@article{deb_jara_lanzas_2023, title={Early evaluation of the Food and Drug Administration (FDA) guidance on antimicrobial use in food animals on antimicrobial resistance trends reported by the National Antimicrobial Resistance Monitoring System (2012-2019)}, volume={17}, ISSN={["2352-7714"]}, url={http://europepmc.org/abstract/med/37448772}, DOI={10.1016/j.onehlt.2023.100580}, abstractNote={Antimicrobial resistance (AMR) is one of the biggest challenges to global public health. To address this issue in the US, governmental agencies have implemented system-wide guidance frameworks and recommendations aimed at reducing antimicrobial use. In particular, the Food and Drug Administration (FDA) prohibited the extra-label use of cephalosporins in food animals in 2012 and issued the guidance for industry (GFI) #213 about establishing a framework to phase out the use of all medically relevant drugs for growth promotion in 2012. Also in 2015, the FDA implemented veterinary feed directive (VFD) drug regulations (GFI# 120) to control the use of certain antimicrobials. To assess the potential early effects of these FDA actions and other concurrent antimicrobial stewardship actions on AMR in the food chain, we compared the patterns of the phenotypic (minimum inhibitory concentration (MIC) and percentage of resistance) and genotypic resistances for selected antimicrobials before and after 2016 across different enteric pathogen species, as reported by the National Antimicrobial Resistance Monitoring System (NARMS). Most of the antimicrobials analyzed at the phenotypic level followed a downward trend in MIC after implementing the guidance. Although, most of those changes were less than one 1-fold dilution. On the other hand, compared to MIC results, the results based on phenotypic resistance prevalence evidenced higher differences in both directions between the pre- and post-guidance implementation period. Also, we did not find relevant differences in the presence of AMR genes between pre- and post-VFD drug regulations. We concluded that the FDA guidance on antimicrobial use has not led to substantial reductions in antimicrobial drug resistance yet.}, journal={ONE HEALTH}, author={Deb, Liton Chandra and Jara, Manuel and Lanzas, Cristina}, year={2023}, month={Dec} }
 @article{janouskova_rokhsar_jara_entezami_horton_dias_machado_prada_2023, title={Quantifying Spillover Risk with an Integrated Bat-Rabies Dynamic Modeling Framework}, volume={2023}, ISSN={["1865-1682"]}, url={https://doi.org/10.1155/2023/2611577}, DOI={10.1155/2023/2611577}, abstractNote={Vampire bat-transmitted rabies has recently become the leading cause of rabies mortality in both humans and livestock in Latin America. Evaluating risk of transmission from bats to other animal species has thus become a priority in the region. An integrated bat-rabies dynamic modeling framework quantifying spillover risk to cattle farms was developed. The model is spatially explicit and is calibrated to the state of São Paulo, using real roost and farm locations. Roost and farm characteristics, as well as environmental data through an ecological niche model, are used to modulate rabies transmission. Interventions aimed at reducing risk in roosts (such as bat culling or vaccination) and in farms (cattle vaccination) were considered as control strategies. Both interventions significantly reduce the number of outbreaks in farms and disease spread (based on distance from source), with control in roosts being a significantly better intervention. High-risk areas were also identified, which can support ongoing programs, leading to more effective control interventions.}, journal={TRANSBOUNDARY AND EMERGING DISEASES}, author={Janouskova, Eva and Rokhsar, Jennifer and Jara, Manuel and Entezami, Mahbod and Horton, Daniel L. and Dias, Ricardo Augusto and Machado, Gustavo and Prada, Joaquin M.}, editor={Diaz, DanielEditor}, year={2023}, month={Jun} }
 @misc{lanzas_jara_tucker_curtis_2022, title={A review of epidemiological models of Clostridioides difficile transmission and control (2009e2021)}, volume={74}, ISSN={["1095-8274"]}, url={https://doi.org/10.1016/j.anaerobe.2022.102541}, DOI={10.1016/j.anaerobe.2022.102541}, abstractNote={Clostridioides difficile is the leading cause of infectious diarrhea and one of the most common healthcare-acquired infections worldwide. We performed a systematic search and a bibliometric analysis of mathematical and computational models for Clostridioides difficile transmission. We identified 33 publications from 2009 to 2021. Models have underscored the importance of asymptomatic colonized patients in maintaining transmission in health-care settings. Infection control, antimicrobial stewardship, active testing, and vaccination have often been evaluated in models. Despite active testing and vaccination being not currently implemented, they are the most commonly evaluated interventions. Some aspects of C. difficile transmission, such community transmission and interventions in health-care settings other than in acute-care hospitals, remained less evaluated through modeling.}, journal={ANAEROBE}, publisher={Elsevier BV}, author={Lanzas, Cristina and Jara, Manuel and Tucker, Rachel and Curtis, Savannah}, year={2022}, month={Apr} }
