Circulating cell-free DNA in patients with alveolar echinococcosis

Circulating free DNA as a diagnostic marker for echinococcosis: a systematic review and meta-analysis

Introduction

Echinococcosis is a chronic zoonotic disease caused by tapeworms of the genus Echinococcus. The World Health Organization (WHO) has identified encapsulated disease as one of 17 neglected diseases to be controlled or eliminated by 2050. There is no accurate, early, non-invasive molecular diagnostic method to detect echinococcosis. The feasibility of circulating free DNA as a diagnostic method for echinococcosis has yielded inconclusive results in a number of published studies. However, there has been no systematic evaluation to date assessing the overall performance of these assays. We report here the first meta-analysis assessing the diagnostic accuracy of cfDNA in plasma, serum, and urine for echinococcosis.

Methods

We systematically searched PubMed, Embase, Cochrane Library, China National Knowledge Infrastructure (CNKI), and WeiPu databases up to 17 January 2024, for relevant studies. All analyses were performed using RevMan 5.3, Meta-DiSc 1.4, Stata 17.0, and R 4.3.1 software. The sensitivity, specificity, and other accuracy indicators of circulating free DNA for the diagnosis of echinococcosis were summarized. Subgroup analyses and meta-regression were performed to identify sources of heterogeneity.

Results

A total of 7 studies included 218 patients with echinococcosis and 214 controls (156 healthy controls, 32 other disease controls (non-hydatid patients), and 26 non-study-targeted echinococcosis controls were included). Summary estimates of the diagnostic accuracy of cfDNA in the diagnosis of echinococcosis were as follows: sensitivity (SEN) of 0.51 (95% CI: 0.45-0.56); specificity (SPE) of 0.99 (95% CI: 0.97-0.99); positive likelihood ratio (PLR) of 11.82 (95% CI: 6.74-20.74); negative likelihood ratio (NLR) of 0.57 (95% CI: 0.41-0.80); diagnostic ratio (DOR) of 36.63 (95% CI: 13.75-97.59); and area under the curve (AUC) value of 0.98 (95% CI: 0.96-1.00).

Conclusion

Existing evidence indicates that the combined specificity of circulating cfDNA for echinococcosis is high. However, the combined sensitivity performance is unsatisfactory due to significant inter-study heterogeneity. To strengthen the validity and accuracy of our findings, further large-scale prospective studies are required.Systematic review registrationThe systematic review was registered in the International Prospective Register of Systematic Reviews PROSPERO [CRD42023454158]. https://www.crd.york.ac.uk/PROSPERO/.

Detection of circulatory E. granulosus-derived cell-free DNA in the plasma and urine of human cystic echinococcosis using an in-house PCR: a potential promising diagnostic biomarker

BACKGROUND

The diagnostic tool for identifying cystic echinococcosis (CE) patients at an early stage is currently lacking. However, circulatory cell-free DNA (cfDNA) has shown potential as a biomarker for parasitic infections and could be used for diagnosing CE.

RESEARCH DESIGN AND METHODS

The plasma and urine samples were collected from 39 patients with confirmed CE through imaging and histopathological techniques. All plasma samples were tested for anti-echinococcal antibodies using a commercial ELISA test. Total plasma and urine cfDNA were extracted and an in-house PCR assay was developed to detect E. granulosus specific cfDNA in the samples of CE patients.

RESULTS

Out of the 39 patients, 30 tested positive for E. granulosus using serology, with a sensitivity of 76.9%. Moreover, the detection rates for the cfDNA were 79.5% in plasma samples and 58.97% in urine samples using the 80 bp COX1 gene. The plasma-based PCR and serology test showed the highest agreement (Kappa = 0.53).

CONCLUSIONS

Plasma-based PCR has been found to be a reliable diagnostic tool for identifying CE patients at different cyst stages. It offers validity, speed, and sufficient sensitivity, making it an alternative to serology in diagnosing CE in endemic areas.

Sensitive detection of specific cell-free DNA in serum samples from sheep with cystic echinococcosis

BACKGROUND

Developing more sensitive methods for the diagnosis of echinococcosis is essential. In this study PCR assay for sensitive detection of specific cell-free DNA (cfDNA) of Echinococcus granulosus sensu lato in the sera of the sheep naturally infected with echinococcosis was investigated.

