Landscape epidemiology: An emerging perspective in the mapping and modelling of disease and disease risk factors

Linking landscape habitats with prevalence of fusarium wilt disease of cashew crop in Tanzania

Epidemic of Cashew Fusarium wilt disease (CFWD) has been a continuous focal challenge in the cashew farming, in Tanzania. Limited to edaphic conditions as a major factor in its epidemic, the current study aimed to assess the habitat-disease relationship. Purposive surveys involving assessment of disease prevalence and habitat compositions were conducted across four landscapes of southeastern zone from 2019 to 2023. Findings revealed a widespread of CFWD across diversified landscapes possessing varying habitat characteristics, mainly cultivated land with mature cashew, brownish sand loamy soils, grassland or shrub vegetation, seasonal river streamlines and natural water wells. The highest disease incidence and severity were noted at Nachingwea/Masasi plain (99.28:88.34%) followed by Liwale inland plain (98.64:89.3%), Coastal zone (72.72:59.83%) and Tunduru dissected plain (62.13:54.54%). The habitat characteristics were strongly similar within the landscape (0.86-Jaccard index) except between villages of the coastal zone (0.71-Jaccard index). Across landscapes, Nachingwea/Masasi plains and the Coastal zone were strongly similar to Tunduru dissected plain (0.63-1.0-Jaccard index), but strongly dissimilar with the Liwale inland plain (0.67-0.70- Jaccard distance). Furthermore, the presence of greater than 0.5 suitability indices across landscapes were revealed, with Liwale inland plain having strongest suitability index of 0.743 followed by Coastal zone (0.681), Tunduru dissected plain (0.617) and Nachingwea/Masasi plain. Significantly, the habitats had an increase of 0.1 suitability index, and positively correlated with disease prevalence by triggering disease incidence of 13.9% and severity of 31.4%. The study for the first time revealed the presence of an association between disease prevalence and landscape habitat characteristics of southeastern, Tanzania; paving the way to inclusive thinking of habitat as one of the drivers in the prevalence of fusarium wilt disease of cashews. Further research on the genetic coevolution of Fusarium oxysporum across landscapes to strengthen disease risk management in the cashew industry is recommended.

Insights from a comprehensive study of Trypanosoma cruzi: A new mitochondrial clade restricted to North and Central America and genetic structure of TcI in the region

More than 100 years since the first description of Chagas Disease and with over 29,000 new cases annually due to vector transmission (in 2010), American Trypanosomiasis remains a Neglected Tropical Disease (NTD). This study presents the most comprehensive Trypanosoma cruzi sampling in terms of geographic locations and triatomine species analyzed to date and includes both nuclear and mitochondrial genomes. This addresses the gap of information from North and Central America. We incorporate new and previously published DNA sequence data from two mitochondrial genes, Cytochrome oxidase II (COII) and NADH dehydrogenase subunit 1 (ND1). These T. cruzi samples were collected over a broad geographic range including 111 parasite DNA samples extracted from triatomines newly collected across North and Central America, all of which were infected with T. cruzi in their natural environment. In addition, we present parasite reduced representation (Restriction site Associated DNA markers, RAD-tag) genomic nuclear data combined with the mitochondrial gene sequences for a subset of the triatomines (27 specimens) collected from Guatemala and El Salvador. Our mitochondrial phylogenetic reconstruction revealed two of the major mitochondrial lineages circulating across North and Central America, as well as the first ever mitochondrial data for TcBat from a triatomine collected in Central America. Our data also show that within mtTcIII, North and Central America represent an independent, distinct clade from South America, named here as mtTcIII_NA-CA, geographically restricted to North and Central America. Lastly, the most frequent lineage detected across North and Central America, mtTcI, was also an independent, distinct clade from South America, noted as mtTcI_NA-CA. Furthermore, nuclear genome data based on Single Nucleotide Polymorphism (SNP) showed genetic structure of lineage TcI from specimens collected in Guatemala and El Salvador supporting the hypothesis that genetic diversity at a local scale has a geographical component. Our multiscale analysis contributes to the understanding of the independent and distinct evolution of T. cruzi lineages in North and Central America regions.

