Evolutionary relationships among members of the genus Chlamydia based on 16S ribosomal DNA analysis

Nucleotide sequences from strains of the four species currently in the genus Chlamydia, C. pecorum, C. pneumoniae, C. psittaci, and C. trachomatis were investigated. In vitro-amplified RNA genes of the ribosomal small subunit from 30 strains of C. pneumoniae and C. pecorum were subjected to solid-phase DNA sequencing of both strands. The human isolates of C. pneumoniae differed in only one position in the 16S rRNA gene, indicating genetic homogeneity among these strains. Interestingly, horse isolate N16 of C. pneumoniae was found to be closely related to the human isolates of this species, with a 98.9% nucleotide similarity between their 16S rRNA sequences. The type strain and koala isolates of C. pecorum were also found to be very similar to each other, possessing two different 16S rRNA sequences with only one-nucleotide difference. Furthermore, the C. pecorum strains truncated the 16S rRNA molecule by one nucleotide compared to the molecules of the other chlamydial species. This truncation was found to result in loss of a unilaterally bulged nucleotide, an attribute present in all other eubacteria. The phylogenetic structure of the genus Chlamydia was determined by analysis of 16S rRNA sequences. All phylogenetic trees revealed a distinct line of descent of the family Chlamydiaceae built of two main clusters which we denote the C. pneumoniae cluster and the C. psittaci cluster. The clusters were verified by bootstrap analysis of the trees and signature nucleotide analysis. The former cluster contained the human isolates of C. pneumoniae and equine strain N16. The latter cluster consisted of C. psittaci, C. pecorum, and C. trachomatis. The members of the C. pneumoniae cluster showed tight clustering and strain N16 is likely to be a subspecies of C. pneumoniae since these strains also share some antigenic cross-reactivity and clustering of major outer membrane protein gene sequences. C. psittaci and strain N16 branched early out of the respective cluster, and interestingly, their inclusion bodies do not stain with iodine. Furthermore, they also share less reliable features like normal elementary body morphology and plasmid content. Therefore, the branching order presented here is very likely a true reflection of evolution, with strain N16 of the species C. pneumoniae and C. psittaci forming early branches of their respective cluster and with C. trachomatis being the more recently evolved species within the genus Chlamydia.     

High-level expression of Chlamydia psittaci major outer membrane protein in COS cells and in skeletal muscles of turkeys

The omp1 genes encoding the major outer membrane proteins (MOMPs) of avian Chlamydia psittaci serovar A and D strains were cloned and sequenced. The nucleotide sequences of the avian C. psittaci serovar A and D MOMP genes were found to be 98.9 and 87.8% identical, respectively, to that of the avian C. psittaci serovar A strain 6BC, 84.6 and 99.8% identical to that of the avian C. psittaci serovar D strain NJ1, 79.1 and 81.1% identical to that of the C. psittaci guinea pig inclusion conjunctivitis strain, 60.9 and 62.5% identical to that of the Chlamydia trachomatis L2 strain, and 57.5 and 60.4% identical to that of the Chlamydia pneumoniae IOL-207 strain. The serovar A or D MOMPs were cloned in the mammalian expression plasmid pcDNA1. When pcDNA1/MOMP A or pcDNA1/MOMP D was introduced into COS7 cells, a 40-kDa protein that was identical in size, antigenicity, and electrophoretic mobility to native MOMP was produced. Recombinant MOMP (rMOMP) was located in the cytoplasm of transfected COS7 cells as well as in the plasma membrane and was immunoaccessible. Intramuscular administration of pcDNA1/MOMP in specific-pathogen-free turkeys resulted in local expression of rMOMP in its native conformation, after which anti-MOMP antibodies appeared in the serum.     

