Rapid nucleotide sequence analysis of the small subunit ribosomal RNA of Toxoplasma gondii: evolutionary implications for the Apicomplexa

What a Difference 30 Years Makes! A Perspective on Changes in Research Methodologies Used to Study Toxoplasma gondii

Toxoplasma gondii is a remarkable species with a rich cell, developmental, and population biology. It is also sometimes responsible for serious disease in animals and humans and the stages responsible for such disease are relatively easy to study in vitro or in laboratory animal models. As a result of all this, Toxoplasma has become the subject of intense investigation over the last several decades, becoming a model organism for the study of the phylum of which it is a member, Apicomplexa. This has led to an ever-growing number of investigators applying an ever-expanding set of techniques to dissecting how Toxoplasma "ticks" and how it interacts with its many hosts. In this perspective piece I first wind back the clock 30 years and then trace the extraordinary pace of methodologies that have propelled the field forward to where we are today. In keeping with the theme of this collection, I focus almost exclusively on the parasite, rather than host side of the equation. I finish with a few thoughts about where the field might be headed-though if we have learned anything, the only sure prediction is that the pace of technological advance will surely continue to accelerate and the future will give us still undreamed of methods for taking apart (and then putting back together) this amazing organism with all its intricate biology. We have so far surely just scratched the surface.

Molecular diagnosis of toxoplasmosis in immunocompromised patients

PURPOSE OF REVIEW

Toxoplasmosis in immunocompromised patients is associated with a high mortality rate. Molecular techniques are important tools to diagnose acute disease in immunocompromised patients, but there are various methods with variable efficiency. Some of them have been validated for the diagnosis of congenital toxoplasmosis, but the impact of their use has not been evaluated in immunocompromised patients.

RECENT FINDINGS

Toxoplasmosis is of increasing importance in non-HIV immunocompromised patients. In addition, the picture of disease shows greater severity in South America, both in immunocompetent study participants and in congenitally infected infants. These epidemiological differences could influence the sensitivity of diagnostic methods. This review analyzes recent data on molecular diagnosis and compares them with older ones, in light of progress gained in molecular techniques and of recent epidemiological findings. Most recent studies were conducted in South America and used PCR targeting the B1 gene. PCR on blood could allow diagnosing a significant proportion of patients with ocular toxoplasmosis in Brazil.

SUMMARY

Quantitative PCR methods with specific probes should be used to improve sensitivity and warrant specificity. Performance of quantitative PCR targeting the repeated 529 bp sequence for the diagnosis of toxoplasmosis in immunocompromised patients needs evaluation in field studies in South America and in western countries.

Rapid ribosomal RNA sequencing and the phylogenetic analysis of protists

A newly described technique for rapidly obtaining the partial nucleotide sequence of ribosomal RNA is being applied to investigate phylogenetic relationships among living organisms. Alan Johnson and Peter Boverstock describe the importance of this method to parasitology in providing new information on the phylogenetic relationships of parasitic organisms previously placed in groups of convenience. The phylum Apicomplexo in particular, has been the object of much study using this technique, but the technology is likely to extend soon to the restructuring of the phylogenetic trees of many groups of parasites.

Molecular genetic approaches to parasite identification: their value in diagnostic parasitology and systematics

A wide range of approaches is available to parasitologists to aid in specific parasite identification and to formulate phylogenetic relationships. This review emphasises the usefulness of molecular genetic techniques, especially DNA-based procedures, in addressing problems of identification, characterisation and phylogeny of parasites. It should be stressed that an understanding of the various DNA approaches, techniques and target genes most likely to be effective in addressing key issues in diagnostic parasitology and systematics is still developing. Nevertheless, DNA methods clearly have great potential with regard to specificity and sensitivity, and applications will increase further with technological advance. Indeed, because of the minimal requirements for material, PCR-based methods especially should prove of immense value in future studies with parasites.

Detection of Toxoplasma gondii by PCR and tissue culture in cerebrospinal fluid and blood of human immunodeficiency virus-seropositive patients

To investigate whether both tissue culture and PCR on a sequence from the repetitive rDNA could contribute to the diagnosis of toxoplasmosis, blood samples and, if they were available, cerebrospinal fluid (CSF) and aqueous humor samples from 72 human immunodeficiency virus-seropositive patients with suspected toxoplasmosis were prospectively tested. For 10 patients with fever of unknown origin but without confirmed toxoplasmosis, no Toxoplasma gondii was detected. For two patients with confirmed toxoplasmic uveitis, only PCR of aqueous humor samples was positive. Of 60 patients (48 with CSF samples) with neurological signs, 25 (from 13 of whom CSF samples were available) had confirmed cerebral toxoplasmosis and 10 had a positive PCR of CSF and/or blood samples, while for 1 patient culture of the CSF sample was also positive. Unlike tissue culture, PCR of rDNA is of value for the detection of cerebral toxoplasmosis in human immunodeficiency virus-seropositive patients, provided that both CSF and blood samples are available (sensitivity, 76.9%; specificity, 100%).