METHODS

To extract cfDNA from 35 infected sheep, the modified phenol-chloroform method was used for two different volumes (0.5 and 2 ml) of serum samples. From each extracted sample, two DNA volumes (5 and 10 μl) were amplified using both standard PCR and semi-nested PCR targeting NADH dehydrogenase subunit I.

RESULTS

Standard and semi-nested PCR on 0.5 ml of serum samples detected Echinococcus DNA in 8 and 12 out of 35 sheep, respectively; however, using 2 ml of serum samples, they detected 24 and 27 samples. By increasing the volume of template DNA, the PCRs could detect 29 and 33 out of 35 samples. The results were confirmed by sequencing of randomly selected PCR amplicons and comparing them with GenBank databases.

CONCLUSIONS

Larger volumes of serum for DNA extraction, greater volumes of DNA template for PCR, and employing a semi-nested PCR protocol, increased the sensitivity of PCR to 95%. This approach can also be applied to the diagnosis of echinococcosis in humans.

Introductory Chapter: Changes in Eco-System Change Echinococci - “One Health Concept” against Echinococci

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Diagnosis of echinococcosis by detecting circulating cell-free DNA and miRNA

INTRODUCTION

Diagnosis of echinococcosis is difficult and usually performed based on clinical findings, imaging, and serological test. However, all of them have limitations, especially in follow-up approaches.

AREAS COVERED

Detection of cell-free DNA (cfDNA) and micro-RNA (miRNA) is currently a hot topic for diagnosis of echinococcosis diseases. For detecting cell-free DNA in echinococcosis patient's samples such as sera, some techniques are based on next-generation sequencing (NGS), DNA-deep sequencing, some are based on PCR-based methods, and a few works related to the detection of miRNA for the diagnosis of human echinococcosis.

EXPERT OPINION

In the detection of cell-free DNA in echinococcosis patient' samples, NGS and DNA-deep sequencing have shown high level of sensitivity, but are not suitable for routine clinical examination as they are expensive and inaccessible in the majority of endemic areas. However, PCR-based methods have shown a sensitivity of about 20-25%. To improve the sensitivity of these tests, improving the DNA extraction method, designing appropriate primers for detecting short-length fragments of circulating DNA, using a higher volume of a serum sample, and application of more sensitive PCR methods are recommended. In the field of miRNA detection, further works are recommended.

Real-time multiplex PCR for human echinococcosis and differential diagnosis

Molecular identification of rare human infectious pathogens appears to be one of the most relevant current methods for rapid diagnosis and management of patients. PCR techniques, in particular real-time quantitative PCR, are best suited for the detection of DNA from the pathogens, even at low concentrations. Echinococcosis infections are due to helminths of the Echinococcus genus, with closely related species involved in parasitic lesions affecting animals and, accidentally, humans. We developed a multiplex qPCR (MLX qPCR) assay allowing for the detection of four Echinococcus species involved in Europe in alveolar echinococcosis (AE) and cystic echinococcosis (CE) (Echinococcus multilocularis, E. granulosus sensu stricto, E. ortleppi, and E. canadensis), based on short mitochondrial targets. A collection of 81 fresh and formalin-fixed paraffin-embedded tissues (FFPE) of AE and CE lesions was assembled. The qPCR assays were performed in triplex for Echinococcus spp. detection, associated with a qPCR inhibitor control. A duplex qPCR was also designed to enable diagnosis of two other dead-end helminthiases (cysticercosis (Taenia solium), and toxocariasis (Toxocara cati and T. canis)). The sensitivity of the qPCR was assessed and ranged from 1 to 5 × 10^-4 ng/μL (seven PCR assays positive), corresponding to 37-42 cycles for quantifiable DNA. The specificity was 100% for all the targets. This multiplex qPCR, adapted to low amounts of DNA can be implemented in the laboratory for the rapid molecular diagnosis of Echinococcosis species.

One-tube nested MGB Probe Real-time PCR assay for detection of Echinococcus multilocularis infection in plasma cell free DNA

INTRODUCTION

The main objective of this study was to develop a One-tube nested MGB probe real-time PCR Assay for detecting Echinococcus multilocularis infection in human plasma cell free DNA (cfDNA).

METHODS

cfDNA was extracted from 10 E.m.-infected patients using a NucleoSnap DNA Plasma Kit and characterized by genomic sequencing. We designed nested PCR primers and MGB probe for Echinococcus multilocularis detection. The specificity, sensitivity and reproducibility of this assay were analyzed, and its validity was confirmed in 13 early stage clinical samples.

