Detection of Chlamydia suis from clinical specimens: comparison of PCR, antigen ELISA, and culture

Prevalence of Chlamydia in Pigs in China from 1985 to 2020: A Systematic Review and Meta-Analysis

Chlamydia is a small gram-negative (G-) microorganism that can be dangerous to human and animals. In this study, we conducted a systematic review and meta-analysis of Chlamydia infection in swine in China. From PubMed, ScienceDirect, Chinese Web of knowledge (CNKI), VIP Chinese journal database, and Wanfang database, we collected a total of 72 publications reported in 1985-2020. The prevalence of Chlamydia was 22.48% in China. In the sampling year subgroup, the prevalence after 2011 was the highest (26.14%). In southern China, the prevalence was 30.97%. By contrast, the prevalence in northern China was only 10.79%. Also the difference was significant (p < 0.05). In the provincial level, Hubei had the highest rate of 36.23%. Boars had a higher prevalence (29.47%). The prevalence of Chlamydia detection in pigs with reproductive disorders (21.86%) was higher than that without reproductive disorders. Among the three age groups, finishing pigs (21.43%) had the highest prevalence. The prevalence in large-scale farmed pigs (28.58%) was the highest in the subgroup of feeding methods. The prevalence in farms was 24.29%, which was the highest in the survey areas. The prevalence in spring was the highest with 40.51%. Other methods had the highest prevalence (39.61%) than enzyme-linked immunosorbent assay (ELISA) and indirect hemagglutination assay. The prevalence of Chlamydia psittaci 18.41% was lower than the prevalence of Chlamydia abortus (41.35%). We also analyzed the impact of different climate factor subgroups (rainfall, temperature, and humidity) on the probability of pigs suffering from the disease. The results showed that Chlamydia was widespread in pigs in China. We suggest that we should strengthen the detection of Chlamydia in the semen of breeding pigs and pigs with reproductive disorders, and reasonably control the environment of large-scale pig farms, so as to reduce further infection of Chlamydia in pigs.

Isolation of Tetracycline-Resistant Chlamydia suis from a Pig Herd Affected by Reproductive Disorders and Conjunctivitis

Due to various challenges in diagnosing chlamydiosis in pigs, antibiotic treatment is usually performed before any molecular or antibiotic susceptibility testing. This could increase the occurrence of tetracycline-resistant Chlamydia (C.) suis isolates in the affected pig population and potentiate the reoccurrence of clinical signs. Here, we present a case of an Austrian pig farm, where tetracycline resistant and sensitive C. suis isolates were isolated from four finishers with conjunctivitis. On herd-level, 10% of the finishers suffered from severe conjunctivitis and sows showed a high percentage of irregular return to estrus. Subsequent treatment of whole-herd using oxytetracycline led to a significant reduction of clinical signs. Retrospective antibiotic susceptibility testing revealed tetracycline resistance and decreased susceptibility to doxycycline in half of the ocular C. suis isolates, and all isolates were able to partially recover following a single-dose tetracycline treatment in vitro. These findings were later confirmed in vivo, when all former clinical signs recurred three months later. This case report raises awareness of tetracycline resistance in C. suis and emphasizes the importance of preventative selection of tetracycline resistant C. suis isolates.

Establishment of a Multiplex Real-Time TaqMan-MGB Polymerase Chain Reaction (PCR) Method for the Simultaneous Detection of Three Animal Chlamydia Species

BACKGROUND Chlamydiae are spread globally and cause infectious diseases in both humans and animals. The existing detection methods for this disease have numerous shortcomings, including low sensitivity, time consuming procedures, and high contamination vulnerability. MATERIAL AND METHODS To overcome shortcomings for detecting animal chlamydiosis, a multiplex quantitative polymerase chain reaction (PCR) assay was established for simultaneously detecting and differentiating 3 Chlamydia species (C. pecorum, C. abortus, and C. psittaci) by real time PCR based on TaqMan-MGB technology. RESULTS The limit of detection was 20.2 copies/µL for Chlamydophila (Cp.) abortus, 30.8 copies/µL for Cp. pecorum, and 16 copies/µL for Cp. psittaci. This method has good repeatability and stability as coefficients of variation range from 0.04% to 1.38%. Furthermore, compared with OIE (World Organization for Animal Health) recommended PCR assay and previously reported animal chlamydia shell PCR, this multiplex PCR assay demonstrated 99% concordance in detecting clinical samples of porcine nasal swabs and vaginal swabs. CONCLUSIONS The novel established method in this study was able to detect 3 types of Chlamydia species simultaneously, and had high sensitivity, strong specificity, and good stability. It provided a rapid, reliable, and convenient method for epidemiological and clinical diagnosis of chlamydiosis in animals.

