Egg intensity and freeze-thawing of fecal samples affect sensitivity of Echinococcus multilocularis detection by PCR

Evaluation of the Allplex GI Parasite and Helminth PCR Assay in a Belgian Travel Clinic

Recently a number of broad-range stool parasite PCR assays have been developed. However, there is ongoing disagreement regarding their diagnostic performance, as various studies have produced contradictory results. In this study, we compared the diagnostic accuracy of the Seegene Allplex GI-Parasite and Allplex GI-Helminth assays (SA) with the conventional methods used at the travel clinic of the Institute of Tropical Medicine (ITM) including microscopy, antigen testing, and molecular detection in order to provide insights into the strengths and limitations of this diagnostic tool which may be crucial to select the most appropriate diagnostic tools for the suspected pathogen. A total of 97 native stool samples from 95 patients with suspected gastrointestinal illness were analyzed, including 26 from a frozen collection and 71 prospectively collected samples. The diagnostic performance of SA was notably superior to the conventional workflow in detecting Dientamoeba fragilis (sensitivity 100% vs. 47.4%) and Blastocystis hominis (sensitivity 95% vs. 77.5%). SA had a comparable performance with the conventional workflow in detecting pathogenic protozoa (sensitivity 90% vs. 95%). In contrast, SA had a much lower diagnostic performance in detecting helminths (59.1%) compared to the conventional workflow (100%). We conclude that the Seegene Allplex GI-Parasite assay may be useful for protozoa screening in low-endemic industrialized countries. However, the Allplex GI-Helminth assay is not recommended due to its suboptimal performance compared to microscopy.

Prevalence and geographic distribution of Echinococcus genus in wild canids in southern Québec, Canada

Echinococcus spp. is an emerging zoonotic parasite of high concern. In Canada, an increase in the number of human and animal cases diagnosed has been reported, but information regarding the parasite's distribution in wildlife reservoir remains limited. A cross-sectional study was conducted to estimate the prevalence of wild canids infected with Echinococcus spp. and Echinococcus multilocularis in areas surrounding populated zones in Québec (Canada); to investigate the presence of areas at higher risk of infection; to evaluate potential risk factors of the infection; and as a secondary objective, to compare coproscopy and RT-PCR diagnostic tests for Taenia spp. and Echinococcus identification. From October 2020 to March 2021, fecal samples were collected from 423 coyotes (Canis latrans) and 284 red foxes (Vulpes vulpes) trapped in 12 administrative regions. Real-time PCR for molecular detection of genus Echinococcus spp. and species-specific Echinococcus multilocularis were performed. A total of 38 positive cases of Echinococcus spp., of which 25 were identified as E. multilocularis, were detected. Two high-risk areas of infection were identified. The prevalence of Echinococcus spp. was 22.7% (95% CI 11.5-37.8%) in the Montérégie centered high-risk area, 26.5% (95% CI 12.9-44.4%) in the Bas-St-Laurent high-risk area, and 3.0% (95%CI 1.8-4.7%) outside those areas. For E. multilocularis, a prevalence of 20.5% (95% CI 9.8-35.3%) was estimated in the high-risk area centered in Montérégie compared to 2.4% (95% CI 1.4-3.9%) outside. Logistic regression did not show any association of infection status with species, sex, or geolocation of capture (p > 0.05). This study shows the circulation of Echinococcus in a wildlife cycle in 9/12 administrative regions of Québec.

Comparison of Clostridioides difficile nucleic acid amplification test (NAAT) results using fresh and frozen stool specimens and rectal swabs

IMPORTANCE

Nucleic acid amplification tests (NAATs) are frequently used in Clostridioides difficile research and diagnostic testing, but the effect of freezing specimens on C. difficile NAAT performance is not well characterized. This study evaluated the concordance of NAAT results between fresh and frozen specimens (fecal and rectal swabs) and found it to be very good to excellent. The results indicate that frozen fecal and rectal swab specimens may be used for C. difficile NAAT testing in research when fresh specimens are not available.

