Comparative proteomic analysis of Trypanosoma cruzi TcI lineage epimastigotes unveils metabolic and phenotypic differences between fast- and slow-dividing strains

Trypanosoma cruzi, the causative agent of Chagas disease, is a genetically and phenotypically diverse species, divided into 5 main phylogenetic lineages (TcI to TcVI). TcI is the most widespread lineage in the Americas. Proteomics is a suitable tool to study the global protein expression dynamics in pathogens. Previous proteomic studies have revealed a link between (i) the genetic variability; (ii) the protein expression; and (iii) the biological characteristics of T. cruzi. Here, two-dimensional electrophoresis (2DE) and mass spectrometry were used to characterize the overall protein expression profiles of epimastigotes from four distinct TcI strains displaying different growth kinetics. Ascending hierarchical clustering analysis based on the global 2DE protein expression profiles grouped the strains under study into two clusters that were congruent with their fast or slow growth kinetics. A subset of proteins differentially expressed by the strains in each group were identified by mass spectrometry. Biological differences between the two groups, including use of glucose as an energy source, flagellum length, and metabolic activity, were predicted by proteomic analysis and confirmed by metabolic tests and microscopic measurements performed on the epimastigotes of each strain. Our results show that protein expression profiles are correlated with parasite phenotypes, which may in turn influence the parasite's virulence and transmission capacity.

Microevolution and subspecific taxonomy of Trypanosoma cruzi

Trypanosoma cruzi, the agent of Chagas disease, is a highly polymorphic species, subdivided into 6 main evolutionary lineages or near-clades (formerly discrete typing units or DTUs). An additional near-clade (TC-bat) has recently been evidenced. This pattern is considered to be the result of predominant clonal evolution (PCE). PCE is compatible with occasional mating/hybridization, which do not break the prevalent pattern of clonal evolution, the main trait of it being the presence of Multigene Bifurcating Trees (MGBTs) at all evolutionary levels ("clonal frame"). The development of highly resolutive genetic (microsatellites*) and genomic (sequencing and multi-single nucleotide polymorphism {SNP}* typing) markers shows that PCE also operates at a microevolutionary* level within each of the near-clades ("Russian doll pattern"), in spite of occasional meiosis and hybridization events. Within each near-clade, one can evidence widespread clonal multilocus genotypes*, linkage disequilibrium*, Multigene Bifurcating Trees and lesser near-clades. The within near-clade population structure is like a miniature picture of that of the whole species, suggesting gradual rather than saltatory evolution. Additional data are required to evaluate the stability of these lesser near-clades in the long run and to evaluate the need for an adequate nomenclature for this microevolutionary level.

Models in parasite and pathogen evolution: Genomic analysis reveals predominant clonality and progressive evolution at all evolutionary scales in parasitic protozoa, yeasts and bacteria

The predominant clonal evolution (PCE) model of pathogenic microorganisms postulates that the impact of genetic recombination in those pathogens' natural populations is not enough to erase a persistent phylogenetic signal at all evolutionary scales from microevolution till geological times in the whole ecogeographical range of the species considered. We have tested this model with a set of representative parasitic protozoa, yeasts and bacteria in the light of the most recent genomic data. All surveyed species, including those that were considered as highly recombining, exhibit similar PCE patterns above and under the species level, from macro- to micro-evolutionary scales (Russian doll pattern), suggesting gradual evolution. To our knowledge, it is the first time that such a strong common evolutionary feature among very diverse pathogens has been evidenced. The implications of this model for basic biology and applied research are exposed. These implications include our knowledge on the pathogens' reproductive mode, their population structure, the possibility to type strain and to follow up epidemics (molecular epidemiology) and to revisit pathogens' taxonomy through a flexible use of the phylogenetic species concept (Cracraft, 1983).

Hybridization in Trypanosoma congolense does not challenge the predominant clonal evolution model. A comment on Tihon et al., 2017, Mol. Ecol

Tihon et al. have just published in Mol. Ecol. a fine genomic study on Trypanosoma congolense, agent of Animal African Trypanosomiasis. They present very convincing evidence that T. congolense underwent several hybridization events between distinct genetic lines in Zambia. They claim that their data challenge our predominant clonal evolution model (PCE) of micropathogens. We point out the main tenets of our model and show that Tihon et al.'s claim is based on a misinterpretation of the PCE model. Actually, their data strongly support PCE in T. congolense at a microevolutionary level.

