MGE-PCR: a novel approach to the analysis of Toxoplasma gondii strain differentiation using mobile genetic elements

High frequency of infection of lung cancer patients with the parasite Toxoplasma gondii

BACKGROUND

Toxoplasma gondii is an intracellular protozoan parasite that can cause a wide range of clinical conditions, including miscarriage and pneumonia. The global prevalence is 30% in humans, but varies by locality (e.g. in the UK it is typically 10%). The association between lung cancer and T. gondii infection was investigated by direct detection in lung tissue samples.

METHODS

Lung tissue samples were taken from patients undergoing lung resection surgery (n=72) for suspected lung cancer (infection prevalence 100% (95% CI: 93.9-100%)). All 72 participants were confirmed as having lung cancer following subsequent diagnostic tests. In addition, bronchial biopsy samples were collected from non-lung cancer healthy control subjects (n=10). Samples were tested for T. gondii using PCR amplification of T. gondii specific gene markers and T. gondii specific immunohistochemistry.

RESULTS

All 72 lung cancer patients were infected with T. gondii (prevalence 100% (95% CI: 93.9-100%)). Of which, 95.8% (n=69) of patients showed evidence of active parasite stages. Infection prevalence in the controls (10%) was significantly lower (p<0.0001).

CONCLUSIONS

Clinicians treating lung cancer patients should be aware of the potential presence of the parasite, the potential for induction of symptomatic complications and interference with treatment success.

iMGEins: detecting novel mobile genetic elements inserted in individual genomes

Background

Recent advances in sequencing technology have allowed us to investigate personal genomes to find structural variations, which have been studied extensively to identify their association with the physiology of diseases such as cancer. In particular, mobile genetic elements (MGEs) are one of the major constituents of the human genomes, and cause genome instability by insertion, mutation, and rearrangement.

Result

We have developed a new program, iMGEins, to identify such novel MGEs by using sequencing reads of individual genomes, and to explore the breakpoints with the supporting reads and MGEs detected. iMGEins is the first MGE detection program that integrates three algorithmic components: discordant read-pair mapping, split-read mapping, and insertion sequence assembly. Our evaluation results showed its outstanding performance in detecting novel MGEs from simulated genomes, as well as real personal genomes. In detail, the average recall and precision rates of iMGEins are 96.67 and 100%, respectively, which are the highest among the programs compared. In the testing with real human genomes of the NA12878 sample, iMGEins shows the highest accuracy in detecting MGEs within 20 bp proximity of the breakpoints annotated.

Conclusion

In order to study the dynamics of MGEs in individual genomes, iMGEins was developed to accurately detect breakpoints and report inserted MGEs. Compared with other programs, iMGEins has valuable features of identifying novel MGEs and assembling the MGEs inserted.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5290-9) contains supplementary material, which is available to authorized users.

Prevalence ofToxoplasma gondiiin localized populations ofApodemus sylvaticusis linked to population genotype not to population location

Toxoplasma gondiiis a globally distributed parasite infecting humans and warm-blooded animals. Although many surveys have been conducted forT. gondiiinfection in mammals, little is known about the detailed distribution in localized natural populations. In this study, host genotype and spatial location were investigated in relation toT. gondiiinfection. Wood mice (Apodemus sylvaticus) were collected from 4 sampling sites within a localized peri-aquatic woodland ecosystem. Mice were genotyped using standardA. sylvaticusmicrosatellite markers andT. gondiiwas detected using 4 specific PCR-based markers: SAG1, SAG2, SAG3 and GRA6 directly from infected tissue. Of 126 wood mice collected, 44 samples were positive giving an infection rate of 34·92% (95% CI: 27·14–43·59%). Juvenile, young adults and adults were infected at a similar prevalence, respectively, 7/17 (41·18%), 27/65 (41·54%) and 10/44 (22·72%) with no significant age-prevalence effect (P = 0·23). Results of genetic analysis of the mice showed that the collection consists of 4 genetically distinct populations. There was a significant difference inT. gondiiprevalence in the different genotypically derived mouse populations (P = 0·035) but not between geographically defined populations (P = 0·29). These data point to either a host genetic/family influence on parasite infection or to parasite vertical transmission.

