Chlamydiae cause a wide variety of diseases in humans and animals, including infections of the eye and the respiratory and the genital tracts (
40,
43). More recently they were also associated with cardiovascular disease, atherosclerosis, and intrinsic asthma (
4,
5,
34,
39). Chlamydiae are characterized by a complicated, obligate intracellular developmental cycle which is unique among the prokaryotes. The metabolically active, obligate intracellular chlamydial reticulate bodies (RB) multiply within their eukaryotic host cells and subsequently differentiate to inactive elementary bodies (EB), which are released and are able to infect new host cells and start a new developmental cycle (
40,
43).
Until recently, the genus
Chlamydia comprised only the four species
Chlamydia pneumoniae,
Chlamydia trachomatis,
Chlamydia psittaci, and
Chlamydia pecorum. This genus was considered the single genus within the family
Chlamydiaceae, the only family within the order
Chlamydiales. However, the recent description of several novel chlamydia-related bacteria (
2,
15,
22,
29,
36) and an encompassing phylogenetic analysis of rRNA and other gene sequences (the major outer membrane protein, GroEL chaperonin, 3-deoxy-
d-manno-octulosonic acid [KDO] transferase, small cysteine-rich lipoprotein and the 60-kDa cysteine-rich protein) changed our view on chlamydial diversity and taxonomy, and led to the reclassification of the
Chlamydiales (
6,
13,
19). Everett and coworkers subdivided the family
Chlamydiaceae into the two genera
Chlamydia (containing
C. trachomatis,
C. muridarum, and
C. suis) and
Chlamydophila (containing
C. pneumoniae,
C. pecorum,
C. psittaci,
C. felis,
C. abortus, and
C. caviae) and established the novel families
Parachlamydiaceae,
Simkaniaceae, and
Waddliaceae, comprising the newly discovered
Chlamydia-related organisms (
13,
36). Since this new classification is not accepted by all members of the scientific community, we use the neutral genus abbreviation “
C.” when possible, leaving the interpretation as
Chlamydia or
Chlamydophila up to the reader.
While
C. trachomatis,
C. psittaci, and
C. pneumoniae are considered as clinically relevant pathogens in humans, it is still unclear whether the novel chlamydia-related bacteria, which were found as endosymbionts in free-living amoebae (
2,
15,
22), as contaminants of a tissue culture (
29), within an aborted bovine fetus (
36), or in a wastewater treatment plant (
21), have any clinical significance.
Diagnosis of chlamydial infections can be attempted by various detection methods, including culture, antigen detection, serology and nucleic acid amplification. However, in spite of the multiplicity of available test methods, the detection of chlamydiae from clinical specimens remains a major challenge, at least for routine laboratories. Especially, laboratory diagnosis of the fastidious
C. pneumoniae is currently hampered by a lack of standardized and validated assays leading to a considerable interlaboratory variation of test results (
18). This is one of the major reasons why the role of
C. pneumoniae in respiratory tract disease as well as in atherosclerosis is still unclear (
9,
38). Therefore, both standardizing of available test assays (
10) and development of new molecular methods are urgently needed to obtain reliable tools for sensitive and specific detection of
C. pneumoniae.
In this study a hierarchical set of oligonucleotide probes for the detection of
C. pneumoniae and all other known members of the
Chlamydiales with FISH was constructed. The described set comprises nine new oligonucleotide probes complementary to order-, genus-, and species-specific sequence stretches on the 16S rRNA of the target organisms and is supplemented by two oligonucleotide probes published previously (
2,
22). Analysis of the developmental cycle of
C. pneumoniae in HeLa 229 cells using the FISH technique and comparison of the results with transmission electron microscopy revealed that 16S rRNA staining might be a suitable marker for viability and metabolic activity of chlamydiae. The specificity of the probes was demonstrated using cell cultures as well as amoebae infected with the different target organisms. The discriminatory power of the probes was further demonstrated using cell cultures, experimentally coinfected with different chlamydial species. Finally, it was shown that FISH can be combined with the direct immunofluorescence antibody (DFA) technique, allowing the concurrent demonstration of chlamydial rRNA and antigen within a single infected cell.