Asymptomatic infections with highly polymorphic Chlamydia suis are ubiquitous in pigs

Background

Chlamydia suis is an important, globally distributed, highly prevalent and diverse obligate intracellular pathogen infecting pigs. To investigate the prevalence and genetic diversity of C. suis in China, 2,137 nasal, conjunctival, and rectal swabs as well as whole blood and lung samples of pigs were collected in 19 regions from ten provinces of China in this study.

Results

We report an overall positivity of 62.4% (1,334/2,137) of C. suis following screening by Chlamydia spp. 23S rRNA-based FRET-PCR and high-resolution melting curve analysis and confirmatory sequencing. For C. suis-positive samples, 33.3 % of whole blood and 62.5% of rectal swabs were found to be positive for the C. suis tetR(C) gene, while 13.3% of whole blood and 87.0% of rectal swabs were positive for the C. suis tet(C) gene. Phylogenetic comparison of partial C. suis ompA gene sequences revealed significant genetic diversity in the C. suis strains. This genetic diversity was confirmed by C. suis-specific multilocus sequence typing (MLST), which identified 26 novel sequence types among 27 examined strains. Tanglegrams based on MLST and ompA sequences provided evidence of C. suis recombination amongst the strains analyzed.

Conclusions

Genetically highly diverse C. suis strains are exceedingly prevalent in pigs. As it stands, the potential pathogenic effect of C. suis on pig health and production of C. suis remains unclear and will be the subject of further investigations. Further study is also required to address the transmission of C. suis between pigs and the risk of 'spill-over' and 'spill-back' of infections to wild animals and humans.

Electronic supplementary material

The online version of this article (10.1186/s12917-017-1295-x) contains supplementary material, which is available to authorized users.

Novel locked nucleic acid (LNA)-based probe for the rapid identification of Chlamydia suis using real-time PCR

Background

As the importance of chlamydial infections in pigs has become more obvious, a rapid and sensitive method to study the prevalence of Chlamydia suis in pig herds is required. Such a method should permit routine diagnostic tests for herds with clinical and subclinical infections, without the need for Chlamydia culture.

Results

The main objective of this study was to develop a specific and rapid method for detecting C. suis in swine herds. A real-time PCR assay using a single locked nucleic acid (LNA)-containing probe specific for C. suis was developed based on the previously described 28S rDNA fragment used to identify Chlamydiales. Use of LNA nucleotides enabled the single probe to target a short, specific fragment of the 23S rRNA. The probe showed high specificity for C. suis and did not show any cross-reactivity with other Chlamydia or Chlamydophila species nor with swine DNA. All of the 86 tested field isolates, earlier identified as C. suis, were confirmed as positive using the newly developed assay.

Conclusions

Using single LNA-based C. suis-specific probe allowed rapid and simple identification of this pathogen without requiring sequencing analysis and culturing. The proposed method may be used to study the prevalence of C. suis infection in pig herds and as a routine diagnostic test for herds with clinical and subclinical infection.

The occurrence of Chlamydia spp. in pigs with and without clinical disease

Background

Within the genera Chlamydia, the development of refined diagnostic techniques has allowed the identification of four species that are capable of infecting pigs. The epidemiology, clinical, and zoonotic impacts of these species are however largely unknown. The study aimed to investigate the presence of Chlamydia spp. in the intestines of growing pigs and in conjunctival swabs from finisher pigs, and relate the findings to clinical signs.

Results

By histology, 20 of 48 pigs had intestinal lesions that may be consistent with chlamydial infection. By PCR, forty-six of the pigs were positive whereas two samples were inhibited. Sequencing of 19 DNA extracts identified these as Chlamydia suis. By immunohistochemistry, 32 of 44 samples were positive and a significant relationship was detected between macroscopically visible intestinal lesions and a high degree of infection. By real-time PCR, a significant difference was detected between pigs with and without conjunctivitis when a Ct value of 36 was employed but not when a Ct value of 38 was employed.

