Integrated genetic epidemiology of infectious diseases: the Chagas model

New insights into Trypanosoma cruzi genetic diversity, and its influence on parasite biology and clinical outcomes

Chagas disease, caused by Trypanosoma cruzi, remains a serious public health problem worldwide. The parasite was subdivided into six distinct genetic groups, called "discrete typing units" (DTUs), from TcI to TcVI. Several studies have indicated that the heterogeneity of T. cruzi species directly affects the diversity of clinical manifestations of Chagas disease, control, diagnosis performance, and susceptibility to treatment. Thus, this review aims to describe how T. cruzi genetic diversity influences the biology of the parasite and/or clinical parameters in humans. Regarding the geographic dispersion of T. cruzi, evident differences were observed in the distribution of DTUs in distinct areas. For example, TcII is the main DTU detected in Brazilian patients from the central and southeastern regions, where there are also registers of TcVI as a secondary T. cruzi DTU. An important aspect observed in previous studies is that the genetic variability of T. cruzi can impact parasite infectivity, reproduction, and differentiation in the vectors. It has been proposed that T. cruzi DTU influences the host immune response and affects disease progression. Genetic aspects of the parasite play an important role in determining which host tissues will be infected, thus heavily influencing Chagas disease's pathogenesis. Several teams have investigated the correlation between T. cruzi DTU and the reactivation of Chagas disease. In agreement with these data, it is reasonable to suppose that the immunological condition of the patient, whether or not associated with the reactivation of the T. cruzi infection and the parasite strain, may have an important role in the pathogenesis of Chagas disease. In this context, understanding the genetics of T. cruzi and its biological and clinical implications will provide new knowledge that may contribute to additional strategies in the diagnosis and clinical outcome follow-up of patients with Chagas disease, in addition to the reactivation of immunocompromised patients infected with T. cruzi.

Analytical performance of a multiplex Real-Time PCR assay using TaqMan probes for quantification of Trypanosoma cruzi satellite DNA in blood samples

Background

The analytical validation of sensitive, accurate and standardized Real-Time PCR methods for Trypanosoma cruzi quantification is crucial to provide a reliable laboratory tool for diagnosis of recent infections as well as for monitoring treatment efficacy.

Methods/Principal Findings

We have standardized and validated a multiplex Real-Time quantitative PCR assay (qPCR) based on TaqMan technology, aiming to quantify T. cruzi satellite DNA as well as an internal amplification control (IAC) in a single-tube reaction. IAC amplification allows rule out false negative PCR results due to inhibitory substances or loss of DNA during sample processing. The assay has a limit of detection (LOD) of 0.70 parasite equivalents/mL and a limit of quantification (LOQ) of 1.53 parasite equivalents/mL starting from non-boiled Guanidine EDTA blood spiked with T. cruzi CL-Brener stock. The method was evaluated with blood samples collected from Chagas disease patients experiencing different clinical stages and epidemiological scenarios: 1- Sixteen Venezuelan patients from an outbreak of oral transmission, 2- Sixty three Bolivian patients suffering chronic Chagas disease, 3- Thirty four Argentinean cases with chronic Chagas disease, 4- Twenty seven newborns to seropositive mothers, 5- A seronegative receptor who got infected after transplantation with a cadaveric kidney explanted from an infected subject.

Conclusions/Significance

The performing parameters of this assay encourage its application to early assessment of T. cruzi infection in cases in which serological methods are not informative, such as recent infections by oral contamination or congenital transmission or after transplantation with organs from seropositive donors, as well as for monitoring Chagas disease patients under etiological treatment.

Chagas disease, caused by the parasite Trypanosoma cruzi, is endemic in several Latin American countries and still represents a major neglected tropical threat. It is transmitted to humans by blood-sucking triatomine bugs, congenital transmission, blood transfusion, organ transplantation and by consuming food and juice contaminated with the parasite. Tools for accurate diagnosis and surrogate markers of parasitological response to treatment remain key needs in the field. This study focused on the evaluation of a novel quantitative PCR assay for the diagnosis and follow-up of patients with Chagas disease, on the basis of international guidelines for analytical validation of molecular diagnostic methods. The method allows the simultaneous amplification of parasite satellite DNA sequence and a heterologous internal amplification control that permits rule out false negative results due to inhibitory substances or loss of DNA during sample processing. It was evaluated in peripheral blood samples from acute and chronic patients as well as in umbilical cord blood samples from newborns to seropositive mothers. The performing characteristics of this assay position it as a promising candidate for application to clinical trials and kit developments.