Detection of Echinococcus multilocularis in repurposed environmental DNA samples from river water

Environmental DNA (eDNA) is an increasingly popular tool in biological and ecological studies. As a biproduct of its increasing use, large number of eDNA samples are being collected and stored, that potentially contain information of many non-target species. One potential use for these eDNA samples is a surveillance and early detection of pathogens and parasites that are otherwise difficult to detect. Echinococcus multilocularis is such a parasite with serious zoonotic concern, and whose range has been expanding. If eDNA samples from various studies can be repurposed in detecting the parasite, it can significantly reduce the costs and efforts in surveillance and early detection of the parasite. We designed and tested a new set of primer-probe for detecting E. multilocularis mitochondrial DNA in environmental medium. Using this primer-probe set, we conducted real-time PCR on repurposed eDNA samples collected from three streams flowing through an area of Japan endemic to the parasite. We detected the DNA of E. multilocularis in one of the 128 samples (0.78%). The discovery suggests that while detecting E. multilocularis using eDNA samples is possible, the rate of detection appear to be very low. However, given the naturally low prevalence of the parasite among wild hosts in endemic areas, the repurposed eDNAs may still be a valid option for surveillance in newly introduced areas with the reduced cost and efforts. Further work is needed to assess and improve the effectiveness of using eDNA for detection of E. multilocularis.

Comparison of multiplex copro PCR with coproscopy followed by PCR on recovered eggs for the detection of Echinococcus granulosus and Taenia spp. infection in dogs

Echinococcosis and taeniasis are important helminth diseases that carry considerable impact on human and animal health. Domestic dogs and other canids are definitive hosts for several parasites of this group, including Echinococcus granulosus, Taenia multiceps, T. ovis, T. hydatigena and E. multilocularis. Detection of infection in dog populations is imperative for estimating the risk to susceptible humans and animals, and for its mitigation through prevention measures in dogs, other animals and humans. To date, identification of taeniid eggs, antigens or DNA in fecal samples are the most practical diagnostic modalities available for canine definitive hosts. Although widely used for this purpose, there is limited information comparing copro PCR and combined coproscopy-PCR protocols for the detection of taeniids. In the current study, a widely used multiplex PCR was performed on a large number of dog fecal samples using DNA extracted directly from feces. The samples were also tested by fecal flotation and coproscopy, eggs were isolated from microscopically-positive samples and extracted DNA was tested using the same multiplex PCR. The total number of taeniid positive samples detected using both methods was 46/317 (14.5%), including 10/317 (3.2%) E. granulosus positive samples. Both copro PCR and coproscopy have identified an equal number of samples as taeniid positive (n = 32). However, for the purpose of identification to species level, the copro PCR was significantly more sensitive than coproscopy followed by PCR on isolated eggs (sensitivity 0.7 vs. 0.41, p = 0.012), with 32/317 (10.1%) and 19/317 (6%) positive samples identified, respectively. The difference in identification of E. granulosus was highly apparent, as the majority of the E. granulosus positive samples (8/10) were detected by the copro PCR only. Coproscopy and egg PCR have identified 5/317 (1.6%) positive samples not detected by the copro PCR, including only a single sample (0.3%) positive for E. granulosus. Adding these positive samples to those identified by the copro PCR did not significantly improve the overall sensitivity (p = 0.074). Therefore, using both copro PCR and coproscopy in parallel may not be advantageous for taeniid detection and identification, at least until the egg PCR is further optimized and performs better. These results should be weighed against the different advantages that coproscopy based approach may offer.

