Microsatellite in the beta-tubulin gene of Toxoplasma gondii as a new genetic marker for use in direct screening of amniotic fluids

Serotyping, a challenging approach for Toxoplasma gondii typing

Genotype analysis has revealed a high genetic diversity in strains of Toxoplasma gondii, isolated from a wide range of intermediate hosts and different geographic origins. Diversity is notably striking for parasites from wild hosts in South America, generally referred as non-archetypal genotypes. Those genotypes are implicated in the etiology of severe clinical disease, multivisceral toxoplasmosis, associated with high rate of mortality in immunocompetent individuals. Can we accept specific antibodies produced during T. gondii infection as biomarkers to identify infecting genotypes? Scientific evidence supports a positive response to this question; however, the genetic diversity of T. gondii genotypes organized into 16 haplogroups and collectively defined in 6 major clades, provides a reminder of the complexity and difficulty for the purpose. This review discusses serological approaches to genotyping T. gondii.

Molecular diagnosis of toxoplasmosis: recent advances and a look to the future

INTRODUCTION

Toxoplasmosis is a globally distributed parasitic infection that can be particularly severe when opportunistic or congenital. Its diagnosis requires accurate and rapid techniques that rely mainly on serology and molecular methods.

AREAS COVERED

The aim of this review was to discuss the positioning of the molecular diagnosis of toxoplasmosis according to the different clinical situations possibly resulting from infection with T. gondii, and to detail recent developments in this technique. The English and French literature were searched with the following keywords: 'Toxoplasmosis', "Molecular diagnosis" and 'PCR'.

EXPERT OPINION

Molecular techniques have revolutionized the diagnosis of toxoplasmosis, and practices have considerably evolved over the past decades. However, there is still a high degree of inter-laboratory heterogeneity which impairs comparisons between results and studies. Efforts to standardize practices are underway.

Is Toxoplasma gondii type related to clinical outcome in human congenital infection? Systematic and critical review

In human congenital toxoplasmosis the effects of parasite burden and pregnancy time at infection on clinical outcome are well known, but there is controversy regarding the role of Toxoplasma gondii type. Through a systematic review of the literature, we aimed to discern if T. gondii type has a role on clinical outcome in human congenital toxoplasmosis. We built up a database of congenital toxoplasmosis from reports of cases, case series and screening-based cohorts, which had information about parasite type, gestation time at maternal infection and/or clinical outcome in the product. Then, we obtained frequencies for loci used to genotype geographical origin of cases and types found. Also, odds ratios were calculated for association between time of maternal infection or parasite type on outcome. Type II parasites were the most common in Europe, Asia and Africa, while in America there were mainly atypical strains. More newborns with clinical problems were born from mothers infected during the first half of gestation than from those acquiring the parasite after week 24, regardless of parasite genotype (92.9 vs. 16.1 %, OR = 67.9, CI95 25.4-181.6). Type I and atypical parasites were associated with clinical problems as opposed to types II and III, regardless of pregnancy period at infection (86.9 vs. 72.9 %, OR = 2.47, CI95 1.1-5.4). A significant and remarkable tendency of type I parasites to be present during early pregnancy was also observed (94.4 vs. 5.6 %, P < 0.009). In addition to parasite burden and period of gestation, T. gondii genotype seems involved in CT clinical outcome.

Genotyping of Toxoplasma gondii Strains Isolated from Patients with Ocular Toxoplasmosis in Iran

BACKGROUND

Toxoplasma gondii is an obligate, intracellular protozoon that develops its sexual stage in cat's intestinal epithelial cells as definitive host and develops its asexual stage in different tissues of a wide range hosts called intermediate host. The protozoon is a food-borne and worldwide parasite that can cause serious complications such as abortion in pregnant women, encephalitis, and ocular toxoplasmosis. The present study aimed to genotype T. gondii strains isolated from patients with toxoplasmic retinochoroiditis.

METHODS

Fifty-two blood samples were taken from patients with ocular toxoplasmosis, from July 2013 to July 2014. The specimens were collected from three ophthalmological hospitals of Tehran, Iran. After that, DNA extraction was performed using kit on separated buffy coats of serologically positive blood samples. Then PCR was done in GRA6 gene. For digestion of products, MseI endonuclease was used. Finally, some of the PCR products were sequenced.

RESULTS

All of 52 samples were found positive by serological and PCR-RFLP methods and all of isolated strains belong to type III genotype. Type III genotype has the highest prevalence in Iranian ocular toxoplasmic patients.