Genetic characterization of Trypanosoma cruzi DTUs in wild Triatoma infestans from Bolivia: predominance of TcI

Background

The current persistence of Triatoma infestans (one of the main vectors of Chagas disease) in some domestic areas could be related to re-colonization by wild populations which are increasingly reported. However, the infection rate and the genetic characterization of the Trypanosoma cruzi strains infecting these populations are very limited.

Methodology/Principal Findings

Of 333 wild Triatoma infestans specimens collected from north to south of a Chagas disease endemic area in Bolivia, we characterized 234 stocks of Trypanosoma cruzi using mini-exon multiplex PCR (MMPCR) and sequencing the glucose phosphate isomerase (Gpi) gene. Of the six genetic lineages (“discrete typing units”; DTU) (TcI-VI) presently recognized in T. cruzi, TcI (99.1%) was overdominant on TcIII (0.9%) in wild Andean T. infestans, which presented a 71.7% infection rate as evaluated by microscopy. In the lowlands (Bolivian Chaco), 17 “dark morph” T. infestans were analyzed. None of them were positive for parasites after microscopic examination, although one TcI stock and one TcII stock were identified using MMPCR and sequencing.

Conclusions/Significance

By exploring large-scale DTUs that infect the wild populations of T. infestans, this study opens the discussion on the origin of TcI and TcV DTUs that are predominant in domestic Bolivian cycles.

Chagas disease is a neglected parasitic disease transmitted by bugs (vectors) and represents a serious health problem in the Americas. Although the transmission generally occurs in the houses where the bugs are living, wild populations of vectors are now considered a problem because these populations might enter the houses and recolonize them after eliminating of house populations by insecticide spraying. This is the case of the Southern countries where Triatoma infestans, the principal vector, transmits Trypanosoma cruzi the agent of the disease. This parasite presents a large genetic variability and it is important to know which T. cruzi genotypes are carried by the vectors. The authors found that in the wild T. infestans from the Bolivian Andean region, a principal group of genotype was circulating. In the lowlands (Bolivian Chaco), another additional genotype group was detected. Together with exploring at large scale which genotypes are infecting T. infestans wild populations, this study opens the discussion on the origin T. cruzi genotype groups. Also this study completes our basic knowledge on T. cruzi subspecific genetic variability, and therefore brings new tools for molecular epidemiology of Chagas disease.

Genetic epidemiology of Chagas disease

Genetic epidemiological approaches hold great promise for improving the understanding of the determinants of susceptibility to infection with Trypanosoma cruzi and the causes of differential disease outcome in T. cruzi-infected individuals. To date, a variety of approaches have been used to understand the role of genetic factors in Chagas disease. Quantitative genetic techniques have been used to estimate the heritabilities for seropositivity for T. cruzi infection and traits that are associated with disease progression in chronic T. cruzi infection. These studies have demonstrated that a significant proportion of the variation in seropositivity and a number of traits related to Chagas disease progression is attributable to genetic factors. Candidate gene studies have provided intriguing evidence for the roles of numerous individual genes in determining cardiac outcomes in chronically infected individuals. Recent results from a long-term study of Chagas disease in a rural area of Brazil have documented that over 60% of the variation in seropositivity status is attributable to genetic factors in that population. Additionally, there are significant genetic effects on a number of electrocardiographic measures and other Chagas disease-related traits. The application of genome-wide approaches will yield new evidence for the roles of specific genes in Chagas disease.

Angiotensin-converting enzyme insertion/deletion gene polymorphism and progression of Chagas' cardiomyopathy

Chagas' disease is common in Latin America and is caused by Trypanosoma cruzi. It is usually associated with chronic cardiomyopathy, the progression of which could be related to genetic factors. As alterations in the renin-angiotensin-aldosterone system have been reported in the disease, the aim of this study was to determine whether associated genetic polymorphisms influence the development of myocardial damage. The study involved 125 patients who were divided into two groups according to whether they had mild or severe cardiomyopathy. The insertion/deletion polymorphism of the angiotensin-converting enzyme gene was investigated using standard techniques and results were correlated with disease stage. The genotypes were in Hardy-Weinberg equilibrium. After adjusting for demographic variables, no significant relationship was found between the polymorphism and progression of chronic Chagas' disease. Although our sample was limited, the results suggest that the progression of cardiomyopathy in chronic Chagas' disease is unrelated to the insertion/deletion polymorphism.