Prevalence and co-infection of Toxoplasma gondii and Neospora caninum in Apodemus sylvaticus in an area relatively free of cats

The protozoan parasite Toxoplasma gondii is prevalent worldwide and can infect a remarkably wide range of hosts despite felids being the only definitive host. As cats play a major role in transmission to secondary mammalian hosts, the interaction between cats and these hosts should be a major factor determining final prevalence in the secondary host. This study investigates the prevalence of T. gondii in a natural population of Apodemus sylvaticus collected from an area with low cat density (<2·5 cats/km2). A surprisingly high prevalence of 40·78% (95% CI: 34·07%-47·79%) was observed despite this. A comparable level of prevalence was observed in a previously published study using the same approaches where a prevalence of 59% (95% CI: 50·13%-67·87%) was observed in a natural population of Mus domesticus from an area with high cat density (>500 cats/km2). Detection of infected foetuses from pregnant dams in both populations suggests that congenital transmission may enable persistence of infection in the absence of cats. The prevalences of the related parasite, Neospora caninum were found to be low in both populations (A. sylvaticus: 3·39% (95% CI: 0·12%-6·66%); M. domesticus: 3·08% (95% CI: 0·11%-6·05%)). These results suggest that cat density may have a lower than expected effect on final prevalence in these ecosystems.

Genomics and molecular genetics of Clonorchis sinensis: current status and perspectives

Clonorchiasis caused by Clonorchis sinensis is an important foodborne parasitosis of humans and animals, and is predominantly a hepatobiliary disease. Globally, nearly 35 million people were infected with C. sinensis, with approximately 15 million being in China. Patients would chronically present fatigue, jaundice, abdominal discomfort, along with the increased risk of developing into a form of cholangiocarcinoma that is fatal to humans. Treatment of clonorchiasis by praziquantel has been very successful, but this is dependent on early accurate diagnosis and correct species identification. The present article reviews the current status of knowledge in genomics and functional genomics of C. sinensis, and summarizes the main DNA-based techniques for the specific diagnosis of C. sinensis infection and studies of genetic variation in C. sinensis, and provides perspectives for future studies. The advances in genomics and molecular genetics of C. sinensis shed new sight on our understanding of population structure of C. sinensis as well as the prevention and control of clonorchiasis.

Evidence for high levels of vertical transmission in Toxoplasma gondii

Toxoplasma gondii is a highly ubiquitous and prevalent parasite. Despite the cat being the only definitive host, it is found in almost all geographical areas and warm blooded animals. Three routes of transmission are recognised: ingestion of oocysts shed by the cat, carnivory and congenital transmission. In natural populations, it is difficult to establish the relative importance of these routes. This paper reviews recent work in our laboratory which suggests that congenital transmission may be much more important than previously thought. Using PCR detection of the parasite, studies in sheep show that congenital transmission may occur in as many as 66% of pregnancies. Furthermore, in families of sheep on the same farm, exposed to the same sources of oocysts, significant divergent prevalences of Toxoplasma infection and abortion are found between different families. The data suggest that breeding from infected ewes increases the risk of subsequent abortion and infection in lambs. Congenital transmission rates in a natural population of mice were found to be 75%. Interestingly, congenital transmission rates in humans were measured at 19.8%. The results presented in these studies differ from those of other published studies and suggest that vertical transmission may be much more important than previously thought.

Molecular epidemiology of African sleeping sickness

Human sleeping sickness in Africa, caused by Trypanosoma brucei spp. raises a number of questions. Despite the widespread distribution of the tsetse vectors and animal trypanosomiasis, human disease is only found in discrete foci which periodically give rise to epidemics followed by periods of endemicity A key to unravelling this puzzle is a detailed knowledge of the aetiological agents responsible for different patterns of disease – knowledge that is difficult to achieve using traditional microscopy. The science of molecular epidemiology has developed a range of tools which have enabled us to accurately identify taxonomic groups at all levels (species, subspecies, populations, strains and isolates). Using these tools, we can now investigate the genetic interactions within and between populations of Trypanosoma brucei and gain an understanding of the distinction between human- and nonhuman-infective subspecies. In this review, we discuss the development of these tools, their advantages and disadvantages and describe how they have been used to understand parasite genetic diversity, the origin of epidemics, the role of reservoir hosts and the population structure. Using the specific case of T.b. rhodesiense in Uganda, we illustrate how molecular epidemiology has enabled us to construct a more detailed understanding of the origins, generation and dynamics of sleeping sickness epidemics.