Neglected Tropical Diseases (NTDs) represents socioeconomic burden in most countries of Latin America. Chagas disease, a NTD, is caused by the parasite Trypanosoma cruzi. The disease can be mild, causing swelling and fever, or it can be long-lasting. Left untreated, it often causes heart failure. This study focused on T. cruzi lineages, emphasizing the gap of information from Central America and complementing what is known in North America. Our diverse collection of kissing bugs from North America (United States and Mexico) and Central America identified two of the major mitochondrial lineages circulating in these regions, both representing distinct clades within the already established three clusters of the T. cruzi parasite (mtTcI-mtTcIII): mtTcI_NA-CA and mtTcIII_NA-CA. At a local scale, population genetic structure of T. cruzi revealed that genetic diversity has a notable geographic component. The important insights into the genetic and evolutionary diversity of T. cruzi in North and Central America provide not only the necessity for referencing genomes to identify lineages but the basis to develop more precise and comprehensive diagnostic assays to better detect T. cruzi infections.

Using urban landscape pattern to understand and evaluate infectious disease risk

COVID-19 case numbers in 161 sub-districts of Wuhan were investigated based on landscape epidemiology, and their landscape metrics were calculated based on land use/land cover (LULC). Initially, a mediation model verified a partially mediated population role in the relationship between landscape pattern and infection number. Adjusted incidence rate (AIR) and community safety index (CSI), two indicators for infection risk in sub-districts, were 25.82∼63.56 ‱ and 3.00∼15.87 respectively, and central urban sub-districts were at higher infection risk. Geographically weighted regression (GWR) performed better than OLS regression with AICc differences of 7.951∼181.261. The adjusted R² in GWR models of class-level index and infection risk were 0.697 to 0.817, while for the landscape-level index they were 0.668 to 0.835. Secondly, 16 key landscape metrics were identified based on GWR, and then a prediction model for infection risk in sub-districts and communities was developed. Using principal component analysis (PCA), development intensity, landscape level, and urban blue-green space were considered to be principal components affecting disease infection risk, explaining 73.1 % of the total variance. Cropland (PLAND and LSI), urban land (NP, LPI, and LSI) and unused land (NP) represent development intensity, greatly affecting infection risk in urban areas. Landscape level CONTAG, DIVISION, SHDI, and SHEI represent mobility and connectivity, having a profound impact on infection risk in both urban and suburban areas. Water (PLAND, NP, LPI, and LSI) and woodland (NP, and LSI) represent urban blue-green spaces, and were particularly important for infection risk in suburban areas. Based on urban landscape pattern, we proposed a framework to understand and evaluate infection risk. These findings provide a basis for risk evaluation and policy-making of urban infectious disease, which is significant for community management and urban planning for infectious disease worldwide.

CHRONIC WASTING DISEASE MODELING: AN OVERVIEW

Chronic wasting disease (CWD) is an infectious and fatal prion disease occurring in the family Cervidae. To update the research community regarding the status quo of CWD epidemic models, we conducted a meta-analysis on CWD research. We collected data from peer-reviewed articles published since 1980, when CWD was first diagnosed, until December 2018. We explored the analytical methods used historically to understand CWD. We used 14 standardized variables to assess overall analytical approaches of CWD research communities, data used, and the modeling methods used. We found that CWD modeling initiated in the early 2000s and has increased since then. Connectivity of the research community was heavily reliant on a cluster of CWD researchers. Studies focused primarily on regression and compartment-based models, population-level approaches, and host species of game management concern. Similarly, CWD research focused on single populations, species, and locations, neglecting modeling using community ecology and biogeographic approaches. Chronic wasting disease detection relied on classic diagnostic methods with limited sensitivity for most stages of infection. Overall, we found that past modeling efforts generated a solid baseline for understanding CWD in wildlife and increased our knowledge on infectious prion ecology. Future analytical efforts should consider more sensitive diagnostic methods to quantify uncertainty and broader scale studies to elucidate CWD transmission beyond population-level approaches. Considering that infectious prions may not follow biological rules of well-known wildlife pathogens (i.e., viruses, bacteria, fungi), assumptions used when modeling other infectious disease may not apply for CWD. Chronic wasting disease is a new challenge in wildlife epidemiology.

A fine scale eco-epidemiological study on endemic visceral leishmaniasis in north ethiopian villages

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We conducted fine-scale eco-epidemiological analyses of factors associated with visceral leishmaniasis transmission.

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The population densities of Phlebotomus orientalis, the vector, were negatively correlated with distance from vertisols.

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Sero-positivity to Ph. orientalis saliva, was found in people living close to vertisol areas.

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Apparent clustering of infections indicates that transmission occurs around houses located close to vertisols.

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Our data suggest that asymptomatic individuals serve as reservoir hosts for anthroponotic transmission inside villages.