Angiotensin-converting enzyme insertion/deletion gene polymorphism and progression of Chagas' cardiomyopathy

Chagas' disease is common in Latin America and is caused by Trypanosoma cruzi. It is usually associated with chronic cardiomyopathy, the progression of which could be related to genetic factors. As alterations in the renin-angiotensin-aldosterone system have been reported in the disease, the aim of this study was to determine whether associated genetic polymorphisms influence the development of myocardial damage. The study involved 125 patients who were divided into two groups according to whether they had mild or severe cardiomyopathy. The insertion/deletion polymorphism of the angiotensin-converting enzyme gene was investigated using standard techniques and results were correlated with disease stage. The genotypes were in Hardy-Weinberg equilibrium. After adjusting for demographic variables, no significant relationship was found between the polymorphism and progression of chronic Chagas' disease. Although our sample was limited, the results suggest that the progression of cardiomyopathy in chronic Chagas' disease is unrelated to the insertion/deletion polymorphism.

The anti-oxidant defence response in individuals with the indeterminate form of Chagas disease (American trypanosomiasis)

In previous studies in animal models, Trypanosoma cruzi-induced oxidative stress and damage have sometimes been controlled by the host's anti-oxidant defence responses. The role of the anti-oxidant defence responses, such as the activities of the anti-oxidant enzymes glutathione peroxidase (GPx) and superoxide dismutase (SOD), in protection against inflammation and damage have now been investigated in humans infected with T. cruzi. The subjects were 32 asymptomatic but seropositive individuals with the indeterminate form of Chagas disease, 18 symptomatic and seropositive patients with the chronic disease, and 50 seronegative and apparently healthy controls. The inflammatory process was explored using serum concentrations of tumour necrosis factor (TNF) and NO. The serum concentrations of GPx in the patients in the indeterminate phase of infection were similar to those in the controls but much higher than those in the chronic cases (P=0.001). The serum concentrations of SOD in the patients in the indeterminate phase of infection were not only significantly higher than those in the cases of chronic Chagas disease (P=0.0004) but also significantly higher than those in the controls (P<0.001). The seropositive subjects had significantly higher serum concentrations of TNF and NO than the controls (P<0.01 for each) and the cases of chronic Chagas disease had significantly higher serum concentrations of TNF and NO than the subjects with the indeterminate form of the disease (P<0.01 for each). It therefore appears that the host's anti-oxidant defence responses (at least in terms of elevated concentrations of SOD) may inhibit inflammation during the indeterminate phase of Chagas disease.

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.

EmsB, a tandem repeated multi-loci microsatellite, new tool to investigate the genetic diversity of Echinococcus multilocularis

In order to explore the genetic diversity within Echinococcus multilocularis (E. multilocularis), the cestode responsible for the alveolar echinococcosis (AE) in humans, a microsatellite, composed of (CA) and (GA) repeats and designated EmsB, was isolated and characterized in view of its nature and potential field application. PCR-amplification with specific primers exhibited a high degree of size polymorphism between E. multilocularis and Echinococcus granulosus sheep (G1) and camel (G6) strains. Fluorescent-PCR was subsequently performed on a panel of E. multilocularis isolates to assess intra-species polymorphism level. EmsB provided a multi-peak profile, characterized by tandemly repeated microsatellite sequences in the E. multilocularis genome. This "repetition of repeats" feature provided to EmsB a high discriminatory power in that eight clusters, supported by bootstrap p-values larger than 95%, could be defined among the tested E. multilocularis samples. We were able to differentiate not only the Alaskan from the European samples, but also to detect different European isolate clusters. In total, 25 genotypes were defined within 37 E. multilocularis samples. Despite its complexity, this tandem repeated multi-loci microsatellite possesses the three important features for a molecular marker, i.e. sensitivity, repetitiveness and discriminatory power. It will permit assessing the genetic polymorphism of E. multilocularis and to investigate its spatial distribution in detail.

