Biotechnological advances in the diagnosis, species differentiation and phylogenetic analysis of Schistosoma spp

Paragonimiasis

Paragonimiasis is a zoonotic disease caused by lung flukes of the genus Paragonimus. Humans usually become infected by eating freshwater crabs or crayfish containing encysted metacercariae of these worms. However, an alternative route of infection exists: ingestion of raw meat from a mammalian paratenic host. Adult worms normally occur in pairs in cysts in the lungs from which they void their eggs via air passages. The pulmonary form is typical in cases of human infection due to P. westermani, P. heterotremus, and a few other species. Worms may occupy other sites in the body, notably the brain, but lung flukes have made their presence felt in almost every organ. Ectopic paragonimiasis is particularly common when infection is due to members of the P. skrjabini complex. Human paragonimiasis occurs primarily in the tropics and subtropics of Asia, Africa, and the Americas, with different species being responsible in different areas (Table 6.1).

Diagnosis of Human Trematode Infections

Digenetic trematodes form a major group of human parasites, affecting a large number of humans, especially in endemic foci. Over 100 species have been reported infecting humans, including blood, lung, liver and intestinal parasites. Traditionally, trematode infections have been diagnosed by parasitological methods based on the detection and the identification of eggs in different clinical samples. However, this is complicated due to the morphological similarity between eggs of different trematode species and other factors such as lack of sensitivity or ectopic locations of the parasites. Moreover, the problem is currently aggravated by migratory flows, international travel, international trade of foods and changes in alimentary habits. Although efforts have been made for the development of immunological and molecular techniques, the detection of eggs through parasitological techniques remains as the gold standard for the diagnosis of trematodiases. In the present chapter, we review the current status of knowledge on diagnostic techniques used when examining feces, urine, and sputum and also analyze the most relevant characteristics used to identify eggs with a quick key for the identification of eggs.

Clinicopathological characteristics and its association with digestive system tumors of 1111 patients with Schistosomiasis japonica

Schistosomiasis japonicum can cause different degrees of organ damage and complex human immune pathological reactions, which often invade the intestine and liver. The purpose of this study was to explore the pathological types and pathological changes of Schistosomiasis and their correlation with some digestive system tumors. Hematoxylin eosin staining was performed on the diseased tissues of 1111 Schistosomiasis cases. We counted the deposition sites of Schistosoma eggs, analyzed the pathological characteristics, and compared the clinicopathological characteristics of Schistosomiasis associated digestive system tumors and non-Schistosomiasis digestive system tumors. We found that Schistosoma japonicum can cause multi organ and multi system damage, with 469 cases of inflammation, 47 cases of adenoma, and 519 cases of adenocarcinoma. Other types include cysts, stromal tumors, malignant lymphomas, and neuroendocrine tumors. Schistosomiasis associated tumors, including gastric cancer, liver cancer, colon cancer and rectal cancer, were compared with non-Schistosomiasis tumors. There were significant differences in age, gender and tumor differentiation between the two groups. Our study shows Schistosomiasis is a systemic disease, causing multiple organ and system damage in the human body. Its clinicopathological types are diverse, and there may be a pathological change process of "Inflammation-adenoma-carcinoma". Schistosomiasis associated digestive system tumors differ from non-Schistosomiasis tumors in some clinicopathological features.

Development of a novel real-time polymerase chain reaction assay for the sensitive detection of Schistosoma japonicum in human stool

BACKGROUND

Elimination and control of Schistosoma japonicum, the most virulent of the schistosomiasis-causing blood flukes, requires the development of sensitive and specific diagnostic tools capable of providing an accurate measurement of the infection prevalence in endemic areas. Typically, detection of S. japonicum has occurred using the Kato-Katz technique, but this methodology, which requires skilled microscopists, has been shown to radically underestimate levels of infection. With the ever-improving capabilities of next-generation sequencing and bioinformatic analysis tools, identification of satellite sequences and other highly repetitive genomic elements for use as real-time PCR diagnostic targets is becoming increasingly common. Assays developed using these targets have the ability to improve the sensitivity and specificity of results for epidemiological studies that can in turn be used to inform mass drug administration and programmatic decision making.

METHODOLOGY/PRINCIPAL FINDINGS

Utilizing Tandem Repeat Analyzer (TAREAN) and RepeatExplorer2, a cluster-based analysis of the S. japonicum genome was performed and a tandemly arranged genomic repeat, which we named SjTR1 (Schistosoma japonicum Tandem Repeat 1), was selected as the target for a real-time PCR diagnostic assay. Based on these analyses, a primer/probe set was designed and the assay was optimized. The resulting real-time PCR test was shown to reliably detect as little as 200 ag of S. japonicum genomic DNA and as little as 1 egg per gram of human stool. Based on these results, the index assay reported in this manuscript is more sensitive than previously published real-time PCR assays for the detection of S. japonicum.

