Quantitative PCR and Digital PCR for Detection of Ascaris lumbricoides Eggs in Reclaimed Water

Present and Future Applications of Digital PCR in Infectious Diseases Diagnosis

Infectious diseases account for about 3 million deaths per year. The advent of molecular techniques has led to an enormous improvement in their diagnosis, both in terms of sensitivity and specificity and in terms of the speed with which a clinically useful result can be obtained. Digital PCR, or 3rd generation PCR, is based on a series of technical modifications that result in more sensitive techniques, more resistant to the action of inhibitors and capable of direct quantification without the need for standard curves. This review presents the main applications that have been developed for the diagnosis of viral, bacterial, and parasitic infections and the potential prospects for the clinical use of this technology.

An update on the current and emerging pharmacotherapy for the treatment of human ascariasis

INTRODUCTION

Globally, Ascaris lumbricoides is the commonest helminthic infection that affects people in underdeveloped countries and returning immigrants in industrialized nations. This article aims to provide latest updates on the epidemiology, clinical manifestations, and pharmacotherapy of ascariasis.

AREAS COVERED

A PubMed search was conducted using Clinical Queries and the key terms 'human ascariasis' OR 'Ascaris lumbricoides.' Ascaris lumbricoides is highly endemic in tropical and subtropic regions and among returning immigrants in industrialized nations. Predisposing factors include poor sanitation and poverty. The prevalence is greatest in young children. Most infected patients are asymptomatic. Patients with A. lumbricoides infection should be treated with anti-helminthic drugs to prevent complications from migration of the worm. Mebendazole and albendazole are indicated for children and nonpregnant women. Pregnant individuals should be treated with pyrantel pamoate.

EXPERT OPINION

Cure rates with anthelmintic treatment are high. No emerging pharmacotherapy can replace these existing drugs of good efficacy, safety profile and low cost for public health. It is opinioned that advances in the management of ascariasis include diagnostic accuracy at affordable costs, Emodepside is highly effective in single doses against ascarids in mammals and in human trials. The drug could be registered for human use in multiple neglected tropical diseases.

Development of a Droplet Digital PCR Assay for Detection and Quantification of Stubby Root Nematode, Paratrichodorus allius, in Soil

The stubby root nematode Paratrichodorus allius is an important plant-parasitic nematode species within the Trichodoridae family. It can directly harm the plants by feeding on the roots or indirectly by transmitting Tobacco rattle virus. These nematodes are mostly diagnosed either by traditional microscopic methods or a polymerase chain reaction (PCR)-based method. Droplet digital PCR (ddPCR) is a novel PCR technique which is sensitive and precise in quantifying DNA templates of the test samples. In this study, we developed a ddPCR assay to detect and quantify P. allius in soil. The specificity and sensitivity of the assay was first determined using P. allius nematode DNA or DNA from sterilized soil artificially inoculated with P. allius, and the assay was used to quantify P. allius populations in field soils. The assay did not detect nematodes other than P. allius, thus showing high specificity. It was able to detect P. allius equivalent to a 0.01 and 0.02 portion of a single nematode in soil DNA and nematode DNA extracts, respectively. Highly linear relationships between DNA copy numbers from ddPCR and serial dilutions of known concentrations were observed with DNA from P. allius nematodes (R2 = 0.9842) and from artificially infested soil (R2 = 0.9464). The P. allius populations from field soils determined by ddPCR were highly correlated with traditional microscopic counts (R2 = 0.7963). To our knowledge, this is the first report of applying ddPCR to detect and quantify stubby root nematode in soil. The results of this study support the potentiality of a ddPCR assay as a new research tool in diagnostics of plant-parasitic nematodes.