CONCLUSION

T. gondii, particularly its type III should not be neglected as a cause of retinochoroiditis.

Genetic characterization of Toxoplasma gondii isolates from chickens in India by GRA6 gene sequence analysis

PCR-RFLP and nucleotide sequencing based genotyping of Toxoplasma gondii Indian isolates (Izatnagar and Chennai isolates and Chennai clone) vis-a vis RH-IVRI strain was conducted by targeting GRA6 as genetic marker. The 791 bp GRA6 product was PCR amplified from the genomic DNA of different T. gondii Indian isolates, including the RH-IVRI strain. Tru1I restriction endonuclease based PCR-RFLP of GRA6 sequence produced polymorphic digestion pattern that discriminated the virulent RH-IVRI strain (as type I) from the moderately virulent local isolates as type III. The PCR amplicon of T. gondii GRA6 from RH-IVRI strain as well as from the local isolates were cloned in cloning vector and custom sequenced. The nucleotide and deduced amino acid sequences of T. gondii isolates were aligned with that of the type I, II and III strains (RH, BEVERLEY, ME49, C56, TONT and NED) available in public domain and analyzed in silico using MEGA version 4.0 software. Nucleotide sequencing and phylogenetic analysis of GRA6 marker from the Indian isolates revealed a close genetic relationship with type III strains of T. gondii. Further, detection of a single nucleotide polymorphism (SNP) at positions 162 and 171 of the GRA6 marker, established the lineage of Indian isolates as type III. This is the first report on characterization of T. gondii lineage as type III in selective chicken population of India based on PCR-RFLP and sequence analysis of GRA6 gene.

Direct genotyping of Toxoplasma gondii from amniotic fluids based on B1 gene polymorphism using minisequencing analysis

Background

Because some Toxoplasma gondii genotypes may be more virulent in pregnant women, discriminating between them appears valuable. Currently, the main genotyping method is based on single copy microsatellite markers, which limit direct genotyping from amniotic fluids (AFs) to samples with a high parasitic load. We investigated whether the multicopy gene B1 could type the parasite with a higher sensitivity. To estimate the amplifiable DNA present in AFs, we first compared three different PCR assays used for Toxoplasma infection diagnosis: the P30-PCR, targeting the single copy gene P30; the B1-PCR, targeting the repeated B1 gene; and RE-PCR, targeting the repeated element.

Results

Of the 1792 AFs analyzed between 2008 and 2011, 73 were RE-PCR positive. Of those, 49 (67.1%) were P30-PCR and B1-PCR positive, and 14 (19.2%) additional AFs were B1-PCR positive only.

All 63 BI-positive AFs (France n = 49; overseas n = 14) could be genotyped based on an analysis of eight nucleotide polymorphisms (SNPs) located within the B1 gene. Following high-resolution melting (HRM) analysis, minisequencing was carried out for each of the eight SNPs. DNA from six reference strains was included in the study, and AFs were assigned to one of the three major lineages (Types I, II, and III). In total, 26 genotypes were observed, and the hierarchical clustering distinguished two clades in lineages II (IIa, n = 30 and IIb, n = 4) and III (IIIa n = 23 and IIIb n = 6). There was an overrepresentation of overseas isolates in Clade IIb (4/4, 100%) and Clade IIIa (8/22; 36.4%) (p <0.0001), whereas medical interruption and fetal death were overrepresented in Clade IIb (2/4, 50%) and Clade IIIa (4/23, 17.4%) (p = 0.049).

Conclusions

Although the current genotyping system cannot pretend to replace multilocus typing, we clearly show that targeting the multicopy B1 gene yields a genotyping capacity of AFs around 20% better than when single copy targets are used. The present genotyping method also allows clear identification of genotypes of potential higher virulence.

Variation of B1 gene and AF146527 repeat element copy numbers according to Toxoplasma gondii strains assessed using real-time quantitative PCR

Using the multicopy B1 gene and AF146527 element for the amplification of Toxoplasma gondii DNA raises the issue of reliable quantification for clinical diagnosis. We applied relative quantification to reference strains using the single-copy P30 gene as a reference. According to the parasite type, the copy numbers for the B1 gene and AF146527 element were found to be 5 to 12 and 4 to 8 times lower than the previous estimations of 35 and 230 copies, respectively.

