A generalized framework for estimating snakebite underreporting using statistical models: A study in Colombia.

BACKGROUND: Snakebite envenoming is a neglected tropical disease affecting deprived populations, and its burden is underestimated in some regions where patients prefer using traditional medicine, case reporting systems are deficient, or health systems are inaccessible to at-risk populations. Thus, the development of strategies to optimize disease management is a major challenge. We propose a framework that can be used to estimate total snakebite incidence at a fine political scale. METHODOLOGY/PRINCIPAL FINDINGS: First, we generated fine-scale snakebite risk maps based on the distribution of venomous snakes in Colombia. We then used a generalized mixed-effect model that estimates total snakebite incidence based on risk maps, poverty, and travel time to the nearest medical center. Finally, we calibrated our model with snakebite data in Colombia from 2010 to 2019 using the Markov-chain-Monte-Carlo algorithm. Our results suggest that 10.19% of total snakebite cases (532.26 yearly envenomings) are not reported and these snakebite victims do not seek medical attention, and that populations in the Orinoco and Amazonian regions are the most at-risk and show the highest percentage of underreporting. We also found that variables such as precipitation of the driest month and mean temperature of the warmest quarter influences the suitability of environments for venomous snakes rather than absolute temperature or rainfall. CONCLUSIONS/SIGNIFICANCE: Our framework permits snakebite underreporting to be estimated using data on snakebite incidence and surveillance, presence locations for the most medically significant venomous snake species, and openly available information on population size, poverty, climate, land cover, roads, and the locations of medical centers. Thus, our algorithm could be used in other countries to estimate total snakebite incidence and improve disease management strategies; however, this framework does not serve as a replacement for a surveillance system, which should be made a priority in countries facing similar public health challenges.

Estimating and forecasting the burden and spread of Colombia's SARS-CoV2 first wave.

Following the rapid dissemination of COVID-19 cases in Colombia in 2020, large-scale non-pharmaceutical interventions (NPIs) were implemented as national emergencies in most of the country's municipalities, starting with a lockdown on March 20th, 2020. Recently, approaches that combine movement data (measured as the number of commuters between units), metapopulation models to describe disease dynamics subdividing the population into Susceptible-Exposed-Asymptomatic-Infected-Recovered-Diseased and statistical inference algorithms have been pointed as a practical approach to both nowcast and forecast the number of cases and deaths. We used an iterated filtering (IF) framework to estimate the model transmission parameters using the reported data across 281 municipalities from March to late October in locations with more than 50 reported deaths and cases in Colombia. Since the model is high dimensional (6 state variables in every municipality), inference on those parameters is highly non-trivial, so we used an Ensemble-Adjustment-Kalman-Filter (EAKF) to estimate time variable system states and parameters. Our results show the model's ability to capture the characteristics of the outbreak in the country and provide estimates of the epidemiological parameters in time at the national level. Importantly, these estimates could become the base for planning future interventions as well as evaluating the impact of NPIs on the effective reproduction number ([Formula: see text]) and the critical epidemiological parameters, such as the contact rate or the reporting rate. However, our forecast presents some inconsistency as it overestimates the deaths for some locations as Medellín. Nevertheless, our approach demonstrates that real-time, publicly available ensemble forecasts can provide short-term predictions of reported COVID-19 deaths in Colombia. Therefore, this model can be used as a forecasting tool to evaluate disease dynamics and aid policymakers in infectious outbreak management and control.

Disentangling snakebite dynamics in Colombia: How does rainfall and temperature drive snakebite temporal patterns?

The role of climate driving zoonotic diseases' population dynamics has typically been addressed via retrospective analyses of national aggregated incidence records. A central question in epidemiology has been whether seasonal and interannual cycles are driven by climate variation or generated by socioeconomic factors. Here, we use compartmental models to quantify the role of rainfall and temperature in the dynamics of snakebite, which is one of the primary neglected tropical diseases. We took advantage of space-time datasets of snakebite incidence, rainfall, and temperature for Colombia and combined it with stochastic compartmental models and iterated filtering methods to show the role of rainfall-driven seasonality modulating the encounter frequency with venomous snakes. Then we identified six zones with different rainfall patterns to demonstrate that the relationship between rainfall and snakebite incidence was heterogeneous in space. We show that rainfall only drives snakebite incidence in regions with marked dry seasons, where rainfall becomes the limiting resource, while temperature does not modulate snakebite incidence. In addition, the encounter frequency differs between regions, and it is higher in regions where Bothrops atrox can be found. Our results show how the heterogeneous spatial distribution of snakebite risk seasonality in the country may be related to important traits of venomous snakes' natural history.

Measuring spatial co-occurrences of species potentially involved in Leishmania transmission cycles through a predictive and fieldwork approach.