Low-Cost Microfluidic Systems for Detection of Neglected Tropical Diseases

Neglected tropical diseases (NTDs) affect tropical and subtropical countries and are caused by viruses, bacteria, protozoa, and helminths. These kinds of diseases spread quickly due to the tropical climate and limited access to clean water, sanitation, and health care, which make exposed people more vulnerable. NTDs are reported to be difficult and inefficient to diagnose. As mentioned, most NTDs occur in countries that are socially vulnerable, and the lack of resources and access to modern laboratories and equipment intensify the difficulty of diagnosis and treatment, leading to an increase in the mortality rate. Portable and low-cost microfluidic systems have been widely applied for clinical diagnosis, offering a promising alternative that can meet the needs for fast, affordable, and reliable diagnostic tests in developing countries. This review provides a critical overview of microfluidic devices that have been reported in the literature for the detection of the most common NTDs over the past 5 years.

Advantages and Limitations of Microscopy and Molecular Detections for Diagnosis of Soil-transmitted Helminths: An Overview

World Health Organization (WHO) reported that over 1.5 billion people are infected by soil-transmitted helminths (STH) worldwide in sub-Saharan Africa, the United States of America, China, and East Asia. Heavy infections and polyparasitism are associated with higher morbidity rates, and the patients are exposed to increased vulnerability to other diseases. Therefore, accurate diagnosis followed by mass treatment for morbidity control is necessary.STH diagnosis commonly involves the microscopic observation of the presence of the STH eggs and larvae in the faecal samples. Furthermore, molecular approaches are increasingly utilised in monitoring and surveillance as they show higher sensitivity. Their capability to differentiate hookworm species is an advantage over the Kato-Katz technique. This review discusses the advantages and limitations of microscopy and various molecular tools used for STH detection.

Advances in diagnosis of gastrointestinal nematodes in livestock and companion animals

Diagnosis of gastrointestinal nematodes in livestock and companion animals has been neglected for years and there has been an historical underinvestment in the development and improvement of diagnostic tools, undermining the undoubted utility of surveillance and control programmes. However, a new impetus by the scientific community and the quickening pace of technological innovations, are promoting a renaissance of interest in developing diagnostic capacity for nematode infections in veterinary parasitology. A cross-cutting priority for diagnostic tools is the development of pen-side tests and associated decision support tools that rapidly inform on the levels of infection and morbidity. This includes development of scalable, parasite detection using artificial intelligence for automated counting of parasitic elements and research towards establishing biomarkers using innovative molecular and proteomic methods. The aim of this review is to assess the state-of-the-art in the diagnosis of helminth infections in livestock and companion animals and presents the current advances of diagnostic methods for intestinal parasites harnessing (i) automated methods for copromicroscopy based on artificial intelligence, (ii) immunodiagnosis, and (iii) molecular- and proteome-based approaches. Regardless of the method used, multiple factors need to be considered before diagnostics test results can be interpreted in terms of control decisions. Guidelines on how to apply diagnostics and how to interpret test results in different animal species are increasingly requested and some were recently made available in veterinary parasitology for the different domestic species.

Potentials and challenges in the isolation and detection of ascarid eggs in complex environmental matrices

Ascarid infections constitute a major concern for both human and animal health risk assessment. Although being effectively transmitted by soil, water and contaminated food, reliable detection of ascarid eggs in environmental media often remains challenging. However, contamination of the environment with ascarid ova has gained more attention as a decisive part of proper risk assessment in recent years. Due to various factors, such as sample matrices, dissociation detergents and flotation solutions, defined and standardised protocols for the isolation of eggs from complex environmental matrices are difficult to establish and therefore limited. Thus, this study reviews common techniques used for the recovery of ascarid eggs from environmental media with special emphasis on sampling strategies, purification procedures and microscopic as well as molecular detection of egg contamination. Despite various advancements, mainly in the field of molecular methods leading to more reliable and sensitive detection, it can be concluded that there is still a need for unified guidelines for sampling and recovery of ascarid eggs derived from complex environmental matrices.