Genotyping of the protozoan pathogen Toxoplasma gondii using high-resolution melting analysis of the repeated B1 gene

Genetic studies of the protozoan parasite Toxoplasma gondii have identified three main distinct types according to virulence in some hosts. Several methods have been developed to differentiate genotypes currently dominated by microsatellite markers targeting single-copy loci. We analyzed the possibility of using the 35-fold repetitive B1 gene via high-resolution melting (HRM) curve analysis. Sequencing of the B1 gene of 14 reference strains (four Type I, six Type II, and four Type III strains) identified 18 single nucleotide polymorphisms (SNP). Primers were designed to amplify eight of them for HRM analysis and for relative quantification of each nucleotide variation using SNaPshot mini-sequencing. Genotyping with five microsatellite markers was performed for comparison. Two to four HRM profiles were obtained depending on the SNP tested. The differences observed relied on the different ratios of nucleotides at the SNP locus as evidenced via SNaPshot mini-sequencing. The three main lineages could be distinguished by using several HRM profiles. Some HRM profiles proved more informative than the analysis based on five microsatellite markers, showing additional differences in Type I and Type II strains. Using HRM analysis, we obtained at least an equally good discrimination of the main lineages than that based on five microsatellite markers.

Polymerase chain reaction in the diagnosis of congenital toxoplasmosis: more than two decades of development and evaluation

Toxoplasmosis, a protozoan disease caused by the coccidian parasite Toxoplasma gondii, is one of the most prevalent parasitic diseases of humans. Although most infections are subclinical and asymptomatic, it has a great importance with respect to immunocompromized hosts and congenitally infected newborns. The diagnosis of T. gondii infection has gained in great interest over the past decades with a wide variety of techniques being investigated from animal inoculation to advanced molecular techniques. This paper reviews and highlights the development and evaluation of polymerase chain reaction in the diagnosis of congenital toxoplasmosis in human population to present the redundant research on it in a chronologically simple approach.

Direct genotypic characterization of Toxoplasma gondii strains associated with congenital toxoplasmosis in Tunisia (North Africa)

Here, we determined the Toxoplasma gondii genotype in amniotic fluid, placenta, and cerebrospinal fluid samples from 14 congenital toxoplasmosis cases in Tunisia, North Africa. Direct genotypic characterization of T. gondii strains was performed by polymerase chain reaction (PCR) amplification of six genetic markers (3'SAG2, 5' SAG2, SAG3, BTUB, GRA6, and APICO) and thereafter, was analyzed by restriction fragment-length polymorphism (RFLP). Samples were sequenced to resolve strain type whenever there were unclear enzyme digestion results. Multilocus analysis revealed that only one specimen harbored the type I allele in all studied loci, whereas the 13 others gave mixed genotype results with different alleles at different markers. Seven specimens produced RFLP profile of the recombinant strains I/III, and three produced a profile of I/II recombinant strains. The last three specimens produced complex digestion patterns. In these cases, sequence analysis revealed double peaks at known polymorphic sites, indicating the presence of multiple alleles.

Management of Toxoplasma gondii infection during pregnancy

Acute infection with Toxoplasma gondii during pregnancy and its potentially tragic outcome for the fetus and newborn continue to occur in the United States, as well as worldwide, despite the fact that it can be prevented. The infection can be acquired through ingestion of infected, undercooked meat or contaminated food or water. Transmission to the fetus occurs almost solely in women who acquire their primary infection during gestation and can result in visual and hearing loss, mental and psychomotor retardation, seizures, hematological abnormalities, hepatosplenomegaly, or death. Systematic education and serological screening of pregnant women are the most reliable and currently available strategies for the prevention, diagnosis, and early treatment of the infection in the offspring; this is largely because toxoplasmosis in pregnant women most often goes unrecognized. Treatment of the infection in the fetus and infant during the first year of life has been demonstrated to significantly improve the clinical outcome.

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.

The relationship between nucleoside triphosphate hydrolase (NTPase) isoform and Toxoplasma strain virulence in rat and human toxoplasmosis

Avirulent strains of Toxoplasma gondii possess only the nucleoside triphosphate hydrolase II (NTPaseII) isoform, whilst virulent strains possess both NTPaseI and NTPaseII. To determine if it is possible to identify the infective strain type (virulent or avirulent) in T. gondii infections by serological methods, we developed isoform-specific peptide ELISAs from the NTPaseI and NTPaseII antigens of T. gondii. When rats were immunized with either recombinant NTPaseI or NTPaseII, the ELISA could differentially identify antibody reactivity to each NTPase isoform. This ELISA was then used to test six groups of rats that were infected with either one of three virulent (RH, P or Ent) or three avirulent (Me49, C or TPR) strains of T. gondii. No differential antibody reactivity was detected by either whole recNTPase ELISA or peptide ELISA in the sera of rats, whether infected by virulent or avirulent strains of T. gondii. We also studied a panel of human sera from patients infected with known laboratory strains of T. gondii or naturally infected patients where the parasite was isolated and its virulence determined in mice. Differential reactivity to whole recNTPase isoforms was detected in some human sera, but this reactivity was not detected by the isoform-specific peptide ELISAs. Although the NTPase peptides do exhibit differential antibody reactivity, this is not correlated with the virulence status of the infecting strain.