 @article{jara_holcomb_wang_goss_machado_2022, title={The Potential Distribution of Pythium insidiosum in the Chincoteague National Wildlife Refuge, Virginia (vol 8, 640339, 2021)}, volume={9}, ISSN={["2297-1769"]}, DOI={10.3389/fvets.2022.893668}, abstractNote={[This corrects the article DOI: 10.3389/fvets.2021.640339.].}, journal={FRONTIERS IN VETERINARY SCIENCE}, author={Jara, Manuel and Holcomb, Kevin and Wang, Xuechun and Goss, Erica M. and Machado, Gustavo}, year={2022}, month={Apr} }
 @article{jara_crespo_roberts_chapman_banda_machado_2021, title={Development of a Dissemination Platform for Spatiotemporal and Phylogenetic Analysis of Avian Infectious Bronchitis Virus}, volume={8}, ISSN={["2297-1769"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85105984090&partnerID=MN8TOARS}, DOI={10.3389/fvets.2021.624233}, abstractNote={Infecting large portions of the global poultry populations, the avian infectious bronchitis virus (IBV) remains a major economic burden in North America. With more than 30 serotypes globally distributed, Arkansas, Connecticut, Delaware, Georgia, and Massachusetts are among the most predominant serotypes in the United States. Even though vaccination is widely used, the high mutation rate exhibited by IBV is continuously triggering the emergence of new viral strains and hindering control and prevention measures. For that reason, targeted strategies based on constantly updated information on the IBV circulation are necessary. Here, we sampled IBV-infected farms from one US state and collected and analyzed 65 genetic sequences coming from three different lineages along with the immunization information of each sampled farm. Phylodynamic analyses showed that IBV dispersal velocity was 12.3 km/year. The majority of IBV infections appeared to have derived from the introduction of the Arkansas DPI serotype, and the Arkansas DPI and Georgia 13 were the predominant serotypes. When analyzed against IBV sequences collected across the United States and deposited in the GenBank database, the most likely viral origin of our sequences was from the states of Alabama, Georgia, and Delaware. Information about vaccination showed that the MILDVAC-MASS+ARK vaccine was applied on 26% of the farms. Using a publicly accessible open-source tool for real-time interactive tracking of pathogen spread and evolution, we analyzed the spatiotemporal spread of IBV and developed an online reporting dashboard. Overall, our work demonstrates how the combination of genetic and spatial information could be used to track the spread and evolution of poultry diseases, providing timely information to the industry. Our results could allow producers and veterinarians to monitor in near-real time the current IBV strain circulating, making it more informative, for example, in vaccination-related decisions.}, journal={FRONTIERS IN VETERINARY SCIENCE}, author={Jara, Manuel and Crespo, Rocio and Roberts, David L. and Chapman, Ashlyn and Banda, Alejandro and Machado, Gustavo}, year={2021}, month={May} }
 @article{machado_corbellini_frias-de-diego_dieh_santos_jara_costa_2021, title={Impact of changes of horse movement regulations on the risks of equine infectious anemia: A risk assessment approach}, volume={190}, ISSN={["1873-1716"]}, url={https://doi.org/10.1016/j.prevetmed.2021.105319}, DOI={10.1016/j.prevetmed.2021.105319}, abstractNote={Equine infectious anemia virus (EIAV) is a transboundary disease affecting a large number of equines worldwide. In this study, we assessed the transmission risk of EIAV in Rio Grande do Sul, Brazil. Serum samples from 1010 animals from 341 farms were initially analyzed using agar gel immunodiffusion to detect viral antibodies, and no antibody-positive animals were found. A risk assessment stochastic model was applied to generate the expected number of potential infections per month and to estimate the time to new infections. Our results estimated 6.5 months as the interval for new infections in the worst-case scenario. Among the variables evaluated, the number of transported animals and the test sensitivity influenced the model the most. These results were then used to revisit the impact of EIAV control regulations, which triggered a change in the diagnostic testing required for animal movement, in which the validity of a negative test for EIAV was extended from 60 to 180 days. Finally, revisiting the annual average of infected farms before and after the new regulation, the number of infected farms increased pre-implementation, and then, the number of culled animals increased, which should impact future EIAV incidence in this region. Our results demonstrated the importance of constant reviews of disease control programs and provided quantitative-based knowledge for decision-makers in official veterinary services.}, journal={PREVENTIVE VETERINARY MEDICINE}, publisher={Elsevier BV}, author={Machado, Gustavo and Corbellini, Luis Gustavo and Frias-De-Diego, Alba and Dieh, Gustavo Nogueira and Santos, Diego Viali and Jara, Manuel and Costa, Eduardo de Freitas}, year={2021}, month={May} }