ISOZYME VARIABILITY IN TRYPANOSOMA CRUZI, THE AGENT OF CHAGAS' DISEASE: GENETICAL, TAXONOMICAL, AND EPIDEMIOLOGICAL SIGNIFICANCE

A genetic interpretation of the zymograms of 524 Trypanosoma cruzi stocks from various hosts and representing a broad geographical range (United States to Southern Brazil) reveals high genetic variability (only one monomorphic locus out of 15) and suggests that this parasite has a diploid structure. The data do not give any indication of Mendelian sexuality, although many opportunities are present for genetic exchange between extremely different genotypes. The population structure of T. cruzi appears to be multiclonal and complex. The natural clones evidenced by isozyme analysis are numerous (43 different ones are recorded among 121 stocks assayed at 15 gene loci) and exhibit a large range of genotypes, in a nonhierarchical structure; it is not possible to cluster them into a few strictly delimited groups which could represent natural taxa. The available data suggest that the genetic variability of T. cruzi reflects the long separate evolution of multiple clones. It is suggested that long clonal evolution may explain the present biological and medical variability of the causative agent of Chagas' disease.

Pioneer study of population genetics of Rhodnius ecuadoriensis (Hemiptera: Reduviidae) from the central coastand southern Andean regions of Ecuador

Effective control of Chagas disease vector populations requires a good understanding of the epidemiological components, including a reliable analysis of the genetic structure of vector populations. Rhodnius ecuadoriensis is the most widespread vector of Chagas disease in Ecuador, occupying domestic, peridomestic and sylvatic habitats. It is widely distributed in the central coast and southern highlands regions of Ecuador, two very different regions in terms of bio-geographical characteristics. To evaluate the genetic relationship among R. ecuadoriensis populations in these two regions, we analyzed genetic variability at two microsatellite loci for 326 specimens (n=122 in Manabí and n=204 in Loja) and the mitochondrial cytochrome b gene (Cyt b) sequences for 174 individuals collected in the two provinces (n=73 and=101 in Manabí and Loja respectively). The individual samples were grouped in populations according to their community of origin. A few populations presented positive F_IS, possible due to Wahlund effect. Significant pairwise differentiation was detected between populations within each province for both genetic markers, and the isolation by distance model was significant for these populations. Microsatellite markers showed significant genetic differentiation between the populations of the two provinces. The partial sequences of the Cyt b gene (578bp) identified a total of 34 haplotypes among 174 specimens sequenced, which translated into high haplotype diversity (Hd=0.929). The haplotype distribution differed among provinces (significant Fisher's exact test). Overall, the genetic differentiation of R. ecuadoriensis between provinces detected in this study is consistent with the biological and phenotypic differences previously observed between Manabí and Loja populations. The current phylogenetic analysis evidenced the monophyly of the populations of R. ecuadoriensis within the R. pallescens species complex; R. pallescens and R. colombiensis were more closely related than they were to R. ecuadoriensis.

Relevant units of analysis for applied and basic research dealing with neglected transmissible diseases: The predominant clonal evolution model of pathogenic microorganisms

The predominant clonal evolution (PCE) model seeks to formulate a common population genetics framework for all micropathogens (namely, parasitic protozoa, fungi and yeasts, bacteria, and viruses). It relies on a definition of clonality that is only based on population structure features (namely, strongly restrained genetic recombination). Its clear-cut properties make it of strong interest for applied and basic research, since it permits the definition of stable, clearly delimited units of analysis below the species level: clonal genotypes and discrete genetic subdivisions (“near-clades”). These units of analysis can be used for clinical and epidemiological studies, vaccine and drug design, species description, and evolutionary studies on natural and experimental populations.

In this review, the evolutionary and population genetics background of the model will be only briefly mentioned, while considerable emphasis will be given to its practical significance for the study and control of neglected tropical diseases. The goal of the paper is to make this practical usefulness accessible to a broad audience of readers, including scientists who are not evolution specialists, such as epidemiologists, field scientists, and clinicians. For extensive developments about the evolutionary background of the model, see our previous papers [1–9]. Citations of these former articles lead to the many references quoted in them, which cannot be listed again here.

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.