Molecular diagnostics in clinical parasitology and mycology: limits of the current polymerase chain reaction (PCR) assays and interest of the real-time PCR assays

Polymerase chain reaction (PCR) represents a major breakthrough for the diagnosis of infectious diseases. However, the absence of standardized kits for commercially unattractive targets, such as most of the parasites and the fungi, has led to the development of numerous in-house PCR assays. The performances reported, both for the sensitivity and the specificity of these assays are very divergent. For instance, for the antenatal diagnosis of toxoplasmosis, the sensitivity is either 97.4%, or 64%. For the diagnosis of toxoplasmosis in HIV-positive patients, the PCR on blood is either of limited value with a sensitivity of 13% or of excellent yield with a sensitivity of 87.5%. Similar results are reported for the diagnosis of invasive aspergillosis in bone-marrow-transplant recipients. The patients and the clinical specimens tested are often different. This can explain some of the discrepancies. However, when performed, the quality controls on identical specimens show different results depending on the laboratories. An analysis of the PCR techniques used shows that the control of false positive results as a result of carry-over and false negative results owing to PCR inhibitors is far from being systematic. These shortcomings of 'classical' PCR should be solved when real-time PCR assays are developed, leading to some standardization. Automated DNA extraction should also be useful to achieve this goal. Comparison between laboratories should then be possible and regular quality controls will be necessary to ensure the reliability of real-time PCR assays.

Comparison of two DNA targets for the diagnosis of Toxoplasmosis by real-time PCR using fluorescence resonance energy transfer hybridization probes

BACKGROUND

Toxoplasmosis is an infectious disease caused by the parasitic protozoan Toxoplasma gondii. It is endemic worldwide and, depending on the geographic location, 15 to 85% of the human population are asymptomatically infected. Routine diagnosis is based on serology. The parasite has emerged as a major opportunistic pathogen for immunocompromised patients, in whom it can cause life-threatening disease. Moreover, when a pregnant woman develops a primary Toxoplasma gondii infection, the parasite may be transmitted to the fetus and cause serious damage. For these two subpopulations, a rapid and accurate diagnosis is required to initiate treatment. Serological diagnosis of active infection is unreliable because reactivation is not always accompanied by changes in antibody levels, and the presence of IgM does not necessarily indicate recent infection. Application of quantitative PCR has evolved as a sensitive, specific, and rapid method for the detection of Toxoplasma gondii DNA in amniotic fluid, blood, tissue samples, and cerebrospinal fluid.

METHODS

Two separate, real-time fluorescence PCR assays were designed and evaluated with clinical samples. The first, targeting the 35-fold repeated B1 gene, and a second, targeting a newly described multicopy genomic fragment of Toxoplasma gondii. Amplicons of different intragenic copies were analyzed for sequence heterogeneity.

RESULTS

Comparative LightCycler experiments were conducted with a dilution series of Toxoplasma gondii genomic DNA, 5 reference strains, and 51 Toxoplasma gondii-positive amniotic fluid samples revealing a 10 to 100-fold higher sensitivity for the PCR assay targeting the newly described 529-bp repeat element of Toxoplasma gondii.

CONCLUSION

We have developed a quantitative LightCycler PCR protocol which offer rapid cycling with real-time, sequence-specific detection of amplicons. Results of quantitative PCR demonstrate that the 529-bp repeat element is repeated more than 300-fold in the genome of Toxoplasma gondii. Since individual intragenic copies of the target are conserved on sequence level, the high copy number leads to an ultimate level of analytical sensitivity in routine practice. This newly described 529-bp repeat element should be preferred to less repeated or more divergent target sequences in order to improve the sensitivity of PCR tests for the diagnosis of toxoplasmosis.

