A multidisciplinary approach to analyze the antimicrobial resistance in natural ecosystems.

Antimicrobial Resistance (AMR) poses a global threat to both human health and environmental well-being. Our study delved into Costa Rican wildlife reserves, uncovering a substantial human impact on these ecosystems and underscoring the imperative to pinpoint AMR hotspots. Embracing a One Health perspective, we advocated for a comprehensive landscape analysis that intricately intertwined geographic, climatic, forest, and human factors. This study illuminated the link between laboratory results and observed patterns of antimicrobial use, thereby paving the way for sustainable solutions. Our innovative methodology involved deploying open-ended questions to explore antimicrobial usage across livestock activities, contributing to establishing a comprehensive methodology. Non-invasive sampling in wildlife emerged as a critical aspect, shedding light on areas contaminated by AMR. Feline species, positioned at the apex of the food chain, acted as sentinels for environmental health due to heightened exposure to improperly disposed waste. Regarding laboratory findings, each sample revealed the presence of at least one antimicrobial resistance gene (ARG). Notably, genes encoding resistance to tetracyclines dominated (94.9%), followed by beta-lactams (75.6%), sulfonamides (53.8%), aminoglycosides (51.3%), quinolones (44.9%), phenicols (25.6%), and macrolides (20.5%). Genes encoding polymyxins were not detected. Moreover, 66% of samples carried a multi-resistant microbiome, with 15% exhibiting resistance to three antimicrobial families and 51% to four. The absence of a correlation between forest coverage and ARG presence underscored the profound human impact on wildlife reserves, surpassing previous estimations. This environmental pressure could potentially modify microbiomes and resistomes in unknown ways. As not all antimicrobial families encoding ARGs were utilized by farmers, our next step involved evaluating other human activities to identify the primary sources of contamination. This comprehensive study contributed crucial insights into the intricate dynamics of AMR in natural ecosystems, paving the way for targeted interventions and sustainable coexistence.

IDENTIFICATION OF ANTHROPOGENIC IMPACT ON NATURAL HABITATS BY ANTIMICROBIAL RESISTANCE QUANTIFICATION IN TWO NEOTROPICAL WILD CATS AND THEIR GEOSPATIAL ANALYSIS.

Human activities such as habitat degradation and fragmentation threaten biodiversity in Neotropical areas. This work proposes an analytical methodology to identify natural areas in Central America with anthropogenic impact, analyzing the presence of antimicrobial resistance genes (ARGs) in accordance with their theoretical relationship with human-related activities. Sixteen ARGs were quantified in feces of different individuals of 13 jaguars (Panthera onca) and 13 pumas (Puma concolor) in three conservation areas in Costa Rica by real-time PCR. At least one ARG was detected in all samples. Of the ARGs encoding tetracycline resistance, the most frequent were tetQ and tetY (85% and 69%, respectively). The sulfonamides (sulI and sulII; 69% each), phenicols (catI and catII; 19% and 54%, respectively), and quinolones (qnrS; 12%) were also detected. The presence of human settlements, livestock farms (pigs, cattle, and poultry), roads, human health centers, flood zones, and rivers were identified within each area to generate an index of human activity. We found no difference between the presence of ARG by roads, agricultural activities, and human settlements (P>0.05). However, tetW showed higher percentages with porcine and bovine farms; both tetY and tetW were more frequent in jaguars than in pumas. Of concern is that many of the most contaminated samples were taken from national parks, such as Braulio Carrillo and Tortuguero, where animals should not have direct contact with humans.

Human disturbance and shifts in vertebrate community composition in a biodiversity hotspot.

