obligate intracellular habitat of the bacterium. In the present study, we report on a molecular typing method termed multiple loci variable number of tandem repeats (VNTR) Analysis (MLVA) for exploring the diversity of C. abortus. An initial analysis performed with 34 selected genetic loci on 34 ruminant strains including the variant Greek strains LLG and POS resulted in the identification of five polymorphic loci, confirming the widely held notion that C. abortus is a very homogeneous species. Analysis of additional 111 samples with the selected five loci resulted in the classification of all strains into six genotypes with distinct molecular patterns termed genotypes [1] through [6]. Interestingly, the classification of the isolates in the six genotypes was partly related to their geographical origin. Direct examination of clinical samples proved the MLVA to be suitable for direct typing. Analysis of the genomic sequences in six C. abortus prototypes of amplicons generated with each of the five selected VNTR primers revealed that variation between genotypes was caused by the presence or absence of coding tandem repeats in three loci. Amplification of Chlamydophila psittaci reference strains with the five selected VNTR primers and of the six C. abortus prototype strains with the eight VNTR primers established for the typing of C. psittaci [Laroucau, K., Thierry, S., Vorimore, F., Blanco, K., Kaleta, E., Hoop, R., Magnino, S., Vanrompay, D., Sachse, K., Myers, G.S., Bavoil, P.M., Vergnaud, G., Pourcel, C., 2008. High resolution typing of Chlamydophila psittaci by multilocus VNTR analysis (MLVA). Infect. Genet. Evol. 8(2), 171-181] showed that both MLVA typing systems were species-specific when all respective VNTR primer sets were used. In conclusion, the newly developed MLVA system provides a highly sensitive, high-resolution and easy-to-perform tool for the differentiation of C. abortus isolates of different origin, which is suitable for molecular epidemiological studies.

Infections with the intracellular bacterium Chlamydophila (C.) pecorum are highly prevalent worldwide in cattle. These infections cause significant diseases such as polyarthritis, pneumonia, enteritis, genital infections and fertility disorders, and occasionally sporadic bovine encephalomyelitis. Subclinical respiratory infections of calves with C. pecorum have been associated with airway obstruction, pulmonary inflammation, and reduced weight gains. This investigation examined four chlamydial strains with biological properties of C. pecorum isolated from feces of clinically normal cattle, from calves with pneumonia, and from bulls with posthitis. The objective was to characterize the evolutionary relationships of these bovine chlamydial isolates to other chlamydiae by genetic analysis of the ompA gene, and by the immunological cross-reactivities in Western immunoblot analysis. PCR typing of the ompA gene identified these isolates as C. pecorum. The OmpA-deduced amino acid dissimilarities between these four strains spanned 10-20%. In phylogenetic analysis, the four isolates clustered with C. pecorum ruminant, porcine, and koala strains of different geographic origins rather than with each other. All four isolates showed different patterns of Western immunoblot reactivity with antiserum against bovine C. pecorum strain LW63, and, interestingly, no cross-reactivity of the OmpA proteins with the anti-LW613 OmpA antibodies. These data underscore the polyphyletic population structure of C. pecorum and suggest that the spectrum of C. pecorum OmpA proteins in a host species can occupy the entire evolutionary bandwidth within C. pecorum. The variant immunoblot reactivities support the notion of considerable genomic plasticity of C. pecorum.

Chlamydophila pecorum is an obligate intracellular bacterium associated with different pathological conditions in ruminants, swine and koala, which is also found in the intestine of asymptomatic animals. A multi-virulence locus sequence typing (MVLST) system was developed using 19 C. pecorum strains (8 pathogenic and 11 non-pathogenic intestinal strains) isolated from ruminants of different geographical origins. To evaluate the ability of MVLST to distinguish the pathogenic from the non-pathogenic strains of C. pecorum, the sequences of 12 genes were analysed: 6 potential virulence genes (ompA, incA, incB, incC, mip and copN), 5 housekeeping genes (recA, hemD, aroC, efp, gap), and the ORF663 gene encoding a hypothetical protein (HP) that includes a variant 15-nucleotides coding tandem repeat (CTR). MVLST provided high discriminatory power (100%) in allowing to distinguish 6 of 8 pathogenic strains in a single group, and overall more discriminatory than MLST targeting housekeeping genes. ompA was the most polymorphic gene and the phylogenetic tree based only on its sequence differentiated 4 groups with high bootstrap values. The number of CTRs (rich in serine, proline and lysine) in ORF663 detected in the pathogenic strains was generally lower than that found in the intestinal strains. MVLST appears to be a promising method for the differential identification of virulent C. pecorum strains, and the ompA, incA and ORF663 genes appear to be good molecular markers for further epidemiological investigation of C. pecorum.