Molecular genetic evidence that dinoflagellates belonging to the genus Symbiodinium freudenthal are haploid

Microscopic and cytological evidence suggest that many dinoflagellates possess a haploid nuclear phase. However, the ploidy of a number of dinoflagellates remains unknown, and molecular genetic support for haploidy in this group has been lacking. To elucidate the ploidy of symbiotic dinoflagellates belonging to the genus Symbiodinium, we used five polymorphic microsatellites to examine populations harbored by the Caribbean gorgonians Plexaura kuna and Pseudopterogorgia elisabethae; we also studied a series of Symbiodinium cultures. In 690 out of 728 Symbiodinium samples in hospite (95% of the cases) and in all 45 Symbiodinium cultures, only a single allele was recovered per locus. Statistical testing of the Symbiodinium populations harbored by P. elisabethae revealed that the observed genotype frequencies deviate significantly from those expected under Hardy-Weinberg equilibrium. Taken together, our results confirm that, in the vegetative life stage, members of Symbiodinium, both cultured and in hospite, are haploid. Furthermore, based on the phylogenetics of the dinoflagellates, haploidy in vegetative cells appears to be an ancestral trait that extends to all 2,000 extant species of these important unicellular protists.

Severe acquired toxoplasmosis in immunocompetent adult patients in French Guiana

The most common presentation of symptomatic postnatally acquired toxoplasmosis in immunocompetent patients is painless cervical adenopathy. Acute visceral manifestations are associated in rare cases. We report 16 cases of severe primary toxoplasmosis diagnosed in French Guiana during a 6.5-year period. All of the subjects were immunocompetent adults hospitalized with clinical presentations consisting of a marked, nonspecific infectious syndrome accompanied by an altered general status with at least one visceral localization, mainly pulmonary involvement (14 cases). Acute toxoplasmosis was diagnosed according to the results of serological tests suggestive of recent primary infection and the absence of an alternative etiology. Recovery was rapid following specific antitoxoplasmosis treatment. Thirteen of the 16 patients had consumed game in the 2 weeks before the onset of the symptoms, and in eight cases the game was considered to have been undercooked. Toxoplasma strains, which were virulent in mice, were isolated from three patients. Microsatellite analysis showed that all of these isolates exhibited an atypical multilocus genotype, with one allele found only for isolates of this region.

Molecular diagnosis of toxoplasmosis

Toxoplasmosis is an anthropozoonotic disease endemic world-wide, caused by the apicomplexan Toxoplasma gondii. Although the course of infection is generally benign, it can cause significant morbidity and mortality in the developing fetus and in immunocompromised individuals. Biological diagnosis classically relies upon serology and direct detection of the parasite by inoculation to laboratory animals. In the past decade, the use of the polymerase chain reaction (PCR) has made a significant improvement in both the prenatal diagnosis of congenital toxoplasmosis and the detection of acute disease in the immunocompromised patient. Nevertheless, like many 'in-house' PCR assays, the PCR-Toxoplasma suffers from lack of standardization and variable performance according to the laboratory. A wide variety of primers has been used in different assays, but few comparative tests have been performed. Moreover, in contrast to other parasitic diseases, PCR-Toxoplasma has not yet attained a sufficient level of sensitivity, regardless of the clinical condition considered. These drawbacks are discussed, together with the undoubted gain that PCR has brought to this difficult diagnosis.

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.

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

The position of mobile genetic elements (MGE) within eukaryotic genomes is often highly variable and we have exploited this phenomenon to develop a novel approach to strain differentiation in Toxoplasma gondii. Two PCR based strategies were designed in which specific primers were used to amplify T. gondii MGE's revealing information on element size and positional variation. The first PCR strategy involved the use of a standard two primer PCR while the second strategy used a single specific primer in a step-up PCR protocol. This approach was applied to T. gondii reference strains which were either acute virulent or avirulent to mice. The use of a standard two primer PCR reaction revealed the presence of a virulence related marker in which all avirulent strains possessed an additional 688 bp band. The single primer PCR strategy demonstrated that all virulent strains had identical banding patterns suggesting invariance within this group of strains. However, all avirulent strains had different banding patterns indicating the presence of a number of individual lineages within this group. The applicability and sensitivity of MGE-PCR in epidemiological studies was demonstrated by direct amplification of T. gondii from sheep tissue samples. All sheep isolates, tested in this way, gave identical banding patterns suggesting the presence of an endemic Toxoplasma strain on this farm.