Conclusions

Chlamydia suis was demonstrated in most samples and overall, no correlation to clinical signs was detected. However, a correlation was noted between samples with a high degree of infection and the presence of clinical signs. It is possible, that the intensive pig production systems studied might predispose for the transmission and maintenance of the infection thus increasing the infectious load and the risk for disease in the pig.

A nested multiplex polymerase chain reaction assay for the differential identification of three zooanthroponotic chlamydial strains in porcine swab samples

Porcine chlamydial infection is an enzootic infectious disease caused by multiple members of the family Chlamydiaceae (e.g. Chlamydophila abortus, Chlamydia suis, and Chlamydophila pneumoniae). Rapid and accurate differentiation of these pathogens is critical in the control and prevention of disease. The aim of the current study was to develop a nested multiplex polymerase chain reaction (nmPCR) assay to simultaneously detect the 3 chlamydial pathogens in clinical samples. In the first round of the nmPCR, 1 pair of family-specific primers were used to amplify the 1,100 base pair (bp) fragment of chlamydial ompA gene. In the second round of the nmPCR, 4 inner primers were designed for Ch. abortus, C. suis, and Ch. pneumoniae. Each pathogen produced a specific amplicon with a size of 340 bp, 526 bp, and 267 bp respectively. The assay was sensitive and specific for detecting target pathogens in both cell cultures and clinical specimens. The results, incorporated with the improved rapid DNA extraction protocol, suggest that the nmPCR could be a promising assay for differential identification of different chlamydial strains in pigs.

Chlamydiaceae in cattle: commensals, trigger organisms, or pathogens?

Epidemiological data indicate that infection of cattle with chlamydiae such as Chlamydophila (C.) pecorum, C. abortus, C. psittaci and Chlamydia suis, is ubiquitous with mixed infections occurring frequently. The apparent lack of association between infection and clinical disease has resulted in debate as to the pathogenic significance of these organisms, and their tendency to sub-clinical and/or persistent infection presents a challenge to the study of their potential effects. However, recent evidence indicates that chlamydial infections have a substantial and quantifiable impact on livestock productivity with chronic, recurrent infections associated with pulmonary disease in calves and with infertility and sub-clinical mastitis in dairy cows. Data also suggest these infections manifest clinically when they coincide with a number of epidemiological risk factors. Future research should: (1) use relevant animal models to clarify the pathogenesis of bovine chlamydioses; (2) quantify the impact of chlamydial infection at a herd level and identify strategies for its control, including sub-unit vaccine development; and (3) evaluate the zoonotic risk of bovine chlamydial infections which will require the development of species-specific serodiagnostics.

Recurrence of Chlamydiasuis infection in pigs after short-term antimicrobial treatment

The effect of short-term antimicrobial treatment on natural excretion of Chlamydia suis in rectal swabs and C. suis and Chlamydophila psittaci in nasal swabs was investigated in 47 clinically normal piglets by quantitative real-time PCR. Pigs were treated IM with 4 mg/kg enrofloxacin for 5 days (n = 22) or 2.5mg/kg enrofloxacin for 3 days followed by 100mg/mL tiamulin (n = 25). Antimicrobial treatment reduced the number of pigs positive for chlamydiae and the quantity of chlamydial DNA in positive swabs for a few days, but chlamydial excretion recurred in both groups. Short-term antimicrobial treatment at dosages recommended for treatment of other bacterial infections in pig herds was not effective in eliminating naturally occurring subclinical chlamydial infection in pigs.

Chlamydial zoonoses

BACKGROUND

Zoonoses were already a subject of intense interest even before the SARS and avian influenza epidemics arose. For many years, chlamydiae have been hypothesized to be important zoonotic pathogens, because of their wide distribution and their infectious cycle. This article provides an overview of the current state of knowledge on this subject.

METHODS

The authors present a selective review of the literature as well as their own findings.

RESULTS

The scientific knowledge of the distribution and infectious cycle of chlamydiae is still inadequate. The laboratory diagnosis of chlamydial zoonoses remains unsatisfactory in both human and veterinary medicine, as there are no commercially available sensitive and species-specific tests. Acute chlamydial infections are usually treated with macrolides, tetracyclines, or quinolones. Persistent varieties are not covered by standard therapy.