CONCLUSIONS/SIGNIFICANCE

The extremely sensitive and specific diagnostic assay described in this manuscript will facilitate the accurate detection of S. japonicum, particularly in regions with low levels of endemicity. This assay will be useful in providing data to inform programmatic decision makers, aiding disease control and elimination efforts.

Diagnosis of Human Trematode Infections

Digenetic trematodes form a major group of human parasites, affecting a large number of humans, especially in endemic foci. Over 100 species have been reported infecting humans, including blood, lung, liver, and intestinal parasites. Traditionally, trematode infections have been diagnosed by parasitological methods based on the detection and the identification of eggs in different clinical samples. However, this is complicated due to the morphological similarity between eggs of different trematode species and other factors such as lack of sensitivity or ectopic locations of the parasites. Moreover, the problem is currently aggravated by migratory flows, international travel, international trade of foods, and changes in alimentary habits. Although efforts have been made for the development of immunological and molecular techniques, the detection of eggs through parasitological techniques remains as the gold standard for the diagnosis of trematodiases. In this chapter, we review the current status of knowledge on diagnostic techniques used when examining feces, urine, and sputum and also analyze the most relevant characteristics used to identify eggs with a quick key for the identification of eggs.

Paragonimiasis

Paragonimiasis is a zoonotic disease caused by lung flukes of the genus Paragonimus. Humans usually become infected by eating freshwater crabs or crayfish containing encysted metacercariae of these worms. However, an alternative route of infection exists: ingestion of raw meat from a mammalian paratenic host. Adult worms normally occur in pairs in cysts in the lungs from which they void their eggs via air passages. The pulmonary form is typical in cases of human infection due to P. westermani, P. heterotremus, and a few other species (Table 5.1). Worms may occupy other sites in the body, notably the brain, but lung flukes have made their presence felt in almost every organ. Ectopic paragonimiasis is particularly common when infection is due to members of the P. skrjabini complex (Table 5.1). Human paragonimiasis occurs primarily in the tropics and subtropics of Asia, Africa, and the Americas, with different species being responsible in different areas (Table 5.1).

Morphological and molecular confirmation of the validity of Trichuris rhinopiptheroxella in the endangered golden snub-nosed monkey (Rhinopithecus roxellana)

The golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered species endemic to China. Relatively little is known about the taxonomic status of soil-transmitted helminths (STH) in these monkeys. Trichuris spp. (syn. Trichocephalus) are among the most important STHs, causing significant socio-economic losses and public health concerns. To date, five Trichuris species have been reported in golden monkeys, including a novel species, T. rhinopiptheroxella, based on morphology. In the present study, molecular and morphological analysis was conducted on adult Trichuris worms obtained from a dead golden snub-nosed monkey, to better understand their taxonomic status. Morphology indicated that the adult Trichuris worms were similar to T. rhinopiptheroxella. To further ascertain their phylogenetic position, the complete mitochondrial (mt) genome of these worms was sequenced and characterized. The mt genome of T. rhinopiptheroxella is 14,186 bp, encoding 37 genes. Phylogenetic analysis based on the concatenated amino acids of 12 protein-coding genes (with the exception of atp8) indicated that T. rhinopiptheroxella was genetically distinct and exhibited 27.5-27.8% genetic distance between T. rhinopiptheroxella and other Trichuris spp. Our results support T. rhinopiptheroxella as a valid Trichuris species and suggest that mt DNA could serve as a marker for future studies on the classification, evolution and molecular epidemiology of Trichuris spp. from golden snub-nosed monkeys.

New Anti-Schistosoma Approaches in The People's Republic of China: Development of Diagnostics, Vaccines and Other New Techniques Belonging to the 'Omics' Group

A new national schistosomiasis elimination programme will be implemented for the period 2016-20. To support this approach, we have performed a systematic review to assess anti-schistosome approaches in The People's Republic of China and defined research priorities for the coming years. A systematic search was conducted for articles published from January 2000 to March 2015 in international journals. Totally 410 references were published in English between 2000 and 2015 related to schistosomiasis after unrelated references and reviews or comments were further excluded. A set of research priorities has been identified for the near future that would improve the progress toward schistosomiasis elimination in The People's Republic of China. In particular, there is a lack of sensitive and specific tests for the detection of schistosomiasis cases with low parasite burdens, as well as an effective vaccine against schistosomiasis, and there is a need for surveillance tools that can evaluate the epidemic status for guiding the elimination strategy. Hence, we think that schistosomiasis control and elimination will be improved in The People's Republic of China through development of new tools.