The population genetics of Trypanosoma cruzi revisited in the light of the predominant clonal evolution model

Comparing the population structure of Trypanosoma cruzi with that of other pathogens, including parasitic protozoa, fungi, bacteria and viruses, shows that the agent of Chagas disease shares typical traits with many other species, related to a predominant clonal evolution (PCE) pattern: statistically significant linkage disequilibrium, overrepresented multilocus genotypes, near-clades (genetic subdivisions somewhat blurred by occasional genetic exchange/hybridization) and "Russian doll" patterns (PCE is observed, not only at the level of the whole species, but also, within the near-clades). Moreover, T. cruzi population structure exhibits linkage with the diversity of several strongly selected genes, with gene expression profiles, and with some major phenotypic traits. We discuss the evolutionary significance of these results, and their implications in terms of applied research (molecular epidemiology/strain typing, analysis of genes of interest, vaccine and drug design, immunological diagnosis) and of experimental evolution. Lastly, we revisit the long-term debate of describing new species within the T. cruzi taxon.

Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi

Trypanosoma cruzi, the aetiological agent of Chagas disease possess extensive genetic diversity. This has led to the development of a plethora of molecular typing methods for the identification of both the known major genetic lineages and for more fine scale characterization of different multilocus genotypes within these major lineages. Whole genome sequencing applied to large sample sizes is not currently viable and multilocus enzyme electrophoresis, the previous gold standard for T. cruzi typing, is laborious and time consuming. In the present work, we present an optimized Multilocus Sequence Typing (MLST) scheme, based on the combined analysis of two recently proposed MLST approaches. Here, thirteen concatenated gene fragments were applied to a panel of T. cruzi reference strains encompassing all known genetic lineages. Concatenation of 13 fragments allowed assignment of all strains to the predicted Discrete Typing Units (DTUs), or near-clades, with the exception of one strain that was an outlier for TcV, due to apparent loss of heterozygosity in one fragment. Monophyly for all DTUs, along with robust bootstrap support, was restored when this fragment was subsequently excluded from the analysis. All possible combinations of loci were assessed against predefined criteria with the objective of selecting the most appropriate combination of between two and twelve fragments, for an optimized MLST scheme. The optimum combination consisted of 7 loci and discriminated between all reference strains in the panel, with the majority supported by robust bootstrap values. Additionally, a reduced panel of just 4 gene fragments displayed high bootstrap values for DTU assignment and discriminated 21 out of 25 genotypes. We propose that the seven-fragment MLST scheme could be used as a gold standard for T. cruzi typing, against which other typing approaches, particularly single locus approaches or systematic PCR assays based on amplicon size, could be compared.

The single-celled parasite Trypanosoma cruzi occurs in mammals and insect vectors in the Americas. When transmitted to humans it causes Chagas disease (American trypanosomiasis) a major public health problem. T. cruzi is genetically diverse and currently split into six groups, known as TcI to TcVI. Multilocus sequence typing (MLST) is a method used for studying the population structure and diversity of pathogens and involves sequencing DNA of several different genes and comparing the sequences between isolates. Here, we assess 13 T. cruzi genes and select the best combination for diversity studies. Outputs reveal that a combination of 7 genes can be used for both lineage assignment and high resolution studies of genetic diversity, and a reduced combination of four loci for lineage assignment. Application of MLST for assigning field isolates of T. cruzi to genetic groups and for detailed investigation of diversity provides a valuable approach to understanding the taxonomy, population structure, genetics, ecology and epidemiology of this important human pathogen.

Discriminating micropathogen lineages and their reticulate evolution through graph theory-based network analysis: the case of Trypanosoma cruzi, the agent of Chagas disease

Micropathogens (viruses, bacteria, fungi, parasitic protozoa) share a common trait, which is partial clonality, with wide variance in the respective influence of clonality and sexual recombination on the dynamics and evolution of taxa. The discrimination of distinct lineages and the reconstruction of their phylogenetic history are key information to infer their biomedical properties. However, the phylogenetic picture is often clouded by occasional events of recombination across divergent lineages, limiting the relevance of classical phylogenetic analysis and dichotomic trees. We have applied a network analysis based on graph theory to illustrate the relationships among genotypes of Trypanosoma cruzi, the parasitic protozoan responsible for Chagas disease, to identify major lineages and to unravel their past history of divergence and possible recombination events. At the scale of T. cruzi subspecific diversity, graph theory-based networks applied to 22 isoenzyme loci (262 distinct Multi-Locus-Enzyme-Electrophoresis -MLEE) and 19 microsatellite loci (66 Multi-Locus-Genotypes -MLG) fully confirms the high clustering of genotypes into major lineages or "near-clades". The release of the dichotomic constraint associated with phylogenetic reconstruction usually applied to Multilocus data allows identifying putative hybrids and their parental lineages. Reticulate topology suggests a slightly different history for some of the main "near-clades", and a possibly more complex origin for the putative hybrids than hitherto proposed. Finally the sub-network of the near-clade T. cruzi I (28 MLG) shows a clustering subdivision into three differentiated lesser near-clades ("Russian doll pattern"), which confirms the hypothesis recently proposed by other investigators. The present study broadens and clarifies the hypotheses previously obtained from classical markers on the same sets of data, which demonstrates the added value of this approach. This underlines the potential of graph theory-based network analysis for describing the nature and relationships of major pathogens, thereby opening stimulating prospects to unravel the organization, dynamics and history of major micropathogen lineages.