RESULTS

Several Echinococcus multilocularis-specific sequences were detected in the cfDNA of E.m.-infected patients, and CBLO020001206.1 was selected as the candidate sequence. We designed the primers and probe for the one tube nested real-time PCR. No cross-reactions with E.g. were observed. The detection limit was as low as 1 copy for Echinococcus multilocularis. The coefficients of variation were lower than 5% in intra- and inter-assays. 11 out of 13 patients were positive with nested MGB Probe PCR Assay and 3 patients were positive without outer primer in early stage Alveolar Echinococcosis pateints.

CONCLUSION

The one-tube nested MGB probe real-time PCR assay is a simple, rapid, and cost-effective method for detection of Echinococcus multilocularis infection in patients' Plasma DNA.

Liquid Biopsy for Promising Non-invasive Diagnostic Biomarkers in Parasitic Infections

BACKGROUND

Liquid biopsy refers to the sampling and molecular analysis of body fluids such as blood, saliva, and urine in contrast to conventional tissue biopsies. Liquid biopsy approach can offer powerful non-invasive biomarkers (circulating markers) for diagnosis and monitoring treatment response of a variety of diseases, including parasitic infections.

METHODS

In this review, we concentrate on cell-free DNA (cfDNA), microRNA (miRNA), and exosomes in the published literature.

RESULTS

Considering the high prevalence and severity of parasitic infections worldwide, circulating biomarkers can provide a new insight into the diagnosis and prognosis of parasites in the near future. Moreover, identifying and characterizing parasite- or host-derived circulating markers are important for a better understanding of the pathogenesis of parasite infection and host-parasite relationship at the molecular level. Profiling of biomarkers for parasitic diseases is a promising potential field, though further studies and optimization strategies are required, both in vitro and in vivo.

CONCLUSION

In this review, we discuss three approaches in the liquid biopsy including circulating cfDNA, miRNAs, and exosomes for diagnosis and evaluation of parasites and summarize circulating biomarkers in non-invasive samples during parasitic infections.

Cell-free DNA as a diagnostic tool for human echinococcosis

Echinococcosis is a major public health problem and an emerging/re-emerging disease. It was proposed that Echinococcus cell-free DNA (cfDNA) could be used in diagnosing human echinococcosis, though earlier attempts failed. Here, we update the research on detecting Echinococcus cfDNA in echinococcosis patients' samples and highlight future research directions.

Parasite Circulating Cell-free DNA in the Blood of Alveolar Echinococcosis Patients as a Diagnostic and Treatment-Status Indicator

BACKGROUND

Alveolar echinococcosis (AE) is a serious parasitic disease caused by the larvae of Echinococcus multilocularis. It is the less common but substantially more deadly of the 2 major echinococcosis diseases that can occur globally but are concentrated in central Asia.

METHODS

We analyzed parasite circulating cell-free DNA (cfDNA) in 149 plasma samples using a DNA sequencing-based method (105 AE, 16 cystic echinococcosis, 4 liver cancer, 4 gallstones, and 20 healthy volunteers). After identifying the Echinococcus-specific cfDNA (Em-cfDNA) sequences in the samples, we determined whether Em-cfDNA could be used for AE diagnosis and as a potential indicator of the effectiveness of surgical treatment. We also examined potential associations between Em-cfDNA levels and clinical features of AE patients.

RESULTS

Our work demonstrates that varying reads of Em-cfDNA were detectable in the plasma of 100% of preoperative AE patients and that all of the non-AE patients and healthy volunteers were negative. Em-cfDNA has good sensitivity and specificity for the diagnosis of AE. We also found that Em-cfDNA levels apparently have reference value for evaluating the therapeutic efficacy of surgery interventions for AE lesions. Finally, our analysis revealed that Em-cfDNA levels can reflect meaningful information about lesion size in preoperative AE patients.