CONCLUSIONS

There is a considerable need for research on chlamydial infections, especially with regard to the diagnosis and treatment of persistent varieties.

Detection of Chlamydophila caviae and Streptococcus equi subsp. zooepidemicus in horses with signs of rhinitis and conjunctivitis

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.

Recent developments in the laboratory diagnosis of chlamydial infections

There are two main approaches to diagnosing infections by Chlamydia and Chlamydophila spp. in mammals and birds. The first involves the direct detection of the agent in tissue or swab samples, while the second involves the serological screening of blood samples for the presence of anti-chlamydial antibodies. Ultimately, the test that is used is dependent on the types of samples that are submitted to the diagnostic laboratory for analysis. The present paper gives an overview on methodologies and technologies used currently in diagnosis of chlamydial infections with emphasis on recently developed tests. The performance characteristics of individual methods, such as the detection of antigen in smears and in pathological samples, the isolation of the pathogen, various antibody detection tests and DNA-based methods utilising conventional and real-time PCR, as well as DNA microarray technology are assessed, and specific advantages and drawbacks are discussed. Further, a combination of a specific real-time PCR assay and a microarray test for chlamydiae is proposed as an alternative reference standard to isolation by cell culture.

The detection of Chlamydophila psittaci genotype C infection in dogs

Reports of canine chlamydiosis are infrequent, possibly because the pathogen is rarely considered to be a cause of disease in dogs. This report presents details of Chlamydophila psittaci infection in four bitches with recurrent keratoconjunctivitis, severe respiratory distress and reduced litter size (up to 50% stillborn or non-viable puppies) in a small dog-breeding facility in Germany. Cell culture and immunofluorescence examination of conjunctival, nasal and pharyngeal swabs revealed chlamydial inclusions. PCR and sequencing of ompA amplification products confirmed the presence of Cp. psittaci genotype C. The zoonotic potential of the pathogen was illustrated by evidence of disease in two children that lived on the premises with the infected dogs. There was circumstantial evidence to suggest infection of dogs and humans may have followed the introduction of two canaries and a parrot to the household. The persistent nature of the chlamydial infection suggests that dogs may be reservoirs of Cp. psittaci, but this putative role and whether or not dogs shed the pathogen require further investigation.

Direct identification of chlamydiae from clinical samples using a DNA microarray assay: a validation study

While DNA microarrays have become a widely accepted tool for mRNA expression monitoring, their use in rapid diagnosis of bacterial and viral pathogens is only emerging. So far, insufficient sensitivity and high costs have been the major limiting factors preventing more widespread use of microarray platforms in direct testing of clinical samples. In the present study, a total of 339 samples, among them 293 clinical specimens from animals and humans, were examined by the ArrayTube (AT) DNA microarray assay to detect chlamydial DNA and identify the species of Chlamydia and Chlamydophila involved. Samples included nasal and conjunctival swabs, formalin-fixed, paraffin-embedded and fresh organ tissue, milk, feces and cell culture. Notably, the AT test was shown to detect mixed infections in clinical samples. The calculated median sensitivity of 0.81 over the entire panel of clinical samples was comparable to conventional 16S PCR, but slightly lower than real-time PCR and other PCR assays. However, when a panel of long-time stored swab samples was excluded from the calculation, the sensitivity was clearly higher (0.87) and equivalent to that of real-time PCR. Altogether, the data demonstrate the suitability of this DNA microarray assay for routine diagnosis.

Field evaluation of a rapid point-of-care assay for targeting antibiotic treatment for trachoma control: a comparative study

BACKGROUND

Trachoma results from repeated episodes of conjunctival infection with Chlamydia trachomatis and is the leading infectious cause of blindness. To eliminate trachoma, control programmes use the SAFE strategy (Surgery, Antibiotics, Face cleanliness, and Environmental improvement). The A component is designed to treat C trachomatis infection, and is initiated on the basis of the prevalence of the clinical sign trachomatous inflammation-follicular (TF). Unfortunately, TF correlates poorly with C trachomatis infection. We sought to assess a newly developed point-of-care (POC) assay compared with presence of TF for guiding the use of antibiotics for trachoma control.