DISCUSSION
Despite the remarkable clinical significance of chlamydial infections, there is still a lack of satisfying approaches for laboratory diagnosis of chlamydiae. Especially for
C. pneumoniae and
C. psittaci one has still to rely on methods which (i) are not well standardized (nucleic acid amplification-based tests), (ii) have insufficient discriminatory power (serology-based methods), or (iii) are time-consuming and technically demanding and carry the risk of laboratory infection (culture). Consequently, there is an urgent need for alternative diagnostic approaches (
10). FISH using rRNA-targeted oligonucleotide probes has become a useful diagnostic tool for detection and identification of bacteria that are slowly growing or difficult to cultivate such as
L. pneumophila (
17,
24) and
H. pylori (
37). In addition, rapid identification of bacteria in blood cultures (
25,
30) and sputum samples (
20) was achieved by FISH. Although Meijer and coworkers recently described the application of a digoxigenin-labeled oligonucleotide probe (fully complementary to a 16S rRNA region of 26 nucleotides in length present in most members of the
Chlamydiales) for ISH of atherosclerotic tissue (
33), no chlamydia-specific oligonucleotide probes with proven suitability for FISH are currently available. We therefore constructed and evaluated a comprehensive and hierarchical set of 16S rRNA-targeted oligonucleotide probes for the specific FISH detection of
C. pneumoniae,
C. psittaci,
C. trachomatis, and all other recognized members of the
Chlamydiales, including the so-called environmental chlamydiae (
21). The last of these groups encompasses more than five novel evolutionary lineages of chlamydia-like bacteria which were discovered during the past 4 years (
2,
15,
23,
31,
36). In addition, there is increasing evidence for an even greater diversity of chlamydiae in the environment (
21,
35). While the clinical significance of these only recently detected
Chlamydia-related bacteria is still unclear, some of them have been associated with respiratory disease in humans (
7,
14,
28,
35; R. J. Birtles, T. J. Rowbotham, C. Storey, T. J. Marrie, and D. Raoult, Letter, Lancet
349:925-926, 1997). Using FISH and the new probe set, a new tool becomes available facilitating a rapid detection of all known chlamydiae and chlamydia-like bacteria, which might help to clarify their role in disease of humans.
The simultaneous application of multiple probes with hierarchical specificity labeled with different dyes increases the reliability of the identification, since nontarget organisms incidentally possessing the target site for one of the probes would not hybridize with the other probes and would thus be characterized by unexpected hybridization patterns. Furthermore, the application of multiple probes labeled with different dyes minimizes the risk of false-positive signals caused by unspecific binding of the fluorescent dyes to nontarget organisms or structures of the host cells. For the new
Chlamydiales probe set, the successful application of multiple probes was, for example, demonstrated for the identification of
C. pneumoniae in experimentally infected HeLa 229 cells by using the
C. pneumoniae-specific probe Cpn-974 and the taxonomically superordinated probes Chlae-574, specific for the family
Chlamydiaceae, and Chls-523, which targets all known members of the order
Chlamydiales, including the recently discovered chlamydia-like bacteria (Fig.
2).
The newly developed oligonucleotide probes also allowed us to clearly differentiate between
C. psittaci and
C. pneumoniae. To our knowledge there is no monoclonal antibody available that enables specific staining of
C. psittaci grown from human as well as from veterinary samples. Unambiguous identification of the highly infectious
C. psittaci is, however, important for patient management as well as for laboratory safety considerations and is currently based mainly on PCR methods or genotyping (
12). FISH using the
C. psittaci-specific 16S rRNA-targeted oligonucleotide probes might offer a rapid alternative for reliable identification of
C. psittaci. However, it should be noted that the
C. psittaci-specific probes designed in this study target all chlamydiae formerly referred to as
Chlamydia psittaci, including the recently described species
Chlamydophila felis,
Chlamydophila abortus, and
Chlamydophila caviae.
In order to visualize the specificity and discriminatory power of the newly designed FISH probes, HeLa 229 cells were simultaneously infected with C. pneumoniae and C. trachomatis. The subsequent application of FISH using C. pneumoniae and C. trachomatis-specific oligonucleotide probes was able to clearly discriminate C. pneumoniae-derived inclusions from C. trachomatis-derived inclusions and demonstrated for the first time that the same HeLa 229 cells can be infected simultaneously with both chlamydia species. The coexistence of related pathogens in the same host cell might facilitate lateral gene transfer events between them. However, fusion of C. pneumoniae inclusions with C. trachomatis inclusions was never observed in the double-infected cells.
The applicability of FISH for basic chlamydia research as well as for diagnostic purposes was further demonstrated by the analysis of the complete developmental cycle of C. pneumoniae, which revealed that chlamydiae can be detected by FISH as early as 12 h after infection. It was, however, not possible to stain purified EB by FISH. This could result either from a low ribosome content of the EB during this metabolically inactive stage of the developmental cycle or from the inaccessibility of the EB for oligonucleotide probes due to their rigid cell wall that is highly cross-linked by disulfide bonds.
A previous study revealed a similar sensitivity of FISH and culture-based methods for the detection of
Pseudomonas aeruginosa from sputa of children with cystic fibrosis (
20). However, the sensitivity of FISH for the detection of chlamydiae in patient samples has still to be investigated in detail in further studies. While the restriction of FISH to detect only the metabolically active forms of chlamydiae might be a disadvantage in terms of the sensitivity of FISH in clinical diagnostics, FISH might be able to circumvent several problems of PCR-based diagnostic methods. These are for example illustrated by the highly discrepant results for PCR detection of
C. pneumoniae in atheromatous lesions by different study groups spanning positivity rates from 0 to 100%, which have contributed to the current confusion about the role of
C. pneumoniae in development of atherosclerosis (
4). The possibility to apply FISH directly on the specimens (in situ), thereby detecting only intact and viable cells (in contrast to PCR, which is susceptible to false-positive results due to the presence of dead bacteria or extracellular DNA), and the encompassing coverage of all chlamydiae render FISH a promising tool for the investigation of blood vessels for the presence of metabolically active
C. pneumoniae or chlamydia-like bacteria. In addition, FISH might help to improve the laboratory diagnosis of, in particular,
C. pneumoniae and
C. psittaci infections.