How often do they have sex? A comparative analysis of the population structure of seven eukaryotic microbial pathogens

The model of predominant clonal evolution (PCE) proposed for micropathogens does not state that genetic exchange is totally absent, but rather, that it is too rare to break the prevalent PCE pattern. However, the actual impact of this “residual” genetic exchange should be evaluated. Multilocus Sequence Typing (MLST) is an excellent tool to explore the problem. Here, we compared online available MLST datasets for seven eukaryotic microbial pathogens: Trypanosoma cruzi, the Fusarium solani complex, Aspergillus fumigatus, Blastocystis subtype 3, the Leishmania donovani complex, Candida albicans and Candida glabrata. We first analyzed phylogenetic relationships among genotypes within each dataset. Then, we examined different measures of branch support and incongruence among loci as signs of genetic structure and levels of past recombination. The analyses allow us to identify three types of genetic structure. The first was characterized by trees with well-supported branches and low levels of incongruence suggesting well-structured populations and PCE. This was the case for the T. cruzi and F. solani datasets. The second genetic structure, represented by Blastocystis spp., A. fumigatus and the L. donovani complex datasets, showed trees with weakly-supported branches but low levels of incongruence among loci, whereby genetic structuration was not clearly defined by MLST. Finally, trees showing weakly-supported branches and high levels of incongruence among loci were observed for Candida species, suggesting that genetic exchange has a higher evolutionary impact in these mainly clonal yeast species. Furthermore, simulations showed that MLST may fail to show right clustering in population datasets even in the absence of genetic exchange. In conclusion, these results make it possible to infer variable impacts of genetic exchange in populations of predominantly clonal micro-pathogens. Moreover, our results reveal different problems of MLST to determine the genetic structure in these organisms that should be considered.

Trypanosoma cruzi: gene expression surveyed by proteomic analysis reveals interaction between different genotypes in mixed in vitro cultures

We have analyzed the comportment in in vitro culture of 2 different genotypes of Trypanosoma cruzi, the agent of Chagas disease, pertaining to 2 major genetic subdivisions (near-clades) of this parasite. One of the stocks was a fast-growing one, highly virulent in mice, while the other one was slow- growing, mildly virulent in mice. The working hypothesis was that mixtures of genotypes interact, a pattern that has been observed by us in empirical experimental studies. Genotype mixtures were followed every 7 days and characterized by the DIGE technology of proteomic analysis. Proteic spots of interest were characterized by the SAMESPOT software. Patterns were compared to those of pure genotypes that were also evaluated every 7 days. One hundred and three spots exhibited changes in time by comparison with T = 0. The major part of these spots (58%) exhibited an under-expression pattern by comparison with the pure genotypes. 32% of the spots wereover-expressed; 10% of spots were not different from those of pure genotypes. Interestingly, interaction started a few minutes after the mixtures were performed. We have retained 43 different proteins that clearly exhibited either under- or over-expression. Proteins showing interaction were characterized by mass spectrometry (MALDI-TOF). Close to 50% of them were either tubulins or heat shock proteins. This study confirms that mixed genotypes of T. cruzi interact at the molecular level. This is of great interest because mixtures of genotypes are very frequent in Chagas natural cycles, both in insect vectors and in mammalian hosts, and may play an important role in the transmission and severity of Chagas disease. The methodology proposed here is potentially applicable to any micropathogen, including fungi, bacteria and viruses. It should be of great interest in the case of bacteria, for which the epidemiological and clinical consequences of mixed infections could be underestimated.

Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE) recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found striking similarities among them. The two main PCE features described by us, namely highly significant linkage disequilibrium and near-clading (stable phylogenetic clustering clouded by occasional recombination), are clearly observed in Cryptococcus and Giardia, and more limited indication of them is also present in Cryptosporidium and Pneumocystis. Moreover, in several cases, these features still obtain when the near-clades that subdivide the species are analyzed separately (“Russian doll pattern”). Lastly, several sets of data undermine the notion that certain microbes form clonal lineages simply owing to a lack of opportunity to outcross due to low transmission rates leading to lack of multiclonal infections (“starving sex hypothesis”). We propose that the divergent taxonomic and population genetic inferences advanced by various authors about these pathogens may not correspond to true evolutionary differences and could be, rather, the reflection of idiosyncratic practices among compartmentalized scientific communities. The PCE model provides an opportunity to revise the taxonomy and applied research dealing with these pathogens and others, such as viruses, bacteria, parasitic protozoa, and fungi.

Micropathogen species definition is extremely difficult, since concepts applied to higher organisms (the biological species concept) are inadequate. In particular, the pathogens here surveyed have given rise to long-lasting controversies about their species status and that of the genotypes that subdivide them. The population genetic approach based on the predominant clonal evolution (PCE) concept proposed by us could bring simple solutions to these controversies, since it permits the description of clearly defined evolutionary entities (clonal multilocus genotypes and near-clades [incompletely isolated clades]) that could be the basis for species description, if the concerned specialists find it justified for applied research. The PCE model also provides a convenient framework for applied studies (molecular epidemiology, vaccine and drug design, clinical research) dealing with these pathogens and others.

New insights into clonality and panmixia in Plasmodium and toxoplasma

Until the 1990s, Plasmodium and Toxoplasma were widely considered to be potentially panmictic species, because they both undergo a meiotic sexual cycle in their definitive hosts. We have proposed that both parasites are able of clonal (nonrecombining) propagation, at least in some cycles. Toxoplasma was soon shown to be a paradigmatic case of clonal population structure in North American and in European cycles. But the proposal provoked an outcry in the case of Plasmodium and still appears as doubtful to many scientists. However, the existence of Plasmodium nonrecombining lines has been fully confirmed, although the origin of these lines is debatable. We discuss the current state of knowledge concerning the population structure of both parasites in the light of the recent developments of pathogen clonal evolution proposed by us and of new hypotheses presented here.

Genetic variation and exchange in Trypanosoma cruzi isolates from the United States

Trypanosoma cruzi, the causative agent of Chagas disease, is a multiclonal parasite with high levels of genetic diversity and broad host and geographic ranges. Molecular characterization of South American isolates of T. cruzi has demonstrated homologous recombination and nuclear hybridization, as well as the presence of 6 main genetic clusters or "discrete typing units" (DTUs). Few studies have extensively investigated such exchange events and genetic diversity in North American isolates. In the current study, we genetically characterized over 50 US isolates from wildlife reservoirs (e.g., raccoons, opossums, armadillos, skunks), domestic dogs, humans, nonhuman primates, and reduviid vectors from nine states (TX, CA, OK, SC, FL, GA, MD, LA, TN) using a multilocus sequencing method. Single nucleotide polymorphisms were identified in sequences of the mismatch-repair class 2 (MSH2) and Tc52 genes. Typing based on the two genes often paralleled genotyping by classic methodologies using mini-exon and 18S and 24Sα rRNA genes. Evidence for genetic exchange was obtained by comparing sequence phylogenies of nuclear and mitochondrial gene targets, dihydrofolate reductase-thymidylate synthase (DHFR-TS) and the cytochrome oxidase subunit II- NADH dehydrogenase subunit I region (COII-ND1), respectively. We observed genetic exchange in several US isolates as demonstrated by incongruent mitochondrial and nuclear genes phylogenies, which confirms a previous finding of a single genetic exchange event in a Florida isolate. The presence of SNPs and evidence of genetic exchange illustrates that strains from the US are genetically diverse, even though only two phylogenetic lineages have been identified in this region.

Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa

We propose that clonal evolution in micropathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure, a definition already widely used for all kinds of pathogens, although not clearly formulated by many scientists and rejected by others. The two main manifestations of clonal evolution are strong linkage disequilibrium (LD) and widespread genetic clustering ("near-clading"). We hypothesize that this pattern is not mainly due to natural selection, but originates chiefly from in-built genetic properties of pathogens, which could be ancestral and could function as alternative allelic systems to recombination genes ("clonality/sexuality machinery") to escape recombinational load. The clonal framework of species of pathogens should be ascertained before any analysis of biomedical phenotypes (phylogenetic character mapping). In our opinion, this model provides a conceptual framework for the population genetics of any micropathogen.