Trypanosoma cruzi: long-term sub-cultures in two different culture media do not confirm the existence of highly versatile multilocus genotypes

Trypanosoma cruzi Y reference strain is found in many laboratories under at least two highly distinct genotypes, A and B corresponding to the 'discrete typing units' T. cruzi IIb and T. cruzi IId, respectively. Previous work has reported reversible switches between these genotypes according to the culture media used in the experiments: genotype A would be associated with blood-enriched culture media, while genotype B would be associated with blood-free culture media. We tried to reproduce this observation, but used a different cloning method of individual organisms. Our cloning was verified visually under the microscope, while the previous studies relied on a cloning by dilution only. The subclones so obtained were submitted to long-term exposure to both media, and no change was observed in isoenzyme and random amplified polymorphic DNA genotypes. The discrepancy is probably explained by the cloning method: clones obtained from the previous method (dilution and plating) could come from several parasite cells while only one cell generates a clone when micro-manipulation is used.

Trypanosoma cruzi: presence of the two major phylogenetic lineages and of several lesser discrete typing units (DTUs) in Chile and Paraguay

Multilocus enzyme electrophoresis (MLEE) of 99 Chilean and 11 Paraguayan stocks of Trypanosoma cruzi, the agent of Chagas disease, was performed for 22 variable genetic loci. As previously shown for this parasite in other geographic areas, a pattern of long-term clonal evolution of T. cruzi genotypes was inferred, both by strong departures of Hardy-Weinberg expectations and high linkage disequilibrium. The presence of the two major phylogenetic lineages that subdivide the species T. cruzi [Tibayrenc, M., 1995. Population genetics of parasitic protozoa and other microorganisms. In: Baker, J.R., Muller, R., Rollinson, D. (Eds.), Advances in Parasitology, vol. 36, Academic Press, New York, pp. 47-115; Souto, R.P., Fernandes, O., Macedo, A.M., Campbell, D.A., Zingales, B., 1996. DNA markers define two major phylogenetic lineages of Trypanosoma cruzi. Mol. Biochem. Parasitol. 83, 141-152], and of several lesser genetic subdivisions ('discrete typing units' or DTUs; Tibayrenc, M., 1998a. Genetic epidemiology of parasitic protozoa and other infectious agents: the need for an integrated approach. Int. J. Parasitol. 28 (1), 85-104; Tibayrenc, M., 1998b. Beyond strain typing and molecular epidemiology: integrated genetic epidemiology of infectious diseases. Parasitol. Today 14, 323-329; Tibayrenc, M., 1998c. Integrated genetic epidemiology of infectious diseases: the Chagas model. Mem. Inst. Oswaldo Cruz 93 (5), 577-580), was recorded in this region. Comparison between clonal populations in sylvatic and domestic transmission cycles of the disease in Chile strongly suggests that these two cycles are at least partially separated from one another.

Analysis of genetic diversity of Trypanosoma cruzi: an application of riboprinting and gradient gel electrophoresis methods

Analysis of restriction fragment length polymorphism (RFLP) profiles derived from digestion of polymerase chain reaction (PCR) products of the ribosomal 18S from Trypanosoma cruzi yields a typical 'riboprint' profile that can vary intraspecifically. A selection of 21 stocks of T. cruzi and three outgroup taxa: T. rangeli, T. conorhini and Leishmania braziliensis were analysed by riboprinting to assess divergence within and between taxa. T. rangeli, T. conorhini and L. braziliensis could be easily differentiated from each other and from T. cruzi. Phenetic analysis of PCR-RFLP profiles indicated that, with one or two exceptions, stocks of T. cruzi could be broadly partitioned into two groups that formally corresponded to T. cruzi I and T. cruzi II respectively. To test if ribosomal 18S sequences were homogeneous within each taxon, gradient gel electrophoresis methods were employed utilising either chemical or temperature gradients. Upon interpretation of the melting profiles of riboprints and a section of the 18S independently amplified by PCR, there would appear to be at least two divergent 18S types present within T. cruzi. Heterogeneity within copies of the ribosomal 18S within a single genome has therefore been demonstrated and interestingly, this dimorphic arrangement was also present in the outgroup taxa. Presumably the ancestral duplicative event that led to the divergent 18S types preceded that of speciation within this group. These divergent 18S paralogues may have, or had, different functional pressures or rates of molecular evolution. Whether or not these divergent types are equally transcriptionally active throughout the life cycle, remain to be assessed.