Occult osseous injuries after ankle sprains: incidence, location, pattern, and age

The 16S rRNA gene sequences were determined for type strains of 21 Bifidobacterium species. A phylogenetic tree was constructed using the determined sequences and sequences from DNA databases, which contain the sequences of 11 type strains of Bifidobacterium species and 11 strains of related genera. All species of the genus Bifidobacterium and Gardnerella vaginalis ATCC 14018 belonged to a cluster phylogenetically distinct from the other genera. The cluster was divided into two subclusters: subcluster 1 composed of most species of Bifidobacterium and G. vaginalis, and subcluster 2 consisting of two species, B. denticolens and B. inopinatum; both of which were isolated from human dental caries. In the genus Bifidobacterium, four groups of species are known to be moderately to highly related by DNA-DNA hybridization. The four groups of species exhibited more than 99% similarity among their 16S rDNA sequences within each group. These results indicated that species with around 99% or more similarity in their 16S rDNA sequences should be confirmed for species identities.     

Differentiation of Chlamydia spp. by sequence determination and restriction endonuclease cleavage of RNase P RNA genes

The amplification of DNA from Chlamydia trachomatis by PCR with degenerated primers yielded a 345-bp fragment of the putative RNase P RNA gene. From the deduced DNA sequence of this gene in C. trachomatis, a modified primer pair was designed. The primer pair was subsequently used to obtain the corresponding gene products from Chlamydia pneumoniae and Chlamydia psittaci. Sequence comparisons revealed similarities of 76.6% between C. trachomatis and C. pneumoniae, 79.5% between C. trachomatis and C. psittaci, and 84.7% between C. pneumoniae and C. psittaci. Furthermore, the three species were differentiated by fragment length polymorphism analysis after restriction enzyme cleavage of the PCR products. Sequence variations among 14 serotypes of C. trachomatis were confined to one purine base substitution in the putative RNase P RNA gene of lymphogranuloma venereum strains L1 to L3. Complete sequence similarity was found for nine strains of C. pneumoniae of different geographic origins. Taken together, our results indicate a possibility of the general application of this method in clinical bacteriology. Analysis of the secondary structures of the putative RNase P RNA genes from the different Chlamydia species suggested that a novel structural element in the domain of RNase P RNA is involved in base pairing with the 3'-terminal CCA motif of a tRNA precursor. This structure has not previously been found among RNase P RNAs of members of the division Bacteria.     

Application of a nested, multiplex PCR to psittacosis outbreaks

We developed a nested, multiplex PCR for simultaneous detection of three species of chlamydiae in human and avian specimens. The PCR was designed to increase sensitivity and to circumvent inhibitors of PCR present in clinical specimens. The target sequence was the 16S rRNA gene. The first-step PCR was genus specific, and the second-step PCR was multiplexed (i.e., had multiple primer sets in the same tube) and could discriminate among Chlamydia pneumoniae, Chlamydia psittaci, and Chlamydia trachomatis on the basis of the molecular weight of the amplicon. The limit of detection of each of the two PCR steps was 5 inclusion-forming units. We used PCR and serologic evidence during outbreaks of psittacosis to infer that C. psittaci had been transmitted from birds purchased in pet stores to humans. We also used this method to test both live and dead birds from pet stores for infection with C. psittaci. Compared with culture, the application of PCR to avian specimens increased the rate of C. psittaci detection.     

Surgical treatment for the recurrence of colorectal cancer

Analysis by two-dimensional gel electrophoresis of the N-laurylsarkosinate(Sarkosyl)-insoluble envelope complexes of L-[35]S-cysteine-labeled elementary bodies of Chlamydia pneumoniae strain IOL-207, Chlamydia trachomatis serovar LGV2, D, and F, and Chlamydia psittaci strain 6BC showed differences in the molecular charges of chlamydial outer membrane proteins. The apparent isoelectric point (pI) of the major outer membrane protein of C. pneumoniae strain IOL-207 was 6.4, whereas the pI of the major outer membrane protein of the C. trachomatis and C. psittaci strains differed little from one another, ranging from 5.3 to 5.5. The 60-kDa cysteine-rich protein of C. pneumoniae was the only 60-kDa chlamydial protein with a pI value (5.9) more acidic than that of the corresponding major outer membrane protein. As a general rule, the charges of both the 60-kDa and the low-molecular-mass (12-15 kDa) cysteine-rich proteins were widely variable, depending on the strain. However, in each individual strain, the variation of the charge of the 60-kDa protein had a compensatory change in the low-molecular-mass cysteine-rich protein.     