The complete mitochondrial genome of Pseudanoplocephala crawfordi and a comparison with closely related cestode species

Pseudanoplocephala crawfordi is an important zoonotic cestode of economic significance and public health concern. In spite of its significance as a pathogen, the systematics, genetics, epidemiology and biology of this parasite remain poorly understood. In the present study, we sequenced and characterized the complete mitochondrial (mt) genome of P. crawfordi, which is 14,192 bp long and encodes 36 genes, including 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. Phylogenetic analysis of the concatenated amino acid sequences using the Bayesian inference (BI) method showed that P. crawfordi was closely related to the family Hymenolepididae. Considering that the taxonomic status of P. crawfordi has been controversial when based only on morphological features, the mt genome obtained here will provide novel molecular markers to ascertain the phylogenetic position of this parasite accurately.

Rapid detection and identification of four major Schistosoma species by high-resolution melt (HRM) analysis

Schistosomiasis, caused by blood flukes belonging to several species of the genus Schistosoma, is a serious and widespread parasitic disease. Accurate and rapid differentiation of these etiological agents of animal and human schistosomiasis to species level can be difficult. We report a real-time PCR assay coupled with a high-resolution melt (HRM) assay targeting a portion of the nuclear 18S rDNA to detect, identify, and distinguish between four major blood fluke species (Schistosoma japonicum, Schistosoma mansoni, Schistosoma haematobium, and Schistosoma mekongi). Using this system, the Schistosoma spp. was accurately identified and could also be distinguished from all other trematode species with which they were compared. As little as 10(-5) ng genomic DNA from a Schistosoma sp. could be detected. This process is inexpensive, easy, and can be completed within 3 h. Examination of 21 representative Schistosoma samples from 15 geographical localities in seven endemic countries validated the value of the HRM detection assay and proved its reliability. The melting curves were characterized by peaks of 83.65 °C for S. japonicum and S. mekongi, 85.65 °C for S. mansoni, and 85.85 °C for S. haematobium. The present study developed a real-time PCR coupled with HRM analysis assay for detection and differential identification of S. mansoni, S. haematobium, S. japonicum, and S. mekongi. This method is rapid, sensitive, and inexpensive. It has important implications for epidemiological studies of Schistosoma.

A specific indel marker for the Philippines Schistosoma japonicum revealed by analysis of mitochondrial genome sequences

In the present study, near-complete mitochondrial (mt) genome sequences for Schistosoma japonicum from different regions in the Philippines and Japan were amplified and sequenced. Comparisons among S. japonicum from the Philippines, Japan, and China revealed a geographically based length difference in mt genomes, but the mt genomic organization and gene arrangement were the same. Sequence differences among samples from the Philippines and all samples from the three endemic areas were 0.57-2.12 and 0.76-3.85 %, respectively. The most variable part of the mt genome was the non-coding region. In the coding portion of the genome, protein-coding genes varied more than rRNA genes and tRNAs. The near-complete mt genome sequences for Philippine specimens were identical in length (14,091 bp) which was 4 bp longer than those of S. japonicum samples from Japan and China. This indel provides a unique genetic marker for S. japonicum samples from the Philippines. Phylogenetic analyses based on the concatenated amino acids of 12 protein-coding genes showed that samples of S. japonicum clustered according to their geographical origins. The identified mitochondrial indel marker will be useful for tracing the source of S. japonicum infection in humans and animals in Southeast Asia.

Development of "-omics" research in Schistosoma spp. and -omics-based new diagnostic tools for schistosomiasis

Schistosomiasis, caused by dioecious flatworms in the genus Schistosoma, is torturing people from many developing countries nowadays and frequently leads to severe morbidity and mortality of the patients. Praziquantel based chemotherapy and morbidity control for this disease adopted currently necessitate viable and efficient diagnostic technologies. Fortunately, those “-omics” researches, which rely on high-throughput experimental technologies to produce massive amounts of informative data, have substantially contributed to the exploitation and innovation of diagnostic tools of schistosomiasis. In its first section, this review provides a concise conclusion on the progresses pertaining to schistosomal “-omics” researches to date, followed by a comprehensive section on the diagnostic methods of schistosomiasis, especially those innovative ones based on the detection of antibodies, antigens, nucleic acids, and metabolites with a focus on those achievements inspired by “-omics” researches. Finally, suggestions about the design of future diagnostic tools of schistosomiasis are proposed, in order to better harness those data produced by “-omics” studies.