The revised Trypanosoma cruzi subspecific nomenclature: rationale, epidemiological relevance and research applications

The protozoan Trypanosoma cruzi, its mammalian reservoirs, and vectors have existed in nature for millions of years. The human infection, named Chagas disease, is a major public health problem for Latin America. T. cruzi is genetically highly diverse and the understanding of the population structure of this parasite is critical because of the links to transmission cycles and disease. At present, T. cruzi is partitioned into six discrete typing units (DTUs), TcI-TcVI. Here we focus on the current status of taxonomy-related areas such as population structure, phylogeographical and eco-epidemiological features, and the correlation of DTU with natural and experimental infection. We also summarize methods for DTU genotyping, available for widespread use in endemic areas. For the immediate future multilocus sequence typing is likely to be the gold standard for population studies. We conclude that greater advances in our knowledge on pathogenic and epidemiological features of these parasites are expected in the coming decade through the comparative analysis of the genomes from isolates of various DTUs.

Microbial molecular epidemiology: an overview

In this introductory chapter, I stress one more time the urgency to better connect molecular epidemiology and evolutionary biology. I show how much population genetics and phylogenetic analyses can confer a considerable added value to all attempts to characterize strains and species of pathogens. The problems dealing with the mere definition of basic concepts, such as species, subspecies, or strains, are briefly summarized. Last, I show the important contribution of molecular epidemiology to our knowledge of the basic biology of pathogens and insist on the necessity not to separate the studies dealing with pathogens from those that concern the hosts and the vectors, in the case of vector-borne diseases.

Molecular typing of Trypanosoma cruzi isolates, United States

Studies have characterized Trypanosoma cruzi from parasite-endemic regions. With new human cases, increasing numbers of veterinary cases, and influx of potentially infected immigrants, understanding the ecology of this organism in the United States is imperative. We used a classic typing scheme to determine the lineage of 107 isolates from various hosts.

Human Genetic Diversity and the Epidemiology of Parasitic and Other Transmissible Diseases

This paper aims to review human genetic studies that are generally poorly known by parasitologists and scientists working on other pathogenic agents. The key proposals of this paper are as follows: (i) human susceptibility to transmissible diseases may often have a complex, multigenic background; (ii) recent discoveries indicate that major genomic rearrangements may be involved, possibly more so than DNA sequence; (iii) it is crucial to have a general population genetics framework of the human species based on neutral/historical markers to analyse reliably genetic susceptibility to infectious diseases; and (iv) the population level is a key factor. Ethnic diversity, a highly adaptive genetically driven phenotypic diversity, is possibly a valuable source for exploring human genetic susceptibility to transmissible diseases, since different populations have been exposed to drastically different geographic/climatic environments and different pathogens and vectors for tens of thousands of years. Studies dealing with human genetic susceptibility to transmissible diseases have mostly been based on the hypothesis that this factor is driven by only one or a few genes, and considered the individual more than the population level. Two different approaches have been developed for identifying the genes involved: (i) candidate genes and (ii) blind association studies (linkage analysis), screening the genome with a large number of high-resolution markers. Some loci involved in susceptibility to leishmaniosis, malaria and schistosomosis, for example, have already been identified. South American trypanosomosis (Chagas disease) is reviewed in detail to show the methodological problems of this classical approach. Current knowledge on the general impact of transmissible diseases on human genetic diversity, mainly HLA polymorphism, and the hopes raised by recent major international programmes such as the Human Genome Project (HGP), Human Genome Diversity Project (HGDP), International Human Haplotype Map Project (Hap Map) and extended databases, networks and networks of networks will also be reviewed.

Clonal propagation and the fast generation of karyotype diversity: An in vitro Leishmania model

In the present work we studied the karyotype stability during long-term in vitro maintenance in 3 cloned strains of Leishmania (Viannia) peruviana, Leishmania (Viannia) braziliensis and a hybrid between both species. Only the L. (V.) peruviana strain showed an unstable karyotype, even after subcloning. Four chromosomes were studied in detail, each of them characterized by homologous chromosomes of different size (heteromorphy). Variations in chromosome patterns during in vitro maintenance were rapid and discrete, involving loss of heteromorphy or appearance of additional chromosome size variants. The resulting pattern was not the same according to experimental conditions (subinoculation rate or incubation temperature), and interestingly, this was associated with differences in growth behaviour of the respective parasites. No change in total ploidy of the cells was observed by flow cytometry. We discuss several mechanisms that might account for this variation of chromosome patterns, but we favour the occurrence of aneuploidy, caused by aberrant chromosome segregation during mitosis. Our results provide insight into the generation of karyotype diversity in natural conditions and highlight the relativity of the clone concept in parasitology.