History and examination of the orofacial pain patient

A polymerase chain reaction (PCR) assay was developed to detect. Chlamydia psittaci DNA in faeces and tissue samples from avian species. Primers were designed to amplify a 264 bp product derived from part of the 5' non-translated region and part of the coding region of the ompA gene which encodes the major outer membrane protein. Amplified sequences were confirmed by Southern hybridization using an internal probe. The sensitivity of the combined assay was found to be between 60 to 600 fg of chlamydial DNA (approximately 6 to 60 genome copies). The specificity of the assay was confirmed since PCR product was not obtained from samples containing several serotypes of C. trachomatis, strains of C. pneumoniae, the type strain of C. pecorum, nor from samples containing microorganisms commonly found in the avian gut flora. In this study, 404 avian faeces and 141 avian tissue samples received by the Central Veterinary Laboratory over a 6 month period were analysed by PCR, antigen detection ELISA and where possible, cell culture isolation. PCR performed favourably compared with ELISA and cell culture, or with ELISA alone. The PCR assay was especially suited to the detection of C. psittaci DNA in avian faeces samples. The test was also useful when applied to tissue samples from small contact birds associated with a case of human psittacosis where ELISA results were negative and chlamydial isolation was a less favourable method due to the need for rapid diagnosis.     

Molecular cloning and sequence comparison of the S1 glycoprotein of the Gray and JMK strains of avian infectious bronchitis virus

The nucleotide sequences of S1 glycoprotein genes of the Gray and JMK strains of avian infectious bronchitis virus (IBV) were determined and compared with published sequences for IBV. The IBV Gray and JMK strains had 99% nucleotide sequence similarity. The overall nucleotide sequence similarity of the Gray and JMK strains compared with other IBV strains was between 82.0% and 87.4%. The similarity of the predicted amino acid sequence for the S1 glycoproteins of the Gray and JMK strains was 98.8%. Six of the 10 differences in the amino acid sequence were found between residues 99 and 127, suggesting a possible role for that region in the tissue trophisms of the viruses. The S1 glycoprotein of the Gray and JMK strains had 79.5%-84.6% amino acid similarity with the published sequence of other IBV strains. Serine instead of phenylalanine was observed in the protease cleavage site between the S1 and S2 glycoprotein subunits for the Gray and JMK strains, which was similar to the published sequence for the Ark99 and SE17 strains. The significance of that amino acid change is not known. Based on the nucleotide sequence of the Gray and JMK strains, the BsmAI restriction enzyme was selected by computer analysis and was used in restriction fragment length polymorphism analysis to differentiate the two strains.     

Evaluation of intraspecies genetic variation within the 16S rRNA gene of Mycoplasma hominis and detection by polymerase chain reaction

Mycoplasma hominis is a heterogeneous species with DNA-DNA hybridization values ranging from 51 to 100%. We report here the sequencing of the 16S rRNA gene of a strain (183) that greatly differs from the type strain (PG21) of this species. Comparison of 16S rDNA sequences from these two strains showed limited differences, indicating that the two strains belong to the same rRNA species complex. Using these nucleotide sequence data, we established a rapid method for the detection of M. hominis by using polymerase chain reaction. This method was shown to be sensitive and specific when tested with reference strains and clinical isolates.     