Evolutionary origin of Plasmodium and other Apicomplexa based on rRNA genes

We have explored the evolutionary history of the Apicomplexa and two related protistan phyla, Dinozoa and Ciliophora, by comparing the nucleotide sequences of small subunit ribosomal RNA genes. We conclude that the Plasmodium lineage, to which the malarial parasites belong, diverged from other apicomplexan lineages (piroplasmids and coccidians) several hundred million years ago, perhaps even before the Cambrian. The Plasmodium radiation, which gave rise to several species parasitic to humans, occurred approximately 129 million years ago; Plasmodium parasitism of humans has independently arisen several times. The origin of apicomplexans (Plasmodium), dinoflagellates, and ciliates may be > 1 billion years old, perhaps older than the three multicellular kingdoms of animals, plants, and fungi. Digenetic parasitism independently evolved several times in the Apicomplexa.

DNA amplification on cerebrospinal fluid for diagnosis of cerebral toxoplasmosis among HIV-positive patients with signs or symptoms of neurological disease

Reactivation of Toxoplasma gondii can lead to a life-threatening intracerebral infection in immunocompromised HIV-positive patients. Due to the current diagnostic limitations for establishing an exact diagnosis of cerebral toxoplasmosis, a nested PCR system was developed for direct detection of T. gondii in cerebrospinal fluid. A storage temperature for samples of -20 degrees C and sample preparation using Proteinase K appeared to be critical for obtaining a high sensitivity of PCR. A total of 56 samples from 38 HIV-positive patients and 12 HIV-negative patients with symptoms or signs of neurological disease were evaluated by PCR. 5 of the 38 HIV-positive patients were diagnosed as having cerebral toxoplasmosis and PCR was positive in samples from all 5 patients. In the remaining 33, PCR was positive in one case and negative in 32. An exact etiological diagnosis other than cerebral toxoplasmosis was established in 5 patients. PCR performed on cerebrospinal fluid samples seems to be a fast, sensitive, specific and valuable tool for establishing the diagnosis of cerebral toxoplasmosis among HIV-positive patients at the time of presentation of symptoms or signs of neurological disease.

Phylogenetic relationships of Sarcocystis species from sheep, goats, cattle and mice based on ribosomal RNA sequences

Partial sequences of the small subunit ribosomal RNA of four species of Sarcocystis were obtained by reverse transcription of total cellular RNA. The semi-conserved regions of these four species were aligned with homologous sequences of two other Sarcocystis species and a range of other eukaryotes including Toxoplasma, Eimeria and Cryptosporidium. Parsimony analysis of the aligned sequences showed that Sarcocystis and Toxoplasma had a more recent common ancestor with Eimeria than with Cryptosporidium. The six Sarcocystis spp. did not cluster together in this analysis; two monophyletic groups were observed, one formed by the two Sarcocystis spp. with felids as definitive hosts, and another by the four Sarcocystis spp. with canids as definitive hosts. These two clades were segregated by Toxoplasma. An analysis of nucleotide divergence suggests that the difference between the two groups of Sarcocystis spp. is similar to that between invertebrates and vertebrates. The results obtained here question the validity of a separation of the genus Sarcocystis from Toxoplasma and refute classifications that place these two genera into two different subfamilies of the Sarcocystidae.

Physical and genetic mapping of cloned ribosomal DNA from Toxoplasma gondii: primary and secondary structure of the 5S gene