Understanding how human modification of the landscape shapes vertebrate community composition is vital to understanding the current status and future trajectory of wildlife. Using a participatory approach, we deployed the largest camera-trap network in Mesoamerica to date to investigate how anthropogenic disturbance shapes the occupancy and co-occurrence of terrestrial vertebrate species in a tropical biodiversity hotspot: the Osa Peninsula, Costa Rica. We estimated species richness in different categories of land protection with rarefaction analysis and estimated the expected occupancy with a joint species distribution model that included covariates for anthropogenic disturbance, land protection, habitat quality, and habitat availability. Areas with the most stringent land-use protections (e.g., Corcovado National Park, 24 species [95% CI 23-25]) harbored significantly more species than unprotected areas (20 species [19.7-20.3]), mainly due to a reduced presence of large-bodied species of conservation concern in unprotected areas (e.g., jaguar Panthera onca and white-lipped peccary Tayassu pecari). Small-bodied generalist species, such as opossums (Didelphidae) and armadillos (Dasypus novemcinctus), in contrast, were more common at disturbed sites, resulting in a significant difference in vertebrate community composition between sites with low and high disturbance. Co-occurrence of species was also mainly associated with response to disturbance. Similar responses to disturbance create two groups of species, those whose site-level occupancy usually increased as anthropogenic disturbance increased and those whose estimated occupancy decreased. The absence of large-bodied species entails an important loss of ecological function in disturbed areas and can hinder forest development and maintenance. Efforts to protect and restore forested landscapes are likely having a positive effect on the abundance of some threatened species. These efforts, however, must be sustained and expanded to increase connectivity and ensure the long-term viability of the wildlife community.

Perturbaciones Humanas y Cambios en la Composición de la Comunidad de Vertebrados en un Punto Caliente de Biodiversidad Resumen El entendimiento de cómo las modificaciones humanas del paisaje conforman la composición de las comunidades de vertebrados es vital para entender el estado actual y la trayectoria futura de la fauna. Mediante una estrategia participativa, desplegamos la mayor red de cámaras trampa en Mesoamérica hasta la fecha para investigar cómo la perturbación antropogénica determina la ocupación y coocurrencia de las especies terrestres de vertebrados en un punto caliente de biodiversidad tropical: la Península de Osa, Costa Rica. Estimamos la riqueza de especies en diferentes categorías de protección de suelo con un análisis de rarefacción y estimamos la ocupación esperada con un modelo de distribución conjunta de especies que incluyó covariables para la perturbación antropogénica, la protección del suelo, la calidad del hábitat y la disponibilidad del hábitat. Las áreas con la protección más estricta de uso de suelo (p. ej.: Parque Nacional Corcovado, 24 especies [95% CI 23-25]) albergaron significativamente a más especies que las áreas desprotegidas (20 especies [19.7-20.3]), principalmente debido a la presencia reducida de especies de talla grande de interés para la conservación en las áreas desprotegidas (p. ej.: el jaguar Panthera onca, el pecarí de labios blancos, Tayassu pecari). Al contrario, las especies generalistas de talla pequeña, como las zarigüeyas (Didelphidae) y el armadillo (Dasypus novemcinctus) fueron más comunes en los sitios perturbados, lo que resulta en una diferencia significativa en la composición de las comunidades de vertebrados entre los sitios con una perturbación baja y alta. La coocurrencia de especies también estuvo asociada principalmente con la respuesta a la perturbación. Las respuestas similares a la perturbación crean dos grupos de especies: aquellas cuya ocupación a nivel de sitio generalmente incrementó conforme incrementó la perturbación antropogénica y aquellas cuya ocupación estimada disminuyó. La ausencia de especies de talla grande conlleva una pérdida importante de la función ecológica en las áreas perturbadas y puede dificultar el desarrollo y mantenimiento del bosque. Los esfuerzos para proteger y restaurar los paisajes forestales probablemente estén teniendo un efecto positivo sobre la abundancia de algunas especies amenazadas. Estos esfuerzos, sin embargo, deben ser sostenidos y expandidos para incrementar la conectividad y asegurar la viabilidad a largo plazo de la comunidad faunística.

Forest cover mediates large and medium-sized mammal occurrence in a critical link of the Mesoamerican Biological Corridor.

