23 research outputs found
Trypanosoma cruzi IIc: phylogenetic and phylogeographic insights from sequence and microsatellite analysis and potential impact on emergent Chagas disease.
Trypanosoma cruzi, the etiological agent of Chagas disease, is highly genetically diverse. Numerous lines of evidence point to the existence of six stable genetic lineages or DTUs: TcI, TcIIa, TcIIb, TcIIc, TcIId, and TcIIe. Molecular dating suggests that T. cruzi is likely to have been an endemic infection of neotropical mammalian fauna for many millions of years. Here we have applied a panel of 49 polymorphic microsatellite markers developed from the online T. cruzi genome to document genetic diversity among 53 isolates belonging to TcIIc, a lineage so far recorded almost exclusively in silvatic transmission cycles but increasingly a potential source of human infection. These data are complemented by parallel analysis of sequence variation in a fragment of the glucose-6-phosphate isomerase gene. New isolates confirm that TcIIc is associated with terrestrial transmission cycles and armadillo reservoir hosts, and demonstrate that TcIIc is far more widespread than previously thought, with a distribution at least from Western Venezuela to the Argentine Chaco. We show that TcIIc is truly a discrete T. cruzi lineage, that it could have an ancient origin and that diversity occurs within the terrestrial niche independently of the host species. We also show that spatial structure among TcIIc isolates from its principal host, the armadillo Dasypus novemcinctus, is greater than that among TcI from Didelphis spp. opossums and link this observation to differences in ecology of their respective niches. Homozygosity in TcIIc populations and some linkage indices indicate the possibility of recombination but cannot yet be effectively discriminated from a high genome-wide frequency of gene conversion. Finally, we suggest that the derived TcIIc population genetic data have a vital role in determining the origin of the epidemiologically important hybrid lineages TcIId and TcIIe
Culture-free genome-wide locus sequence typing (GLST) provides new perspectives on Trypanosoma cruzi dispersal and infection complexity
El análisis del polimorfismo genético es una poderosa herramienta para la vigilancia epidemiológica y investigar. Sin embargo, la inferencia poderosa de la variación genética del patógeno es a menudo restringido por el acceso limitado al ADN objetivo representativo, especialmente en el estudio de especies parásitas obligadas para las cuales el cultivo ex vivo requiere muchos recursos o es propenso a sesgos. Los métodos modernos de captura de secuencias permiten analizar directamente la variación genética de los patógenos del material del huésped/vector, pero a menudo son demasiado complejos y costosos para entornos de escasos recursos donde prevalecen las enfermedades infecciosas. Este estudio propone un método sencillo y rentable Herramienta de tipificación de secuencias de locus de todo el genoma (GLST) basada en la amplificación paralela masiva de puntos crÃticos de información en todo el genoma del patógeno objetivo. el multiplexado La reacción en cadena de la polimerasa amplifica cientos de objetivos genéticos diferentes definidos por el usuario en un único tubo de reacción y la posterior limpieza basada en gel de agarosa y código de barras completan la preparación de la biblioteca por menos de 4 USD por muestra. Nuestro estudio genera un modelo flexible Flujo de trabajo de diseño de panel de imprimación GLST para Trypanosoma cruzi, el agente parásito de Chagas enfermedad. Aplicamos con éxito nuestro panel GLST de 203 objetivos a extractos nómicos metagénicos directos y sin cultivo de vectores triatominos que contienen un mÃnimo de 3,69 pg/μl de ADN de T. cruzi y elaborar más sobre el rendimiento del método mediante la secuenciación de bibliotecas GLST de T. cruzi clones de referencia que representan unidades de tipificación discretas (DTU) TcI, TcIII, TcIV, TcV y TcVI. Los 780 sitios SNP que identificamos en el conjunto de muestras distinguen parásitos de forma repetitiva infectar vectores simpátricos y detectar correlaciones entre distancias genéticas y geográficas a escala regional (< 150 km), asà como continental. Los marcadores también separan claramente TcI, TcIII, TcIV y TcV + TcVI y parecen distinguir infecciones multiclonales dentro de TcI. Discutimos las ventajas, limitaciones y perspectivas de nuestro método a través de un espectro de la investigación epidemiológica.Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obli gate parasitic species for which ex vivo culture is resource-intensive or bias-prone. Mod ern sequence capture methods enable pathogen genetic variation to be analyzed directly from host/vector material but are often too complex and expensive for resource-poor set tings where infectious diseases prevail. This study proposes a simple, cost-effective ‘genome-wide locus sequence typing’ (GLST) tool based on massive parallel amplifica tion of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding com pletes library preparation at under 4 USD per sample. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metage nomic extracts from triatomine vectors containing a minimum of 3.69 pg/μl T. cruzi DNA and further elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, TcV and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic dis tances at regional (< 150 km) as well as continental scales. The markers also clearly sep arate TcI, TcIII, TcIV and TcV + TcVI and appear to distinguish multiclonal infections within TcI. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research
Geographical Distribution of Trypanosoma cruzi Genotypes in Venezuela
Chagas disease is an endemic zoonosis native to the Americas and is caused by the kinetoplastid protozoan parasite Trypanosoma cruzi. The parasite is also highly genetically diverse, with six discrete typing units (DTUs) reported TcI – TcVI. These DTUs broadly correlate with several epidemiogical, ecological and pathological features of Chagas disease. In this manuscript we report the most comprehensive evaluation to date of the genetic diversity of T. cruzi in Venezuela. The dataset includes 778 samples collected and genotyped over the last twelve years from multiple hosts and vectors, including nine wild and domestic mammalian host species, and seven species of triatomine bug, as well as from human sources. Most isolates (732) can be assigned to the TcI clade (94.1%); 24 to the TcIV group (3.1%) and 22 to TcIII (2.8%). Importantly, among the 95 isolates genotyped from human disease cases, 79% belonged to TcI - a DTU common in the Americas, however, 21% belonged to TcIV- a little known genotype previously thought to be rare in humans. Furthermore, were able to assign multiple oral Chagas diseases cases to TcI in the area around the capital, Caracas. We discuss our findings in the context of T. cruzi DTU distributions elsewhere in the Americas, and evaluate the impact they have on the future of Chagas disease control in Venezuela
Culture-free genome-wide locus sequence typing (GLST) provides new perspectives on Trypanosoma cruzi dispersal and infection complexity.
Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obligate parasitic species for which ex vivo culture is resource-intensive or bias-prone. Modern sequence capture methods enable pathogen genetic variation to be analyzed directly from host/vector material but are often too complex and expensive for resource-poor settings where infectious diseases prevail. This study proposes a simple, cost-effective 'genome-wide locus sequence typing' (GLST) tool based on massive parallel amplification of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding completes library preparation at under 4 USD per sample. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metagenomic extracts from triatomine vectors containing a minimum of 3.69 pg/μl T. cruzi DNA and further elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, TcV and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic distances at regional (< 150 km) as well as continental scales. The markers also clearly separate TcI, TcIII, TcIV and TcV + TcVI and appear to distinguish multiclonal infections within TcI. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research
Venezuela's humanitarian crisis, resurgence of vector-borne diseases, and implications for spillover in the region.