Trypanosoma cruzi strains isolated from human, vector, and animal reservoir in the same endemic region in Mexico and typed as T. cruzi I, discrete typing unit 1 exhibit considerable biological diversity

In this study, three strains of Trypanosoma cruzi were isolated at the same time and in the same endemic region in Mexico from a human patient with chronic chagasic cardiomyopathy (RyC-H); vector (Triatoma barberi) (RyC-V); and rodent reservoir (Peromyscus peromyscus) (RyC-R). The three strains were characterized by multilocus enzyme electrophoresis, random amplified polymorphic DNA, and by pathological profiles in experimental animals (biodemes). Based on the analysis of genetic markers the three parasite strains were typed as belonging to T. cruzi I major group, discrete typing unit 1. The pathological profile of RyC-H and RyC-V strains indicated medium virulence and low mortality and, accordingly, the strains should be considered as belonging to biodeme Type III. On the other hand, the parasites from RyC-R strain induced more severe inflammatory processes and high mortality (> 40%) and were considered as belonging to biodeme Type II. The relationship between genotypes and biological characteristics in T. cruzi strains is still debated and not clearly understood. An expert committee recommended in 1999 that Biodeme Type III would correspond to T. cruzi I group, whereas Biodeme Type II, to T. cruzi II group. Our findings suggest that, at least for Mexican isolates, this correlation does not stand and that biological characteristics such as pathogenicity and virulence could be determined by factors different from those identified in the genotypic characterization.

Trypanosoma cruzi: sequence analysis of the variable region of kinetoplast minicircles

The comparisons of 170 sequences of kinetoplast DNA minicircle hypervariable region obtained from 19 stocks of Trypanosoma cruzi and 2 stocks of Trypanosoma cruzi marenkellei showed that only 56% exhibited a significant homology one with other sequences. These sequences could be grouped into homology classes showing no significant sequence similarity with any other homology group. The 44% remaining sequences thus corresponded to unique sequences in our data set. In the DTU I ("Discrete Typing Units") 51% of the sequences were unique. In contrast, in the DTU IId, 87.5% of sequences were distributed into three classes. The results obtained for T. cruzi marinkellei, showed that all sequences were unique, without any similarity between them and T. cruzi sequences. Analysis of palindromes in all sequence sets show high frequency of the EcoRI site. Analysis of repetitive sequences suggested a common ancestral origin of the kDNA. The editing mechanism that occurs in kinetoplastidae is discussed.

Phylogenetic analysis of the glucose-6-phosphate isomerase gene in Trypanosoma cruzi

Trypanosoma cruzi, the agent of Chagas disease, has a basically clonal population structure with rare hybridization events. The species is subdivided into six "Discrete Typing Units" called DTUs I, IIa-e, distributed into two major phylogenetic lineages, T. cruzi I and II (TC I and II). The glucose-6-phosphate isomerase (Gpi) is a specific isoenzymic locus that presents homozygous profiles for DTUs I, IIa-c, and typical heterozygous patterns, for DTUs IId and IIe. The gene was sequenced in 12 T. cruzi stocks and in three stocks pertaining to related species. The phylogenetic relationships observed confirm that the DTUs I, IIa-c do constitute monophyletic groups. Nevertheless, the phylogenetic hierarchy of the DTUs is not clearly resolved with the GPI gene. The hybrid status of DTUs IId and IIe was clearly supported. Sequence analysis revealed that the allele 4 present in both DTUs IIa and IIc, previously considered as unique, displayed in fact two distinct sequences, specific for each DTU. The level of recombination between alleles has been investigated.

The species concept in parasites and other pathogens: a pragmatic approach?

Although the problem of speciation is a puzzle for evolutionists, species are not mere fantasies. In many cases, it is possible to identify evolutionary entities that deserve to be attributed the name 'species' and that are relevant to medical researchers and decision makers. All approaches to the problem of speciation in pathogens are specific cases of four main concepts (or combinations thereof): biological, phylogenetic, phenetic and phenotypic. Modern genetic concepts and technologies help to juggle these concepts.

Bridging the gap between molecular epidemiologists and evolutionists

Molecular epidemiology designates the various molecular methods that aim to identify the relevant units of analysis of pathogens involved in transmissible diseases: species, subspecies, strains, clones and genes of interest. It is frequently based on an empirical approach. I advocate that evolutionary concepts enrich this discipline considerably and should be considered as an integral part. In turn, the experience and questioning of field experts are crucial to evolutionists who use transmissible diseases as models. A molecular epidemiology aim gives evolutionary studies a practical goal, putting a stop to approaches that are overly speculative.