The Leishmaniases are a group of neglected tropical diseases caused by different species of the protozoan parasite Leishmania, transmitted to its mammalian hosts by the bites of several species of female Phlebotominae sand flies. Many factors have contributed to shifts in the disease distribution and eco epidemiological outcomes, resulting in the emergence of Cutaneous Leishmaniasis outbreaks and the incrimination of vectors in unreported regions. New research development is vital for establishing the new paradigms of the present transmission cycles, hoping to facilitate new control strategies to reduce parasite transmission. Hereafter, this work aims to model and infer the current transmission cycles of Cutaneous Leishmaniasis in Colombia defined by vector and mammal species distributed and interacting in the different regions and validate them by performing sand fly and mammal collections. Vector-host co-occurrences were computed considering five ecoregions of the Colombian territory defined by the World Wide Fund for Nature (WWF) and downloaded from The Nature Conservancy TNC Maps website. Four validation sites were selected based on Cutaneous Leishmaniasis prevalence reports. Sand flies and mammals captured in the field were processed, and species were defined using conventional taxonomic guidelines. Detection of infection by Leishmania was performed to identify transmission cycles in the selected areas. This study uses predictive models based on available information from international gazetteers and fieldwork to confirm sand fly and mammalian species' sustaining Leishmania transmission cycles. Our results show an uneven distribution of mammal samples in Colombia, possibly due to sampling bias, since only two departments contributed 50% of the available samples. Bats were the vertebrates with the highest score values, suggesting substantial spatial overlap with sand flies than the rest of the vertebrates evaluated. Fieldwork allowed identifying three circulating Leishmania species, isolated from three sand fly species. In the Montane Forest ecosystem, one small marsupial, Gracilinanus marica, was found infected with Leishmania panamensis, constituting the first record of this species infected with Leishmania. In the same locality, an infected sand fly, Pintomyia pia, was found. The overall results could support the understanding of the current transmission cycles of Leishmaniasis in Colombia.

Diversity patterns, Leishmania DNA detection, and bloodmeal identification of Phlebotominae sand flies in villages in northern Colombia.

Leishmaniases are neglected tropical diseases exhibiting complex transmission cycles due to the number of parasite species circulating, sand fly species acting as vectors and infected mammals, including humans, which are defined in the New World as accidental hosts. However, current transmission scenarios are changing, and the disease is no longer exclusively related to forested areas but urban transmission foci occur, involving some species of domestic animals as suspected reservoirs. The aim of this study was to determine the transmission cycles in urban environments by evaluating sand fly diversity, detection of Leishmania DNA, and bloodmeal sources through intra and peridomestic collections. The study was carried out in Colombia, in 13 municipalities of Cordoba department, implementing a methodology that could be further used for the evaluation of vector-borne diseases in villages or towns. Our sampling design included 24 houses randomly selected in each of 15 villages distributed in 13 municipalities, which were sampled in two seasons in 2015 and 2016. Sand flies were collected using CDC light traps placed in intra and peridomestic habitats. In addition to the morphological identification, molecular identification through DNA barcodes was also performed. A total of 19,743 sand flies were collected and 13,848 of them (10,268 females and 3,580 males) were used in molecular procedures. Circulation of two known parasite species-Leishmania infantum and Leishmania panamensis was confirmed. Blood source analyses showed that sand flies fed on humans, particularly in the case of the known L. infantum vector, P. evansi; further analyses are advised to evaluate the reservoirs involved in parasite transmission. Our sampling design allowed us to evaluate potential transmission cycles on a department scale, by defining suspected vector species, parasite species present in different municipalities and feeding habits.

Using agent based modeling to assess the effect of increased Bus Rapid Transit system infrastructure on walking for transportation.

The effect of transport infrastructure on walking is of interest to researchers because it provides an opportunity, from the public policy point of view, to increase physical activity (PA). We use an agent based model (ABM) to examine the effect of transport infrastructure on walking. Particular relevance is given to assess the effect of the growth of the Bus Rapid Transit (BRT) system in Bogotá on walking. In the ABM agents are assigned a home, work location, and socioeconomic status (SES) based on which they are assigned income for transportation. Individuals must decide between the available modes of transport (i.e., car, taxi, bus, BRT, and walking) as the means of reaching their destination, based on resources and needed travel time. We calibrated the model based on Bogota's 2011 mobility survey. The ABM results are consistent with previous empirical findings, increasing BRT access does indeed increase the number of minutes that individuals walk for transportation, although this effect also depends on the availability of other transport modes. The model indicates a saturation process: as more BRT lanes are added, the increment in minutes walking becomes smaller, and eventually the walking time decreases. Our findings on the potential contribution of the expansion of the BRT system to walking for transportation suggest that ABMs may prove helpful in designing policies to continue promoting walking.

TransMilenio, a Scalable Bus Rapid Transit System for Promoting Physical Activity.