Sequence-based differentiation of strains in the Mycobacterium avium complex

The complete 16S-23S rDNA internal transcribed spacer (ITS) was sequenced in 35 reference strains of the Mycobacterium avium complex. Twelve distinct ITS sequences were obtained, each of which defined a "sequevar"; a sequevar consists of the strain or strains which have a particular sequence. ITS sequences were identified which corresponded to M. avium (16 strains, four ITS sequevars) and Mycobacterium intracellulare (12 strains, one ITS sequevars). The other seven M. avium complex strains had ITS sequences which varied greatly from those of M. avium and M. intracellulare and from each other. The 16S-23S rDNA ITS was much more variable than 16S rDNA, which is widely used for genus and species identification. Phylogenetic trees based on the ITS were compatible with those based on 16S rDNA but were more detailed and had longer branches. The results of ITS sequencing were consistent with the results of hybridization with M. avium and M. intracellulare probes (Gen-Probe) for 30 of 31 strains tested. Serologic testing correlated poorly with ITS sequencing. Strains with the same sequence were different serovars, and those of the same serovar had different sequences. Sequencing of the 16S-23S rDNA ITS should be useful for species and strain differentiation for a wide variety of bacteria and should be applicable to studies of epidemiology, diagnosis, virulence, and taxonomy.     

Relationship between retinal lesions and axial length, age and sex in high myopia

Questionnaires (3426; 72.8%) and blood samples (3890; 82.6%) were analysed from 4704 women post-natally. The answers to the questionnaire confirmed that those patients living in areas with the highest percentage employed in agriculture were most likely to be in direct or indirect contact with sheep or sheep products. When the 788 (20.3%) of the sera with group specific antibody were examined for type-specific antibody, 291 (7.5%) reacted with Chlamydia trachomatis, 153 (3.9%) with Chlamydia pneumoniae, but only one (0.03%) with Chlamydia psittaci. Thus, it would appear that C. psittaci was not an important pathogen in this survey, despite the largest proportion of blood samples being submitted from those most likely to be employed in agriculture. However, in the course of this survey the three patients who had previously suffered chlamydia-associated abortion had successful pregnancies and submitted blood specimens. Serological studies on the serial bloods from these patients showed that, despite developing antibody to the C. psittaci pool and the ovine abortion strain of C. psittaci following abortion, this antibody waned. At the time of the subsequent successful pregnancy, serological results would not have detected a previous C. psittaci infection, but one due to C. pneumoniae. Thus, the results of a survey such as this must be interpreted with caution.     

Comparison of type I and type II Chlamydia psittaci strains infecting koalas (Phascolarctos cinereus)

The native Australian marsupial Phascolarctos cinereus, otherwise known as the koala, is prone to infection by the obligate intracellular parasite Chlamydia psittaci, which causes ocular 'pink eye' and urogenital 'dirty tail' diseases. Several chlamydial DNA probes to both chromosomal and plasmid sequences were used to type by Southern blot analysis 51 samples taken from wild and captive koalas from habitats on the eastern seaboard of Australia as far apart as Queensland and Victoria. Two types of C. psittaci were observed and called types I and II. Type II was found more frequently than type I and occurred in both ocular and urogenital samples, while type I showed a strong but not absolute preference for ocular sites. Cross-hybridization analyses indicated that type I and type II had about 10% DNA sequence identity to each other. DNA analyses showed that type II was very closely related to some ovine and bovine chlamydiae but type I could not be related to any other C. psittaci strain available. Light and electron microscopic analyses of infected BGM monolayers revealed that the two strains were similar in morphological characteristics. The type I strain was considerably more infectious than the type II strain in BGM cells and in the yolk sacs of embryonated eggs. A PCR based assay detected both type I and type II koala chlamydiae in samples that had been negative by Southern blot and tissue culture and provided the first evidence that both types can occur simultaneously at the one site of infection.     

Polypeptidic composition analysis of "Chlamydia" purified elementary bodies by polyacrylamide slab gel electrophoresis (author's transl)

The study of the polypeptidic components of elementary bodies of various strains of Chlamydia might help in the classification of these bacteria. The use of a satisfactory method for the preparation of purified elementary bodies has permitted the electrophoretic analysis of their crude lysate on polyacrylamide gel in the presence of sodium dodecyl sulfate. Differences between the strain LB 1 C. trachomatis and the strains Loth and MP 1 C. psittaci were found.     