Tracking transmission of the zoonosis Toxoplasma gondii

Toxoplasma gondii is a highly successful parasite that infects many host species and has colonised a wide range of habitats. Review of the parasite's life cycle demonstrates that it has become adapted to exploit multiple routes of transmission through a sexual cycle in the definitive host and asexually, through carnivory, and by vertical transmission. These alternative routes may operate synergistically to enhance transmission, but they might also provide a vehicle for selection leading to partitioning of strains in the environment. Genetic analysis has shown that parasite population structure varies globally. In South America, there is high strain diversity while in North America, Europe and Africa three clonal strain types predominate. This may imply a shift from sexual to asexual transmission. Mapping of the parasite genome has provided a wealth of markers for strain characterisation. Close genotyping of isolates gives evidence of multiple infection and recombination in natural populations and reveals differences in both the distribution and the phenotype of strains. More intensive epidemiological studies are now required to unravel the networks of transmission operating within defined habitats.

Molecular genetic profiles among individual Clonorchis sinensis adults collected from cats in two geographic regions of China revealed by RAPD and MGE-PCR methods

Clonorchis sinensis causes the important food-borne zoonosis, clonorchiasis, which is endemic in East Asia, especially in China mainly in Guangdong, Guangxi and Heilongjiang provinces and Korea. Although comparisons on isoenzymes and some molecular profiles of C. sinensis collected from different parts of China and Korea have been studied, few works on the genetic variation among the individuals from different regions of China has been reported. In the present study, individual adults of C. sinensis were collected from cats in two geographic locations (Guangdong province in the South and Heilongjiang province in the North) of China and 44 of them were examined by using random amplified polymorphic DNA (RAPD)-PCR and mobile genetic elements (MGEs)-PCR techniques to assess the individual genetic variability within and between the two groups of this parasite. Six arbitrary primers and two pairs of MGE primers were employed in the genomic DNA amplification. The molecular patterns showed significant polymorphism among the individuals. The RAPD data displayed that the similarity coefficient (SC) of the individuals within Heilongjiang group was much higher than that of the Guangdong group, which was further confirmed by MGE-PCR results. Individuals from Heilongjiang were found genetically closer with lesser polymorphisms than those collected from Guangdong province. These results demonstrated that RAPD and MGE-PCR techniques, particularly RAPD method, could be useful for investigating genetic variations among C. sinensis individuals. They may also indicate that the genetic variation of C. sinensis occurs in the subtropical region--Guangdong--faster than that in the cold-region--Heilongjiang province--due to more generations (life cycle) occurred.

The urban house mouse (Mus domesticus) as a reservoir of infection for the human parasite Toxoplasma gondii: an unrecognised public health issue?

Toxoplasma gondii is a protozoan parasite capable of infecting almost all warm-blooded animals. The cat is the definitive host and becomes infected by consuming contaminated meat or infected prey. Humans can act as intermediate hosts and in healthy individuals the infection is mild and self-limiting. In pregnant women it can cause spontaneous abortions and foetal abnormalities and is capable of inducing serious illness in immuno-compromised patients. In infested dwellings, mice could act as intermediate hosts and play a role in the persistence/propagation of the disease. A total of 200 mice were trapped alive in 27 infested properties in Manchester, UK, and screened for Toxoplasma infection; 59% tested positive. Evidence of vertical transmission from infected dams to foetus was found, possibly maintaining the infection in urban areas. These findings have important implications when considering approaches to rodent control.

Evidence that primary infection of Charollais sheep withToxoplasma gondiimay not prevent foetal infection and abortion in subsequent lambings

A study carried out on a sheep farm examined whetherToxoplasma gondiifoetal infection and associated abortion occur in successive lambings. We identified 29 ewes that gave birth to lambs on at least 2 successive years over our study period, 2000–2003. Tissue samples from the progeny of these ewes were analysed by PCR to determine infection status withT. gondii.T. gondii-infected lambs were born in 31% of successive pregnancies.T. gondii-positive lambs were aborted in successive pregnancies in 21% of lambings during study period, 2000–2003. The frequency of successive abortions within this flock over the period 1992–2003 was 18%. If a lamb was congenitally infected there was a high risk (69%) that the successive lamb from that ewe would also be congenitally infected. Similarly, if a lamb was aborted there was a high risk (55%) of abortion in the next lamb produced. These data suggest that life-long immunity toT. gondiiinfections may not always be acquired following an initial infection and raises the question as to whether the mechanisms ofT. gondiitransmission prior to and during ovine pregnancies are fully understood.