Diagnostic tools for the detection of taeniid eggs in different environmental matrices: A systematic review

The cestode family Taeniidae consists of the genera Echinococcus and Taenia, both of which include zoonotic tapeworms of serious public health importance. Various environmental matrices have been identified from which parasite transmission to animals and humans can occur, and many techniques for detecting taeniid eggs in different environments have been developed. However, the majority lack appropriate validation, and standardized egg isolation procedures are absent. This hampers interstudy comparisons and poses a challenge for future researchers when deciding which technique to implement for assessing taeniid egg contamination in a particular matrix. Therefore, the aim of this systematic review was to present an overview of the detection methods for taeniid eggs in the environment, to discuss and compare them, and to provide recommendations for future studies. In total, 1814 publications were retrieved from scientific databases, and, ultimately, data were systematically reviewed from 90 papers. The results provide an overview of numerous diagnostic tests for taeniid egg detection in (or on) water, food, soil, insects, objects, and air. These tools could be categorized as either conventional (light microscopy), molecular, or immunodetection tools. The relatively cheap microscopy techniques often lack sensitivity and are unable to identify a taeniid egg at the genus level. Nevertheless, several records ascribed a genus, or even species, to taeniid eggs that had been detected by light microscopy. Molecular and immunodetection tools offer better specificity, but still rely on the preceding egg recovery steps that also affect overall sensitivity. Finally, the majority of the methods lacked any attempt at performance evaluation and standardization, especially at the earlier stages of the analysis (e.g., sampling strategy, storage conditions, egg recovery), and viability was rarely addressed. As such, our review highlights the need for standardized, validated detection tools, that not only assess the extent of environmental contamination, but also the egg genus or species, and address viability.

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The cestode family Taeniidae contains species of serious public health importance.

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Parasite transmission may occur from several environmental matrices.

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Many methods for environmental detection of taeniid eggs have been developed.

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These often lack standardization, performance evaluation, and viability assessment.

Rapid and Reliable Detection of Echinococcus multilocularis from Faeces Using Droplet Digital PCR

Purpose

Alveolar echinococcosis is a severe helminthic disease in humans caused by larvae of the fox tapeworm Echinococcus multilocularis. Austria is considered an endemic area with hotspots having up to 45% prevalence (Bagó et al. in Proceedings of the Zoo and Wildlife Health Conference 2019, Berlin, p. 91, 2019). At our facility, we have registered a notifiable increase of animals submitted for the diagnosis of E. multilocularis since 2016. Therefore, we investigated high throughput diagnostic methods to provide rapid and reliable results in comparison with our current method.

Methods

We have developed and compared a novel method of detection using droplet digital PCR (ddPCR) combined with previous target specific extraction according to Maas et al. (Vet Parasitol 230:20–24, 2016), with our current macroscopic method “Shaking in a Vessel Technique” (SVT) by Duscher et al. (Parasitol Res 95(1):40–42, 2005). We investigated 77 wild canids (72 red foxes, 5 golden jackals) using both methods. The data were analyzed using a non-Bayesian approach, applying bootstrapping to create confidentiality intervals.

Results

Sensitivity for droplet digital PCR was 90.51% with the 95% credibility interval ranging from 82.50 to 96.92%, whereas mean sensitivity for SVT was 92.04% with a 95% credibility interval ranging from 84.75% to 98.36%. Additionally, a non-linear regression similar to R² could be pointed out between the counted worms and the results gathered from ddPCR.

Conclusion

Magnetic capture extraction followed by ddPCR shows strong potential as a high throughput method for diagnosing E. multilocularis prevalence in diverse canid populations as well as infection intensities of individual animals, giving valuable epidemiological insights of the distribution amongst wild canids as an alternative to conventional qPCR or macroscopic methods.