METHODS

We compared performance outcomes of the POC assay and presence of TF using commercial PCR as a comparator in 664 children aged 1-9 years in remote, trachoma-endemic villages in Tanzania. Signs of trachoma were graded according to the WHO simplified trachoma grading system.

FINDINGS

Of 664 participants, 128 (19%) were positive for ocular C trachomatis infection by PCR. Presence of TF had a sensitivity of 64.1% (95% CI 55.8-72.4), specificity of 80.2% (76.8-83.6), and positive predictive value of 43.6% (36.5-50.7). By contrast, the POC assay had a sensitivity of 83.6% (77.2-90.0), specificity of 99.4% (98.8-100.0), and positive predictive value of 97.3% (94.2-100.3). Interagreements and intra-agreements between four novice operators were 0.988 (0.973-1.000) and 0.950 (0.894-1.000), respectively.

INTERPRETATION

The POC assay is substantially more accurate than TF prevalence in identifying the presence or absence of infection. Additional studies should assess the use of the assay in the planning and monitoring of trachoma control activities.

BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species

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.

Effects of a probiotic strain of Enterococcus faecium on the rate of natural chlamydia infection in swine

Chlamydiae are obligately intracellular pathogens which cause infections associated with a broad range of diseases in both livestock and humans. In addition, a large proportion of animals may become persistently infected asymptomatic carriers and serve as reservoirs for other animals which also shed these potential zoonotic pathogens. Reducing the chlamydial load of animals is therefore of major importance, and since large-scale antibiotic treatment is neither desired nor feasible, alternative means of prevention are needed. Here we performed a study comparing the efficacy of a probiotic strain of Enterococcus faecium on the reduction of both the rate of natural infection and the shedding of chlamydiae in swine. The presence of Chlamydiaceae was detected by species-specific PCR of fecal samples of sows taken at three times prior to the birth of piglets. Piglets delivered from chlamydia-positive sows in either the control or the probiotic group were also examined for the frequency of chlamydiae at various ages. Eighty-five percent of the piglets from the control group were found to be chlamydia positive, whereas chlamydiae were found in only 60% of piglets from the probiotic group, results confirmed by fluorescence in situ hybridization and immunohistology, which showed higher rates of infection in the control group. In addition to the reduced frequency of chlamydia-positive piglets in the probiotic group, the time of appearance of positive samples was delayed. To our knowledge, these data show for the first time that a probiotic strain of E. faecium can reduce the rate of carryover infections of piglets by obligate intracellular pathogens.

DNA microarray-based detection and identification of Chlamydia and Chlamydophila spp

A microarray hybridization assay for identification of chlamydiae was developed using the ArrayTube platform. The technology is comparatively inexpensive and involves plastic tube-integrated microchips and signal amplification by enzyme-catalyzed silver precipitation. Hybridization probes were designed on the basis of the most variable window approach, which identified species-specific nucleotide polymorphisms in a region of generally high sequence similarity. The selected 26-nt probe sequences were used on two different series of customized microarrays, i.e. combinatorial high-density in situ synthesized arrays and low-density spotted arrays. Target DNA was prepared by consensus PCR amplifying a 1-kbp segment of the ribosomal RNA operon. Unique species-specific hybridization patterns were obtained for all nine species of the family Chlamydiaceae on both microarray types. The present assay proved suitable for unambiguous species identification of chlamydial cell cultures and showed a potential for direct detection of these bacteria from clinical tissue.

Tetracycline resistance in Chlamydia suis mediated by genomic islands inserted into the chlamydial inv-like gene

Many strains of Chlamydia suis, a pathogen of pigs, express a stable tetracycline resistance phenotype. We demonstrate that this resistance pattern is associated with a resistance gene, tet(C), in the chlamydial chromosome. Four related genomic islands were identified in seven tetracycline-resistant C. suis strains. All resistant isolates carry the structural gene tet(C) and the tetracycline repressor gene tetR(C). The islands share significant nucleotide sequence identity with resistance plasmids carried by a variety of different bacterial species. Three of the four tet(C) islands also carry a novel insertion sequence that is homologous to the IS605 family of insertion sequences. In each strain, the resistance gene and associated sequences are recombined into an identical position in a gene homologous to the inv gene of the yersiniae. These genomic islands represent the first examples of horizontally acquired DNA integrated into a natural isolate of chlamydiae or within any other obligate intracellular bacterium.