Connectivity of natural areas through biological corridors is essential for ecosystem resilience and biodiversity conservation. However, robust assessments of biodiversity in corridor areas are often hindered by logistical constraints and the statistical challenges of modeling data from multiple species. Herein, we used a hierarchical community occupancy model in a Bayesian framework to evaluate the status of medium and large-sized mammals in a critical link of the Mesoamerican Biological Corridor (MBC) in Costa Rica. We used camera traps deployed from 2013-2017 to detect 18 medium (1-15 kg) and 6 large (>15 kg) mammal species in a portion of two Jaguar Conservation Units (JCUs) and the Corridor linking them. Camera traps operated for 16,904 trap nights across 209 stations, covering an area of 880 km2. Forest cover was the most important driver of medium and large-sized mammal habitat use, with forest specialists such as jaguars (Panthera onca) and pumas (Puma concolor) strongly associated with high forest cover, while habitat generalists such as coyotes (Canis latrans) and raccoons (Procyon lotor) were associated with low forest cover. Medium and large-sized mammal species richness was lower in the Corridor area ([Formula: see text] = 9.78±1.84) than in the portions evaluated of the two JCUs ([Formula: see text] = 11.50±1.52). Puma and jaguar habitat use probabilities were strongly correlated with large prey species richness (jaguar, r = 0.59, p<0.001; puma, r = 0.72, p<0.001), and correlated to a lesser extent with medium prey species richness (jaguar, r = 0.36, p = 0.003; puma, r = 0.23, p = 0.064). Low estimated jaguar habitat use probability in one JCU (Central Volcanic Cordillera: [Formula: see text] = 0.15±0.11) suggests that this is not the jaguar stronghold previously assumed. In addition, the western half of the Corridor has low richness of large mammals, making it necessary to take urgent actions to secure habitat connectivity for mammal populations.

Estimating large carnivore populations at global scale based on spatial predictions of density and distribution - Application to the jaguar (Panthera onca).

Broad scale population estimates of declining species are desired for conservation efforts. However, for many secretive species including large carnivores, such estimates are often difficult. Based on published density estimates obtained through camera trapping, presence/absence data, and globally available predictive variables derived from satellite imagery, we modelled density and occurrence of a large carnivore, the jaguar, across the species' entire range. We then combined these models in a hierarchical framework to estimate the total population. Our models indicate that potential jaguar density is best predicted by measures of primary productivity, with the highest densities in the most productive tropical habitats and a clear declining gradient with distance from the equator. Jaguar distribution, in contrast, is determined by the combined effects of human impacts and environmental factors: probability of jaguar occurrence increased with forest cover, mean temperature, and annual precipitation and declined with increases in human foot print index and human density. Probability of occurrence was also significantly higher for protected areas than outside of them. We estimated the world's jaguar population at 173,000 (95% CI: 138,000-208,000) individuals, mostly concentrated in the Amazon Basin; elsewhere, populations tend to be small and fragmented. The high number of jaguars results from the large total area still occupied (almost 9 million km2) and low human densities (< 1 person/km2) coinciding with high primary productivity in the core area of jaguar range. Our results show the importance of protected areas for jaguar persistence. We conclude that combining modelling of density and distribution can reveal ecological patterns and processes at global scales, can provide robust estimates for use in species assessments, and can guide broad-scale conservation actions.

Impact of jaguar Panthera onca (Carnivora: Felidae) predation on marine turtle populations in Tortuguero, Caribbean coast of Costa Rica.

Little is known about the effects of jaguars on the population of marine turtles nesting in Tortuguero National Park, Costa Rica. This study assessed jaguar predation impact on three species of marine turtles (Chelonia mydas, Dermochelys coriacea and Eretmochelys imbricata) that nest in Tortuguero beach. Jaguar predation data was obtained by using two methodologies, literature review (historical records prior the year 2005) and weekly surveys along the 29 km stretch of beach during the period 2005-2013. Our results indicated that jaguar predation has increased from one marine turtle in 1981 to 198 in 2013. Jaguars consumed annually an average of 120 (SD = 45) and 2 (SD = 3) green turtles and leatherbacks in Tortuguero beach, respectively. Based on our results we concluded that jaguars do not represent a threat to the population of green turtles that nest in Tortuguero beach, and it is not the main cause for population decline for leatherbacks and hawksbills. Future research should focus on continuing to monitor this predator-prey relationship as well as the factors that influence it so the proper management decisions can be taken.