Prenatal diagnosis of congenital toxoplasmosis by duplex real-time PCR using fluorescence resonance energy transfer hybridization probes

The diagnosis of congenital toxoplasmosis frequently relies on PCR tests of amniotic fluid (AF). A duplex real-time quantitative PCR test based on fluorescence resonance energy transfer was developed to quantify the parasite load and to decrease the risk of contamination. An internal control based on the detection of 10 pg mouse DNA added to the AF was included to check for PCR efficiency. The relationship between the parasite load and the occurrence of ultrasonographic abnormalities in 87 samples of AF was analyzed. Seven AF (8%) had a parasitic load > 10(3); 14 (16%) had > 10(2)-< or =10(3); 26 (30%) had > 10-< or = 10(2); and 40 (46%) had < or = 10 parasites/ml. Four of the six AF with cerebral ventriculomegaly had >10(3) parasites/ml. The other two had 130 and 24 parasites/ml, respectively. No parasitic loads of > 10(3) parasites/ml and no ultrasonographic abnormalities were observed in the 11 AF with maternal toxoplasmosis in the third trimester. Therefore, there is a trend to associate high parasite count with ultrasonographic abnormality, but the main concern remains early maternal infection. The importance of quantification should be better evaluated with postnatal studies. The duplex LightCycler PCR test currently provides rapid and safe results.

Real-time PCR for quantitative detection of Toxoplasma gondii

The protozoan Toxoplasma gondii is one of the most common infectious pathogenic parasites and can cause severe medical complications in infants and immunocompromised individuals. We report here the development of a real-time PCR-based assay for the detection of T. gondii. Oligonucleotide primers and a fluorescence-labeled TaqMan probe were designed to amplify the T. gondii B1 gene. After 40 PCR cycles, the cycle threshold values (C(T)) indicative of the quantity of the target gene were determined. Typically, a C(T) of 25.09 was obtained with DNA from 500 tachyzoites of the T. gondii RH strain. The intra-assay coefficients of variation (CV) were 0.4, 0.16, 0.24, and 0.79% for the four sets of quadruplicate assays, with a mean interassay CV of 0.4%. These values indicate the reproducibility of this assay. Upon optimization of assay conditions, we were able to obtain a standard curve with a linear range (correlation coefficient = 0.9988) across at least 6 logs of DNA concentration. Hence, we were able to quantitatively detect as little as 0.05 T. gondii tachyzoite in an assay. When tested with 30 paraffin-embedded fetal tissue sections, 10 sections (33%) showed a C(T) of <40 and were scored as positive for this test. These results were consistent with those obtained through our nested-PCR control experiments. We have developed a rapid, sensitive, and quantitative real-time PCR for detection of T. gondii. The advantages of this technique for the diagnosis of toxoplasmosis in a clinical laboratory are discussed.

Detection and characterisation of parasites causing emerging zoonoses

Understanding the epidemiology of zoonotic parasitic infections is dependent upon the availability of accurate and sensitive diagnostic techniques. The development of molecular diagnostic methods, particularly those utilising PCR for the detection of zoonoses will contribute greatly to the identification and control of these pathogens, by increasing the speed of diagnosis, specificity and sensitivity, reproducibility and ease of interpretation. Molecular characterisation studies allow us to distinguish between closely related infectious agents and to document the patterns of transmission of 'strains' and species within populations. This will allow precise determinations to be made about the aetiological agent, its characteristics and the source of infection. This review focuses on recent detection and characterisation techniques for both emerging and re-emerging parasite zoonoses.

Strain typing of Toxoplasma gondii: comparison of antigen-coding and housekeeping genes

Molecular characterization of Toxoplasma gondii isolates is central for understanding differences in disease transmission and manifestations. Only 3 subgroups (lineages) have been discerned with subtle within-lineage variation, permitting low-resolution classification of isolates. Because proteins, coding sequences, and especially antigen-coding genes have been used extensively in previous studies, we focused on sequence variation in introns of housekeeping genes, which may be more informative for phylogenetic analysis because they evolve under lower selection. We compared sequence variation in introns of 5 housekeeping genes with 2 antigen-coding genes. Introns of housekeeping genes were slightly more polymorphic than coding and noncoding regions of antigen-coding genes and only the former showed intralineage variation. Intragenic linkage disequilibrium was complete, but intergenic linkage, although highly significant, was incomplete, suggesting that genes are partially uncoupled. Six of 7 substitutions found within the region coding for the tachyzoite surface antigen, SAG2, were nonsynonymous, indicating that diversifying selection acts on this locus. Typing isolates on the basis of housekeeping and antigen-coding genes was consistent, but the phylogenetic relationships among the resulting groups was inconsistent. A cougar isolate typed as lineage II using a restriction fragment length polymorphism assay possessed multiple unique polymorphisms, suggesting that it represents a new lineage. We concluded that introns of housekeeping genes are preferred markers for phylogenetic study, and that multilocus genotyping is preferred for typing parasites, especially from feral or unstudied environments.

