Phase II evaluation of sensitivity and specificity of PCR and NASBA followed by oligochromatography for diagnosis of human African trypanosomiasis in clinical samples from D.R. Congo and Uganda

A Systematic Review on Suitability of Molecular Techniques for Diagnosis and Research into Infectious Diseases of Concern in Resource-Limited Settings

Infectious diseases significantly impact the health status of developing countries. Historically, infectious diseases of the tropics especially have received insufficient attention in worldwide public health initiatives, resulting in poor preventive and treatment options. Many molecular tests for human infections have been established since the 1980s, when polymerase chain reaction (PCR) testing was introduced. In spite of the substantial innovative advancements in PCR technology, which currently has found wide application in most viral pathogens of global concern, the development and application of molecular diagnostics, particularly in resource-limited settings, poses potential constraints. This review accessed data from sources including PubMed, Google Scholar, the Web of Knowledge, as well as reports from the World Health Organization’s Annual Meeting on infectious diseases and examined these for current molecular approaches used to identify, monitor, or investigate some neglected tropical infectious diseases. This review noted some growth efforts in the development of molecular techniques for diagnosis of pathogens that appear to be common in resource limited settings and identified gaps in the availability and applicability of most of these molecular diagnostics, which need to be addressed if the One Health goal is to be achieved.

Viral outbreaks detection and surveillance using wastewater-based epidemiology, viral air sampling, and machine learning techniques: A comprehensive review and outlook

A viral outbreak is a global challenge that affects public health and safety. The coronavirus disease 2019 (COVID-19) has been spreading globally, affecting millions of people worldwide, and led to significant loss of lives and deterioration of the global economy. The current adverse effects caused by the COVID-19 pandemic demands finding new detection methods for future viral outbreaks. The environment's transmission pathways include and are not limited to air, surface water, and wastewater environments. The wastewater surveillance, known as wastewater-based epidemiology (WBE), can potentially monitor viral outbreaks and provide a complementary clinical testing method. Another investigated outbreak surveillance technique that has not been yet implemented in a sufficient number of studies is the surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in the air. Artificial intelligence (AI) and its related machine learning (ML) and deep learning (DL) technologies are currently emerging techniques for detecting viral outbreaks using global data. To date, there are no reports that illustrate the potential of using WBE with AI to detect viral outbreaks. This study investigates the transmission pathways of SARS-CoV-2 in the environment and provides current updates on the surveillance of viral outbreaks using WBE, viral air sampling, and AI. It also proposes a novel framework based on an ensemble of ML and DL algorithms to provide a beneficial supportive tool for decision-makers. The framework exploits available data from reliable sources to discover meaningful insights and knowledge that allows researchers and practitioners to build efficient methods and protocols that accurately monitor and detect viral outbreaks. The proposed framework could provide early detection of viruses, forecast risk maps and vulnerable areas, and estimate the number of infected citizens.

Analytical sensitivity of loopamp and quantitative real-time PCR on dried blood spots and their potential role in monitoring human African trypanosomiasis elimination

The objective set by WHO to reach elimination of human African trypanosomiasis (HAT) as a public health problem by 2020 is being achieved. The next target is the interruption of gambiense-HAT transmission in humans by 2030. To monitor progress towards this target, in areas where specialized local HAT control capacities will disappear, is a major challenge. Test specimens should be easily collectable and safely transportable such as dried blood spots (DBS). Monitoring tests performed in regional reference centres should be reliable, cheap and allow analysis of large numbers of specimens in a high-throughput format. The aim of this study was to assess the analytical sensitivity of Loopamp, M18S quantitative real-time PCR (M18S qPCR) and TgsGP qPCR as molecular diagnostic tests for the presence of Trypanosoma brucei gambiense in DBS. The sensitivity of the Loopamp test, with a detection limit of 100 trypanosomes/mL, was in the range of parasitaemias commonly observed in HAT patients, while detection limits for M18S and TgsGP qPCR were respectively 1000 and 10,000 trypanosomes/mL. None of the tests was entirely suitable for high-throughput use and further development and implementation of sensitive high-throughput molecular tools for monitoring HAT elimination are needed.

Barcoding in trypanosomes

Trypanosomes (genus Trypanosoma) are parasites of humans, and wild and domestic mammals, in which they cause several economically and socially important diseases, including sleeping sickness in Africa and Chagas disease in the Americas. Despite the development of numerous molecular diagnostics and increasing awareness of the importance of these neglected parasites, there is currently no universal genetic barcoding marker available for trypanosomes. In this review we provide an overview of the methods used for trypanosome detection and identification, discuss the potential application of different barcoding techniques and examine the requirements of the 'ideal' trypanosome genetic barcode. In addition, we explore potential alternative genetic markers for barcoding Trypanosoma species, including an analysis of phylogenetically informative nucleotide changes along the length of the 18S rRNA gene.

