Development of a simplified polymerase chain reaction-enzyme immunoassay for the detection of Chlamydia pneumoniae

Reliable and Sensitive Nested PCR for the Detection of Chlamydia in Sputum

Chlamydia are Gram-negative, intracellular pathogens colonizing epithelial mucosa. They cause primarily atypical pneumonia and have recently been associated with chronic diseases. Diagnostics relies almost exclusively on serological methods; PCR tests are used rarely because in patients with positive ELISA, it is nearly impossible to identify chlamydial DNA. This paradox is associated with DNA degradation in sputum samples, low abundance, and low sensitivity of PCR systems. In a newly designed and validated “nested” PCR (NPCR) assay, it was possible to amplify DNA of Chlamydia known to infect humans in 31% samples. The reliability of the assay was confirmed by DNA sequencing, and all PCR products belonged exclusively to the Chlamydiales, mainly recognized as Chlamydia pneumoniae. Three samples were related to Ca. Rhabdochlamydia porcellionis and Ca. Renichlamydia lutjani, which infect arthropods. In one case, samples were taken from sick individual, indicating the potential as a human pathogen.

Assessment of Chlamydia suis Infection in Pig Farmers

Chlamydia suis infections are endemic in domestic pigs in Europe and can lead to conjunctivitis, pneumonia, enteritis and reproductive failure. Currently, the knowledge on the zoonotic potential of C. suis is limited. Moreover, the last decades, porcine tetracycline resistant C. suis strains have been isolated, which interfere with treatment of chlamydial infections. In this study, the presence of C. suis was examined on nine Belgian pig farms, using Chlamydia culture and a C. suis specific real-time PCR in both pigs and farmers. In addition to diagnosis for C. suis, the farmers' samples were examined using a Chlamydia trachomatis PCR. Additionally, the Chlamydia isolates were tested for the presence of the tet(C) resistance gene. C. DNA was demonstrated in pigs on all farms, and eight of nine farmers were positive in at least one anatomical site. None of the farmers tested positive for C. trachomatis. Chlamydia suis isolates were obtained from pigs of eight farms. Nine porcine C. suis isolates possessing a tet(C) gene were retrieved, originating from three farms. Moreover, C. suis isolates were identified in three human samples, including one pharyngeal and two rectal samples. These findings suggest further research on the zoonotic transfer of C. suis from pigs to humans is needed.

Longitudinal monitoring for respiratory pathogens in broiler chickens reveals co-infection of Chlamydia psittaci and Ornithobacterium rhinotracheale

Chlamydia psittaci is prevalent in broiler chicken production. However, the role of C. psittaci in the respiratory disease complex needs to be clarified. Our aim was to identify the time point when a C. psittaci infection appeared on a broiler farm and to examine the presence of other respiratory pathogens at that time. We focused on the 'major' respiratory pathogens occurring in Belgian broilers, namely infectious bronchitis virus (IBV), avian metapneumovirus (aMPV), Ornithobacterium rhinotracheale, Mycoplasma gallisepticum and Mycoplasma synoviae, and examined their co-occurrence with C. psittaci on three commercial broiler farms. For all farms, 1-day-old broilers showed high maternal antibody titres against C. psittaci in the presence of viable C. psittaci. Maternal antibodies seemed to protect against respiratory signs. Maternal antibodies declined and clinical outbreaks could be identified serologically even before maternal antibodies completely disappeared. Mixed infections with genotypes B/C and B/C/D were observed. Broilers with C. psittaci antibody increases showed conjunctivitis, signs of upper respiratory disease and dyspnoea. C. psittaci always preceded an O. rhinotracheale infection. Infections with aMPV, IBV or Mycoplasma spp. were not observed. Evidence was provided that C. psittaci could occur at an early age in broilers without a predisposing respiratory infection. Both C. psittaci and O. rhinotracheale should be considered when developing prevention strategies for respiratory disease in broilers.

Evaluation of the presence and zoonotic transmission of Chlamydia suis in a pig slaughterhouse

Background

A significant number of studies on pig farms and wild boars worldwide, demonstrate the endemic presence of Chlamydia suis in pigs. However, the zoonotic potential of this pathogen, phylogenetically closely related to Chlamydia trachomatis, is still uninvestigated. Therefore, this study aims to examine the zoonotic transmission in a Belgian pig abattoir.

Methods

Presence of Chlamydia suis in pigs, contact surfaces, air and employees was assessed using a Chlamydia suis specific real-time PCR and culture. Furthermore, Chlamydia suis isolates were tested for the presence of the tet(C) gene.