CONCLUSIONS

We demonstrate that sequencing-based monitoring of Em-cfDNA can be used in the clinic as a powerful diagnostic indicator for AE. We also note that there is a strong potential for use of this liquid-biopsy method to monitor ongoing disease status in postintervention AE patients.

microRNA-125b-5p is a promising novel plasma biomarker for alveolar echinococcosis in patients from the southern province of Qinghai

Background

Alveolar echinococcosis (AE) is caused by parasitic infection by Echinococcus multilocularis. Its diagnosis is usually based on clinical symptoms, ultrasound, and other imaging methods. MicroRNAs (miRNAs) play important roles in disease processes and can exist in a highly stable cell-free form in body fluids. It is important to identify specific, sensitive diagnostic markers for early diagnosis and evaluation of AE. In this study, we examined hsa-miR-125b-5p as a potential plasma biomarker of E. multilocularis infection.

Methods

Plasma samples from patients with AE and healthy individuals were screened for the presence of five miRNAs using miRNA chips. We used quantitative polymerase chain reaction to measure miRNA expression levels in plasma and liver tissue samples from patients with AE.

Results

hsa-miR-125b-5p was stably upregulated in the plasma and liver tissue samples from patients with AE.

Conclusions

The results suggest that hsa-miR-125b-5p may be a promising biomarker for early, non-invasive diagnosis of AE.

Characterizing dynamic changes of plasma cell-free Echinococcus granulosus DNA before and after cystic echinococcosis treatment initiation

Over one million people are living with cystic echinococcosis (CE) and alveolar echinococcosis (AE). For CE, long-term albendazole treatment is often needed, which requires regular follow-up. Follow-up is mainly through imaging which is insensitive to subtle changes and subjective to experience. We investigated the changes of Echinococcus granulosus (Eg) cell-free DNA (cfDNA) in plasma of CE patients before and after albendazole treatment to evaluate its potential as an objective marker for treatment follow-up. Plasma samples of nine CE patients were collected before and after treatment. We identified Eg cfDNA from every sample through high-throughput sequencing. Eg cfDNA concentration and fragment length increased significantly after the treatment period. Ultrasound examination before and after the treatment initiation reflected the drug effects to a certain extent, as the cyst size of four patients reduced. Our findings indicated that Eg cfDNA from plasma could be a potential marker in the monitoring of CE treatment.

Cell-free DNA and RNA-measurement and applications in clinical diagnostics with focus on metabolic disorders

Circulating cell-free DNA (cfDNA) and RNA (cfRNA) hold enormous potential as a new class of biomarkers for the development of noninvasive liquid biopsies in many diseases and conditions. In recent years, cfDNA and cfRNA have been studied intensely as tools for noninvasive prenatal testing, solid organ transplantation, cancer screening, and monitoring of tumors. In obesity, higher cfDNA concentration indicates accelerated cellular turnover of adipocytes during expansion of adipose mass and may be directly involved in the development of adipose tissue insulin resistance by inducing inflammation. Furthermore, cfDNA and cfRNA have promising diagnostic value in a range of obesity-related metabolic disorders, such as nonalcoholic fatty liver disease, type 2 diabetes, and diabetic complications. Here, we review the current and future applications of cfDNA and cfRNA within clinical diagnostics, discuss technical and analytical challenges in the field, and summarize the opportunities of using cfDNA and cfRNA in the diagnostics and prognostics of obesity-related metabolic disorders.

Diagnostic urinary cfDNA detected in human cystic echinococcosis

Cystic echinococcosis (CE) is a major neglected tropical zoonotic disease caused by the tissue-dwelling larval stage of the cestode parasite Echinococcus granulosus. For individuals suspected of CE, the diagnostic standard is imaging using ultrasonography, X rays, or computed tomography. These resource-demanding and expensive procedures are rarely available in endemic rural areas where CE is most prevalent. There is a critical need for a new approach to identify CE patients so that they can be managed early in the course of their infection. This study reports on the results of a diagnostic approach that identifies E. granulosus-derived cell-free DNA (cfDNA) in the urine of CE patients. Utilizing PCR to amplify a fragment of a major tandem repeat element found in E. granulosus nuclear DNA, urine samples from all seven imaging-confirmed CE patients who harbored active liver cysts were positive. In addition, the urine samples from 2/4 patients who presented with non-viable/calcified liver cysts were also PCR positive for the repeat fragment. To our knowledge, this is the first report of using parasite cfDNA from urine to diagnose CE. This approach provides an easy to implement and cost-effective method to survey for the prevalence of E. granulosus in humans populations.

Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics

Advances in sequencing technologies facilitate personalized disease-risk profiling and clinical diagnosis. In recent years, some great progress has been made in noninvasive diagnoses based on cell-free DNAs (cfDNAs). It exploits the fact that dead cells release DNA fragments into the circulation, and some DNA fragments carry information that indicates their tissues-of-origin (TOOs). Based on the signals used for identifying the TOOs of cfDNAs, the existing methods can be classified into three categories: cfDNA mutation-based methods, methylation pattern-based methods and cfDNA fragmentation pattern-based methods. In cfDNA mutation-based methods, the SNP information or the detected mutations in driven genes of certain diseases are employed to identify the TOOs of cfDNAs. Methylation pattern-based methods are developed to identify the TOOs of cfDNAs based on the tissue-specific methylation patterns. In cfDNA fragmentation pattern-based methods, cfDNA fragmentation patterns, such as nucleosome positioning or preferred end coordinates of cfDNAs, are used to predict the TOOs of cfDNAs. In this paper, the strategies and challenges in each category are reviewed. Furthermore, the representative applications based on the TOOs of cfDNAs, including noninvasive prenatal testing, noninvasive cancer screening, transplantation rejection monitoring and parasitic infection detection, are also reviewed. Moreover, the challenges and future work in identifying the TOOs of cfDNAs are discussed. Our research provides a comprehensive picture of the development and challenges in identifying the TOOs of cfDNAs, which may benefit bioinformatics researchers to develop new methods to improve the identification of the TOOs of cfDNAs.

Comprehensive characterization of plasma cell-free Echinococcus spp. DNA in echinococcosis patients using ultra-high-throughput sequencing

Background

Echinococcosis is a life-threatening parasitic disease caused by Echinococcus spp. tapeworms with over one million people affected globally at any time. The Echinococcus spp. tapeworms in the human body release DNA to the circulatory system, which can be a biomarker for echinococcosis. Cell-free DNA (cfDNA) is widely used in medical research and has been applied in various clinical settings. As for echinococcosis, several PCR-based tests had been trialed to detect cell-free Echinococcus spp. DNA in plasma or serum, but the sensitivity was about 20% to 25%. Low sensitivity of PCR-based methods might be related to our limited understanding of the features of cell-free Echinococcus spp. DNA in plasma, including its concentration, fragment pattern and release source. In this study, we applied ultra-high-throughput sequencing to comprehensively investigate the characteristics of cell-free Echinococcus spp. DNA in plasma of echinococcosis patients.

Methodology/Principal findings

We collected plasma samples from 23 echinococcosis patients. Total plasma cfDNA was extracted and sequenced with a high-throughput sequencing platform. An average of 282 million read pairs were obtained for each plasma sample. Sequencing data were analyzed with bioinformatics workflow combined with Echinococcus spp. sequence database. After identification of cell-free Echinococcus spp. reads, we found that the cell-free Echinococcus spp. reads accounted for 1.8e-5 to 4.0e-9 of the total clean reads. Comparing fragment length distribution of cfDNA between Echinococcus spp. and humans showed that cell-free Echinococcus spp. DNA of cystic echinococcosis (CE) had a broad length range, while that of alveolar echinococcosis (AE) had an obvious peak at about 135 bp. We found that most of the cell-free Echinococcus spp. DNA reads were from the nuclear genome with an even distribution, which might indicate a random release pattern of cell-free Echinococcus spp. DNA.

Conclusions/Significance

With ultra-high-throughput sequencing technology, we analyzed the concentration, fragment length, release source, and other characteristics of cell-free Echinococcus spp. DNA in the plasma of echinococcosis patients. A better understanding of the characteristics of cell-free Echinococcus spp. DNA in plasma may facilitate their future application as a biomarker for diagnosis.