Bacteria of the family Chlamydiaceae are obligate intracellular pathogens of human and animals. Chlamydophila pecorum is associated with different pathological conditions in ruminants, swine and koala. To characterize a coding tandem repeat (CTR) identified at the 3' end of incA gene of C. pecorum, 51 strains of different chlamydial species were examined. The CTR were observed in 18 of 18 tested C. pecorum isolates including symptomatic and asymptomatic animals from diverse geographical origins. The CTR were also found in two strains of C. abortus respectively isolated from faeces from a healthy ewe and from a goat belonging to asymptomatic herds, but were absent in C. abortus strains isolated from clinical disease specimens, and in tested strains of C. psittaci, C. caviae, C. felis and C. trachomatis. The number of CTR repeats is variable and encode several motifs that are rich in alanine and proline. The CTR-derived variable structure of incA, which encode the Chlamydiaceae-specific type III secreted inclusion membrane protein, IncA, may be involved in the adaptation of C. pecorum to its environment by allowing it to persist in the host cell.

We have identified the gene product of locus 766 in the transmembrane head region (TMH/Inc-region) in the Chlamydophila abortus genome by using mass spectrometry and a monoclonal antibody that reacted with the inclusion membrane. The identified protein at 32 kDa, termed Inc766, formed highly stable oligomers when solubilized in the absence of beta-mercaptoethanol. These oligomers were resistant to SDS, to heat denaturation and to 8M urea, but very sensitive to beta-mercaptoethanol, consistent with conformations resulting from protein-protein interactions stabilized through disulphide bonds. Mass spectrometry analysis of immunoprecipitated infected cell lysates indicated that a dimer at 56 kDa was the most prominent form in solution. Cross-linking with DSP provided supporting evidence for the formation of oligomers in situ. Inc766 was expressed at 20-24h post infection and its localization pattern in the extra-inclusion space was common in all C. abortus strains tested. Taken together, Inc766 displays unique biochemical and cellular features not encountered in other Incs from other Chlamydiaceae species. Future studies of the particular characteristics especially the interactive properties of Inc766 should contribute to our understanding of the relationship of the different chlamydial species with their respective hosts.

Background: Reports worldwide indicate high prevalence of Chlamydophila spp. infection in cattle. To assess the prevalence in Sweden, 525 cows in 70 dairy herds with reproductive disorders was investigated., Methods: To detect antibodies two commercially available kits were used. Moreover, 107 specimens, including vaginal swabs, organ tissues and milk were analysed by Polymerase Chain Reaction (PCR)., Results: Two (0.4%) cows were seropositive in the Pourquier Cp. abortus ELISA. The seroprevalence with the Chekit ELISA was 28% with no difference between cases and controls. Five specimens were positive in real-time PCR and further analysed by nested PCR. Cp. pecorum was confirmed by partial omp1 DNA sequencing of the nested PCR product of vaginal swabs from control cows., Conclusion: The results suggest that Cp. abortus infection is absent or rare in Swedish cows whereas Cp. pecorum is probably more spread. They also suggest that Chlamydophila spp. are not related to reproduction disorders in Swedish cattle.

A DNA fragment encoding the MOMP gene of Chlamydophila psittaci was fused to the heat-labile toxin B subunit gene (LTB-MOMP) and transferred into rice callus by Agrobacterium tumefaciens-mediated transformation. The LTB-MOMP fusion gene was detected in genomic DNA from transformed rice leaves by Southern blot and RT-PCR amplification. Synthesis and assembly of the LTB-MOMP fusion protein into pentamers was detected in transformed leaf extracts by immunoblot analysis. Binding of the pentamers to intestinal epithelial cell membrane glycolipid receptors was quantified by GM1-ganglioside enzyme-linked immunosorbent assay (GM1-ELISA). The ELISA results indicated that LTB-MOMP fusion protein made up 0.0033-0.0054% of the total soluble leaf protein. Meanwhile, this suggested that the fusion protein retained both its native antigenicity and the ability to form pentamers.