Paragonimiasis

Paragonimiasis is a zoonotic disease caused by lung flukes of the genus Paragonimus. Humans usually become infected by eating freshwater crabs or crayfish containing encysted metacercariae of these worms. However, an alternative route of infection exists: ingestion of raw meat from a mammalian paratenic host. Adult worms normally occur in pairs in cysts in the lungs from which they void their eggs via air passages. The pulmonary form is typical in cases of human infection due to P. westermani, P. heterotremus, and a few other species (Table 5.1). Worms may occupy other sites in the body, notably the brain, but lung flukes have made their presence felt in almost every organ. Ectopic paragonimiasis is particularly common when infection is due to members of the P. skrjabini complex (Table 5.1). Human paragonimiasis occurs primarily in the tropics and subtropics of Asia, Africa, and the Americas, with different species being responsible in different areas (Table 5.1).

Significant variance in genetic diversity among populations of Schistosoma haematobium detected using microsatellite DNA loci from a genome-wide database

BACKGROUND

Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium.

METHODS

We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium.

RESULTS

We designed >13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at http://www.cebio.org/projetos/schistosoma-haematobium-genome). The three Schistosoma genomes contained similar overall frequencies of microsatellites, but the frequency and length distributions of specific motifs differed among species. We identified 15 primer pairs that amplified consistently and were easily scored. We genotyped these 15 loci in S. haematobium individuals from six locations: Zanzibar had the highest levels of diversity; Malawi, Mauritius, Nigeria, and Senegal were nearly as diverse; but the sample from South Africa was much less diverse.

CONCLUSIONS

About half of the primers in the database of Schistosoma haematobium microsatellite DNA loci should yield amplifiable and easily scored polymorphic markers, thus providing thousands of potential markers. Sequence conservation among S. haematobium, S. japonicum, and S. mansoni is relatively high, thus it should now be possible to identify markers that are universal among Schistosoma species (i.e., using DNA sequences conserved among species), as well as other markers that are specific to species or species-groups (i.e., using DNA sequences that differ among species). Full genome-sequencing of additional species and specimens of S. haematobium, S. japonicum, and S. mansoni is desirable to better characterize differences within and among these species, to develop additional genetic markers, and to examine genes as well as conserved non-coding elements associated with drug resistance.

Repeated Schistosoma japonicum infection following treatment in two cohorts: evidence for host susceptibility to helminthiasis?

Background

In light of multinational efforts to reduce helminthiasis, we evaluated whether there exist high-risk subpopulations for helminth infection. Such individuals are not only at risk of morbidity, but may be important parasite reservoirs and appropriate targets for disease control interventions.

Methods/Principal Findings

We followed two longitudinal cohorts in Sichuan, China to determine whether there exist persistent human reservoirs for the water-borne helminth, Schistosoma japonicum, in areas where treatment is ongoing. Participants were tested for S. japonicum infection at enrollment and two follow-up points. All infections were promptly treated with praziquantel. We estimated the ratio of the observed to expected proportion of the population with two consecutive infections at follow-up. The expected proportion was estimated using a prevalence-based model and, as highly exposed individuals may be most likely to be repeatedly infected, a second model that accounted for exposure using a data adaptive, machine learning algorithm. Using the prevalence-based model, there were 1.5 and 5.8 times more individuals with two consecutive infections than expected in cohorts 1 and 2, respectively (p<0.001 in both cohorts). When we accounted for exposure, the ratio was 1.3 (p = 0.013) and 2.1 (p<0.001) in cohorts 1 and 2, respectively.

Conclusions/Significance

We found clustering of infections within a limited number of hosts that was not fully explained by host exposure. This suggests some hosts may be particularly susceptible to S. japonicum infection, or that uncured infections persist despite treatment. We propose an explanatory model that suggests that as cercarial exposure declines, so too does the size of the vulnerable subpopulation. In low-prevalence settings, interventions targeting individuals with a history of S. japonicum infection may efficiently advance disease control efforts.

Approximately 1 billion people are infected with one or more helminthes – a class of parasites that can impair physical, mental and economic development. We are interested in whether there exist groups who are repeatedly infected with helminthes over time in areas where treatment is ongoing. Such individuals may be at risk of morbidity and may also serve as parasite reservoirs, making them appropriate targets for disease control programs. We followed two cohorts in rural Sichuan, China in order to evaluate whether the same individuals were repeatedly infected with the water-borne helminth, Schistosoma japonicum. Each participant was tested for infection at enrollment and two follow-up points – all infections were promptly treated. We conducted detailed interviews to assess exposures to S. japonicum. We found infections repeatedly occurred in a subgroup of individuals and this clustering of infections was only partly explained by differences in exposure. This suggests some individuals may be particularly susceptible to S. japonicum infection. Further exploration of the interplay of exposure and susceptibility suggest that as exposure declines, so too does the fraction of the population vulnerable to infection. Helminth control programs that target people with a history of infection may efficiently reduce helminth infections and morbidity.