A TaqMan quantitative polymerase chain reaction assay for the detection of Lawsonia intracellularis in fecal and tissue samples from pigs

Detection and quantification by molecular techniques of early infection by Lawsonia intracellularis in suckling piglets

BACKGROUND

Lawsonia intracellularis is the causative agent of Porcine Proliferative Enteropathy (PPE), one of the most prevalent pig enteric diseases worldwide, but with sparse information about early infections in suckling piglets in the epidemiology of PPE. With that aim, this study evaluates the prevalence of L. intracellularis in 3-week-old piglets by analysing ileal digesta content and mucosal scrapings from 383 pigs from 16 farms (aprox., 25 pigs/batch) by real-time qPCR and droplet digital PCR (ddPCR).

RESULTS

Forty-nine samples yielded a qPCR positive result. Eleven samples from eight farms were confirmed as positive with concentrations of L. intracellularis from 3.5 log10 to 4.5 log10 bacteria/g of sample. Another 16 samples, eight farms, were classified as low positive (2.07-2.38 log10 bacteria/g) and 22 provided an uncertain result. Finally, 334 samples tested negative for L. intracellularis. At batch level, half of the farms included in the study had at least one positive sample and in 10 farms (62.5%) there was at least one low positive sample. The ddPCR was run in 50 of the 383 samples based on their PCR output (including low positive, uncertain and negative samples). Correlation analyses revealed a strong association between qPCR and the ddPCR results (ρ = 0.75; p < 0.001). The ddPCR allowed us to detect and confirm a positive result in the 19 samples classified as uncertain by the qPCR and detect L. intracellularis in 8 of 15 negatives by qPCR.

CONCLUSIONS

The results of the study demonstrate that a number of piglets are already infected with L. intracellularis during the suckling period evidencing early infection in certain animals, adding information of PPE epidemiology and opening new research topics such as sow-piglet transmission. Study results also evidence the usefulness of a combination of qPCR and ddPCR to improve qPCR sensitivity but assuring high specificity.

Epidemiology Tools to Evaluate the Control of Proliferative Enteropathy in Commercial Pig Herds

Proliferative enteropathy (PE) is characterized by diarrhea and reduced weight gains in growing pigs and intestinal hemorrhage in finishers. Vaccination, antibiotic medication, and improved hygiene can control PE, but their efficacy depends upon the epidemiology of PE. This study monitored the timing and severity of PE in 84 commercial pens across seven treatments, including disinfection, vaccination, no treatment, medication with olaquindox (50, 25 and 12.5 ppm), and combined disinfection and vaccination. Vaccination with or without lime disinfection suppressed clinical signs of PE and reduced the number of excreted L. intracellularis relative to untreated pigs housed in cleaned or cleaned and disinfected pens between 9 and 17 weeks of age. Continuous olaquindox mediation to 17 weeks of age prevented L. intracellularis infection, leaving finisher pigs naïve. These finisher pigs suffered an outbreak of hemorrhagic enteropathy with significant reductions in weight gain, feed intake, and mortalities of 4.6%. Over the 13 week grow/finish period, vaccinated pigs housed in disinfected pens showed significantly higher weight gain and feed intake relative to all other treatments, equating to a weight gain difference of between 3.6 and 3.9 kg per pig. Monitoring the immune response and fecal excretion of L. intracellularis in pens of pigs enabled effective PE control strategies to be evaluated on the farm.