The ribosomal DNA (rDNA encoding rRNA) of the obligately intracellular protozoan parasite, Toxoplasma gondii, was identified, cloned, physically mapped, its copy number determined, and the 5S gene sequenced. Using total RNA as a probe, a collection of recombinant lambda phages containing copies of rDNA were isolated from a lambda 2001 tachyzoite genomic library. Northern gel hybridization confirmed specific homology of the 7.5-kb rDNA unit, subcloned into pTZ18R, to T. gondii rRNA. The mapped rDNA found in pTOX1 contained small ribosomal subunit (SS; 18S)- and large ribosomal subunit (LS; 26S)-encoding genes localized using intragenic heterologous probes from the conserved sequences of the SS (18S) and LS (28S) Xenopus laevis genes. the physical mapping data, together with partial digestion experiments and Southern gel hybridization, confirmed a 7.5-kb rDNA unit arranged in a simple head-to-tail fashion that is tandemly repeated. We estimated the rDNA repeat copy number in T. gondii to be 110 copies per haploid tachyzoite genome. Parts of the SS gene and the complete 5S gene were sequenced. The 5S gene was found to be within the rDNA locus, a rare occurrence found only in some fungi and protozoa. Secondary-structure analysis revealed an organization remarkably similar to the 5S RNA of eukaryotes.

Contribution of a new PCR assay to the prenatal diagnosis of congenital toxoplasmosis

A polymerase chain reaction (PCR) assay has been developed for the detection of Toxoplasma gondii. The target sequence (88 bp) is part of a rDNA repetitive gene. A signal can be observed with only one parasite. It is directly and rapidly detected by electrophoresis and ethidium bromide staining. We report a prospective study of 80 documented cases of toxoplasmic seroconversions during pregnancy. The PCR assay of the amniotic fluids was compared with the current standard methods for diagnosis of fetal infection. Seventy specimens gave no PCR signal, and were negative according to prenatal tests and postnatal examinations. The presence of T. gondii was detected in ten specimens by PCR analysis. Four were confirmed by isolation of the parasite from the amniotic fluid; four by biological study of the fetal blood. For the remaining two, infection was diagnosed after birth. Together with ultrasonographic and biological data, this technique permits prenatal diagnosis within 1 day.

Improved sensitivity of the polymerase chain reaction for detection of Toxoplasma gondii in biological and human clinical specimens

The aim of the present study was to improve the sensitivity of the polymerase chain reaction for detection of Toxoplasma gondii in biological and clinical specimens. Using a pair of primers amplifying a 634 bp fragment of the B1 gene of this parasite, it was possible to detect ten parasites in 100 microliters of sample suspensions containing a high concentration of concomitant host cells. A comparison of different DNA purification methods indicated that cell-rich clinical specimens intended for use as samples for the polymerase chain reaction should be digested with proteinase K prior to DNA amplification. By using the described sample preparation methods and the polymerase chain reaction, Toxoplasma gondii DNA was demonstrated in ten of 52 clinical specimens of patients with clinical or serological indications of toxoplasmosis.

Use of polymerase chain reaction to detect Toxoplasma

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The troublesome parasites--molecular and morphological evidence that Apicomplexa belong to the dinoflagellate-ciliate clade

Large insertions and deletions in the variable regions of eukaryotic 16S-like rRNA relative to the archaebacterial structure have been defined as a marker for rapidly evolving taxa. Deletions in the rRNA occur in the diplomonad Giardia and the microsporidian Vairimorpha, whereas insertions occur in Euglenozoa (Euglena and the kinetoplastids), Acanthamoeba, Naegleria, Physarum, Dictyostelium, the apicomplexan Plasmodium, the ciliate Euplotes, and some metazoa. Except Acanthamoeba and Euplotes, all of these protists were previously placed at the base of the eukaryote phylogeny. A re-analysis of the 16S-like rRNA and 5S rRNA data with the neighborliness method revealed a close relationship of Apicomplexa to the dinoflagellate-ciliate clade, most probably closer to the dinoflagellates. Morphological evidence that supports this grouping is the layer of sacs underneath the plasma membrane in all three taxa and the identical structure of trichocysts in the apicomplexan Spiromonas and dinoflagellates. The remaining rapidly evolving organisms might still be misplaced in the 16S-like rRNA trees.

Genetic exchange and evolutionary relationships in protozoan and helminth parasites