Antigenic characterization of Chlamydia pneumoniae isolated in Hiroshima, Japan

The morphology and antigenic property of elementary bodies (EBs) of new Chlamydia pneumoniae YK-41 strain isolated in Hiroshima, Japan, were compared with those of C. pneumoniae strains TW-183 and AR-39, C. trachomatis L2/434/Bu strain and C. psittaci Cal 10 and Budgerigar-1 strains by SDS-PAGE and immunoblotting techniques. In spite of a clear difference in EB morphology between the YK-41 and the other C. pneumoniae strains used, protein profile of the YK-41 strain in SDS-PAGE was similar to that of the other strains. However, some quantitative difference in 200 and 98 kDa peptides and a faint difference in SDS-PAGE pattern was also observed in the molecular masses from 42 to 50 kDa. Immunoblot analysis with the patient serum at the convalescent stage revealed the presence of genus-specific and species-specific antigens in YK-41 EBs: i.e., the major outer membrane protein and 73 kDa peptides were genus-specific and the peptides of 43, 46, 53, 60 and 98 kDa appeared to be C. pneumoniae-specific.     

Development of a PCR-restriction fragment length polymorphism assay using the nucleotide sequence of the Helicobacter hepaticus urease structural genes ureAB

Infection with Helicobacter hepaticus causes chronic active hepatitis in certain strains of mice and is associated with hepatocellular carcinoma in A/JCr mice. Like the gastric helicobacters, H. pylori and H. mustelae, H. hepaticus possesses a high level of urease activity. However, the H. hepaticus urease structural gene sequences have not been previously determined, and the role of the urease enzyme in colonization and in pathogenesis is not known. PCR was used to amplify a portion of the urease structural genes from H. hepaticus genomic DNA. Amplified DNA fragments were cloned, and the nucleotide sequence was determined. The deduced amino acid sequence of the partial H. hepaticus ureA gene product was found to exhibit 60% identity and 75% similarity to the predicted H. pylori UreA. The deduced amino acid sequence of a partial H. hepaticus ureB gene product exhibited 75% identity and 87% similarity to the predicted H. pylori UreB. Diversity among H. hepaticus isolates was evaluated by means of a restriction fragment length polymorphism (RFLP) assay. The 1.6-kb fragments within the ureAB open reading frames, amplified from 11 independent isolates, were digested with the restriction endonuclease HhaI. Three distinct RFLP patterns were observed. Identical RFLP profiles were noted in sequential isolates of one strain of H. hepaticus during an 18 month in vivo colonization study, suggesting that the urease genes of H. hepaticus are stable. The urease genes among H. hepaticus strains were also well conserved, showing 98.8 to 99% nucleotide sequence identity among three isolates analyzed. These findings indicate that H. hepaticus has urease structural genes which are homologous to those of the gastric Helicobacter species and that these gene sequences can be used in a PCR and RFLP assay for diagnosis of this important murine pathogen.     

Comparison of herpesvirus isolates from falcons, pigeons and psittacines by restriction endonuclease analysis

Field isolates of herpesviruses recovered from falcon, pigeon, and psittacine birds were compared by restriction endonuclease (RE) analysis using four separate enzymes. Pigeon and falcon herpesviruses had strikingly similar DNA cleavage patterns, while DNA cleavage pattern of virus isolates from a double-yellow headed Amazon and an African grey parrot had different genomic patterns to both the pigeon and falcon herpesviruses. These findings support the field observations that pigeon herpesvirus causes a fatal herpesviral infection in the livers of pigeon-eating falcons.     

Differences in physicochemical and antigenic properties of chlamydial strains

Antigenic analysis of Chlamydia psittaci, C. trachomatis, and Lymphogranuloma venereum (LGV) revealed basic physicochemical differences among the three chlamydial strains. These were manifested in structural, isoelectric points, absorption spectra, and in the characteristics of the chromophobe-containing proteins. The effective period of sonication for C. psittaci and C. trachomatis is around 60 min during which the linkages most susceptible to external sonication forces were broken, releasing all attainable cellular components. Denaturation studies demonstrated that less than 50% of protein content of C. psittaci was denatured after 1 h of sonication, only 5% in the case of C. trachomatis. The protein and carbohydrate content of the most reactive fractions in macrophage-spreading inhibition test were different for LGV and C. trachomatis. The structural differences appear to determine the antigenic properties observed among the chlamydial strains as well as the specificity and probably the mechanisms (s) of cellular immune reactivity to Chlamydiae. This in turn may explain the failure of chlamydial vaccines, prepared from stock strains, to protect immunized children against 'wild' chlamydial strains.     