Fecal PCR survey and genome analysis of Lawsonia intracellularis in China

Proliferative enteropathy caused by Lawsonia intracellularis is an important economic associated disease to pig industry, but the knowledge about the prevalence of L. intracellularis in pig farms in China is limited. In addition, there is no complete genome sequence available for L. intracellularis isolates from China. In this study, we developed a TaqMan qPCR for the screening of L. intracellularis by targeting the bacterial 16S rDNA gene. Laboratory evaluations revealed a good sensitivity and specificity on detecting L. intracellularis nucleic acid. Using this method, we investigated 891 fecal samples from apparently healthy pigs in 47 farms. The results demonstrated a screening positive rate of 37.3% (95% CI, 34.1-40.5%) for the samples, and a farm screening positive rate of 93.6% (95% CI, 65.3-94.4%). The screening positive rate at herd level ranged from 6.67% (95% CI, 0.2-31.9%) to 40% (95% CI, 38-79.6%), while at animal level, the highest screening positive rate was found in 12-week-old pigs [85.7% (95% CI, 67.3-96.0%)]. Investigation of 705 diarrheal or bloody feces from symptomatic pigs revealed that the highest positive rate was found in replacement gilts which was 37.18% (95% CI, 45.1-89.5%). Secondly, we conducted the complete genome sequence of a L. intracellularis PPE-GX01-2022 from China through PacBio sequencing. The genome of PPE-GX01-2022 consisted of a chromosome of 1,439,110 bp in length and three plasmids of 193,063, 39,799, and 27,067 bp, respectively. This genome encoded 1,428 predicted proteins, 44 tRNAs, and 6 rRNAs. Sequence comparisons demonstrated that the genome sequence of PPE-GX01-2022 was highly homologous to those of two isolates from US, and these three isolates shared 1,378 core genes. The screening results suggest a high prevalence rate of L. intracellularis in Chinese pig farms. In addition, the genome sequence of the Chinese isolate was highly homologous to those of the field isolates from the US.

The Effects of a Phytogenic Additive on the Histomorphometric Characteristics of the Intestines in Weaned Pigs with a Subclinical Natural Infection with Lawsonia intracellularis

Proliferative enteropathy, also known as proliferative ileitis, is considered to be one of the most economically important diseases in pig production worldwide. The estimated losses per affected growing pig usually range from US $1 to $5. The disease is caused by Lawsonia intracellularis, a Gram-negative, obligately intracellular bacterium. Control of the disease can be achieved with the use of vaccines or antibiotics. Recently there has been an increase in the efforts in the control of certain pathologies of the digestive system with phytogenic additives. The aim of this work was to assess the effects of a phytogenic additive on the histomorphometric characteristics of the intestines in weaned pigs with a subclinical infection with L. intracellularis acquired spontaneously. Histomorphometry analysis showed that crypt depth was significantly shorter (P<0.05), and the villus-height-to-crypt-depth ratio (P<0.05) significantly greater in the treatment group than the control. This improvement in the histological parameters of the intestine, considered to be indicators of its health, proved the positive effect of the tested additive on the digestive system in pigs.

Rapid and visual detection of Lawsonia intracellularis with an improved recombinase polymerase amplification assay combined with a lateral flow dipstick

Background

Lawsonia intracellularis (L. intracellularis) is the etiologic agent of porcine proliferative enteropathy (PPE), which is reported in many swine breeding countries all over the world, and has caused enormous economic losses in intensive pig production systems. Therefore, the aim of this study was to develop a simple and rapid method for on-site detection of Lawsonia intracellularis (L. intracellularis). As the isothermal recombinase polymerase amplification (RPA) can be performed at a constant temperature and its product is directly observed on a lateral-flow dipstick (LFD) with naked eyes without electrophoresis, the RPA-LFD assay should be useful for field diagnosis of L. intracellularis as well as its detection from clinical samples.

Results

The established RPA-LFD assay could be finished in 30 min at a wide temperature range of 25 to 40 °C, and the amplicons could be visualized by naked eyes. The developed RPA-LFD assay was specific to dnaA gene of L. intracellularis, and did not detect nucleic acids extracted from other common gastrointestinal pathogens. The minimum detection of this RPA-LFD method was 400 L. intracellularis per reaction, which was as sensitive as conventional PCR. Further, the RPA-LFD assay was performed with 150 clinical fecal samples and the detection results were compared with conventional PCR. Results showed that the coincidence rate of RPA-LFD and conventional PCR was 100%.

Conclusions

The combined RPA with LFD assay provides a simple, rapid, specific and sensitive alternative for field diagnosis of L. intracellularis infection.