The prevalence of Neospora caninum and co-infection with Toxoplasma gondii by PCR analysis in naturally occurring mammal populations

Neospora caninum and Toxoplasma gondii are closely related intracellular protozoan parasites associated with bovine and ovine abortion respectively. Little is known about the extent of Neospora/Toxoplasma co-infection in naturally infected populations of animals. Using nested PCR techniques, based on primers from the Nc5 region of N. caninum and SAG1 for T. gondii, the prevalence of N. caninum and its co-infection with T. gondii were investigated in populations of Mus domesticus, Rattus norvegicus and aborted lambs (Ovis aries). A low frequency of infection with N. caninum was detected in the Mus domesticus (3%) and Rattus norvegicus (4.4%) populations. A relatively high frequency of infection with N. caninum was detected in the brains of aborted lambs (18.9%). There was no significant relationship between N. caninum and T. gondii co-infection. Investigation of the tissue distribution of Neospora, in aborted lambs, showed that Neospora could not be detected in tissues other than brain and this was in contrast to Toxoplasma where the parasite could be frequently detected in a range of tissues.

Molecular tools--advances, opportunities and prospects

Modern molecular technologies are having a substantial impact in many fundamental and applied areas of parasitology. In particular, polymerase chain reaction (PCR)-coupled approaches have found broad applicability because their sensitivity permits the enzymatic amplification of gene fragments from minute quantities of nucleic acids from tiny amounts of parasite material. Also, high-resolution electrophoretic and genomic methods are finding increased utility. This paper briefly discusses some developments and applications of DNA methods to parasites and highlights their usefulness or potential for those of veterinary importance. Selected examples of applications with implications in fundamental (systematics, population genetics, epidemiology and ecology) and applied (diagnosis, prevention and control) areas are presented. The focus is mainly on tools for the accurate identification of parasitic nematodes and protozoa of socio-economic importance, the diagnosis of infections and the detection of genetic variability using PCR-coupled mutation scanning technology.

Application of multiple DNA fingerprinting techniques to study the genetic relationships among three members of the subgenus Trypanozoon (Protozoa: Trypanosomatidae)

Three different DNA fingerprinting techniques, the mobile genetic element (MGE)-PCR, simple sequence repeat (SSR)-PCR and random amplified polymorphic DNA (RAPD)-PCR, were used to define a large set of genetic markers to study genetic similarity within and among Trypanosoma brucei, Trypanosoma equiperdum and Trypanosoma evansi strains (n=18) from China, Africa and South America and to investigate their genetic relationships. Using the three fingerprinting techniques, >890 bands (ranging in size from 0.2 to 2kb) were defined for all 18 strains of Trypanosoma. Within each of the strains, 39-59 bands were defined. The similarity coefficients between strains ranged from approximately 41 to 94%, with a mean of 65%. There was more genetic similarity among strains within T. evansi (mean of approximately 79%) compared with T. equiperdum ( approximately 65%) and T. brucei ( approximately 59%). The similarity coefficient data were used to construct the dendrogram, which revealed that (irrespective of species) the majority of strains from China and South America grouped together to the exclusion of those from Africa. The exceptions were a T. brucei strain from Africa and a T. equiperdum strain of unknown origin. Hence, employing data sets generated using the three different fingerprinting methods, it was not possible to unequivocally distinguish among T. brucei, T. evansi and T. equiperdum, although there was a tendency for T. evansi strains to group together to the exclusion of T. brucei. The findings provide support for the hypothesis that T. evansi originated from a mutated form of T. equiperdum and stimulate further investigations of the genetic make-up and evolution of members of the subgenus Trypanozoon.