Application of digital PCR for public health-related water quality monitoring

Digital polymerase chain reaction (dPCR) is emerging as a reliable platform for quantifying microorganisms in the field of water microbiology. This paper reviews the fundamental principles of dPCR and its application for health-related water microbiology. The relevant literature indicates increasing adoption of dPCR for measuring fecal indicator bacteria, microbial source tracking marker genes, and pathogens in various aquatic environments. The adoption of dPCR has accelerated recently due to increasing use for wastewater surveillance of Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) - the virus that causes Coronavirus Disease 2019 (COVID-19). The collective experience in the scientific literature indicates that well-optimized dPCR assays can quantify genetic material from microorganisms without the need for a calibration curve and often with superior analytical performance (i.e., greater sensitivity, precision, and reproducibility) than quantitative polymerase chain reaction (qPCR). Nonetheless, dPCR should not be viewed as a panacea for the fundamental uncertainties and limitations associated with measuring microorganisms in water microbiology. With dPCR platforms, the sample analysis cost and processing time are typically greater than qPCR. However, if improved analytical performance (i.e., sensitivity and accuracy) is critical, dPCR can be an alternative option for quantifying microorganisms, including pathogens, in aquatic environments.

Human Ascariasis: An Updated Review

Background:

Ascaris lumbricoides is the most common helminthic infection. More than 1.2 billion people have ascariasis worldwide.

Objective:

This article aimed to provide an update on the evaluation, diagnosis, and treatment of ascariasis.

Methods:

A PubMed search was conducted in February 2020 in Clinical Queries using the key terms “ascariasis” OR “Ascaris lumbricoides”. The search strategy included meta-analyses, randomized controlled trials, clinical trials, observational studies, and reviews published within the past 10 years. The search was restricted to English literature. The information retrieved from the above search was used in the compilation of the present article. Patents were searched using the key term “ascariasis” OR “Ascaris lumbricoides” in www.freepatentsonline.com.

Results:

Ascaris lumbricoides is transmitted through the ingestion of embryonated eggs from fecal- contaminated material. Ascariasis has high endemicity in tropical and subtropical areas. Predisposing factors include poverty, poor sanitation, inadequate sewage disposal, and poor personal hygiene. The prevalence is greatest in children younger than 5 years of age. The majority of patients with intestinal ascariasis are asymptomatic. For those with symptoms, anorexia, nausea, bloating, abdominal discomfort, recurrent abdominal pain, abdominal distension, and intermittent diarrhea are not uncommon. Other clinical manifestations vary widely, depending on the underlying complications. Complications include Löeffler syndrome, intestinal obstruction, biliary colic, recurrent pyogenic cholangitis, cholecystitis, acalculous cholecystitis, obstructive jaundice, cholelithiasis, pancreatitis, and malnutrition. The diagnosis is best established by microscopic examination of fecal smears or following concentration techniques for the characteristic ova. Patients with A. lumbricoides infection warrant anthelminthic treatment, even if they are asymptomatic, to prevent complications from migration of the parasite. Albendazole and mebendazole are the drugs of choice for children and nonpregnant individuals with ascariasis. Pregnant women with ascariasis should be treated with pyrantel pamoate. Recent patents related to the management of ascariasis are also discussed.

Conclusion:

The average cure rate with anthelminthic treatment is over 95%. Unfortunately, most treated patients in endemic areas become re-infected within months. Health education, personal hygiene, improved sanitary conditions, proper disposal of human excreta, and discontinuing the use of human fecal matter as a fertilizer are effective long-term preventive measures. Targeting deworming treatment and mass anthelminthic treatment should be considered in regions where A. lumbricoides is prevalent.

Diagnostic Techniques of Soil-Transmitted Helminths: Impact on Control Measures

Soil-transmitted helminth (STH) infections are common in the tropical and subtropical countries. The burden of disease is highest in endemic areas with limited access to good quality water supply and poor sanitary conditions. Major approaches to control and reduce morbidity caused by worm infections include the periodic deworming of pre-school and school-aged children with anthelminthic drugs. Population-based studies and individual patient management including interventional studies can only be successful when accurate diagnostic techniques are used. The lack of appropriate diagnostic tools providing accurate results concerning both infectious status and intensity of infection-as these two factors vary in regions of low infection intensities-is a major challenge. Currently, available techniques show limited sensitivity and specificity and as such, a combination of several techniques is usually used to diagnose the large variety of parasite species. The objective of this review was to describe the advantages and disadvantages of the different available techniques for the diagnosis of STH infections and to highlight their use in control programs.