The prevalence of feline herpesvirus-1 (FHV-1), feline calicivirus (FCV), and Chlamydophila (C.) felis was studied in cats of an animal shelter in Korea. Total 78 cats without ocular and upper respiratory tract disease were examined. Specimens were obtained from ocular conjunctiva and oropharynx. Using multiplex polymerase chain reaction (PCR) and reverse transcription PCR, three pathogens were simultaneously detected. In examined 78 cats, 49 (63%) cats were positive for FHV-1. However, all specimens were negative for C. felis and FCV. In conclusion, many cats recovered from FHV-1 infection remain subclinical carriers in shelter environment.

Chlamydia trachomatis is the leading cause of preventable blindness and bacterial sexually transmitted diseases worldwide. Plaque assays have been used to clonally segregate laboratory-adapted C. trachomatis strains from mixed infections, but no assays have been reported to segregate clones from recent clinical samples. We developed a novel shotgun cell culture harvest assay for this purpose because we found that recent clinical samples do not form plaques. Clones were strain-typed by using outer membrane protein A and 16S rRNA sequences. Surprisingly, ocular trachoma reference strain A/SA-1 contained clones of Chlamydophila abortus. C. abortus primarily infects ruminants and pigs and has never been identified in populations where trachoma is endemic. Three clonal variants of reference strain Ba/Apache-2 were also identified. Our findings reflect the importance of clonal isolation in identifying constituents of mixed infections containing new or emerging strains and of viable clones for research to more fully understand the dynamics of in vivo strain-mixing, evolution, and disease pathogenesis.

A group of genes thought to encode members of the unique chlamydial polymorphic membrane protein (pmp) family were recently described in the Chlamydophila felis genome. This study aimed to commence characterisation of a subset of 12 of these putative pmp genes by developing and using gene-specific real-time (Q)PCR assays to confirm their presence in a wide range of C. felis field isolates and laboratory strains, and to look for pmp mRNA expression during in vitro infection. Sequencing of 525-698 base pair regions of pmp genes 7, 9-11, 13-20 for two laboratory strains of C. felis and alignment with the published Fe/C-56 sequence found only a single nucleotide polymorphism present in pmp9. Following the development of gene-specific (Q)PCR assays, analysis of genomic DNA extracted from 40 C. felis field isolates and 4 laboratory strains found that all 12 pmp genes were represented in all cases. Reverse transcription (RT)-QPCR analysis of RNA extracted from cell cultures at 24 and 48 h post inoculation with 1 of 5 different strains of C. felis detected transcripts for all 12 pmp genes at both time points. Analysis of the relative levels of pmp gene transcription suggested that down-regulation of the expression of multiple C. felis pmp genes occurs between 24 and 48 h post inoculation. This study provides the first evidence that 12 of the putative pmp C. felis genes are transcribed during in vitro infection, and shows that these genes are present in a large range of C. felis field isolates and multiple passage laboratory-grown strains.

In order to evaluate the relevance of multiple infections in domestic cats with Upper Respiratory Tract Disease (URTD) one hundred animals with clinical signs were investigated for detection of Feline Herpesvirus type-1 (FHV-1), Chlamydophila felis, Feline Calicivirus (FCV) and Bordetella bronchiseptica from mucosal swabs. Forty-seven cats were positive for FCV, 42 cats for FHV-1, 26 for B. bronchiseptica and 8 for C. felis. Dual or multiple infections were found in 33 of examined animals. Our results document that FCV and FHV-1 are the major recognized cause of URTD, although infections associated with other pathogens such as B. bronchiseptica or C. felis are also common in cats.

Background: Prevention and control of ovine enzootic abortion (OEA) can be achieved by application of a live vaccine. In this study, five sheep flocks with different vaccination and infection status were serologically tested using a competitive enzyme-linked immunosorbent assay (cELISA) specific for Chlamydophila (Cp.) abortus over a two-year time period., Results: Sheep in Flock A with recent OEA history had high antibody values after vaccination similar to Flock C with natural Cp. abortus infections. In contrast, OEA serology negative sheep (Flock E) showed individual animal-specific immunoreactions after vaccination. Antibody levels of vaccinated ewes in Flock B ranged from negative to positive two and three years after vaccination, respectively. Positive antibody values in the negative control Flock D (without OEA or vaccination) are probably due to asymptomatic intestinal infections with Cp. abortus. Excretion of the attenuated strain of Cp. abortus used in the live vaccine through the eye was not observed in vaccinated animals of Flock E., Conclusion: The findings of our study indicate that, using serology, no distinction can be made between vaccinated and naturally infected sheep. As a result, confirmation of a negative OEA status in vaccinated animals by serology cannot be determined.