The beta-tubulin gene of Babesia and Theileria parasites is an informative marker for species discrimination

A fragment of the beta-tubulin gene was polymerase chain reaction (PCR) amplified from genomic DNAs of Babesia bovis, Babesia bigemina, Babesia divergens, Babesia major, Babesia caballi, Babesia equi, Babesia microti, Theileria annulata and Theileria sergenti. Single amplification products were obtained for each of these species, but the size of the amplicons varied from 310 to 460 bp. Sequence analysis revealed that this variation is due to the presence of a single intron, which ranged from 20 to 170 bp. The extensive genetic variability at the beta-tubulin locus has been exploited to develop two types of species identification assays. The first assay can be used on samples containing mostly parasite DNA, like those prepared from infected erythrocytes. Following PCR amplification, the species identification is obtained directly from the size of the products (for Babesia species infecting human or horse) or using a simple PCR-restriction fragment length polymorphism (RFLP) protocol (for Babesia species infecting cattle). The second assay can be used on samples prepared from whole blood, that contain both parasite and host DNAs. In this case, due to the strong conservation of the beta-tubulin gene, co-amplification of a gene fragment from the host DNA was observed. A nested PCR assay was developed for the specific amplification of parasite DNA, using a primer designed to span the exon-intron boundary. Direct identification of Babesia species infecting human and horse is again obtained after the electrophoretic separation of the amplification products, while for Babesia and Theileria species infecting cattle, differentiation is based on a nested PCR-RFLP protocol. These methods may be used for the simultaneous identification of horses and cattle carrying multiple parasites by means of a single PCR or using the PCR-RFLP protocol.

Strain and stage specific variation in Toxoplasma gondii antigens

The antigenic profile of virulent (RH, ENT, Martin) and avirulent (RRA, DEG, ME49) Toxoplasma strains was compared directly by western blotting using a panel of immune mouse sera. Dominant antigens of approximate MR 30-33, 21 and 25 x 10(3) were common to tachyzoites of all strains, however, there were significant quantitative and qualitative differences in the antigen profiles, indicating a moderate degree of strain specific polymorphism in tachyzoite antigens. We found no specific association between antigenic variation and strain virulence. Comparison of tachyzoite and bradyzoite antigens from homologous strains (RRA, DEG, ME49) confirmed the existence of stage specific antigens and demonstrated a conserved antigen profile among bradyzoites.

Intergenic spacer (IGS) polymorphism: a new genetic marker for differentiation of Toxoplasma gondii strains and Neospora caninum

The region between the 28S and 18S rRNA genes, including the intergenic spacer (IGS) region and the 5S rRNA gene, from 32 strains of Toxoplasma gondii and the NC1 strain of Neospora caninum was amplified and used for DNA sequencing and/or restriction fragment length polymorphism (RFLP) analysis. The 5S rDNA sequences from 20 strains of T. gondii were identical. The IGS region between the 5S and 18S rRNA genes (nontranscribed spacer 2 or NTS 2) showed 10 nucleotide variations. Six of the 10 variant positions correlated with the murine virulence of the strains. Intraspecific polymorphisms distinguished the virulent strains of zymodemes 5, 6, and 8 from other virulent strains (in zymodeme 1). RFLP methods (IGS-RFLP) were developed and used to characterize the virulent and avirulent patterns among 29 T. gondii strains. Sequence diversity of 19.8% was found between T. gondii and N. caninum when comparing a region of 919 bp at the 3' end of NTS 2. The sequence variation in ribosomal IGS could therefore be a useful marker for Toxoplasma strain identification and for distinguishing N. caninum from T. gondii.

Molecular typing of Toxoplasma gondii strains by GRA6 gene sequence analysis

The utility of sequence polymorphisms in the dense granule antigen GRA6 gene as typing markers for Toxoplasma gondii was investigated. The coding region of GRA6 was amplified, sequenced and compared for 30 Toxoplasma strains from eight different zymodemes (Z1-Z8). Sequence alignment identified nucleotide polymorphisms at 24 positions out of 690 bp, which correlated with murine-virulence. Types I, II, and III could be distinguished from each other on the basis of three, 10, and six variable positions, respectively. Two deletions of 15 bp and 3 bp existed in the avirulent (type II) strains. With one exception, all polymorphic positions resulted in amino acid substitutions, and the two gaps of 15 bp and 3 bp caused the deletion of six amino acids in type II strains. Intra-specific polymorphisms were also found in the virulent group. A high degree of sequence polymorphism correlating with the phenotypes of T. gondii strains points to the GRA6 gene being a good marker for strain characterisation and typing of the isolates of this apicomplexan. The large variety of amino acid changes supports the view that the GRA6 protein plays an important role in the antigenicity and pathogenicity of T. gondii. The existence of polymorphic restriction sites for endonuclease MseI was used to develop a PCR-RFLP method which could simply differentiate the three different groups (types I, II, III) of T. gondii.