Development and evaluation of a loop-mediated isothermal amplification (LAMP) diagnostic test for detection of whipworm, Trichuris trichiura, in faecal samples

Whipworm infection or trichuriasis caused by Trichuris trichiura is of major public health concern in sub-Saharan Africa, particularly among pre-school and school-going children. It is among the neglected tropical diseases targeted for elimination through mass drug administration (MDA). One of the outcomes of MDA is a rapid decline in levels of infection intensity, making it difficult to monitor effectiveness of control measures using the conventional Kato-Katz procedure, which relies on the microscopic detection of parasite ova in faecal samples. In the present study, a loop-mediated isothermal amplification (LAMP) test was developed for the detection of T. trichiura infection in faecal samples. LAMP technology offers greater sensitivity and specificity than the microscopy-based tests. A set of four specific primers targeting the internal transcribed spacer 2 region of the ribosomal DNA were designed using Primer Explorer software. DNA was extracted from faecal samples using the alkaline lysis method (HotSHOT) and the LAMP reaction performed at 63°C for 1 h. The amplicons were visualized by both gel electrophoresis and with the naked eye following staining with SYBR green dye. Sensitivity and specificity tests were determined using the standard Kato-Katz diagnostic procedure as a reference test. The developed LAMP assay reliably detected T. trichiura DNA in faecal samples, with a specificity and sensitivity of 88% and 77%, respectively. No cross-reactivity was observed with several common helminth parasites. The developed LAMP assay is an appropriate diagnostic method for the detection of T. trichiura DNA in human faecal samples due to its simplicity, low cost, high sensitivity and specificity.

Detection of Helminth Ova in Wastewater Using Recombinase Polymerase Amplification Coupled to Lateral Flow Strips

Ascaris lumbricoides is a major soil-transmitted helminth that is highly infective to humans. The ova of A. lumbricoides are able to survive wastewater treatment, thus making it an indicator organism for effective water treatment and sanitation. Hence, Ascaris ova must be removed from wastewater matrices for the safe use of recycled water. Current microscopic techniques for identification and enumeration of Ascaris ova are laborious and cumbersome. Polymerase chain reaction (PCR)-based techniques are sensitive and specific, however, major constraints lie in having to transport samples to a centralised laboratory, the requirement for sophisticated instrumentation and skilled personnel. To address this issue, a rapid, highly specific, sensitive, and affordable method for the detection of helminth ova was developed utilising recombinase polymerase amplification (RPA) coupled with lateral flow (LF) strips. In this study, Ascaris suum ova were used to demonstrate the potential use of the RPA-LF assay. The method was faster (< 30 min) with optimal temperature at 37 °C and greater sensitivity than PCR-based approaches with detection as low as 2 femtograms of DNA. Furthermore, ova from two different helminth genera were able to be detected as a multiplex assay using a single lateral flow strip, which could significantly reduce the time and the cost of helminth identification. The RPA-LF system represents an accurate, rapid, and cost-effective technology that could replace the existing detection methods, which are technically challenged and not ideal for on-site detection in wastewater treatment plants.

Digital PCR—An Emerging Technology with Broad Applications in Microbiology

BACKGROUND

The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR.

CONTENT

Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing.

SUMMARY

dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.

Validation of droplet digital Polymerase Chain Reaction for the detection and absolute quantification of Taenia solium eggs in spiked soil samples

To enable the detection of taeniid eggs in environmental samples, a sensitive technology is required. In this study, we validated the effectiveness of a digital droplet Polymerase Chain Reaction (ddPCR) assay for detection, identification and absolute quantification of taeniid DNA from artificially contaminated soils with varying numbers of taeniid eggs using a set of universal primers, JB3 & JB4.5. The results showed that the number of cox1 copies detected increased gradually for both species with the number of taeniid eggs added to the different soil types. The highest cox1 DNA copies recovery for Taenia solium and T. lynciscapreoli was from the sand soil with lowest recovery being observed in clay soils. Therefore, ddPCR is a promising technology for screening of taeniid eggs from soil samples collected in the environment irrespective of the soil type and the number of eggs. The potential of the ddPCR protocol to detect taeniid egg DNA in spiked soil samples has great practical application for taeniid egg screening in soils from endemic areas. However, when universal primers are used in screening environmental samples, the identity of ddPCR positive samples must be confirmed by sequencing. In addition, more validation studies using species-specific primers and field soil samples is recommended.