Echinococcosis is one of the most neglected tropical diseases caused by the metacestodes of Echinococcus spp. tapeworms, which affect both humans and livestock. Plasma cell-free DNA (cfDNA) consists of nucleic acid fragments found extracellularly and may contain DNA released from the parasites. Research shows that a variety of parasites can be detected from plasma cfDNA. Cell-free Echinococcus spp. DNA in plasma or serum had been tested with PCR-based methods, but these PCR methods had low sensitivity ranged from 20% to 25%. Low sensitivity may be due to our limited understanding of cell-free Echinococcus spp. DNA in plasma. Here, we take advantage of high-throughput sequencing to get a comprehensive characterization of cell-free Echinococcus spp. DNA. Our results showed that with high-throughput sequencing we could detect cell-free Echinococcus spp. DNA in all samples, though at a very low level. Based on the sequencing data, we found that cell-free Echinococcus spp. DNA in plasma had a different fragment length distribution to cell-free human DNA, and fragment length distribution of cell-free Echinococcus spp. DNA is also different between cystic echinococcosis (CE) and alveolar echinococcosis (AE). The sequencing data can also help trace the release source of cell-free Echinococcus spp. DNA from the genome. According to the mapping results of cell-free Echinococcus spp. DNA reads, we found that most of them were from the nuclear genome rather than the mitochondrial genome, and their release position showed an even distribution on the genome. These characteristics of cell-free Echinococcus spp. DNA in echinococcosis patients’ plasma could facilitate their future application in research or clinical settings.

Targeted Sequencing of Genomic Repeat Regions Detects Circulating Cell-free Echinococcus DNA

Background

Echinococcosis is a chronic zoonosis caused by tapeworms of the genus Echinococcus. Treatment of the disease is often expensive and complicated, sometimes requiring extensive surgery. Ultrasonographic imaging is currently the main technique for diagnosis, while immunological analysis provides additional information. Confirmation still needs pathological analysis. However, these diagnostic techniques generally detect infection in late stages of the disease. An accurate, early and non-invasive molecular diagnostic method is still unavailable.

Methodology/Principal findings

We sequenced the cell-free DNA (cfDNA) from plasma of echinococcosis patients and confirmed the presence of Echinococcus DNA. To improve detection sensitivity, we developed a method based on targeted next-generation sequencing of repeat regions. Simulation experiments demonstrate that the targeted sequencing is sensitive enough to detect as little as 0.1% of an Echinococcus genome in 1 mL of plasma. Results obtained using patient plasma shows that the Area Under the Curve (AUC) of the method is 0.862, with a detection sensitivity of 62.50% and specificity of 100%, corresponding to a Youden-index of 0.625.

Conclusions/Significance

This study provides evidence that hydatid cysts release cfDNA fragments into patient plasma. Using the repeat region targeted sequencing method, highly specific detection of Echinococcus infection was achieved. This study paves a new avenue for potential non-invasive screening and diagnosis of echinococcosis.

Echinococcosis is a severe chronic parasitic disease caused by tapeworms of the genus Echinococcus. According to the World Health Organization, there are more than 1 million people living with echinococcosis worldwide. For decades, little progress has been made to develop a molecular diagnosis and specific treatment for the disease. Although imaging and immunological detection are used for diagnosis, these technologies are either only effective for late stages of the disease or hardly conclusive. The detection of cell-free DNA has been a powerful tool for precise diagnosis. In this study, we showed the presence of Echinococcus-derived cell-free DNA in plasma of echinococcosis patients. We further established an assay to detect parasite DNA in blood samples based on amplification of Echinococcus specific repeat regions followed by targeted next-generation sequencing. This technique provides a new method for potential extensive screening and precision diagnosis of echinococcosis with high specificity.

A novel technique for retrospective genetic analysis of the response to vaccination or infection using cell-free DNA from archived sheep serum and plasma

Genetic variation is associated with differences in disease resistance and susceptibility among individuals within a population. To date, molecular genetic analyses of host responses have relied on extraction of genomic DNA from whole blood or tissue samples. However, such samples are not routinely collected during large-scale field studies. We demonstrate that cell-free genomic DNA (cfDNA) may be extracted and amplified from archived plasma samples, allowing retrospective analysis of host genetic diversity. This technique was also applicable to archived serum samples up to 35 years old and to different ruminant species. As proof of concept, we used this cfDNA approach to genotype the major histocompatibility complex (MHC) class II DRB1 locus of 224 Merino sheep which had participated in field trials of a commercial Haemonchus contortus vaccine, Barbervax^®, in Australia. This identified a total of 51 different DRB1 alleles and their relative frequencies. This is the first study to examine host MHC diversity using DNA extracted from archived plasma samples, an approach that may be applied to retrospective analyses of genetic diversity and responses to vaccination or infection across different species and populations.