A real-time loop-mediated isothermal amplification method for rapid detection of Lawsonia intracellularis in porcine fecal samples

Porcine proliferative enteritis is a common diarrheal disease characterized by thickening of the intestinal mucosa in swine due to enterocyte proliferation, which is caused by Lawsonia intracellularis. In this study, a real-time loop-mediated isothermal amplification (LAMP) assay was developed to detect L. intracellularis based on the conserved region of the 16S ribosomal RNA gene. The optimal reaction conditions of the real-time LAMP was 65 °C for 60 min. The LAMP products could be detected by both real-time turbidity and direct visual inspection. The assay was specific for L. intracellularis, as no cross-reaction was observed with other pathogens. The detection limit of the real-time LAMP assay was 1.4 × 10^-1pg of L. intracellularis DNA, which was the same as that of real-time PCR and approximately 100 times more sensitive than that of conventional PCR. Of the 136 clinical samples, L. intracellularis DNA was identified in 60 samples by real-time LAMP, which was the same as real-time PCR and higher than conventional PCR (36.8%, 50/136). The specific, sensitive and rapid real-time LAMP assay developed in this study could be a useful alternative tool in point-of-care (POC) diagnosis of L. intracellularis infection.

Influence of phytogenic feed additive on Lawsonia intracellularis infection in pigs

Lawsonia intracellularis is known to cause proliferative enteropathy (PE), one of the economically most important swine diseases with global distribution. Not unlike other enteric diseases, PE is a frequent indication for antibiotic therapy. However, their unjustified use leads to an emerging problem - antimicrobial resistance. Thus, the aim of this research was to assess if a phytogenic additive may replace antibiotics in the control of PE in 144 weaned piglets (72 treated and 72 controls) naturally infected with L. intracellularis. The quantity of L. intracellularis faecal shedding was monitored by real-time polymerase chain reaction (PCR) assay in faecal samples on day 0, 14 and 28, whilst the level of the ileum damage was determined by immunohistochemistry (IHC) assay performed on gut sections. Real-time PCR assay revealed that cycle-threshold (Ct) values in the treatment group increased significantly over time and were higher than in the control. These results indicate that the use of the phytogenic additive decreases the faecal excretion of L. intracellularis both throughout the experiment and in comparison to the control. The expression of the L. intracellularis antigen in IHC assay was lower in treated animals, implying that the additive leads to the decrease in the pathogen quantity in the ileum. Significantly higher feed conversion ratio was recorded in the treatment group. The results indicate that the phytogenic additive may be beneficial in the control of PE, but additional research is necessary to assess its use in various pig categories and define the optimum concentrations.

Stereomicroscopic 3D-pattern profiling of murine and human intestinal inflammation reveals unique structural phenotypes

Histology is fundamental to assess two-dimensional intestinal inflammation; however, inflammatory bowel diseases (IBDs) are often indistinguishable microscopically on the basis of mucosal biopsies. Here, we use stereomicroscopy (SM) to rapidly profile the entire intestinal topography and assess inflammation. We examine the mucosal surface of >700 mice (encompassing >16 strains and various IBD-models), create a profiling catalogue of 3D-stereomicroscopic abnormalities and demonstrate that mice with comparable histological scores display unique sub-clusters of 3D-structure-patterns of IBD pathology, which we call 3D-stereoenterotypes, and which are otherwise indiscernible histologically. We show that two ileal IBD-stereoenterotypes ('cobblestones' versus 'villous mini-aggregation') cluster separately within two distinct mouse lines of spontaneous ileitis, suggesting that host genetics drive unique and divergent inflammatory 3D-structural patterns in the gut. In humans, stereomicroscopy reveals 'liquefaction' lesions and hierarchical fistulous complexes, enriched with clostridia/segmented filamentous bacteria, running under healthy mucosa in Crohn's disease. We suggest that stereomicroscopic (3D-SMAPgut) profiling can be easily implemented and enable the comprehensive study of inflammatory 3D structures, genetics and flora in IBD.