Impact of jaguar Panthera onca(Carnívora: Felidae) predation on marine turtle populations in Tortuguero, Caribbean coast of Costa Rica / Efecto de la depredación por jaguares, Panthera onca (Carnívora: Felidae), sobre las poblaciones de tortugas marinas de Tortuguero, costa caribeña de Costa Rica

Little is known about the effects of jaguars on the population of marine turtles nesting in Tortuguero National Park, Costa Rica. This study assessed jaguar predation impact on three species of marine turtles (Chelonia mydas, Dermochelys coriáceaand Eretmochelys imbricata)that nest in Tortuguero beach. Jaguar predation data was obtained by using two methodologies, literature review (historical records prior the year 2005) and weekly surveys along the 29 km stretch of beach during the period 2005-2013. Our results indicated that jaguar predation has increased from one marine turtle in 1981 to 198 in 2013. Jaguars consumed annually an average of 120 (SD= 45) and 2 (SD= 3) green turtles and leatherbacks in Tortuguero beach, respectively. Based on our results we concluded that jaguars do not represent a threat to the population of green turtles that nest in Tortuguero beach, and it is not the main cause for population decline for leatherbacks and hawksbills. Future research should focus on continuing to monitor this predator-prey relationship as well as the factors that influence it so the proper management decisions can be taken.

Existe poco conocimiento sobre el impacto que tienen los jaguares sobre las tortugas marinas que anidan en el Parque Nacional Tortuguero, Costa Rica. Este estudio evaluó el impacto de la depredación de jaguar sobre tres especies de tortugas marinas (Chelonia mydas, Dermo-chelys coriáceay Eretmochelys imbricata)que anidan en Tortuguero. Los reportes de depredación fueron obtenidos empleando dos metodologías, revisión literaria (eventos registrados antes del 2005) y monitoreos semanales a lo largo de la playa (durante el periodo 2005-2013). La depredación del jaguar se ha incrementado de una tortuga en 1981 a 198 tortugas en 2013. Asimismo, los jaguares consumieron anualmente un promedio de 120 (SD= 45) y 2 (SD= 3) tortugas verdes y tortugas baula en Tortugue-ro, respectivamente. Nuestros resultados indican que los jaguares no representan una amenaza para la población de tortugas verdes que anida en Tortuguero, y no son la causa principal de la disminución poblacional de la tortuga baula y carey. No obstante, se recomienda continuar con el monitoreo con el fin de entender cómo esta interacción depredador-presa evolucionará en el futuro.

Habitat features influencing jaguar Panthera onca (Carnivora: Felidae) occupancy in Tortuguero National Park, Costa Rica / Características del hábitat que influyen en la presencia del jaguar Panthera onca (Carnivora: Felidae) en el Parque Nacional Tortuguero, Costa Rica

Habitat characteristics and human activities are known to play a major role in the occupancy of jaguars Panthera onca across their range, however the key variables influencing jaguar distribution in Tortuguero National Park, Costa Rica, have yet to be identified. This study evaluated jaguar occupancy in Tortuguero National Park and the surrounding area. Jaguar detection/non-detection data was collected using digital camera traps distributed within the boundaries of the protected area. Local community members were also interviewed to determine jaguar occurrence in the Park’s buffer zone. Occupancy models were then applied to identify the habitat characteristics that may better explain jaguar distribution across the study area. From June 2012 to June 2013, a total of 4 339 camera trap days were used to identify 18 individual jaguars inside the protected area; 17 of these jaguars were exclusively detected within the coastal habitat, whilst the remaining individual was detected solely within the interior of the Park. Interviewees reported 61 occasions of jaguar presence inside the buffer zone, between 1995 and 2013, with 80% of these described by the communities of Lomas de Sierpe, Barra de Parismina and La Aurora. These communities also reported the highest levels of livestock predation by jaguars (85% of attacks). In the study area, jaguar occurrence was positively correlated with the seasonal presence of nesting green turtles Chelonia mydas, and negatively correlated with distance to the Park boundary. Our findings suggested that the current occupancy of the jaguar in the study area may be a response to: 1) the vast availability of prey (marine turtles) on Tortuguero beach, 2) the decline of its primary prey species as a result of illegal hunting inside the Park, and 3) the increase in anthropogenic pressures in the Park boundaries. Rev. Biol. Trop. 62 (4): 1449-1458. Epub 2014 December 01.