AFLP allows the identification of genomic markers of ruminant Chlamydia psittaci strains useful for typing and epidemiological studies

Amplified fragment length polymorphism (AFLP), a novel method for molecular typing, was evaluated for its ability to differentiate among a group of highly related Chlamydia psittaci strains isolated from ruminants and belonging to serotype 1. A total set of 12 strains were included in this study, 10 strains inducing abortion in ruminants and 2 strains from faecal samples. For the AFLP analysis, the total purified genomic DNA of each strain was submitted to a one-step digestion-ligation reaction for 3 h at 37 degrees C. DNA was digested with a single restriction endonuclease Mspl and ligated to specially constructed adapters. Subsequently, restricted fragments were selectively amplified under high stringency PCR conditions using primers complementary to the adapters. Amplified products were then resolved on agarose gel electrophoresis. The method is easy to perform, fast and reproducible. AFLP enabled characterization of C. psittaci strains at the infra-subspecific level. Thus, AFLP led to the identification of a cluster of strains on the basis of their AFLP patterns, constituted by French chlamydial isolates. It also permitted differentiation among strains in relation to host origin and to clinical syndromes. These data confirmed the highly discriminative power of AFLP towards the differentiation of closely related ruminant C. psittaci strains. The analysis will need to be applied to more samples to check the usefulness of AFLP markers in epidemiological and evolutionary studies.     

Ribosomal genes of Histoplasma capsulatum var. duboisii and var. farciminosum

A total of 1704 basepairs of the 18S rDNA of Histoplasma capsulatum var. duboisii (HCD, strain CBS175.57) and H. capsulatum var. farciminosum (HCF, strain CBS478.64) were sequenced (EMBL accession no. Z75306 and no. Z75307). The 18S rDNA of HCD was 100% identical to a published sequence of H. capsulatum var. capsulatum (HCC). The 18S rDNA of HCF showed one transversional point mutation at the nucleotide position 114 (ref. Saccharomyces cerevisiae). Hybridization confirmed that, in the 18S rDNA of two out of five strains of HCF, guanine was substituted for cytosine at the nucleotide position 114. Furthermore, identical group 1C1 introns (403 bp) were found to be inserted after position 1165 in four out of five strains of HCF, including the two strains with point mutations in the 18S rDNA, and a slightly different group 1C1 intron (408 bp) was detected in one strain of HCC without this point mutation. Intraspecific sequence variability in the highly conserved 18S rDNA because of occurrence of introns and mutations as a possible source of error in molecular diagnostics is discussed. In addition, internal transcribed spacer regions between the 18S rDNA and the 5.8S rDNA (ITS1) of three strains of HCF, and one strain each of HCC and HCD showed significant sequence variability between varieties and strains of H. capsulatum.     

Vaccination against feline pneumonitis

A commercially available modified live chlamydial vaccine against feline pneumonitis was tested in 26 cats for its ability to protect against aerosol challenge exposure to the feline pneumonitis strain of Chlamydia psittaci. After cats were challenge exposed (30 days after vaccination), pyrexia of greater than 40.0 C occurred in 81% of nonvaccinated (control) cats and in 13% of vaccinated cats (principals). Evidence of upper respiratory tract disease and the presence of the agent in ocular fluids were observed less frequently in principals than in nonvaccinated cats. In the cats euthanatized at intervals of 3 days after challenge exposure, C psittaci was demonstrated in 60% of tissues tested from nonvaccinated controls and in 34% of similar tissues obtained from principals.