Copro-polymerase chain reaction has higher sensitivity compared to centrifugal fecal flotation in the diagnosis of taeniid cestodes, especially Echinococcus spp, in canids

Prompt and reliable diagnostic tests for taeniid infection in canids are important due to the risk of zoonoses like Echinococcus spp. Current diagnostic methods relying on fecal flotation lack sensitivity and specificity, but this has rarely been quantified due to the challenges in performing adult cestode recovery (the gold standard) in domestic dogs (Canis familiaris). Therefore, we recovered adult Taenia and Echinococcus spp. from intestines, as well as fecal/intestinal material from 484 wild canids trapped for fur in two Canadian provinces (276 foxes - primarily Vulpes vulpes, coyotes - Canis latrans, and wolves - Canis lupus in Québec and 208 coyotes in Saskatchewan). The performances of a newly developed coproPCR for tapeworm DNA detection in dogs, and centrifugal fecal flotation using Sheather's solution, were evaluated against adult cestode recovery. Overall, adult taeniid cestode prevalence (Taenia and/or Echinococcus) was 28 % (95 % CI: 23-33 %) in Québec (62 % (CI: 51-73%) of 74 coyotes, 65 % (CI: 44-82) of 23 wolves, and 11 % (CI: 7-16%) of 179 foxes) and 79 % (CI: 73-84%) of 208 coyotes in Saskatchewan. In Québec, E. canadensis and Taenia spp. were detected in coyotes and wolves, and foxes were only infected with Taenia spp., whereas Saskatchewan coyotes were predominantly infected with E. multilocularis (at significantly higher prevalence, but not intensity, than coyotes in Québec). Compared with centrifugal fecal flotation, the new coproPCR had at least double the sensitivity (58 % vs 23 % in QC coyotes, 57 % vs 23 % in QC wolves, 24 % vs 0% in QC foxes, and 80 % vs 25 % in SK coyotes). Notably, no taeniid eggs were detected on flotations from foxes infected with Taenia spp., and the new coproPCR had highest sensitivity in Saskatchewan coyotes, which were predominantly infected with E. multilocularis. CoproPCR has promising prospects for use in Veterinary clinics and diagnostic laboratories to detect taeniid cestode infections because of its higher sensitivity than faecal flotation methods. This is particularly important for zoonotic Echinococcus spp. where, from a public health perspective, false negatives are a much greater concern than false positives.

Comparison of Two DNA Extraction Methods and Two PCRs for Detection of Echinococcus multilocularis in the Stool Samples of Naturally Infected Red Foxes

Simple Summary

The goal of the study was to compare the efficiency of two commercial DNA extraction kits together with two different Polymerase Chain Reaction (PCR) protocols in the detection of Echinococcus multilocularis in the feces of naturally infected foxes. Stool samples from red foxes were collected in a highly endemic area in Poland. Sedimentation and counting technique (SCT) was used as a reference method. From 48 samples, 35 were positive in SCT. Further investigations showed that 40.0% of samples (from those with SCT positive result) after Z—DNA extraction and 45.7% after Q—DNA extraction gave positive results in nested PCR. In multiplex PCR, positive results were obtained in 54.3% of samples after Z isolation and 48.6% of samples after Q. Additionally, one sample negative in SCT gave a positive result in PCR. The number of worms detected in the intestines had no influence on the PCR results. Both of the extraction methods showed similar efficiency in DNA isolation and dealing with inhibitors; however, they showed relatively low sensitivity.

Abstract

(1) Background: Due to the increasing distribution of Echinococcus multilocularis infections in final hosts, epidemiological investigations are important for recognizing the spreading pattern of this parasite and also to estimate risk infection for humans. (2) Methods: Investigations were conducted with two commercial kits dedicated for DNA extraction from feces: ZR Fecal DNA Mini Prep (Zymo Research, Freiburg, Germany) and QIAamp FAST DNA Stool Mini Kit (Qiagen, Hilden, Germany) (marked as Z and Q), together with two common PCR protocols (nested PCR and multiplex PCR). The goal was to compare their efficiency in detecting the genetic material of E. multilocularis in the samples of feces. Stool samples from red foxes were collected in a highly endemic area in Poland. Sedimentation and counting technique (SCT) was used as a reference method. (3) Results: From 48 samples, 35 were positive in SCT. Further investigations showed that 40.0% of samples (from those with SCT positive result) after Z-DNA extraction and 45.7% after Q-DNA extraction gave positive results in nested PCR. In multiplex PCR, positive results were obtained in 54.3% of samples after Z isolation and 48.6% of samples after Q. Additionally, one sample that resulted in being negative in SCT gave a positive result in PCR. The number of worms detected in the intestines had no influence on PCR results. (4) Conclusions: Both of the extraction methods showed similar efficiency in DNA isolation and dealing with inhibitors; however, they showed relatively low sensitivity. This was probably caused by degradation of genetic material in the field-collected samples.