Las características del hábitat y las actividades humanas juegan un papel importante en la presencia del jaguar Panthera onca en toda su área de distribución, sin embargo, las variables clave que influyen en la distribución del jaguar en el Parque Nacional Tortuguero, Costa Rica, aún no se han identificado. Por lo tanto se evaluó la presencia del jaguar Panthera onca en este parque nacional y su área de amortiguamiento. Se recolectaron datos de detección/no detección del jaguar mediante cámaras trampa ubicadas dentro del parque, y se realizaron encuestas en las comunidades del área de amortiguamiento. Posteriormente, se emplearon modelos de ocupación para identificar los atributos del hábitat que mejor explicaban la presencia del felino en el área. Se identificaron 18 jaguares dentro del parque, de los cuales 17 estuvieron exclusivamente en el hábitat costero. En el área de amortiguamiento, las comunidades con una mayor presencia del felino (Lomas de Sierpe, Barra de Parismina y La Aurora) coincidieron con las zonas más conflictivas, en relación a la cacería y la depredación de jaguar sobre el ganado. La probabilidad de ocupación del jaguar se incrementa a medida que aumenta la presencia de la tortuga verde Chelonia mydas, y disminuye conforme la distancia al límite del parque se incrementa. Nuestros resultados indican que la actual presencia del jaguar se debe a: 1) la alta disponibilidad de presas (tortugas marinas) en el hábitat costero, 2) la disminución de las principales especies presa como resultado de la cacería y 3) al incremento de las actividades humanas en el área de amortiguamiento del parque.

Habitat features influencing jaguar Panthera onca (Carnivora: Felidae) occupancy in Tortuguero National Park, Costa Rica.

Habitat characteristics and human activities are known to play a major role in the occupancy of jaguars Panthera onca across their range, however the key variables influencing jaguar distribution in Tortuguero National Park, Costa Rica, have yet to be identified. This study evaluated jaguar occupancy in Tortuguero National Park and the surrounding area. Jaguar detection/non-detection data was collected using digital camera traps distributed within the boundaries of the protected area. Local community members were also interviewed to determine jaguar occurrence in the Park's buffer zone. Occupancy models were then applied to identify the habitat characteristics that may better explain jaguar distribution across the study area. From June 2012 to June 2013, a total of 4,339 camera trap days were used to identify 18 individual jaguars inside the protected area; 17 of these jaguars were exclusively detected within the coastal habitat, whilst the remaining individual was detected solely within the interior of the Park. Interviewees reported 61 occasions of jaguar presence inside the buffer zone, between 1995 and 2013, with 80% of these described by the communities of Lomas de Sierpe, Barra de Parismina and La Aurora. These communities also reported the highest levels of livestock predation by jaguars (85% of attacks). In the study area, jaguar occurrence was positively correlated with the seasonal presence of nesting green turtles Chelonia mydas, and negatively correlated with distance to the Park boundary. Our findings suggested that the current occupancy of the jaguar in the study area may be a response to: 1) the vast availability of prey (marine turtles) on Tortuguero beach, 2) the decline of its primary prey species as a result of illegal hunting inside the Park, and 3) the increase in anthropogenic pressures in the Park boundaries.