Value of prenatal diagnosis and early postnatal diagnosis of congenital toxoplasmosis: retrospective study of 110 cases

We reviewed the files of 110 women with Toxoplasma seroconversion during pregnancy. Prenatal diagnosis was attempted for 94 women by amniotic fluid sampling. Toxoplasma gondii was detected by PCR, with or without tissue culture and mouse inoculation. The early neonatal diagnostic procedure included placental testing by PCR and/or mouse inoculation, cord blood serological testing, and comparison of maternal and newborn antibodies by Western blotting (WB). Serological follow-up of the infants was conducted during the first year of life or until the diagnosis of congenital toxoplasmosis (CT) could be ruled out. Congenital infection was diagnosed in 27 individuals (20 live births) in the prenatal and/or neonatal period. The sensitivity and specificity of prenatal diagnosis were 81 and 100%, respectively. Placental examination was positive for 66.7% of individuals with CT and was always negative for neonates without CT. Cord blood serology detected immunoglobulin M (IgM) and/or IgA in 80% of infected newborns, with respective specificities of 91.2 and 87.7%. By WB we detected bands on IgG and IgM blots recognized by the newborn serum but not by the maternal serum (neosynthesized IgG and/or IgM) for 88.2% of infected infants within the first 2 months of life with a specificity of 100%. Early postnatal diagnosis was negative for 2 of the 20 neonates with CT. Both of these newborns had a negative prenatal diagnosis and were asymptomatic, suggesting a very low parasite load. In conclusion, despite the use of advanced methods, some cases of congenital toxoplasmosis cannot be detected early, which underlines the importance of careful follow-up of newborns who are at risk.

Detection of Toxoplasma gondii in 94 placentae from infected women by polymerase chain reaction, in vivo, and in vitro cultures

The biological diagnosis of congenital toxoplasmosis at birth is important to determine the infant's treatment. The aim of this study was to evaluate the placenta results in the congenital toxoplasmosis diagnosis and to compare them with those obtained with other samples collected at birth (cord blood and newborn blood). A total of 94 placentas, of which 33 came from fetuses suspected of or with proven congenital toxoplasmosis (CT+) and 61 from definitely or probably non-infected fetuses (CT-), was analysed by in vitro culture, mouse inoculation and polymerase chain reaction (PCR). The PCR sensitivity was higher (60.9 per cent) than that of cell culture (29.6 per cent) and mouse inoculation (51.5 per cent) but the number of PCR positive results in CT - patients was also higher (9.5 per cent). The presence of Toxoplasma gondii in the placenta tissues was the only argument at birth (IgM and neosynthesized Ig were negative) in three out of the 33 CT+ cases. The detection of IgM by ELISA and ISAGA and the detection of neosynthesized Ig by immunoblotting were more satisfactory to diagnose congenital toxoplasmosis but the placenta analysis was important to improve the sensitivity of the diagnosis at birth, especially when the prenatal diagnosis was negative or not performed.

Lack of consistent short sequence repeat polymorphisms in genetically homologous colonizing and invasive Candida albicans strains

Short sequence repeats (SSRs), potentially representing variable numbers of tandem repeat (VNTR) loci, were identified for the human-pathogenic yeast species Candida albicans by computerized DNA sequence scanning. The individual SSR regions were investigated in different clinical isolates of C. albicans. Most of the C. albicans SSRs were identified as genuine VNTRs. They appeared to be present in multiple allelic variants and were demonstrated to be diverse in length among nonrelated strains. As such, these loci provide adequate targets for the molecular typing of C. albicans strains. VNTRs encountered in other microbial species sometimes participate in regulation of gene expression and function as molecular switches at the transcriptional or translational level. Interestingly, the VNTRs identified here often encode polyglutamine stretches and are frequently located within genes potentially involved in the regulation of transcription. DNA sequencing of these VNTRs demonstrated that the length variability was restricted to the CAA/CAG repeats encoding the polyglutamine stretches. For these reasons, paired C. albicans isolates of similar genotype, either found as noninvasive colonizers or encountered in an invasive state in the same individual, were studied with respect to potentially invasion-related alterations in the VNTR profiles. However, none of the VNTRs analyzed thus far varied systematically with the transition from colonization to invasion. In contrast to the situation described for some prokaryotic species, this finding suggests that VNTRs of C. albicans may not simply function as contingency loci related to straightforward on/off regulation of invasion-related gene expression.