The study of genetic exchange systems and the use of genetic analysis has been relatively limited in parasites leading to considerable gaps in our basic knowledge. This lack of knowledge makes it difficult to draw firm conclusions as to how these systems evolved. An additional problem is also raised by the difficulties in defining evolutionary distances particularly with the unicellular protozoa, using classical ultrastructural and cytological criteria. While these difficulties have by no means been overcome, the use of rapid sequencing techniques applied to the ribosomal genes has allowed measurement of evolutionary distances, and considerable advances in our understanding of the genetic exchange systems in a few parasitic protozoa have recently been made. The conclusions from these recent sets of analyses are reviewed and then examined together in order to discuss the evolution of genetic exchange systems in parasitic protozoa. The evolutionary distances defined by ribosome sequence analysis show that parasites are an extremely divergent group, with distances which, in some cases, are orders of magnitude greater than the distances between mammals and fish; furthermore these studies suggest that the parasitic protozoa or their free-living ancestors are extremely ancient. These findings support the view that parasitism has occurred independently many times and that the parasitic life-style has been adopted by evolutionarily distinct groups. The recent observation of a non-obligatory genetic system in the diploid but evolutionary ancient kinetoplastid Trypanosoma brucei suggests that diploidy and meiosis are extremely old. The observation, in parasitic protozoa and helminths, that selfing or non-obligatory mating is a common feature suggests that these processes may be strategies to overcome the cost of meiosis. In this context, the question of what selective forces maintain genetic exchange is discussed.

Comparison of dinucleotide frequency and codon usage in Toxoplasma and Plasmodium: evolutionary implications

The weight-averaged observed/expected dinucleotide frequencies for the sum total of the coding regions of five Toxoplasma genes were compared with the same parameters previously determined for the coding regions of 21 Plasmodium genes. In addition, codon usage in the five Toxoplasma genes was compared with that in the 21 Plasmodium genes, and the percent distribution of amino acids in the Toxoplasma protein pool and the Plasmodium protein pool were compared with that in a general protein pool of 314 proteins. The results are consistent with the hypothesis that, contrary to currently held opinion, the genera Toxoplasma and Plasmodium are not especially closely related.

Phylogenetic relationships of Cryptosporidium determined by ribosomal RNA sequence comparison

Reverse transcription of total cellular RNA was used to obtain a partial sequence of the small subunit ribosomal RNA of Cryptosporidium, a protist currently placed in the phylum Apicomplexa. The semi-conserved regions were aligned with homologous sequences in a range of other eukaryotes, and the evolutionary relationships of Cryptosporidium were determined by two different methods of phylogenetic analysis. The prokaryotes Escherichia coli and Halobacterium cuti were included as outgroups. The results do not show an especially close relationship of Cryptosporidium to other members of the phylum Apicomplexa.

Pneumocystis carinii: sequence from ribosomal RNA implies a close relationship with fungi

Pneumocystis carinii is the etiologic agent of a lethal pneumonia which occurs in patients with the acquired immune deficiency syndrome (AIDS) and other immunocompromised hosts. The basic biochemical and genetic characteristics of P. carinii are poorly understood and its taxonomic classification as a protozoan is uncertain. To address the taxonomic question, a method was developed for the extraction of total RNA from P. carinii. Denaturing agarose gel electrophoresis showed the two ribosomal RNA species of P. carinii to be similar in size to those of other lower eukaryotes, including Saccharomyces cerevisiae. Three portions of the small ribosomal RNA of P. carinii were sequenced by reverse transcription from oligonucleotide primers. Three hundred seventy-two nucleotides of sequence were obtained. The sequence derived from P. carinii RNA contained regions that previous phylogenetic studies have shown to be highly variable among species, as well as regions that are highly conserved. Comparison of the P. carinii sequence to corresponding sequences of organisms from other taxa showed the P. carinii sequence to be more similar to sequences from the fungi (Saccharomyces cerevisiae, Neurospora crassa, Candida albicans, and Cryptococcus diffuens) than to protozoan sequences. These data suggest that P. carinii is more closely related to fungi than to protozoa.

Blastocystis hominis: phylogenetic affinities determined by rRNA sequence comparison

In 1912 Blastocystis hominis was identified as a new species and classified as a yeast (Brumpt 1912). In the early 1920s several groups confirmed its classification as a yeast, specifically a member of the genus Schizosaccharomyces (discussed by Zierdt et al. 1967). Apart from an occasional case report, the classification of B. hominis and its role as a harmless intestinal yeast was not questioned for another 50 years. Then, Zierdt (1967) suggested that it should be classified in the phylum Protozoa, subphylum Sporozoa, and that it should be considered as a potential pathogen. The likely role of B. hominis as a human pathogen has recently become more firmly established (Garcia et al. 1984; Sheehan et al. 1986) and its classification has been changed. Although the classification of B. hominis as a protozoon was assumed widely, classification as a sporozoon was not accepted, and the most recent definitive classification of the Protozoa did not even list B. hominis (Lee et al. 1985). Then, based essentially on a review of the known characteristics of the organism, it was recently reclassified into the subphylum Sarcodina (Zierdt 1988). Clearly, the phylogeny of this emerging human pathogen needs definitive analysis (Mehlhorn 1988).