Trypanosoma brucei s.l.: Characterisation of stocks from Central Africa by PCR analysis of mobile genetic elements

To better understand the epidemiology of sleeping sickness in the Central African sub-region, notably the heterogeneity of Human African Trypanosomiasis (HAT) foci, the mobile genetic element PCR (MGE-PCR) technique was used to genotype Trypanosoma brucei s.l. (T. brucei s.l.) isolates from this sub-region. Using a single primer REV B, which detects positional variation of the mobile genetic element RIME, via amplification of flanking regions, MGE-PCR revealed a micro genetic variability between Trypanosoma brucei gambiense (T. b. gambiense) isolates from Central Africa. The technique also revealed the presence of several T. b. gambiense genotypes and allowed the identification of minor and major ubiquitous genotypes in HAT foci. The presence of several T. b. gambiense genotypes in HAT foci may explain the persistence and the resurgence phenomena of the disease and also the epidemic and the endemic status of some Central African sleeping sickness foci. The MGE-PCR technique represents a simple, rapid, and specific method to differentiate Central African T. brucei s.l. isolates.

Recent trends in molecular diagnostics for Toxoplasma gondii infections

Toxoplasmosis is an important parasitic infection of man and animals. It is well-known that the progression and severity of disease depend on the immunological status of the host, but recent studies suggest that the genetics of the parasite can also play a role. Diagnosis based on clinical appearance and serology is not always easy. However, molecular methods do not depend on an immune response, and allow direct detection of the parasite in biological samples. Thus they can be used to establish a diagnosis when serological tests are not definitive. Multicopy sequences specific for Toxoplasma gondii, e.g., the B1 gene or the 529-bp sequence, are especially useful in molecular tests. Real-time PCR is very sensitive and is a promising technique that is capable of providing a quantitative result. Molecular methods are also used for genotypic characterisation of T. gondii isolates. Analysis of polymorphic sequences determines the precise strain. The choice of sequence is critical when undertaking studies on the correlation between clinical signs and symptoms of disease and the T. gondii genotype. Further studies involving direct genotyping of T. gondii from clinical samples are needed.

Significant familial differences in the frequency of abortion and Toxoplasma gondii infection within a flock of Charollais sheep

A study was carried out to investigate the frequencies of abortion and congenital Toxoplasma gondii infection within 27 families (765 individuals) of a pedigree Charollais sheep flock maintained on a working farm in Worcestershire, UK, since 1992. Pedigree lambing records were analysed to establish the frequency of abortion for each family. The frequency of congenital infection was determined for each family by PCR analysis of tissue samples taken from newborn lambs. A total of 155 lambs were tested for congenital T. gondii infection, which were all born during the study period 2000–2003. Significant differences in the frequency of abortion between sheep families within this flock were observed with frequencies ranging between 0% and 48% (P<0·01). Significantly different infection frequencies with T. gondii were also observed for different families and ranged between 0% and 100% (P<0·01). Although the actual cause of each abortion was not verified, a highly significant positive correlation was found to exist between the frequency of abortion and the frequency of T. gondii infection in the same families (P<0·01). The data presented here raise further questions regarding the significance of congenital transmission of T. gondii within sheep populations, the possible successive vertical transmission of T. gondii within families of sheep, and the potential role of inherited genetic susceptibility to abortion with respect to T. gondii infection. This work invites further study into the epidemiology of ovine toxoplasmosis and may have implications for sheep husbandry methods in the future.

Structure analysis of two Toxoplasma gondii and Neospora caninum satellite DNA families and evolution of their common monomeric sequence

A family of repetitive DNA elements of approximately 350 bp-Sat350-that are members of Toxoplasma gondii satellite DNA was further analyzed. Sequence analysis identified at least three distinct repeat types within this family, called types A, B, and C. B repeats were divided into the subtypes B1 and B2. A search for internal repetitions within this family permitted the identification of conserved regions and the design of PCR primers that amplify almost all these repetitive elements. These primers amplified the expected 350-bp repeats and a novel 680-bp repetitive element (Sat680) related to this family. Two additional tandemly repeated high-order structures corresponding to this satellite DNA family were found by searching the Toxoplasma genome database with these sequences. These studies were confirmed by sequence analysis and identified: (1). an arrangement of AB1CB2 350-bp repeats and (2). an arrangement of two 350-bp-like repeats, resulting in a 680-bp monomer. Sequence comparison and phylogenetic analysis indicated that both high-order structures may have originated from the same ancestral 350-bp repeat. PCR amplification, sequence analysis and Southern blot showed that similar high-order structures were also found in the Toxoplasma-sister taxon Neospora caninum. The Toxoplasma genome database (http://ToxoDB.org ) permitted the assembly of a contig harboring Sat350 elements at one end and a long nonrepetitive DNA sequence flanking this satellite DNA. The region bordering the Sat350 repeats contained two differentially expressed sequence-related regions and interstitial telomeric sequences.