In the past 5-10 years, Venezuela has faced a severe economic crisis, precipitated by political instability and declining oil revenue. Public health provision has been affected particularly. In this Review, we assess the impact of Venezuela's health-care crisis on vector-borne diseases, and the spillover into neighbouring countries. Between 2000 and 2015, Venezuela witnessed a 359% increase in malaria cases, followed by a 71% increase in 2017 (411 586 cases) compared with 2016 (240 613). Neighbouring countries, such as Brazil, have reported an escalating trend of imported malaria cases from Venezuela, from 1538 in 2014 to 3129 in 2017. In Venezuela, active Chagas disease transmission has been reported, with seroprevalence in children (<10 years), estimated to be as high as 12·5% in one community tested (n=64). Dengue incidence increased by more than four times between 1990 and 2016. The estimated incidence of chikungunya during its epidemic peak is 6975 cases per 100 000 people and that of Zika virus is 2057 cases per 100 000 people. The re-emergence of many vector-borne diseases represents a public health crisis in Venezuela and has the possibility of severely undermining regional disease elimination efforts. National, regional, and global authorities must take action to address these worsening epidemics and prevent their expansion beyond Venezuelan borders
Geographical Distribution of Trypanosoma cruzi Genotypes in Venezuela
<p>Chagas disease is caused by a protozoan parasite called<br>Trypanosoma cruzi. T. cruzi infects a wide variety of<br>mammal species in Latin America as well as man, and is<br>spread by multiple species of blood sucking triatomine<br>insect vectors. The presence of genetic diversity in T. cruzi<br>in the Americas is well established, with six different major<br>genetic types in circulation. The genetic diversity of T. cruzi<br>in Venezuela is relatively poorly understood. In this work<br>we present the results from the genotyping of over seven<br>hundred isolates from 17 of the 24 states. Our dataset<br>comprises strains isolated from wild and domestic animals,<br>several species of triatomine vector, as well as from human<br>Chagas disease cases, including those associated with oral<br>transmission of T. cruzi. Amongst other findings, our data<br>reveal a surprisingly high frequency of atypical genotypes<br>in humans, particularly TcIV, which has rarely been<br>reported. We evaluate our findings in the context of T.<br>cruzi diversity elsewhere in the Americas, and assess the<br>impact they have on the future of Chagas disease control<br>in Venezuela.</p
Culture-free genome-wide locus sequence typing (GLST) provides new perspectives on Trypanosoma cruzi dispersal and infection complexity
El análisis del polimorfismo genético es una poderosa herramienta para la vigilancia epidemiológica y investigar. Sin embargo, la inferencia poderosa de la variación genética del patógeno es a menudo restringido por el acceso limitado al ADN objetivo representativo, especialmente en el estudio de especies parásitas obligadas para las cuales el cultivo ex vivo requiere muchos recursos o es propenso a sesgos. Los métodos modernos de captura de secuencias permiten analizar directamente la variación genética de los patógenos del material del huésped/vector, pero a menudo son demasiado complejos y costosos para entornos de escasos recursos donde prevalecen las enfermedades infecciosas. Este estudio propone un método sencillo y rentable Herramienta de tipificación de secuencias de locus de todo el genoma (GLST) basada en la amplificación paralela masiva de puntos crÃticos de información en todo el genoma del patógeno objetivo. el multiplexado La reacción en cadena de la polimerasa amplifica cientos de objetivos genéticos diferentes definidos por el usuario en un único tubo de reacción y la posterior limpieza basada en gel de agarosa y código de barras completan la preparación de la biblioteca por menos de 4 USD por muestra. Nuestro estudio genera un modelo flexible Flujo de trabajo de diseño de panel de imprimación GLST para Trypanosoma cruzi, el agente parásito de Chagas enfermedad. Aplicamos con éxito nuestro panel GLST de 203 objetivos a extractos nómicos metagénicos directos y sin cultivo de vectores triatominos que contienen un mÃnimo de 3,69 pg/μl de ADN de T. cruzi y elaborar más sobre el rendimiento del método mediante la secuenciación de bibliotecas GLST de T. cruzi clones de referencia que representan unidades de tipificación discretas (DTU) TcI, TcIII, TcIV, TcV y TcVI. Los 780 sitios SNP que identificamos en el conjunto de muestras distinguen parásitos de forma repetitiva infectar vectores simpátricos y detectar correlaciones entre distancias genéticas y geográficas a escala regional (< 150 km), asà como continental. Los marcadores también separan claramente TcI, TcIII, TcIV y TcV + TcVI y parecen distinguir infecciones multiclonales dentro de TcI. Discutimos las ventajas, limitaciones y perspectivas de nuestro método a través de un espectro de la investigación epidemiológica.Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obli gate parasitic species for which ex vivo culture is resource-intensive or bias-prone. Mod ern sequence capture methods enable pathogen genetic variation to be analyzed directly from host/vector material but are often too complex and expensive for resource-poor set tings where infectious diseases prevail. This study proposes a simple, cost-effective ‘genome-wide locus sequence typing’ (GLST) tool based on massive parallel amplifica tion of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding com pletes library preparation at under 4 USD per sample. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metage nomic extracts from triatomine vectors containing a minimum of 3.69 pg/μl T. cruzi DNA and further elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, TcV and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic dis tances at regional (< 150 km) as well as continental scales. The markers also clearly sep arate TcI, TcIII, TcIV and TcV + TcVI and appear to distinguish multiclonal infections within TcI. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research
Molecular epidemiologic source tracking of orally transmitted Chagas disease, Venezuela.