Transport systems can play an important role in increasing physical activity (PA). Bogotá has been recognized for its bus rapid transit (BRT) system, TransMilenio (TM). To date, BRTs have been implemented in over 160 cities worldwide. The aim of this study was to assess the association between PA and the use of TM among adults in Bogotá. The study consists of a cross-sectional study conducted from 2010 to 2011 with 1000 adults. PA was measured using the International Physical Activity Questionnaire. In a subsample of 250 adults, PA was objectively measured using ActiGraph accelerometers. Analyses were conducted using multilevel logistic regression models. The use of TM was associated with meeting moderate-to-vigorous PA (MVPA). TM users were more likely to complete an average of >22 min a day of MVPA (odds ratio [OR] = 3.1, confidence interval [CI] = 95 % 1.4-7.1) and to walk for transportation for ≥150 min per week (OR = 1.5; CI = 95 % 1.1-2.0). The use of TM was associated with 12 or more minutes of MVPA (95 % CI 4.5-19.4, p < 0.0001). Associations between meeting PA recommendations and use of TM did not differ by socioeconomic status (p value = 0.106) or sex (p value = 0.288). The use of TM is a promising strategy for enhancing public health efforts to reduce physical inactivity through walking for transport. Given the expansion of BRTs, these results could inform the development of transport PA programs in low- to high-income countries.

Spatial Distribution of Sand Fly Vectors and Eco-Epidemiology of Cutaneous Leishmaniasis Transmission in Colombia.

BACKGROUND: Leishmania is transmitted by Phlebotominae insects that maintain the enzootic cycle by circulating between sylvatic and domestic mammals; humans enter the cycles as accidental hosts due to the vector's search for blood source. In Colombia, leishmaniasis is an endemic disease and 95% of all cases are cutaneous (CL), these cases have been reported in several regions of the country where the intervention of sylvatic areas by the introduction of agriculture seem to have an impact on the rearrangement of new transmission cycles. Our study aimed to update vector species distribution in the country and to analyze the relationship between vectors' distribution, climate, land use and CL prevalence. METHODS: A database with geographic information was assembled, and ecological niche modeling was performed to explore the potential distribution of each of the 21 species of medical importance in Colombia, using thirteen bioclimatic variables, three topographic and three principal components derived from NDVI. Binary models for each species were obtained and related to both land use coverage, and a CL prevalence map with available epidemiological data. Finally, maps of species potential distribution were summed to define potential species richness in the country. RESULTS: In total, 673 single records were obtained with Lutzomyia gomezi, Lutzomyia longipalpis, Psychodopygus panamensis, Psathyromyia shannoni and Pintomyia evansi the species with the highest number of records. Eighteen species had significant models, considering the area under the curve and the jackknife results: L. gomezi and P. panamensis had the widest potential distribution. All sand fly species except for Nyssomyia antunesi are mainly distributed in regions with rates of prevalence between 0.33 to 101.35 cases per 100,000 inhabitants and 76% of collection data points fall into transformed ecosystems. DISCUSSION: Distribution ranges of sand flies with medical importance in Colombia correspond predominantly to disturbed areas, where the original land coverage is missing therefore increasing the domiciliation potential. We highlight the importance of the use of distribution maps as a tool for the development of strategies for prevention and control of diseases.

New scenarios of Trypanosoma cruzi transmission in the Orinoco region of Colombia

Rhodnius prolixus, a blood-sucking triatomine with domiciliary anthropophilic habits, is the main vector of Chagas disease. The current paradigm of Trypanosoma cruzi transmission in Columbia includes a sylvatic and domiciliary cycle co-existing with domestic and sylvatic populations of reservoirs. The aim of this study is to evaluate the population densities and relative abundance of triatomines and mammals that may be involved in the sylvatic cycle of Chagas disease to clarify the epidemiological scenario in an endemic area in the province of Casanare. Insect vectors on Attalea butyracea palms were captured using both manual searches and bait traps. The capture of mammals was performed using Sherman and Tomahawk traps. We report an infestation index of 88.5% in 148 palms and an index of T. cruzi natural infection of 60.2% in 269 dissected insects and 11.9% in 160 captured mammals. High population densities of triatomines were observed in the sylvatic environment and there was a high relative abundance of reservoirs in the area, suggesting a stable enzootic cycle. We found no evidence of insect domiciliation. Taken together, these observations suggest that eco-epidemiological factors shape the transmission dynamics of T. cruzi, creating diverse scenarios of disease transmission.

New scenarios of Trypanosoma cruzi transmission in the Orinoco region of Colombia.

Rhodnius prolixus, a blood-sucking triatomine with domiciliary anthropophilic habits, is the main vector of Chagas disease. The current paradigm of Trypanosoma cruzi transmission in Columbia includes a sylvatic and domiciliary cycle co-existing with domestic and sylvatic populations of reservoirs. The aim of this study is to evaluate the population densities and relative abundance of triatomines and mammals that may be involved in the sylvatic cycle of Chagas disease to clarify the epidemiological scenario in an endemic area in the province of Casanare. Insect vectors on Attalea butyracea palms were captured using both manual searches and bait traps. The capture of mammals was performed using Sherman and Tomahawk traps. We report an infestation index of 88.5% in 148 palms and an index of T. cruzi natural infection of 60.2% in 269 dissected insects and 11.9% in 160 captured mammals. High population densities of triatomines were observed in the sylvatic environment and there was a high relative abundance of reservoirs in the area, suggesting a stable enzootic cycle. We found no evidence of insect domiciliation. Taken together, these observations suggest that eco-epidemiological factors shape the transmission dynamics of T. cruzi, creating diverse scenarios of disease transmission.