Detection and genetic characterization of Echinococcus granulosus mitochondrial DNA in serum and formalin-fixed paraffin embedded cyst tissue samples of cystic echinococcosis patients

Cystic echinococcosis (CE) is a worldwide zoonotic disease caused by the larval stage of Echinococcus granulosus. We investigated the presence of E. granulosus-specific DNA in the serum of CE patients by detecting the cytochrome c oxidase I (cox1) and NADH dehydrogenase subunit I (nad1) mitochondrial genes. Serum and formalin-fixed paraffin embedded (FFPE) cyst tissue samples of 80 CE patients were analyzed. The extracted DNA of samples was submitted to PCR amplification of cox1 and nad1 genes, and products were sequenced and genotyped. Nineteen (23.8%; 95% CI 15.8-34.1) serum and 78 (97.5%; 95% CI 91.3-99.3) FFPE cyst tissue samples were successfully amplified with at least one gene. Echinococcus DNA was detected in the sera of 15.0% (95% CI: 8.8-24.4) and 10.0% (95% CI: 5.2-18.5) and in cyst tissue of 91.3% (95% CI: 83.0-95.7) and 83.8% (95% CI: 74.2-90.3) of 80 patients by cox1 and nad1 gene, respectively. Four genotypes of E. granulosus were distinguished in the CE patients, with predominance of genotype G1, followed by G3, G2, and G6. The finding of E. granulosus DNA in 23.8% of serum samples from CE patients confirmed that E. granulosus releases cell-free DNA into the circulatory system, but quantities may be inadequate for the diagnosis of CE. Genotype G1 predominance suggests the sheep-dog cycle as the primary route of human infection.

Digital PCR: a new technology for diagnosis of parasitic infections

BACKGROUND

Parasitic infections are responsible for a significant burden of disease worldwide as a result of international travel and immigration. More accurate diagnostic tools are necessary in support to parasite control and elimination programmes in endemic regions as well as for rapid case detection in non-endemic areas. Digital PCR (dPCR) is a powerful technology with recent applications in parasitology.

AIMS

This review provides for the first time an overview of dPCR as a novel technology applied to detection of parasitic infections, and highlights the most relevant potential benefits of this assay.

SOURCES

Peer-reviewed literature pertinent to this review based on PubMed, Cochrane and Embase databases as well as laboratory experience of authors.

CONTENT

Among the 86 studies retrieved, 17 used the dPCR applied to parasites belonging to protozoa (8), helminths (8) and arthropods (1) of clinical human interest. dPCR was adopted in four studies, respectively, for Plasmodium and Schistosoma japonicum. dPCR led to clear advantages over quantitative real-time PCR in P. falciparum and spp., and in S. japonicum showing higher sensitivity; and in Cryptosporidium with higher stability to inhibitors from stool. For all parasites, dPCR allows absolute quantitation without the need of a standard curve. Various dPCR platforms were used. A few critical factors need consideration: DNA load, choice of platform and reaction optimization.

IMPLICATIONS

Owing to its sensitivity and quantitative characteristics, dPCR is a potential candidate to become an appealing new method among the molecular technologies for parasite detection and quantitative analysis in the future. In general, it has more applications than genomic DNA detection only, such as quantitation in mixed infections, gene expression and mutation analysis. dPCR should be considered in malaria screening and diagnosis as a complement to routine assays and in schistosomiasis elimination programmes. Standardized strategies and further studies are needed for the integration of dPCR in routine clinical laboratory.

Echinococcosis: Advances in the 21st Century

Echinococcosis is a zoonosis caused by cestodes of the genus Echinococcus (family Taeniidae). This serious and near-cosmopolitan disease continues to be a significant public health issue, with western China being the area of highest endemicity for both the cystic (CE) and alveolar (AE) forms of echinococcosis. Considerable advances have been made in the 21st century on the genetics, genomics, and molecular epidemiology of the causative parasites, on diagnostic tools, and on treatment techniques and control strategies, including the development and deployment of vaccines. In terms of surgery, new procedures have superseded traditional techniques, and total cystectomy in CE, ex vivo resection with autotransplantation in AE, and percutaneous and perendoscopic procedures in both diseases have improved treatment efficacy and the quality of life of patients. In this review, we summarize recent progress on the biology, epidemiology, diagnosis, management, control, and prevention of CE and AE. Currently there is no alternative drug to albendazole to treat echinococcosis, and new compounds are required urgently. Recently acquired genomic and proteomic information can provide a platform for improving diagnosis and for finding new drug and vaccine targets, with direct impact in the future on the control of echinococcosis, which continues to be a global challenge.