Results

Chlamydia suis bacteria could be demonstrated in samples from pigs, the air and contact surfaces. Moreover, eye swabs of two employees were positive for Chlamydia suis by both PCR and culture. The tet(C) gene was absent in both human Chlamydia suis isolates and no clinical signs were reported.

Conclusions

These findings suggest the need for further epidemiological and clinical research to elucidate the significance of human ocular Chlamydia suis infections.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-014-0560-x) contains supplementary material, which is available to authorized users.

Emerging Chlamydia psittaci infections in chickens and examination of transmission to humans

Chlamydia psittaci and atypical Chlamydiaceae infections are (re)-emerging in chickens. We therefore examined the prevalence of C. psittaci, atypical Chlamydiaceae and their zoonotic transmission on 19 Belgian chicken farms. Atypical Chlamydiaceae were not detected in chickens but 18 out of 19 farms were positive for C. psittaci by culture and PCR. C. psittaci ompA genotypes A and D were discovered. None of the examined humans (n = 31) was infected with atypical Chlamydiaceae, but 29 (93.5%) of them were positive for C. psittaci by culture and PCR. Genotypes A, D and a mixed infection with genotypes C and D were found. Humans (n = 2) working at the C. psittaci-negative farm never had respiratory complaints, while 25 out of 29 positive farmers (86.2%) reported yearly medical complaints potentially related to psittacosis. Four of them currently experienced respiratory disease and one of them was being treated with antibiotics. Four farmers (12.5%) mentioned that they had pneumonia after starting to keep chickens. Occupational physicians should be aware of emerging Chlamydiaceae infections in chickens.

Tetracycline-resistant Chlamydia suis in cases of reproductive failure on Belgian, Cypriote and Israeli pig production farms

Similar cases of severe reproductive failure associated with the presence of Chlamydia suis in two Belgian, one Cypriote and one Israeli pig farrowing to slaughter farms are presented. Vaginal and rectal swabs from 39 sows were examined by culture and DNA microarray. Nineteen of 23 (83 %) C. suis-positive sows were infected with tetracycline-resistant C. suis strains, as determined by MIC tests. Furthermore, boar semen from a German artificial insemination centre, intended for export, was positive for C. suis. Emergence of tetracycline-resistant C. suis strains was confirmed.

Chlamydia pneumoniae is genetically diverse in animals and appears to have crossed the host barrier to humans on (at least) two occasions

Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of diseases. Since the first isolation of C. pneumoniae TWAR in 1965, all human isolates have been essentially clonal, providing little evolutionary insight. To address this gap, we investigated the genetic diversity of 30 isolates from diverse geographical locations, from both human and animal origin (amphibian, reptilian, equine and marsupial). Based on the level of variation that we observed at 23 discreet gene loci, it was clearly evident that the animal isolates were more diverse than the isolates of human origin. Furthermore, we show that C. pneumoniae isolates could be grouped into five major genotypes, A-E, with A, B, D and E genotypes linked by geographical location, whereas genotype C was found across multiple continents. Our evidence strongly supports two separate animal-to-human cross species transfer events in the evolutionary history of this pathogen. The C. pneumoniae human genotype identified in the USA, Canada, Taiwan, Iran, Japan, Korea and Australia (non-Indigenous) most likely originated from a single amphibian or reptilian lineage, which appears to have been previously geographically widespread. We identified a separate human lineage present in two Australian Indigenous isolates (independent geographical locations). This lineage is distinct and is present in Australian amphibians as well as a range of Australian marsupials.

Chlamydia pneumoniae is an intracellular bacterial pathogen with an extremely diverse host range (humans, amphibians, reptiles and marsupials). We selected 23 target genes in order to investigate genetic diversity: seven of these had been lost or gained by C. pneumoniae, a further six were conserved, four were polymorphic (defined by greater than 20 SNPs per 1 kbp; in this study), and six were truncated or length polymorphic in one strain or the other. Our research highlights that C. pneumoniae animal isolates are much more genetically diverse than C. pneumoniae human isolates, and have crossed the host barrier to humans on at least two occasions. Our study provides new insights into the evolution of this complex pathogen.