Detecting co-infections of Echinococcus multilocularis and Echinococcus canadensis in coyotes and red foxes in Alberta, Canada using real-time PCR

The continued monitoring of Echinococcus species in intermediate and definitive hosts is essential to understand the eco-epidemiology of these parasites, as well to assess their potential impact on public health. In Canada, co-infections of Echinococcus canadensis and Echinococcus multilocularis based on genetic characterization have been recently reported in wolves, but not yet in other possible hosts such as coyotes and foxes. In this study, we aimed to develop a quantitative real-time PCR assay to detect E. multilocularis and E. canadensis and estimate the occurrence of co-infections while inferring about the relative abundance of the two parasites within hosts. We tested DNA extracted from aliquots of Echinococcus spp. specimens collected from intestinal tracts of 24 coyote and 16 fox carcasses from Alberta, Canada. We found evidence of co-infections of E. multilocularis and E. canadensis in 11 out of 40 (27%) samples, with 8 out of 24 (33%) in coyote samples and 3 out of 16 (19%) in red fox samples. DNA concentrations were estimated in three samples with Cq values within the range of the standard curve for both parasites; two of them presented higher DNA concentrations of E. multilocularis than E. canadensis. The use of qPCR aided detection of co-infections when morphological discrimination was difficult and quantification of DNA for samples within the standard curve. This is the first molecularly confirmed record of E. canadensis in coyotes and the first evidence of co-infections of E. multilocularis and E. canadensis in coyotes and red foxes.

Latent class models for Echinococcus multilocularis diagnosis in foxes in Switzerland in the absence of a gold standard

Background

In Europe the principal definitive host for Echinococcus multilocularis, causing alveolar echinococcosis in humans, is the red fox (Vulpes vulpes). Obtaining reliable estimates of the prevalence of E. multilocularis and relevant risk factors for infection in foxes can be difficult if diagnostic tests with unknown test accuracies are used. Latent-class analysis can be used to obtain estimates of diagnostic test sensitivities and specificities in the absence of a perfect gold standard. Samples from 300 foxes in Switzerland were assessed by four different diagnostic tests including necropsy followed by sedimentation and counting technique (SCT), an egg-PCR, a monoclonal and a polyclonal copro-antigen ELISA. Information on sex, age and presence of other cestode species was assessed as potential covariates in the Bayesian latent class models. Different Bayesian latent-class models were run, considering dichotomized test results and, additionally, continuous readings resulting in empirical ROC curves.

Results

The model without covariates estimated a true parasite prevalence of 59.5% (95% CI: 43.1–66.4%). SCT, assuming a specificity of 100%, performed best among the four tests with a sensitivity of 88.5% (95% CI: 82.7–93.4%). The egg-PCR showed a specificity of 93.4% (95% CI: 87.3–99.1%), although its sensitivity of 54.8% was found moderately low (95% CI: 48.5–61.0%). Relatively higher sensitivity (63.2%, 95% CI: 55.3–70.8%) and specificity (70.0%, 95% CI: 60.1–79.4%) were estimated for the monoclonal ELISA compared to the polyclonal ELISA with a sensitivity and specificity of 56.0% (95% CI: 48.0–63.9%) and 65.9% (95% CI: 55.8–75.6%), respectively. In the Bayesian models, adult foxes were found to be less likely infected than juveniles. Foxes with a concomitant cestode infection had double the odds of an E. multilocularis infection. ROC curves following a Bayesian approach enabled the empirical determination of the best cut-off point. While varying the cut-offs of both ELISAs, sensitivity and specificity of the egg-PCR and SCT remained constant in the Bayesian latent class models.