Revisiting zoonotic human African trypanosomiasis control in Uganda

OBJECTIVES

Human migration and concomitant HIV infections are likely to bring about major changes in the epidemiology of zoonotic parasitic infections. Human African trypanosomiasis (HAT) control is particularly fraught with intricacies. The primarily zoonotic form, T.b. rhodesiense, and the non-zoonotic T.b. gambiense co-exist in Northern Uganda, leading to a potential geographic and genetic overlap of the two foci. This region also has the highest HIV prevalence in Uganda plus poor food security. We examine the bottlenecks facing the control program in a changed political and economic context.

METHOD

We searched the literature in July 2015 using three databases: MEDLINE, Google Scholar, and Web of Science.

FINDINGS

Decentralized zoonotic HAT control for animal reservoirs and vectors compromise sustainability of the control programs. Human transmission potential may be underestimated in a region with other endemic diseases and where an HIV-HAT epidemic, could merge two strains.

CONCLUSION

Our comprehensive literature review concludes that enhanced collaboration is imperative not only between human and animal health specialists, but also with political science. Multi-sectorial collaborations may need to be nurtured within existing operational national HIV prevention frameworks, with an integrated surveillance framework.

Human african trypanosomiasis diagnosis in first-line health services of endemic countries, a systematic review

While the incidence of Human African Trypanosomiasis (HAT) is decreasing, the control approach is shifting from active population screening by mobile teams to passive case detection in primary care centers. We conducted a systematic review of the literature between 1970 and 2011 to assess which diagnostic tools are most suitable for use in first-line health facilities in endemic countries. Our search retrieved 16 different screening and confirmation tests for HAT. The thermostable format of the Card Agglutination Test for Trypanosomiasis (CATT test) was the most appropriate screening test. Lateral flow antibody detection tests could become alternative screening tests in the near future. Confirmation of HAT diagnosis still depends on visualizing the parasite in direct microscopy. All other currently available confirmation tests are either technically too demanding and/or lack sensitivity and thus rather inappropriate for use at health center level. Novel applications of molecular tests may have potential for use at district hospital level.

New insights in staging and chemotherapy of African trypanosomiasis and possible contribution of medicinal plants

Human African trypanosomiasis (HAT) is a fatal if untreated fly-borne neuroinflammatory disease caused by protozoa of the species Trypanosoma brucei (T.b.). The increasing trend of HAT cases has been reversed, but according to WHO experts, new epidemics of this disease could appear. In addition, HAT is still a considerable burden for life quality and economy in 36 sub-Saharan Africa countries with 15-20 million persons at risk. Following joined initiatives of WHO and private partners, the fight against HAT was re-engaged, resulting in considerable breakthrough. We present here what is known at this day about HAT etiology and pathogenesis and the new insights in the development of accurate tools and tests for disease staging and severity monitoring in the field. Also, we elaborate herein the promising progresses made in the development of less toxic and more efficient trypanocidal drugs including the potential of medicinal plants and related alternative drug therapies.

Towards Point-of-Care Diagnostic and Staging Tools for Human African Trypanosomiaisis

Human African trypanosomiasis is a debilitating disease prevalent in rural sub-Saharan Africa. Control of this disease almost exclusively relies on chemotherapy that should be driven by accurate diagnosis, given the unacceptable toxicity of the few available drugs. Unfortunately, the available diagnostics are characterised by low sensitivities due to the inherent low parasitaemia in natural infections. Demonstration of the trypanosomes in body fluids, which is a prerequisite before treatment, often follows complex algorithms. In this paper, we review the available diagnostics and explore recent advances towards development of novel point-of-care diagnostic tests.

Diagnostic accuracy of molecular amplification tests for human African trypanosomiasis--systematic review

Background

A range of molecular amplification techniques have been developed for the diagnosis of Human African Trypanosomiasis (HAT); however, careful evaluation of these tests must precede implementation to ensure their high clinical accuracy. Here, we investigated the diagnostic accuracy of molecular amplification tests for HAT, the quality of articles and reasons for variation in accuracy.

Methodology

Data from studies assessing diagnostic molecular amplification tests were extracted and pooled to calculate accuracy. Articles were included if they reported sensitivity and specificity or data whereby values could be calculated. Study quality was assessed using QUADAS and selected studies were analysed using the bivariate random effects model.

