Parasite associations predict infection risk: incorporating co-infections in predictive models for neglected tropical diseases

Coinfection by multiple Trypanosoma cruzi clones: a new perspective on host-parasite relationship with consequences for pathogenesis and management of Chagas disease

SUMMARYChagas disease (CD) is caused by the protozoan parasite Trypanosoma cruzi (Tc), infecting 6-7 million people. It is transmitted by insect vectors, orally, through infected tissues, or congenitally. Tc infection can progress toward chronic cardiac and/or digestive severe and fatal CD in 20%-40% of patients. Tc exhibits an important genetic and phenotypic intraspecies diversity and a preponderant clonal population structure. The impact of multiclonal coinfections has been little studied in CD patients. Relationships between the currently used discrete typing unit (DTU)-based classification of Tc lineages and the occurrence of the different clinical forms of CD, its congenital transmission, as well as the efficacy of trypanocidal molecules (benznidazole and nifurtimox) could not be established. In this review, we revisit the different aspects of Tc diversity and analyze the impact of infections with multiple clones and their variants on the dynamic and pathogenesis of CD and its maternal-fetal transmission. We propose to call "cruziome" all the Tc clones and their variants infecting a given host and provide strong evidence that (i) multiclonal Tc infections are likely the rule rather than the exception; (ii) each "cruziome" is associated with a unique combination of virulence factors, tissular tropisms, and host immune responses; (iii) accordingly, some particularly harmful "cruziomes" likely trigger the occurrence and progression of CD and might also favor the congenital transmission of parasites. We propose that our concept of "cruziome" should be taken into consideration because of its practical consequences in epidemiological studies, laboratory diagnosis, clinical management, and treatment of CD.

A systematic review and guide for using multi-response statistical models in co-infection research

The simultaneous infection of organisms with two or more co-occurring pathogens, otherwise known as co-infections, concomitant infections or multiple infections, plays a significant role in the dynamics and consequences of infectious diseases in both humans and animals. To understand co-infections, ecologists and epidemiologists rely on models capable of accommodating multiple response variables. However, given the diversity of available approaches, choosing a model that is suitable for drawing meaningful conclusions from observational data is not a straightforward task. To provide clearer guidance for statistical model use in co-infection research, we conducted a systematic review to (i) understand the breadth of study goals and host-pathogen systems being pursued with multi-response models and (ii) determine the degree of crossover of knowledge among disciplines. In total, we identified 69 peer-reviewed primary studies that jointly measured infection patterns with two or more pathogens of humans or animals in natural environments. We found stark divisions in research objectives and methods among different disciplines, suggesting that cross-disciplinary insights into co-infection patterns and processes for different human and animal contexts are currently limited. Citation network analysis also revealed limited knowledge exchange between ecology and epidemiology. These findings collectively highlight the need for greater interdisciplinary collaboration for improving disease management.

Evolutionary consequences of vector-borne transmission: how using vectors shapes host, vector and pathogen evolution

Transmission mode is a key factor that influences host–parasite coevolution. Vector-borne pathogens are among the most important disease agents for humans and wildlife due to their broad distribution, high diversity, prevalence and lethality. They comprise some of the most important and widespread human pathogens, such as yellow fever, leishmania and malaria. Vector-borne parasites (in this review, those transmitted by blood-feeding Diptera) follow unique transmission routes towards their vertebrate hosts. Consequently, each part of this tri-partite (i.e. parasite, vector and host) interaction can influence co- and counter-evolutionary pressures among antagonists. This mode of transmission may favour the evolution of greater virulence to the vertebrate host; however, pathogen–vector interactions can also have a broad spectrum of fitness costs to the insect vector. To complete their life cycle, vector-borne pathogens must overcome immune responses from 2 unrelated organisms, since they can activate responses in both vertebrate and invertebrate hosts, possibly creating a trade-off between investments against both types of immunity. Here, we assess how dipteran vector-borne transmission shapes the evolution of hosts, vectors and the pathogens themselves. Hosts, vectors and pathogens co-evolve together in a constant antagonistic arms race with each participant's primary goal being to maximize its performance and fitness.

Household profiles of neglected tropical disease symptoms among children: A latent class analysis of built-environment features of Tanzanian households using the Demographic and Health Survey

Background

While malaria and neglected tropical disease (NTD) morbidity and mortality rates among children <5 years old have decreased through public health efforts in the United Republic of Tanzania, associations between household environments and disease outcomes are relatively unknown.