Molecular diagnosis of natural fasciolosis by DNA detection in sheep faeces

Fasciolosis is an important parasitic zoonosis considered the most important helminth infection of ruminants in tropical countries. The aim of this study was to develop a PCR assay for the sensitive and specific detection of F. hepatica in formalin preserved sheep faeces. A 405-bp fragment of the cytochrome c oxidase subunit 1 gene of F. hepatica was amplified from stool samples of infected sheep. The PCR assay showed a detection limit of 20 pg of F. hepatica DNA. No cross-reactions were observed with samples containing coccidian oocysts or gastrointestinal nematodes eggs. Our PCR technique showed to be effective for specific detection of F. hepatica infections in sheep.

Nonculture Molecular Techniques for Diagnosis of Bacterial Disease in Animals

The past decade has seen remarkable technical advances in infectious disease diagnosis, and the pace of innovation is likely to continue. Many of these techniques are well suited to pathogen identification directly from pathologic or clinical samples, which is the focus of this review. Polymerase chain reaction (PCR) and gene sequencing are now routinely performed on frozen or fixed tissues for diagnosis of bacterial infections of animals. These assays are most useful for pathogens that are difficult to culture or identify phenotypically, when propagation poses a biosafety hazard, or when suitable fresh tissue is not available. Multiplex PCR assays, DNA microarrays, in situ hybridization, massive parallel DNA sequencing, microbiome profiling, molecular typing of pathogens, identification of antimicrobial resistance genes, and mass spectrometry are additional emerging technologies for the diagnosis of bacterial infections from pathologic and clinical samples in animals. These technical advances come, however, with 2 caveats. First, in the age of molecular diagnosis, quality control has become more important than ever to identify and control for the presence of inhibitors, cross-contamination, inadequate templates from diagnostic specimens, and other causes of erroneous microbial identifications. Second, the attraction of these technologic advances can obscure the reality that medical diagnoses cannot be made on the basis of molecular testing alone but instead through integrated consideration of clinical, pathologic, and laboratory findings. Proper validation of the method is required. It is critical that veterinary diagnosticians understand not only the value but also the limitations of these technical advances for routine diagnosis of infectious disease.

Lawsonia intracellularis infection and proliferative enteropathy in foals

Equine proliferative enteropathy (EPE) is a disease of foals caused by the obligate intracellular organism Lawsonia intracellularis. This organism is unique in that it causes proliferation of infected enterocytes, resulting in thickening of the intestinal epithelium, most often the small intestine. This disease affects mainly weanling foals and causes fever, lethargy, peripheral edema, diarrhea, colic and weight loss. The diagnosis of EPE may be challenging and relies on the presence of hypoproteinemia, thickening of segments of the small intestinal wall observed on abdominal ultrasonography, positive serology and molecular detection of L. intracellularis in feces. The epidemiology and genetic basis for pathogenesis for this disease is beginning to be elucidated. Phenotypic traits, genomic features, and gene expression profiles during L. intracellularis infection in vitro and in vivo are presented. In addition, this article reviews the epidemiology, pathological and clinicopathological findings, diagnosis, and control of EPE.

Equine proliferative enteropathy--a review of recent developments

Equine proliferative enteropathy (EPE) is a disease of foals caused by the obligate intracellular organism Lawsonia intracellularis. This emerging disease affects mainly weanling foals and causes fever, lethargy, peripheral oedema, diarrhoea, colic and weight loss. The diagnosis of EPE may be challenging and relies on the presence of hypoproteinaemia, thickening of segments of the small intestinal wall observed upon abdominal ultrasonography, positive serology and molecular detection of L. intracellularis in faeces. Although the clinical entity, diagnostic approach and treatment of EPE are well established and described, the epidemiology for this disease has remained largely unaddressed. This article focuses on new developments in the field of EPE, including epidemiology, pathophysiology, clinical signs, diagnosis, treatment and prevention.

The Summary is available in Chinese – see Supporting information.

Association between faecal load of lawsonia intracellularis and pathological findings of proliferative enteropathy in pigs with diarrhoea

Background

The study was designed to investigate correlation between histological findings of Lawsonia intracellularis in porcine cases of diarrhoea and the quantitative detection of Lawsonia intracellularis in faeces. A total of 156 pigs (10 to 70 days post weaning) with diarrhoea were randomly selected from 20 herds: The pigs were subjected to necropsy, histopathology, immunohistochemistry and faecal quantification of Lawsonia intracellularis by real time PCR.