Oral outbreaks of Chagas disease are increasingly reported in Latin America. The transitory presence of Trypanosoma cruzi parasites within contaminated foods, and the rapid consumption of those foods, precludes precise identification of outbreak origin. We report source attribution for 2 peri-urban oral outbreaks of Chagas disease in Venezuela via high resolution microsatellite typing
Signatures of the Venezuelan Humanitarian Crisis in the First Wave of COVID-19: Fuel Shortages and Border Migration
Testing and isolation have been crucial for controlling the COVID-19 pandemic. Venezuela has one of the weakest testing infrastructures in Latin America and the low number of reported cases in the country has been attributed to substantial underreporting. However, the Venezuelan epidemic seems to have lagged behind other countries in the region, with most cases occurring within the capital region and four border states. Here, we describe the spatial epidemiology of COVID-19 in Venezuela and its relation to the population mobility, migration patterns, non-pharmaceutical interventions and fuel availability that impact population movement. Using a metapopulation model of SARS-CoV-2 transmission dynamics, we explore how movement patterns could have driven the observed distribution of cases. Low within-country connectivity most likely delayed the onset of the epidemic in most states, except for those bordering Colombia and Brazil, where high immigration seeded outbreaks. NPIs slowed early epidemic growth and subsequent fuel shortages appeared to be responsible for limiting the spread of COVID-19 across the country
Genetic diversification of Panstrongylus geniculatus (Reduviidae: Triatominae) in northern South America
Triatomines are the vectors of Trypanosoma cruzi, the etiological agent of Chagas disease. Although Triatoma and Rhodnius are the most-studied vector genera, other triatomines, such as Panstrongylus, also transmit T. cruzi, creating new epidemiological scenarios. Panstrongylus has at least 13 reported species but there is limited information about its intraspecific genetic variation and patterns of diversification. Here, we begin to fill this gap by studying populations of P. geniculatus from Colombia and Venezuela and including other epidemiologically important species from the region. We examined the pattern of diversification of P. geniculatus in Colombia using mitochondrial and nuclear ribosomal data. Genetic diversity and differentiation were calculated within and among populations of P. geniculatus. Moreover, we constructed maximum likelihood and Bayesian inference phylogenies and haplotype networks using P. geniculatus and other species from the genus (P. megistus, P. lignarius, P. lutzi, P. tupynambai, P. chinai, P. rufotuberculatus and P. howardi). Using a coalescence framework, we also dated the P. geniculatus lineages. The total evidence tree showed that P. geniculatus is a monophyletic species, with four clades that are concordant with its geographic distribution and are partly explained by the Andes orogeny. However, other factors, including anthropogenic and eco-epidemiological effects must be investigated to explain the existence of recent geographic P. geniculatus lineages. The epidemiological dynamics in structured vector populations, such as those found here, warrant further investigation. Extending our knowledge of P. geniculatus is necessary for the accurate development of effective strategies for the control of Chagas disease vectors. © 2019 Caicedo-Garzón et al