Methods

We conducted latent class analysis (LCA) on 2015-2016 Tanzania Demographic Health Survey data from mothers with children <5 years old (N = 10 233) to identify NTD household risk profiles. The outcome of child NTD was assessed by mothers’ reports of recent diarrhoea, cough, treatment for enteric parasites, and fever symptoms. Household-built environment indicators included urban/rural designation, electricity access, water source, cooking fuel, flooring, wall, and roofing materials. External environmental covariates were considered to further differentiate profiles.

Results

Five profiles were identified in the sample: rural finished walls households (40.2%) with the lowest NTD risk; rural rudimentary households (20.9%) with intermediate-low NTD risk; finished material households (22.5%) with intermediate NTD risk; urban households (14.4%) with intermediate-high NTD risk and high likelihood of enteric parasites; rural finished roof/walls households (2.1%) with the highest overall NTD risk.

Conclusions

This study is among the first to use LCA to examine household environment characteristics to assess child NTD risk in Tanzania. This paper serves as a framework for community-level rapid NTD risk assessment for targeted health promotion interventions.

Using Routinely Collected Health Records to Identify the Fine-Resolution Spatial Patterns of Soil-Transmitted Helminth Infections in Rwanda

Background. Soil-transmitted helminths (STH) are parasitic diseases with significant public health impact. Analysis is generally based on cross-sectional prevalence surveys; outcomes are mostly aggregated to larger spatial units. However, recent research demonstrates that infection levels and spatial patterns differ between STH species and tend to be localized. Methods. Incidence data of STHs including roundworm (Ascaris lumbricoides), whipworm (Trichuris trichiura) and hookworms per primary health facility for 2008 were linked to spatially delineated primary health center service areas. Prevalence data per district for individual and combined STH infections from the 2008 nationwide survey in Rwanda were also obtained. Results. A comparison of reported prevalence and incidence data indicated significant positive correlations for roundworm (R2 = 0.63) and hookworm (R2 = 0.27). Weak positive correlations were observed for whipworm (R2 = 0.02) and the three STHs combined (R2 = 0.10). Incidence of roundworm and whipworm were found to be focalized with significant spatial autocorrelation (Moran’s I > 0: 0.05−0.38 and p ≤ 0.03), with (very) high incidence rates in some focal areas. In contrast, hookworm incidence is ubiquitous and randomly distributed (Moran’s I > 0: 0.006 and p = 0.74) with very low incidence rates. Furthermore, an exploratory regression analysis identified relationships between helminth infection cases and potential environmental and socio-economic risk factors. Conclusions. Findings show that the spatial distribution of STH incidence is significantly associated with soil properties (sand proportion and pH), rainfall, wetlands and their uses, population density and proportion of rural residents. Identified spatial patterns are important for guiding STH prevention and control programs.

Parasite co-infection: an ecological, molecular and experimental perspective

Laboratory studies of pathogens aim to limit complexity in order to disentangle the important parameters contributing to an infection. However, pathogens rarely exist in isolation, and hosts may sustain co-infections with multiple disease agents. These interact with each other and with the host immune system dynamically, with disease outcomes affected by the composition of the community of infecting pathogens, their order of colonization, competition for niches and nutrients, and immune modulation. While pathogen-immune interactions have been detailed elsewhere, here we examine the use of ecological and experimental studies of trypanosome and malaria infections to discuss the interactions between pathogens in mammal hosts and arthropod vectors, including recently developed laboratory models for co-infection. The implications of pathogen co-infection for disease therapy are also discussed.

Retrospective analysis and time series forecasting with automated machine learning of ascariasis, enterobiasis and cystic echinococcosis in Romania

The epidemiology of neglected tropical diseases (NTD) is persistently underprioritized, despite NTD being widespread among the poorest populations and in the least developed countries on earth. This situation necessitates thorough and efficient public health intervention. Romania is at the brink of becoming a developed country. However, this South-Eastern European country appears to be a region that is susceptible to an underestimated burden of parasitic diseases despite recent public health reforms. Moreover, there is an evident lack of new epidemiologic data on NTD after Romania's accession to the European Union (EU) in 2007. Using the national ICD-10 dataset for hospitalized patients in Romania, we generated time series datasets for 2008-2018. The objective was to gain deep understanding of the epidemiological distribution of three selected and highly endemic parasitic diseases, namely, ascariasis, enterobiasis and cystic echinococcosis (CE), during this period and forecast their courses for the ensuing two years. Through descriptive and inferential analysis, we observed a decline in case numbers for all three NTD. Several distributional particularities at regional level emerged. Furthermore, we performed predictions using a novel automated time series (AutoTS) machine learning tool and could interestingly show a stable course for these parasitic NTD. Such predictions can help public health officials and medical organizations to implement targeted disease prevention and control. To our knowledge, this is the first study involving a retrospective analysis of ascariasis, enterobiasis and CE on a nationwide scale in Romania. It is also the first to use AutoTS technology for parasitic NTD.