Results

16 articles evaluating molecular amplification tests fulfilled the inclusion criteria: PCR (n = 12), NASBA (n = 2), LAMP (n = 1) and a study comparing PCR and NASBA (n = 1). Fourteen articles, including 19 different studies were included in the meta-analysis. Summary sensitivity for PCR on blood was 99.0% (95% CI 92.8 to 99.9) and the specificity was 97.7% (95% CI 93.0 to 99.3). Differences in study design and readout method did not significantly change estimates although use of satellite DNA as a target significantly lowers specificity. Sensitivity and specificity of PCR on CSF for staging varied from 87.6% to 100%, and 55.6% to 82.9% respectively.

Conclusion

Here, PCR seems to have sufficient accuracy to replace microscopy where facilities allow, although this conclusion is based on multiple reference standards and a patient population that was not always representative. Future studies should, therefore, include patients for which PCR may become the test of choice and consider well designed diagnostic accuracy studies to provide extra evidence on the value of PCR in practice. Another use of PCR for control of disease could be to screen samples collected from rural areas and test in reference laboratories, to spot epidemics quickly and direct resources appropriately.

A range of molecular amplification techniques has been developed for the diagnosis of HAT, with polymerase chain reaction (PCR) at the forefront. As laboratory strengthening in endemic areas increases, it is expected that the applicability of molecular tests will increase. However, careful evaluation of these tests against the current reference standard, microscopy, must precede implementation. Therefore, we have investigated the published diagnostic accuracy of molecular amplification tests for HAT compared to microscopy for both initial diagnosis as well as for disease staging.

Here, PCR tests seem to have an acceptably high specificity and sensitivity for diagnosis of stage I HAT. This conclusion is, however, based on multiple-microscopy based techniques as reference standards, which may have low sensitivity, and a patient population that was not always representative. Future studies should, therefore, first and foremost include those patients for which PCR may become the test of choice. More certainty about the practical value of PCR tests for HAT diagnosis should come from non-accuracy design studies, like feasibility or cost-effectiveness studies.

Molecular diagnosis of infections and resistance in veterinary and human parasites

Since 1977, >2000 research papers described attempts to detect, identify and/or quantify parasites, or disease organisms carried by ecto-parasites, using DNA-based tests and 148 reviews of the topic were published. Despite this, only a few DNA-based tests for parasitic diseases are routinely available, and most of these are optional tests used occasionally in disease diagnosis. Malaria, trypanosomiasis, toxoplasmosis, leishmaniasis and cryptosporidiosis diagnosis may be assisted by DNA-based testing in some countries, but there are very few cases where the detection of veterinary parasites is assisted by DNA-based tests. The diagnoses of some bacterial (e.g. lyme disease) and viral diseases (e.g. tick borne encephalitis) which are transmitted by ecto-parasites more commonly use DNA-based tests, and research developing tests for these species makes up almost 20% of the literature. Other important uses of DNA-based tests are for epidemiological and risk assessment, quality control for food and water, forensic diagnosis and in parasite biology research. Some DNA-based tests for water-borne parasites, including Cryptosporidium and Giardia, are used in routine checks of water treatment, but forensic and food-testing applications have not been adopted in routine practice. Biological research, including epidemiological research, makes the widest use of DNA-based diagnostics, delivering enhanced understanding of parasites and guidelines for managing parasitic diseases. Despite the limited uptake of DNA-based tests to date, there is little doubt that they offer great potential to not only detect, identify and quantify parasites, but also to provide further information important for the implementation of parasite control strategies. For example, variant sequences within species of parasites and other organisms can be differentiated by tests in a manner similar to genetic testing in medicine or livestock breeding. If an association between DNA sequence and phenotype has been demonstrated, then qualities such as drug resistance, strain divergence, virulence, and origin of isolates could be inferred by DNA-based tests. No such tests are in clinical or commercial use in parasitology and few tests are available for other organisms. Why have DNA-based tests not had a bigger impact in veterinary and human medicine? To explore this question, technological, biological, economic and sociological factors must be considered. Additionally, a realistic expectation of research progress is needed. DNA-based tests could enhance parasite management in many ways, but patience, persistence and dedication will be needed to achieve this goal.

Latent Trypanosoma brucei gambiense foci in Uganda: a silent epidemic in children and adults?