A Case for Using Genomics and a Bioinformatics Pipeline to Develop Sensitive and Species-Specific PCR-Based Diagnostics for Soil-Transmitted Helminths

The balance of expense and ease of use vs. specificity and sensitivity in diagnostic assays for helminth disease is an important consideration, with expense and ease often winning out in endemic areas where funds and sophisticated equipment may be scarce. In this review, we argue that molecular diagnostics, specifically new assays that have been developed with the aid of next-generation sequence data and robust bioinformatic tools, more than make up for their expense with the benefit of a clear and precise assessment of the situation on the ground. Elimination efforts associated with the London Declaration and the World Health Organization (WHO) 2020 Roadmap have resulted in areas of low disease incidence and reduced infection burdens. An accurate assessment of infection levels is critical for determining where and when the programs can be successfully ended. Thus, more sensitive assays are needed in locations where elimination efforts are approaching a successful conclusion. Although microscopy or more general PCR targets have a role to play, they can mislead and cause study results to be confounded. Hyper-specific qPCR assays enable a more definitive assessment of the situation in the field, as well as of shifting dynamics and emerging diseases.

A Review on the Current Knowledge and Prospects for the Development of Improved Detection Methods for Soil-Transmitted Helminth Ova for the Safe Reuse of Wastewater and Mitigation of Public Health Risks

Climate change, increase in population and scarcity of freshwater have led to a global demand for wastewater reuse in irrigation. However, wastewater has to be treated in order to minimize the presence of pathogens, in particular, the ova of soil-transmitted helminthes (STHs). Limiting the transmission via removal of STH ova, accurate assessment of risks and minimizing the exposure to the public have been recommended by health regulators. The World Health Organization (WHO) guideline specifies a limit of ≤1 ova/L for safe wastewater reuse. Additionally, the Australian Guidelines for Water recycling (AGWR) recommend a hydraulic retention time of over 25 days in a lagoon or stabilization pond to ensure a 4 log reduction value of helminth ova and to mitigate soil-transmitted helminths associated risks to humans. However, the lack of fast and sensitive methods for assessing the concentration of STH ova in wastewater poses a considerable challenge for an accurate risk assessment. Consequently, it has been difficult to control soil-transmitted helminthiasis despite effective mass drug administration. This limitation can be overcome with the advent of novel techniques for the detection of helminth ova. Therefore, this review presents an assessment of the current methods to detect the viable ova of soil-transmitted helminths in wastewater. Furthermore, the review focuses on the perspectives for the emerging state-of-the-art research and developments that have the potential to replace currently available conventional and polymerase chain reaction based methods and achieve the guidelines of the WHO in order to allow the safe reuse of wastewater for non-potable applications, thereby minimizing public health risks.

Detection of helminth ova genera using in-situ biosynthesis of gold nanoparticles

In this study, a presumptive colorimetric method was used to detect and differentiate the ova of two major soil transmitted helminths in wastewater, Ascaris and Trichuris. Gold nanoparticles were synthesised following the reduction of tetrachloroauric acid by the surface moiety of Ascaris suum, resulting in a colour change. In contrast there was no colour change with Trichuris suis indicating the absence of gold nanoparticle synthesis. Analysis of the ova using scanning electron microscopy (SEM) revealed that the synthesis of nanoparticles on the surface of ova was confirmed as gold nanoparticles (91 w/w %) by energy dispersive X-ray analysis (EDX). This study indicated that the surface moieties of helminth ova could be a potential target for ova detection and differentiation using the biosynthesis of nanoparticles by colorimetry methods.

Three advantages:

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Simple colorimetry based method requiring no sophisticated devices.

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No trained personnel required.

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Cost-effective and can be a potential candidate for biosensors.