Identification and characterization of a type III secretion system in Chlamydophila psittaci

Chlamydiaceae are obligate intracellular Gram-negative bacteria replicating in vacuoles inside eukaryotic cells. It has been proven that most of them possess a type III secretion system (T3SS) allowing them to transfer effector molecules in the host cell. We examined the existence of a T3SS in Chlamydophila psittaci by studying the expression of three essential structural proteins SctW, SctC, and SctN, and one putative effector protein IncA. Immunofluorescence assays showed SctW and IncA to be associated with the bacteria and the inclusion membrane, while SctC and SctN were only localized to the bacteria itself. Immuno electron microscopy could confirm these results for SctW, IncA, and SctC. Unfortunately, SctN was not investigated with this technique. Additionally, we sequenced 14 full-length T3S genes (scc1, sctW, sctJ, sctL, sctR, sctS, scc2, copD1, sctN, sctQ, sctC, incA, ca037, and cadd) and examined the transcription of 26 Cp. psittaci T3S genes namely cluster 1 (scc1, sctW, sctV, sctU), cluster 2 (sctJ, sctL, sctR, sctS, sctT, scc2, copB1, copD1), cluster 3 (sctD, sctN, ca037, sctQ, pkn5, sctC) and non-clustered genes (incA, incC, scc3, copD2, cap1, tarp, ca530, cadd). The gene expression study indicated the T3S structural protein encoding genes to be transcribed from mid-cycle (12-18 h post infection (p.i.)) on. Genes encoding effector proteins and putative T3S related proteins were expressed early (1.5 h-8 h p.i.) or late (>24 h p.i.) during the developmental cycle. We hereby provided evidence for the existence of a T3SS and possible effectors in avian Cp. psittaci.

Molecular characterization of Chlamydophila pneumoniae isolates from Western barred bandicoots

Chlamydophila pneumoniae is an obligate intracellular respiratory pathogen that has been associated with pneumonia and chronic bronchitis, atherosclerosis, asthma and other chronic diseases in humans. However, C. pneumoniae is not restricted to humans, as originally thought, and can cause infections in several animal hosts. C. pneumoniae was isolated in cell culture from nine Western barred bandicoots (Perameles bougainville) from Australia. The sequences of five genomic regions were determined, including full-length sequences of the 16S rRNA and ompA genes and the ygeD-urk intergenic spacer, and partial sequences of the 23S rRNA and rpoB genes. Sequence analysis of the entire 16S rRNA and ompA genes from bandicoot isolates demonstrated that they were 98.2-98.3% similar to human isolates, 94.6-99.3% similar to the equine biovar and almost identical, with 99.5-99.9% similarity, to the koala biovar. Comparative genotyping of the variable domain 4 region of the ompA gene demonstrated that bandicoot isolates seemed to be identical to the animal genotype that has been recently identified in human carotid plaque specimens. Minor sequence polymorphism observed in ompA, 16S rRNA and rpoB genes of animal isolates, indicating genomic diversity within C. pneumoniae, may have important implications for diagnostic PCR assays leading to false negative results. Forty percent of selected published species-specific PCR assays were found to have sequence variability in primer and/or probe that might affect their performance in detecting bandicoot isolates of C. pneumoniae, or possibly other animal and human strains where minor sequence polymorphisms may be present. The data from this study support the previous observations that C. pneumoniae is not restricted to humans and may be widespread in an animal reservoir with a potential risk of transmission to humans.

Use of a nested PCR-enzyme immunoassay with an internal control to detect Chlamydophila psittaci in turkeys

Background

Laboratory diagnosis of Chlamydophila psittaci, an important turkey respiratory pathogen, is difficult. To facilitate the diagnosis, a nested PCR-enzyme immunoassay (PCR-EIA) was developed to detect the Cp. psittaci outer membrane protein A (ompA) gene in pharyngeal swabs.

Methods

The fluorescein-biotin labelled PCR products were immobilized on streptavidin-coated microtiter plates and detected with anti-fluorescein peroxidase conjugate and a colorimetric substrate. An internal inhibition control was included to rule out the presence of inhibitors of DNA amplification. The diagnostic value of the ompA nested PCR-EIA in comparison to cell culture and a 16S-rRNA based nested PCR was assessed in pharyngeal turkey swabs from 10 different farms experiencing respiratory disease.

Results

The sensitivity of the nested PCR-EIA was established at 0.1 infection forming units (IFU). Specificity was 100%. The ompA nested PCR-EIA was more sensitive than the 16S-rRNA based nested PCR and isolation, revealing 105 out of 200 (52.5%) positives against 13 and 74 for the latter two tests, respectively. Twenty-nine (23.8%) out of 122 ompA PCR-EIA negatives showed the presence of inhibitors of DNA amplification, although 27 of them became positive after diluting (1/10) the specimens in PCR buffer or after phenol-chloroform extraction and subsequent ethanol precipitation.