Differential gene expression in benznidazole-resistant Trypanosoma cruzi parasites

We analyzed the differential gene expression among representative Trypanosoma cruzi stocks in relation to benznidazole exposures using a random differentially expressed sequences (RADES) technique. Studies were carried out with drug pressure both at the natural susceptibility level of the wild-type parasite (50% inhibitory concentration for the wild type) and at different resistance levels. The pattern of differential gene expression performed with resistant stocks was compared to the population structure of this parasite, established by random amplified polymorphic DNA analysis and multilocus enzyme electrophoresis. A RADES band polymorphism was observed, and over- or underexpression was linked to the resistance level of the stock. The analysis of RADES bands suggested that different products may be involved in benznidazole resistance mechanisms. No significant association was found between phylogenetic clustering and benznidazole susceptibility. Benznidazole resistance may involve several mechanisms, depending on the level of drug exposure.

Population structure of malaria parasites: the driving epidemiological forces

The population structure of Plasmodial parasites, especially Plasmodium falciparum, has received much attention in the recent years. Like many other micropathogens, the debate has focused on the clonality/sexuality question. Considered a panmictic species for very long, P. falciparum actually exhibits strong departures from panmictic expectations in many of its populations, which corroborates the proposal that it is able to undergo uniparental propagation.(1) The currently accepted idea to account for this surprising result is kind of "mechanical" self-fertilization due to the lack of availability of gametes with different genetic make-ups in low transmission areas. However, it could be misleading to make this simple working hypothesis a dogma, for many other explanations are possible (unknown cycles, sibling species, mating types) that deserve to be explored as well. The consequences of this combination of uniparental(1) and sexual propagation on the circulation of genes of interest (drug resistance, antigenic variability, pathogenicity) are discussed, together with the need to use more sophisticated technologies, analysing much broader samples and considering better the host and vector factors in P. falciparum population dynamics.

A hard lesson for Europeans: the ASEAN CDC

Despite the growing threat of major pandemics, the European Union is planning no more than a meager surveillance agency staffed with 70 people on the 2007 horizon: the new European Centre for Disease Control. I argue that an effective structure should be much larger and include a strong research activity. Asian countries, inspired by the US CDC, are now taking this concept in hand and creating an ASEAN Center For Disease Control, with sophisticated laboratory facilities to be included. This is a tough lesson for us Europeans, and our avarice in this domain could have tragic consequences in the future.

Genetic characterization of Trypanosoma cruzi natural clones from the state of Paraíba, Brazil

Eighteen Trypanosoma cruzi stocks from the state of Paraíba, Brazil, isolated from man, wild mammals, and triatomine bugs were studied by multilocus enzyme electrophoresis and random primed amplified polymorphic DNA. Despite the low number of stocks, a notable genetic, genotypic, and phylogenetic diversity was recorded. The presence of the two main phylogenetic subdivisions, T. cruzi I and II, was recorded. The strong linkage disequilibrium observed in the population under survey suggests that T. cruzi undergoes predominant clonal evolution in this area too, although this result should be confirmed by a broader sample. The pattern of clonal variation does not suggests a recent origin by founder effect with a limited number of different genotypes.

Entamoeba, giardia and toxoplasma: clones or cryptic species?

The availability of molecular markers has renewed interest in the taxonomy of parasitic protozoa at the subspecific and specific levels. Nevertheless, the conclusions reached are heavily dependent upon the way the data are analyzed. Some authors have emphasized the value of genetic distances to propose the creation o f new species, while others have rather favoured a population genetic approach to account for the intraspecific variability of parasites. In this article, using three illustrative cases, Michel Tibayrenc shows that dissimilar taxonomic approaches can be built from quite comparable sets of data.

Towards a population genetics of microorganisms: The clonal theory of parasitic protozoa

Over the past 15 years, molecular investigations, including the study of isozymes and DNA markers, have provided much information on the genetic variation, population structure, breeding system and other population characteristics of parasitic protozoa. For some parasitic protozoa, but not for others, the evidence indicates that their reproduction is prevailingly clonal. In this article, Michel Tibayrenc and Francisco Ayala propose that the issue of whether the predominant mode of reproduction of a given micro-organism is clonal or sexual can only be settled by population genetics information, and they summarize evidence favoring a clonal population structure for a number of parasitic protozoa.