Conclusions

Adoption of a Bayesian latent class approach helps to overcome the absence of a perfectly accurate diagnostic test and gives a more reliable indication of the test performance and the impact of covariates on the prevalence adjusted for diagnostic uncertainty.

Electronic supplementary material

The online version of this article (10.1186/s13071-017-2562-1) contains supplementary material, which is available to authorized users.

Comparison of different commercial DNA extraction kits and PCR protocols for the detection of Echinococcus multilocularis eggs in faecal samples from foxes

Effective and sensitive methods for the molecular detection of Echinococcus multilocularis in faecal samples of final hosts are crucial for the prevention and control of human alveolar echinococcosis and for studies on the epidemiology of the parasite. Little is known about the suitability of commercial test kits for isolating DNA of E. multilocularis from fox faeces and the performance of standard Polymerase Chain Reaction (PCR) protocols in relation to the quality of DNA extracted by these kits. We compared four different kits: ZR Faecal DNA MiniPrep™ (Zymo Research), FastDNA^® SPIN Kit for Soil (MP Biomedicals), QIAamp^® Fast DNA Stool Mini Kit (QIAGEN) and NucleoSpin^® Soil Kit (Macherey-Nagel) for the extraction of DNA from E. multilocularis eggs present in faeces of foxes. Negative faecal samples were spiked with 600, 300, 150, 75, 37, 18, 9, 5 or 2 E. multilocularis eggs, and each egg concentration was tested 10 times with each of the DNA extraction kits. Each extracted DNA sample was amplified using three PCR protocols: i. conventional PCR (cPCR, Platinum^®Taq, Invitrogen), ii. qPCR with the iQ™ Supermix (Bio-Rad) and iii. qPCR with the QuantiTect^® Multiplex-Master Mix (QIAGEN). The highest analytical sensitivities for molecular detection of E. multilocularis eggs in spiked fox faeces were observed when combining either the QIAamp^® Fast DNA Stool Mini Kit or the ZR Faecal DNA MiniPrep™ kit with the qPCR using the QuantiTect^® Multiplex-Master Mix (Sensitivities 97% and 94%, respectively). Combinations including the remaining test kits (NucleoSpin^® Soil Kit and FastDNA^® SPIN Kit for Soil) showed a markedly lower analytical sensitivity for PCR examinations. The results of the present study indicate that it is of utmost importance to select suitable DNA extraction kits in combination with robust PCR methods or reagents to achieve acceptable analytical sensitivity in the molecular detection of E. multilocularis eggs in fox faecal samples.

Evaluation by latent class analysis of a magnetic capture based DNA extraction followed by real-time qPCR as a new diagnostic method for detection of Echinococcus multilocularis in definitive hosts

A new method, based on a magnetic capture based DNA extraction followed by qPCR, was developed for the detection of the zoonotic parasite Echinococcus multilocularis in definitive hosts. Latent class analysis was used to compare this new method with the currently used phenol-chloroform DNA extraction followed by single tube nested PCR. In total, 60 red foxes and coyotes from three different locations were tested with both molecular methods and the sedimentation and counting technique (SCT) or intestinal scraping technique (IST). Though based on a limited number of samples, it could be established that the magnetic capture based DNA extraction followed by qPCR showed similar sensitivity and specificity as the currently used phenol-chloroform DNA extraction followed by single tube nested PCR. All methods have a high specificity as shown by Bayesian latent class analysis. Both molecular assays have higher sensitivities than the combined SCT and IST, though the uncertainties in sensitivity estimates were wide for all assays tested. The magnetic capture based DNA extraction followed by qPCR has the advantage of not requiring hazardous chemicals like the phenol-chloroform DNA extraction followed by single tube nested PCR. This supports the replacement of the phenol-chloroform DNA extraction followed by single tube nested PCR by the magnetic capture based DNA extraction followed by qPCR for molecular detection of E. multilocularis in definitive hosts.