Dark diversity of flea assemblages of small mammalian hosts: effects of environment, host traits and host phylogeny

An assemblage of species in a locality comprises two components, namely (i) species that are present (realised diversity) and (ii) species from the regional pool that may potentially inhabit this locality due to suitable ecological conditions, but that are absent (dark diversity). We investigated factors affecting the dark diversity of component communities of fleas parasitic on small mammals in the northern Palearctic at two scales. First, we considered the dark diversity of flea assemblages of the same host (for 13 host species) across regions and tested for the effects of environmental factors and the number of available host species on the dark diversity of within-region flea assemblages. Second, we considered the dark diversity of fleas across host species within a region (for 20 regions) and asked whether within-host dark diversity is associated with host phylogeny and/or traits. We found that the dark diversity of flea assemblages harboured by small mammals varied substantially (i) within the same host species across space (in 12 of 13 host species) and (ii) between host species within a region (in eight of 20 regions). The size of the dark diversity of flea assemblages of the same host across regions was generally affected by environmental factors (mainly by the amount of green vegetation), whereas the size of the dark diversity of flea assemblages of a host species within a region was affected by host traits (mainly by the degree of host sociality and the structure of its shelter and, to a lesser degree, by its geographic range size) but was not associated with host phylogenetic affinities. We conclude that application of the dark diversity concept to parasite communities across space or hosts allows a better understanding of the factors affecting the species richness and composition of these communities.

Environmental, anthropogenic, and spatial factors affecting species composition and species associations in helminth communities of water frogs (Pelophylax esculentus complex) in Latvia

We investigated factors affecting species composition and patterns of species associations in parasite communities of water frogs (Pelophylax esculentus complex), applying the distance-based redundancy analysis for component communities (assemblages harboured by host populations) and Markov random fields modelling for infracommunities (assemblages harboured by individual hosts), respectively. We asked (a) What are the relative effects of variation in environmental, land use (i.e., anthropogenic), and spatial factors on the variation in the species composition of component communities (i.e., in a locality)? and (b) What is the dominant pattern of species associations in infracommunities (in a host individual), and how do these associations vary along environmental and/or anthropogenic gradients? In component communities, the greatest portion of variation in helminth species composition was explained by the combined effects of space, anthropogenic pressure, and NDVI, with the pure effect of the spatial predictor being much stronger than the effects of the remaining predictors. In infracommunities, the probability of occurrence of some, but not all, helminth species depended on the occurrence of another species, with the numbers of negative and positive co-occurrences being equal. The strength and/or sign of associations of some species pairs were spatially stable, whereas interactions between other species pairs varied along the gradient of the amount of green vegetation, from negative to positive and vice versa. We conclude that the processes in parasite infracommunities and component communities in frogs are intertwined, with both bottom-up and top-down effects acting at different hierarchical scales.

Soil-Transmitted Helminth Vaccines: Are We Getting Closer?

Parasitic helminths infect over one-fourth of the human population resulting in significant morbidity, and in some cases, death in endemic countries. Despite mass drug administration (MDA) to school-aged children and other control measures, helminth infections are spreading into new areas. Thus, there is a strong rationale for developing anthelminthic vaccines as cost-effective, long-term immunological control strategies, which, unlike MDA, are not haunted by the threat of emerging drug-resistant helminths nor limited by reinfection risk. Advances in vaccinology, immunology, and immunomics include the development of new tools that improve the safety, immunogenicity, and efficacy of vaccines; and some of these tools have been used in the development of helminth vaccines. The development of anthelminthic vaccines is fraught with difficulty. Multiple lifecycle stages exist each presenting stage-specific antigens. Further, helminth parasites are notorious for their ability to dampen down and regulate host immunity. One of the first significant challenges in developing any vaccine is identifying suitable candidate protective antigens. This review explores our current knowledge in lead antigen identification and reports on recent pre-clinical and clinical trials in the context of the soil-transmitted helminths Trichuris, the hookworms and Ascaris. Ultimately, a multivalent anthelminthic vaccine could become an essential tool for achieving the medium-to long-term goal of controlling, or even eliminating helminth infections.