Conclusion

The present study stresses the need for an internal control to confirm PCR true-negatives and demonstrates the high prevalence of chlamydiosis in Belgian turkeys and its potential zoonotic risk. The ompA nested PCR-EIA described here is a rapid, highly sensitive and specific diagnostic assay and will help to facilitate the diagnosis of Cp. psittaci infections in both poultry and man.

Sequencing of the Chlamydophila psittaci ompA gene reveals a new genotype, E/B, and the need for a rapid discriminatory genotyping method

Twenty-one avian Chlamydophila psittaci isolates from different European countries were characterized using ompA restriction fragment length polymorphism, ompA sequencing, and major outer membrane protein serotyping. Results reveal the presence of a new genotype, E/B, in several European countries and stress the need for a discriminatory rapid genotyping method.

Single-run, parallel detection of DNA from three pneumonia-producing bacteria by real-time polymerase chain reaction

A molecular assay for parallel detection of three bacteria, Chlamydia (C.) pneumoniae, Legionella (L.) spp., and Mycoplasma (M.) pneumoniae, in clinical specimens by a set of real-time polymerase chain reactions (PCRs) in a single run was evaluated. Bacterial DNAs were extracted by an automated DNA extraction protocol on the MagNA Pure LC System. Amplification and detection were done by real-time PCR on the LightCycler (LC) instrument. For amplification, specific oligonucleotides derived from the 16s rRNA genes of C. pneumoniae, L. spp., and M. pneumoniae were used. The three assays were complemented with an internal control (IC), a specially designed DNA fragment which contains the specific primer binding sites for the three PCRs. The IC was added to the samples, co-extracted, and co-amplified. Primers and hybridization probes were designed to suit one LC PCR program. LC PCRs were established, detection limits were determined, and clinical samples were tested. The detection limits were found between 5.0 and 0.5 IFU/CFU per PCR reaction for each of the bacteria. A total number of 100 clinical specimens were tested for validation of the molecular assay. Tested samples included 63 bronchoalveolar lavages (BALs) and 37 induced sputa specimens. The internal control was detected in all negative and low-positive samples; no inhibition was found throughout the whole study. Additionally, samples underwent testing by culture for L. spp., and M. pneumoniae; for C. pneumoniae, the serological microimmunofluorescence (MIF) test was used. In conclusion, the developed set of LC PCR assays permits parallel detection of C. pneumoniae, L. spp., and M. pneumoniae in a single LC run. This molecular assay may lead to accurate and early diagnosis of pneumonia produced by these three types of bacteria. The assay proved to be suitable for the high-throughput routine diagnostic laboratory.

Comparison of an industry-derived LCx Chlamydia pneumoniae PCR research kit to in-house assays performed in five laboratories

In a multicenter comparison of PCR assays utilizing 120 quantitated samples of 16 Chlamydia pneumoniae isolates, an LCx research-use-only (RUO) PCR developed by Abbott Laboratories demonstrated 100% sensitivity on 48 samples with >1 copy of DNA per microl of specimen. The sensitivities of five in-house PCR assays ranged from 54 to 94% for the same samples. All six assays showed decreased sensitivities as the DNA copy numbers of the samples decreased. Overall, sensitivities ranged from 68% for the LCx PCR assay to 29% for one of the in-house tests. The LCx RUO PCR and three of the five in-house PCR tests reported no false positives with the 24 negative samples. Increasing the number of replicates tested increased the sensitivities of all of the assays, including the LCx PCR. The LCx RUO assay showed high reproducibility for a single technologist and between technologists, with a kappa agreement of 0.77. The within-center agreements of the five in-house PCR tests varied from 0.19 to 0.74 on two challenges of 60 specimens 1 month apart. The LCx C. pneumoniae RUO PCR shows excellent potential for use in clinical studies, which could enable standardization of results in the field.

Standardizing Chlamydia pneumoniae assays: recommendations from the Centers for Disease Control and Prevention (USA) and the Laboratory Centre for Disease Control (Canada)

Chlamydia pneumoniae has been associated with atherosclerosis and several other chronic diseases, but reports from different laboratories are highly variable and "gold standards" are lacking, which has led to calls for more standardized approaches to diagnostic testing. Using leading researchers in the field, we reviewed the available approaches to serological testing, culture, DNA amplification, and tissue diagnostics to make specific recommendations. With regard to serological testing, only use of microimmunofluorescence is recommended, standardized definitions for "acute infection" and "past exposure" are proposed, and the use of single immunoglobulin (Ig) G titers for determining acute infection and IgA for determining chronic infection are discouraged. Confirmation of a positive culture result requires propagation of the isolate or confirmation by use of polymerase chain reaction (PCR). Four of 18 PCR assays described in published reports met the proposed validation criteria. More consistent use of control antibodies and tissues and improvement in skill at identifying staining artifacts are necessary to avoid false-positive results of immunohistochemical staining. These standards should be applied in future investigations and periodically modified as indicated.