A PCR was used to detect the genome of Chlamydophila abortus in samples of uterine tissue collected from 304 sheep by a sterile technique at an abattoir. The stage of pregnancy of the sheep was determined by measuring the dimensions of the embryo/fetus, and its morphology was recorded. Only samples from non-pregnant sheep and sheep up to 100 days of gestation were retained; the clinical history of the animals was unknown. The total prevalence of the chlamydial genome was 30.9 per cent, with a significantly higher prevalence in the pregnant animals (46.9 per cent). Higher detection rates were recorded during early gestation than during mid-gestation.

The obligate intracellular nature of chlamydiae presents challenges to the characterization of its phages, which are potential tools for a genetic transfer system. An assay for phage infectivity is described, and the infectious properties of phage Chp2 were determined.

Polymerase chain reaction (PCR) has gained increasing importance as a tool for directly demonstrating the presence of Chlamydophila in the placentas of aborted sheep and goats. However, because of the zoonotic potential of the disease, it is advisable to use fixed materials. To evaluate 4 different DNA extraction protocols in paraffin-embedded sections for PCR, previously immunohistochemically diagnosed placental samples from outbreaks of abortions in goats and sheep were used. The samples were also used to evaluate the effect of the duration of fixation in formalin on PCR. A protocol that uses Tris-HCl pH 8.5 with EDTA and subsequent digestion with proteinase K was found to be an easy protocol for obtaining excellent PCR products for Chlamydophila abortus diagnosis from formalin-fixed and paraffin-embedded specimens. It was also found that if samples are fixed in formalin for more than 2 weeks, the PCR technique is affected more adversely than immunohistochemical methods.

Objective: To use PCR assays to determine the prevalence of feline herpesvirus 1 (FHV-1), Chlamydophila felis, and Mycoplasma spp DNA in conjunctival cells collected from cats with and without conjunctivitis; to compare results of conventional and real-time fluorogenic PCR assays for amplification of FHV-1 DNA; and to determine whether copy numbers of FHV-1 DNA are correlated with conjunctivitis., Animals: 55 cats with active conjunctivitis, 39 healthy cats that never had conjunctivitis, and 32 cats with a history of conjunctivitis that had been resolved for at least 3 months., Procedures: Samples were obtained by rolling cotton-tipped applicators on the ventral conjunctiva of awake cats treated topically with proparacaine. The DNA was extracted from the swab specimens and assessed in PCR assays to detect DNA of FHV-1 (fluorogenic PCR assay and conventional PCR assay), Mycoplasma spp (conventional PCR assay), and C felis (conventional PCR assay)., Results: Overall prevalence rates of FHV-1, C felis, and Mycoplasma spp as assessed by the conventional PCR assays were 6.7%, 3.2%, and 9.6%, respectively. Percentage concordance between conventional PCR and fluorogenic PCR assays for FHV-1 was 92.5%. There were no significant differences among the 3 groups of cats for the mean copy number of FHV-1 divided by the copy number of glyceraldehyde-3-phosphate dehydrogenase., Conclusions and Clinical Relevance: Mycoplasma spp were the most prevalent organism detected and was associated with conjunctivitis. This study could not confirm that there are increased copy numbers of FHV-1 DNA in cats with conjunctivitis, compared with the copy numbers for cats without conjunctivitis.

Infections with Chlamydophila abortus and C. pecorum are highly prevalent in cattle and have been associated with bovine mastitis. A prospective cohort study was conducted with a herd of 140 Holstein dairy cows to investigate the influence of Chlamydophila infection on subclinical inflammation of the bovine mammary gland as characterized by somatic cell numbers in milk. PCR detection of C. abortus and low serum antibody levels against Chlamydophila spp. were significantly associated with subclinical mastitis. To examine the effect of the infection by response modification, immune perturbation was done by two subcutaneous administrations of an experimental vaccine preparation of inactivated C. abortus and C. pecorum elementary bodies. Vaccination against Chlamydophila highly significantly decreased milk somatic cell numbers, thus reducing bovine mastitis, and increased antibody levels against Chlamydophila but did not eliminate shedding of C. abortus in milk as detected by PCR. The protective effect peaked at 11 weeks after vaccination and lasted for a total of 14 weeks. Vaccination with the Chlamydophila vaccine, a mock vaccine, or a combination vaccine against bovine viral diseases highly significantly increased C. abortus shedding in milk for 1 week, presumably mediated by the vaccine adjuvant. In summary, this study shows an etiological involvement of the widespread Chlamydophila infections in bovine mastitis, a herd disease of critical importance for the dairy industry. Furthermore, this investigation shows the potential for temporary improvement of chlamydial disease by therapeutic vaccination. Chlamydophila vaccination of cattle might serve as a testing ground for vaccines against human chlamydial infections.