Results

The median Lawsonia intracellularis excretion was significantly higher in pigs with gross lesions of proliferative enteropathy (median excretion: 5.92 log₁₀ bacteria/g faeces) compared to pigs without gross lesions of proliferative enteropathy (median excretion: <3.3 log₁₀ bacteria/g faeces) (P<0.001). Spearman’s correlation coefficient between the measureable PE lesions and L. intracellularis excretion was 0.50 (P<0.001). A significantly increasing trend in Lawsonia intracellularis excretion level for increasing proliferative enteropathy histopathology and immunohistochemistry scores was demonstrated (P<0.001; P<0.001). Spearman’s correlation coefficient between the histopathology scores and L. intracellularis excretion was 0.67 (P<0.001). Spearman’s correlation coefficient between the IHC scores and L. intracellularis excretion was 0.77 (P<0.001).

Conclusions

The histological and quantitative PCR detection of Lawsonia intracellularis were correlated in pigs with diarrhoea. Overall the results suggest that clinically important levels for Lawsonia intracellularis excretion in faeces may be established. Such clinical threshold levels may be used in practice to confirm a diagnosis of Lawsonia intracellularis associated diarrhoea.

Association between average daily gain, faecal dry matter content and concentration of Lawsonia intracellularis in faeces

Background

The objective of this study was to investigate the association between average daily gain and the number of Lawsonia intracellularis bacteria in faeces of growing pigs with different levels of diarrhoea.

Methods

A longitudinal field study (n = 150 pigs) was performed in a Danish herd from day 29 to 47 post weaning. Every third day all pigs were weighed, subjected to a clinical examination and faecal samples were obtained. Faecal samples were subjected to dry matter determination and absolute quantification by PCR for L. intracellularis and porcine circovirus type 2 (PCV2). Association between average daily gain, faecal dry matter content, numbers of L. intracellularis bacteria and PCV2 genome copies in faeces was investigated in a multilevel mixed-effects linear model.

Results

Increasing numbers of L. intracellularis log₁₀ bacteria/g faeces were significantly associated with decreasing average daily gain (P < 0.001). The association was decreasing with increasing faecal dry matter content (P < 0.01). The number of PCV2 log₁₀ copies/g faeces was not significantly associated with average daily gain of the pigs (P > 0.5).

Conclusion

The results suggest a potential application of a PCR quantifying L. intracellularis in growing pigs. Faecal dry matter content must be taken into consideration in interpretation of such test results.

Colonisation and shedding of Lawsonia intracellularis in experimentally inoculated rodents and in wild rodents on pig farms

Lawsonia intracellularis is an intracellular bacterium causing proliferative enteropathy in various animal species, and is considered an economically important pathogen of pigs. Rats and mice have been implicated as external vectors for a wide range of pig pathogens, including L. intracellularis. Previous studies have demonstrated L. intracellularis infection and proliferative enteropathy in rodents, but did not show the duration of shedding or the number of L. intracellularis shed by infected rodents, and therefore the infection risk that rodents pose to pigs. In this study, the number of L. intracellularis shed in the faeces and intestinal mucosa of wild rats trapped on pig farms was determined by a quantitative real time polymerase chain reaction assay. The prevalence of L. intracellularis in wild rats trapped on pig farms with endemic proliferative enteropathy (PE) was very high (≥ 70.6%), and large numbers of L. intracellularis were shed (10(10)/g of faeces) in a small proportion of wild rats. The duration of colonisation in laboratory rats and mice challenged with porcine isolates of L. intracellularis was also shown. Faecal shedding of L. intracellularis persisted for 14-21 days in rats and mice that were mildly affected with histological lesions of PE. The humoral immune response to L. intracellularis persisted for 40 days in both species. This study demonstrates that rodents may be an important reservoir of L. intracellularis on piggeries, and hence rodent control is important in disease eradication programs on pig farms.