Touchdown enzyme time release-PCR for detection and identification of Chlamydia trachomatis, C. pneumoniae, and C. psittaci using the 16S and 16S-23S spacer rRNA genes

Three touchdown enzyme time release (TETR)-PCR assays were used to amplify different DNA sequences in the variable regions of the 16S and 16S-23S spacer rRNA genes specific for Chlamydia trachomatis, Chlamydia pneumoniae, and Chlamydia psittaci as improved tests for sensitive diagnosis and rapid species differentiation. The TETR-PCR protocol used 60 cycles of amplification, which provided improved analytical sensitivity (0.004 to 0.063 inclusion-forming unit of Chlamydia species per PCR). The sensitivity of TETR-PCR with primer set CTR 70-CTR 71 was 96.7%, and the specificity was 99.6%, compared to those of the AMPLICOR PCR for the detection of C. trachomatis in vaginal swab samples. TETR-PCR for C. pneumoniae with primer set CPN 90-CPN 91 was 90% sensitive and 93.3% specific compared with a nested PCR with primer set CP1/2-CPC/D for clinical respiratory samples. TETR-PCR for C. psittaci with primer set CPS 100-CPS 101 showed substantial agreement with cell culturing (kappa, 0.78) for animal tissue samples. Primer sets were then combined into a single multiplex TETR-PCR test. The respective 315-, 195-, and 111-bp DNA target products were precisely amplified when DNA from each of the respective Chlamydia species or combinations of them was used. Multiplex chlamydia TETR-PCR correctly identified one strain of each of the 15 serovars of C. trachomatis, 22 isolates of C. pneumoniae, and 20 isolates of C. psittaci. The primer sets were specific for each species. No target products were amplified when DNA from C. pecorum or a variety of other microorganisms was tested for specificity. TETR-PCR with primers selected for specific sequences in the 16S and 16S-23S spacer rRNA genes is a valuable test that could be used either with individual primers or in a multiplex assay for the identification and differentiation of Chlamydia species from culture isolates or for the detection of chlamydiae in clinical samples.

PCR-enzyme-linked immunosorbent assay and partial rRNA gene sequencing: a rational approach to identifying mycobacteria

A PCR-enzyme-linked immunosorbent assay (ELISA) for amplification and rapid identification of mycobacterial DNA coding for 16S rRNA was developed. The PCR selectively targeted and amplified part of the 16S rRNA gene from all mycobacteria while simultaneously labelling one strand of the amplified product with a 5' fluorescein-labelled primer. The identity of the labelled strand was subsequently determined by hybridization to a panel of mycobacterial species-specific capture probes, which were immobilized via their 5' biotin ends to a streptavidin-coated microtiter plate. Specific hybridization of a 5' fluorescein-labelled strand to a species probe was detected colorimetrically with an anti-fluorescein enzyme conjugate. The assay was able to identify 10 Mycobacterium spp. A probe able to hybridize to all Mycobacterium species (All1) was also included. By a heminested PCR, the assay was sensitive enough to detect as little as 10 fg of DNA, which is equivalent to approximately three bacilli. The assay was able to detect and identify mycobacteria directly from sputa. The specificities of the capture probes were assessed by analysis of 60 mycobacterial strains corresponding to 18 species. Probes Avi1, Int1, Kan1, Xen1, Che1, For1, Mal1, Ter1, and Gor1 were specific. The probe Tbc1 cross-hybridized with the Mycobacterium terrae amplicon. Analysis of 35 strains tested blind resulted in 34 strains being correctly identified. This method could be used for rapid identification of early cultures and may be suitable for the detection and concurrent identification of mycobacteria within clinical specimens.

Analysis of partial 16S rRNA nucleotide sequences of Chlamydia pecorum and C. psittaci

Partial 16S nucleotide sequences of Chlamydia psittaci isolates S26/3 (abortion), P94/1 (pigeon) and Chlamydia pecorum isolates W73 (enteric) and E58 (encephalomyelitis) were determined. Analysis of these data indicates very high levels of interspecies sequence conservation, with C. psittaci being more closely related to C. pecorum than to C. pneumoniae or C. trachomatis. Restriction enzyme analysis of nucleotide sequences indicated that BslI can be used to clearly distinguish C. psittaci and C. pecorum isolates. Psittacine and non-psittacine (pigeon) avian isolates of C. psittaci were distinguished using MaeI.