The aim was to evaluate the "strategical place" of the new commercial test Chlamylege (Argene-Biosoft-France) which allows the simultaneous detection in respiratory samples of Chlamydophila pneumoniae, Mycoplasma pneumoniae and most Legionella species using a PCR multiplex. 41 patients with an atypical pneumonia were included, all standard procedures of diagnosis were done and in addition the chamylege test. A pathogen was identified in 12 patients, an other microorganisms than the 3 targeted by our study was found in 8 patients. 4 positive PCR were obtained, 3 with M. pneumoniae and 1 with Legionella pneumophila 1. That means that for 29 patients no aetiology was found. Among them 23 clearly improved under antibiotic treatment. Though that PCR multiplex is an attractive test, easy to perform, sensitive, specific and convenient, we need further studies to approach the place of this PCR test in the diagnosis of multifaceted atypical pneumonia. We also need to know if the cost associated with the microbiological diagnosis (culture, serology, immunofluorescence, urinary antigen test, PCR...) for atypical pneumonia worth value? An algorithm as to be drawn to determine the value of intensive microbiological investigation. An other point to discuss, may be this kind of rapid and multiplex PCR technique could lead to spare the use of some antibiotics.

Chlamydiae are one of the causative agents of various diseases in animals and human beings, which include abortion, pneumonia, gastroenteritis, encephalomyelitis, conjunctivitis, arthritis and sexually transmitted diseases. Much work has been carried out to attempt to develop an efficient pathogen detection strategy. Here, we presented a Chlamydiaceae-specific 23S rRNA-based real-time PCR assay for simultaneous detection and quantification of four members of Chlamydiaceae family, C. trachomatis, C. psittaci, C. pneumoniae and C. pecorum, using SYBR Green and Lightcycler. The assay was characterized using plasmid constructs of the bacteria and verified on standard strains of all four species of the Chlamydiaceae and a large cohort of clinical samples collected from human and animals by comparison with fluorescence immunohistochemistry method. The results showed that the present real-time PCR assay was of high specificity and sensitivity. It was capable of detecting as few as 250fg of chlamydial DNA (equivalent to 10(-1)IFU) and was applicable to both liquid cultures and clinical samples. This assay may therefore offer a rapid, economic and reliable means for screening of the chlamydiaceae pathogens.

Background: Chlamydiae species are of much importance from a clinical viewpoint. Their diversity both in terms of their numbers as well as clinical involvement are presently believed to be significantly underestimated. The obligate intracellular nature of chlamydiae has also limited their genetic and biochemical studies. Thus, it is of importance to develop additional means for their identification and characterization., Results: We have carried out analyses of available chlamydiae genomes to identify sets of unique proteins that are either specific for all Chlamydiales genomes, or different Chlamydiaceae family members, or members of the Chlamydia and Chlamydophila genera, or those unique to Protochlamydia amoebophila, but which are not found in any other bacteria. In total, 59 Chlamydiales-specific proteins, 79 Chlamydiaceae-specific proteins, 20 proteins each that are specific for both Chlamydia and Chlamydophila and 445 ORFs that are Protochlamydia-specific were identified. Additionally, 33 cases of possible gene loss or lateral gene transfer were also detected., Conclusion: The identified chlamydiae-lineage specific proteins, many of which are highly conserved, provide novel biomarkers that should prove of much value in the diagnosis of these bacteria and in exploration of their prevalence and diversity. These conserved protein sequences (CPSs) also provide novel therapeutic targets for drugs that are specific for these bacteria. Lastly, functional studies on these chlamydiae or chlamydiae subgroup-specific proteins should lead to important insights into lineage-specific adaptations with regards to development, infectivity and pathogenicity.

Due to its highly parallel approach, DNA microarray technology opens up new possibilities that may be particularly beneficial for laboratory diagnosis of infectious diseases. We developed a microarray assay for detection and differentiation of all currently defined chlamydial species belonging to the genera Chlamydia and Chlamydophila using the ArrayTube system, which we found to be particularly user-friendly and economical. The test includes PCR amplification of a 23S rDNA target region with concurrent biotinylation and subsequent hybridisation in the ArrayTube, a micro-reaction tube carrying the microarray chip on the bottom. In addition to high specificity, the assay was shown to allow detection and genetic characterisation of single PCR-amplifiable target DNA copies.