Detection of high levels of congenital transmission of Toxoplasma gondii in natural urban populations of Mus domesticus

The relative importance of different transmission routes of Toxoplasma gondii has been a matter for debate. This ubiquitous parasite is generally thought to be transmitted by infective oocysts excreted by the definitive host, the cat. Ingestion of undercooked meat has also been considered an important route of transmission in many mammals while congenital transmission has generally been considered relatively rare. Experimental studies demonstrate the ability of T. gondii to be transmitted congenitally, but few studies have investigated the frequency of this transmission route in natural populations. We use PCR amplification of the SAG1 gene to investigate the frequency of congenital transmission in a wild population of mice (Mus domesticus) and show that congenital transmission is occurring in 75% of pregnancies in this population. Furthermore, for infected pregnant mice, transmission occurs to at least one foetus in 100% of cases while variable penetrance of congenital infection is observed. These high levels of congenital transmission in this wild population of mice, taken together with other recent data on congenital transmission in sheep, suggests that this phenomenon might be more widespread than previously thought.

Analysis of the SAG5 locus reveals a distinct genomic organisation in virulent and avirulent strains of Toxoplasma gondii

We have recently characterised, in the virulent strain RH of Toxoplasma gondii, three glycosylphosphatidylinositol-anchored surface antigens related to SAG1 (p30) and encoded by highly homologous, tandemly arrayed genes named SAG5A, SAG5B and SAG5C. In the present study, we compared the genomic organisation of the SAG5 locus in strains belonging to the three major genotypes of T. gondii. Southern blot analysis using a SAG5-specific probe produced two related but distinct hybridisation patterns, one exclusive of genotype I virulent strains, the other shared by avirulent strains of either genotype II or genotype III. To understand the molecular bases of this intergenotypic heterogeneity, we cloned and sequenced the SAG5 locus in the genotype II strain Me49. We found that in this isolate the SAG5B gene is missing, with SAG5A and SAG5C laying contiguously. This genomic arrangement explains the hybridisation profiles observed for all the avirulent strains examined and indicates that the presence of SAG5B is a distinctive trait of genotype I. Furthermore, we identified two novel SAG1-related genes, SAG5D and SAG5E, mapping respectively 1.8 and 4.0 kb upstream of SAG5A. SAG5D is transcribed in tachyzoites and encodes a polypeptide of 362 amino acids sharing 50% identity with SAG5A-C, whereas SAG5E is a transcribed pseudogene. We also evaluated polymorphisms at the SAG5 locus by comparing the coding regions of SAG5A-E from strains representative of the three archetypal genotypes. In agreement with the strict allelic dimorphism of T. gondii, we identified two alleles for SAG5D, whereas SAG5A, SAG5C and SAG5E were found to be three distinct nucleotide variants. The higher intergenotypic polymorphism of SAG5A, SAG5C and SAG5E suggests that these genes underwent a more rapid genetic drift than the other members of the SAG1 family. Finally, we developed a new PCR-restriction fragment length polymorphism method based on the SAG5C gene that is able to discriminate between strains of genotype I, II and III by a single endonuclease digestion.

A rapid and simple method of detection of Blepharisma japonicum using PCR and immobilisation on FTA paper

Background

The rapid expansion in the availability of genome and DNA sequence information has opened up new possibilities for the development of methods for detecting free-living protozoa in environmental samples. The protozoan Blepharisma japonicum was used to investigate a rapid and simple detection system based on polymerase chain reaction amplification (PCR) from organisms immobilised on FTA paper.

Results

Using primers designed from the α-tubulin genes of Blepharisma, specific and sensitive detection to the equivalent of a single Blepharisma cell could be achieved. Similar detection levels were found using water samples, containing Blepharisma, which were dried onto Whatman FTA paper.

Conclusion

This system has potential as a sensitive convenient detection system for Blepharisma and could be applied to other protozoan organisms.