Visceral Leishmaniasis (VL) is a disseminated protozoan infection caused by Leishmania donovani that affects almost half a million people annually. In Northern Ethiopia, VL is common in migrant agricultural laborers returning from the lowland sesame fields of Metema and Humera. Recent VL foci have emerged in resident rural populations near the town. In the current study, we evaluate multilevel entomological, epidemiological and ecological factors associated with infection and disease through fine-scale eco-epidemiological analyses in three villages. Satellite images showed that villages constructed in or close to vertisols, were likely to become endemic for VL. Vertisols or black-cotton soil, are characterized by high contents of smectitic clay minerals, which swell when hydrated and shrink upon desiccation, causing extensive deep cracking during the dry season. The population densities of Phlebotomus orientalis, the vector, were negatively correlated with distance from vertisols and persons living close to vertisols were more likely to be bitten by sand flies, as evidenced by sero-positivity to Ph. orientalis saliva. Apparent (albeit non-significant) clustering of VL cases and abundant asymptomatic infections close to vertisols, suggest anthroponotic transmission around houses located close to vertisols. Comparable rates of male and female volunteers, mostly under 15 years of age, were infected with L. donovani but a significantly higher proportion of males succumbed to VL indicating a physiological gender-linked male susceptibility. Our data suggest that the abundant infected persons with high parasitemias who remain asymptomatic, may serve as reservoir hosts for anthroponotic transmission inside villages. Only limited insights on the transmission dynamics of L. donovani were gained by the study of environmental factors such as presence of animals, house structure and vegetation cover.

Application of landscape epidemiology to assess potential public health risk due to poor sanitation

Clear identification of areas vulnerable to waterborne diseases is essential for protecting community health. This is particularly important in developing countries where unsafe disposal of domestic wastewater and limited potable water supply pose potential public health risks. However, data paucity can be a compounding issue. Under these circumstances, landscape epidemiology can be applied as a resource efficient approach for mapping potential disease risk areas associated with poor sanitation. However, in order to realise the full potential offered by this approach, an in-depth understanding of the impact of different classes of an explanatory variable on a target disease and the validity of hotspot analysis using limited datasets is needed. Accordingly, this research study focused on typhoid and diarrhoea incidence with respect to different classes of elevation, flood inundation, land use, soil permeability, population density and rainfall as explanatory variables. An integrated methodology consisting of hot spot analysis and Poisson regression was employed to map potential disease risk areas. The study findings confirmed the significant differences in the influence exerted by the various classes of an explanatory variable in relation to a target disease. The results also confirmed the feasibility of the hotspot analysis for identifying areas vulnerable to the target diseases using a limited dataset. The study outcomes are expected to contribute to creating an in-depth understanding of the relationship between disease prevalence and associated landscape factors for the delineation of disease risk zones in the context of data paucity.

Geophysiology of Wood Frogs: Landscape Patterns of Prevalence of Disease and Circulating Hormone Concentrations across the Eastern Range

One of the major challenges for conservation physiologists is to determine how current or future environmental conditions relate to the health of animals at the population level. In this study, we measured prevalence of disease, mean condition of the body, and mean resting levels of corticosterone and testosterone in a total of 28 populations across the years 2011 and 2012, and correlated these measures of health to climatic suitability of habitat, using estimates from a model of the ecological niche of the wood frog's geographic range. Using the core-periphery hypothesis as a theoretical framework, we predicted a higher prevalence and intensity of infection of Batrachochytrium dendrobatidis (Bd) and ranaviruses, two major amphibian pathogens causing disease, and higher resting levels of circulating corticosterone, an indicator of allostatic load incurred from living in marginal habitats. We found that Bd infections were rare (2% of individuals tested), while infections with ranavirus were much more common: ranavirus-infected individuals were found in 92% of ponds tested over the 2 years. Contrary to our predictions, rates of infection with ranaviruses were positively correlated with quality of the habitat with the highest prevalence at the core of the range, and plasma corticosterone concentrations measured when frogs were at rest were not correlated with quality of the habitat, the prevalence of ranavirus, or the intensity of infection. Prevalence and mean viral titers of ranavirus infection were higher in 2012 than in 2011, which coincided with lower levels of circulating corticosterone and testosterone and an extremely early time of breeding due to relatively higher temperatures during the winter. In addition, the odds of having a ranavirus infection increased with decreased body condition, and if animals had an infection, viral titers were positively correlated to levels of circulating testosterone concentration. By resolving these patterns, experiments can be designed to test hypotheses about the mechanisms that produce them, such as whether transmission of the ranavirus and tolerance of the host are greater or whether virulence is lower in populations within core habitats. While there is debate about which metrics serve as the best bioindicators of population health, the findings of this study demonstrate the importance of long-term monitoring of multiple physiological parameters to better understand the dynamic relationship between the environment and the health of wildlife populations over space and time.