Trypanosoma brucei gambiense sleeping sickness follows a long asymptomatic phase and persists in ancient foci from which epidemic clinical disease arises. A putative focus of T. b. gambiense infections has been identified, initially in mothers and young children, on the Lake Albert shoreline of Western Uganda leading to mass screening of 6207 individuals in September 2008. T. b. gambiense infections were identified by Card Agglutination Test for Trypanosomiasis (CATT) and sub-species-specific PCR although parasitological methods failed to confirm any patent trypanosome infections. In April 2009, CATT positives were re-visited; diagnosis of individuals by CATT and PCR was unstable over the two time points and parasites remained undetected, even using mini Anion Exchange Centrifugation Technique (mAECT). These observations suggest the possibility of a silent focus of disease, where all infected individuals are in a latent stage, and highlight our limited understanding of the local natural history and disease progression of T. b. gambiense in children and adults.

Comparison of short-term and long-term protocols for stabilization and preservation of RNA and DNA of Leishmania, Trypanosoma, and Plasmodium

Molecular tools continue to be important in the prevention and control of parasitic diseases. However, using these techniques directly in the field remains a major challenge. Therefore, the preservation of clinical samples collected from endemic field areas for later analysis remains an important preanalytical process. This study aimed at identifying a suitable protocol for stabilization and preservation of RNA and DNA in bioclinical specimens for Trypanosoma, Leishmania, and Plasmodium research. Both spiked and unspiked blood samples were preserved in 7 protocols (different media; storage temperatures). Samples were evaluated for possible degradation of DNA and RNA along the storage duration up to the 10th week. Nucleic acid targets were assessed as follows: (i) Trypanosoma and Plasmodium RNA analysis was done using real-time nucleic acid sequence-based amplification (RT-NASBA) for 18S rRNA and for stage-specific Pfs25 mRNA, respectively; (ii) Trypanosoma DNA assessment analysis was conducted by using a conventional PCR for 18S rDNA; (iii) Leishmania RNA analysis was performed with a quantitative NASBA for 18S rRNA and Leishmania DNA assessment with an RT-PCR for 18S rDNA. Findings suggested that a newly developed L3™ buffer proved to be reliable and suitable for both short- and long-term preservation of parasite nucleic acid material. This buffer is envisaged to be suitable for utilization in field situations where resources are limited.

Diagnostic accuracy of PCR in gambiense sleeping sickness diagnosis, staging and post-treatment follow-up: a 2-year longitudinal study

Background

The polymerase chain reaction (PCR) has been proposed for diagnosis, staging and post-treatment follow-up of sleeping sickness but no large-scale clinical evaluations of its diagnostic accuracy have taken place yet.

Methodology/Principal Findings

An 18S ribosomal RNA gene targeting PCR was performed on blood and cerebrospinal fluid (CSF) of 360 T. brucei gambiense sleeping sickness patients and on blood of 129 endemic controls from the Democratic Republic of Congo. Sensitivity and specificity (with 95% confidence intervals) of PCR for diagnosis, disease staging and treatment failure over 2 years follow-up post-treatment were determined. Reference standard tests were trypanosome detection for diagnosis and trypanosome detection and/or increased white blood cell concentration in CSF for staging and detection of treatment failure. PCR on blood showed a sensitivity of 88.4% (84.4–92.5%) and a specificity of 99.2% (97.7–100%) for diagnosis, while for disease staging the sensitivity and specificity of PCR on cerebrospinal fluid were 88.4% (84.8–91.9%) and 82.9% (71.2–94.6%), respectively. During follow-up after treatment, PCR on blood had low sensitivity to detect treatment failure. In cerebrospinal fluid, PCR positivity vanished slowly and was observed until the end of the 2 year follow-up in around 20% of successfully treated patients.

Conclusions/Significance

For T.b. gambiense sleeping sickness diagnosis and staging, PCR performed better than, or similar to, the current parasite detection techniques but it cannot be used for post-treatment follow-up. Continued PCR positivity in one out of five cured patients points to persistence of living or dead parasites or their DNA after successful treatment and may necessitate the revision of some paradigms about the pathophysiology of sleeping sickness.

Post-treatment follow-up is crucial for sleeping sickness patient management and still relies on microscopic examination of the cerebrospinal fluid (CSF). Detection of the parasites DNA with the polymerase chain reaction (PCR) is proposed as a promising and possibly non-invasive alternative for monitoring treatment outcome, but has never been evaluated. We performed PCR on blood and CSF of 360 Trypanosoma brucei gambiense sleeping sickness patients, before treatment and during 2 years after treatment, and on blood of 129 controls. We found that performance of PCR to diagnose sleeping sickness and detect brain involvement was better or similar to current diagnostic techniques. However, we observed that PCR was unreliable for monitoring treatment outcome. Continued PCR positivity in cured patients points to persistence of parasites, or their DNA, after successful treatment, challenging the dogma that in sleeping sickness cure equals parasite elimination. In conclusion, we do not recommend PCR for treatment outcome assessment in sleeping sickness.