Trypanosoma brucei: trypanosome strain typing using PCR analysis of mobile genetic elements (MGE-PCR)

We describe the development of a single-primer amplification system, which uses the trypanosomal mobile genetic element RIME as a molecular marker for the differentiation of Trypanosoma brucei stocks. Using a well-characterised set of T. brucei stocks from southeast Uganda, Kenya and Zambia, we have evaluated the application of this technique, termed MGE-PCR (mobile genetic element PCR) for the typing of trypanosome strains. The technique revealed considerable variation between stocks and was sufficiently specific to amplify trypanosomal DNA in the presence of host DNA. The results showed a clear distinction between human-infective and non-human-infective stocks. Comparative studies on these stocks using markers for the human serum resistance associated (SRA) gene, which identifies human-infective stocks, demonstrated complete agreement between MGE-PCR derived groups and human-infectivity status. Furthermore, MGE-PCR detects high levels of variability within the T. b. brucei and T. b. rhodesiense groups and is therefore a powerful discriminatory tool for tracking individual T. brucei genotypes and strains.

Molecular biology techniques in parasite ecology

Molecular techniques are increasingly being used to study the ecology of a variety of organisms. These techniques represent important tools for the study of the systematics, population genetics, biogeography and ecology of parasites. Here, we review the techniques that have been employed to study the ecology and systematics of parasites (including bacteria and viruses). Particular emphasis is placed on the techniques of isoenzyme electrophoresis, in situ hybridisation and nucleic acid amplification to characterise parasite/microbial communities. The application of these techniques will be exemplified using ticks, bacterial endosymbionts and parasitic protozoa.

Microsatellite analysis of Toxoplasma gondii shows considerable polymorphism structured into two main clonal groups

Previous studies on Toxoplasma gondii population structure, based essentially on multilocus restriction fragment length polymorphism analysis or on multilocus enzyme electrophoresis, indicated that T. gondii comprises three clonal lineages. These studies showed a weak polymorphism of the markers (2-4 alleles by locus). In this study, we used eight microsatellite markers to type 84 independent isolates from humans and animals. Two microsatellite markers were present in the introns of two genes, one coding for beta-tubulin and the other for myosin A, and six were found in expressed sequence tags. With 3-16 alleles detected, these markers can be considered as the most discriminating multilocus single-copy markers available for typing T. gondii isolates. This high discriminatory power of microsatellites made it possible to detect mixed infections and epidemiologically related isolates. Evolutionary genetic analyses of diversity show that the T. gondii population structure consists of only two clonal lineages that can be equated to discrete typing units, but there is some evidence of occasional genetic exchange that could explain why one of these discrete typing units is less clearly individualised than the other.

High levels of congenital transmission of Toxoplasma gondii in a commercial sheep flock

Our current understanding of congenital transmission of Toxoplasma gondii from ewe to lamb dictates that infection frequently results in abortion and the death of the developing foetus, that the birth of live infected lambs occurs rarely and that the cat is the predominant source of infection in ewes. Using direct polymerase chain reaction detection of T. gondii, we report high levels of congenital transmission occurring in a commercially managed sheep flock. We sampled foetal-derived placental tissue and tissues from aborted lambs and showed that congenital transmission was detected in these tissues from 61% of all pregnancies. Where pregnancies resulted in the death of one or more lambs, T. gondii was detected in the lamb tissue for all but one of 18 (94%) pregnancies. Of the successful pregnancies resulting in the birth of live lambs we were able to detect T. gondii in foetal-derived placental tissue from 37 of 70 (42%) pregnancies. These results show that congenital transmission is occurring in a high percentage of lambings including normal healthy lambings, at this farm, suggesting that this route of transmission from generation to generation may be much more significant than that reported previously. These results may have implications for sheep husbandry and future epidemiological studies of T. gondii.

Use of mobile genetic elements as tools for molecular epidemiology

Trypanosomiasis is a complex zoonotic disease where human-infective and non-human-infective strains of Trypanosoma brucei interact in the same transmission cycles. Differentiating these strains is paramount to understanding disease epidemiology. Restriction fragment length polymorphism analysis of repetitive DNA has provided such a method for distinguishing human and non-human isolates. Unfortunately, this approach requires large amounts of material and a more rapid approach is required. We have developed a novel technique, mobile genetic element-PCR, for assaying for positional variation of the mobile genetic element, RIME. The trypanosome genome contains up to 400 copies of RIME. Using this approach we have observed considerable variation between strains of T. brucei. Such a technique may offer potential as a method for differentiating non-human- and human-infective trypanosomes and shows promise as a rapid sensitive tool for investigating the epidemiology of sleeping sickness.