 @article{jara_holcomb_wang_goss_machado_2021, title={The Potential Distribution of Pythium insidiosum in the Chincoteague National Wildlife Refuge, Virginia}, volume={8}, ISBN={2297-1769}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85102310807&partnerID=MN8TOARS}, DOI={10.3389/fvets.2021.640339}, abstractNote={Pythium insidiosumis a widespread pathogen that causes pythiosis in mammals. Recent increase in cases reported in North America indicates a need to better understand the distribution and persistence of the pathogen in the environment. In this study, we reconstructed the distribution ofP. insidiosumin the Chincoteague National Wildlife Refuge, located on Assateague Island, Virginia, and based on 136 environmental water samples collected between June and September of 2019. The Refuge hosts two grazing areas for horses, also known as the Chincoteague Ponies. In the past 3 years, 12 horses have succumbed to infection byP. insidiosum. Using an ecological niche model framework, we estimated and mapped suitable areas forP. insidiosumthroughout the Refuge. We foundP. insidiosumthroughout much of the study area. Our results showed significant monthly variation in the predicted suitability, where the most influential environmental predictors were land-surface water and temperature. We found that June, July, and August were the months with the highest suitability forP. insidiosumacross the Refuge, while December through March were less favorable months. Likewise, significant differences in suitability were observed between the two grazing areas. The suitability map provided here could also be used to make management decisions, such as monitoring horses for lesions during high risk months.}, journal={FRONTIERS IN VETERINARY SCIENCE}, author={Jara, Manuel and Holcomb, Kevin and Wang, Xuechun and Goss, Erica M. and Machado, Gustavo}, year={2021} }
 @article{pincheira-donoso_harvey_grattarola_jara_cotter_tregenza_hodgson_2021, title={The multiple origins of sexual size dimorphism in global amphibians}, volume={30}, ISSN={["1466-8238"]}, DOI={10.1111/geb.13230}, abstractNote={Abstract}, number={2}, journal={GLOBAL ECOLOGY AND BIOGEOGRAPHY}, author={Pincheira-Donoso, Daniel and Harvey, Lilly P. and Grattarola, Florencia and Jara, Manuel and Cotter, Sheena C. and Tregenza, Tom and Hodgson, Dave J.}, year={2021}, month={Feb}, pages={443–458} }
 @article{binkley_deressa_shi_jara_escobar_mauldin_matheny_o'quin_pieracci_kling_et al._2021, title={Use of partial N-gene sequences as a tool to monitor progress on rabies control and elimination efforts in Ethiopia}, volume={221}, ISSN={["1873-6254"]}, DOI={10.1016/j.actatropica.2021.106022}, abstractNote={Ethiopia is one of the African countries most affected by rabies. A coarse catalog of rabies viruses (RABV) was created as a benchmark to assess the impact of control and elimination activities. We evaluated a 726 bp amplicon at the end of the N-gene to infer viral lineages in circulation using maximum likelihood and Bayesian methods for phylogenetic reconstruction. We sequenced 228 brain samples from wild and domestic animals collected in five Ethiopian regions during 2010-2017. Results identified co-circulating RABV lineages that are causing recurrent spillover infections into wildlife and domestic animals. We found no evidence of importation of RABVs from other African countries or vaccine-induced cases in the area studied. A divergent RABV lineage might be involved in an independent rabies cycle in jackals. This investigation provides a feasible approach to assess rabies control and elimination efforts in resource-limited countries.}, journal={ACTA TROPICA}, author={Binkley, Laura and Deressa, Asefa and Shi, Mang and Jara, Manuel and Escobar, Luis E. and Mauldin, Mathew R. and Matheny, Audrey and O'Quin, Jeanette and Pieracci, Emily G. and Kling, Chantal and et al.}, year={2021}, month={Sep} }
 @article{frias-de-diego_jara_pecoraro_crisci_2021, title={Whole Genome or Single Genes? A Phylodynamic and Bibliometric Analysis of PRRSV}, volume={8}, ISSN={2297-1769}, url={http://dx.doi.org/10.3389/fvets.2021.658512}, DOI={10.3389/fvets.2021.658512}, abstractNote={Diversity, ecology, and evolution of viruses are commonly determined through phylogenetics, an accurate tool for the identification and study of lineages with different pathological characteristics within the same species. In the case of PRRSV, evolutionary research has divided into two main branches based on the use of a specific gene (i.e., ORF5) or whole genome sequences as the input used to produce the phylogeny. In this study, we performed a review on PRRSV phylogenetic literature and characterized the spatiotemporal trends in research of single gene vs. whole genome evolutionary approaches. Finally, using publicly available data, we produced a Bayesian phylodynamic analysis following each research branch and compared the results to determine the pros and cons of each particular approach. This study provides an exploration of the two main phylogenetic research lines applied for PRRSV evolution, as well as an example of the differences found when both methods are applied to the same database. We expect that our results will serve as a guidance for future PRRSV phylogenetic research.}, journal={Frontiers in Veterinary Science}, publisher={Frontiers Media SA}, author={Frias-De-Diego, Alba and Jara, Manuel and Pecoraro, Brittany M. and Crisci, Elisa}, year={2021}, month={Jun} }
 @article{krasteva_jara_frias-de-diego_machado_2020, title={Nairobi Sheep Disease Virus: A Historical and Epidemiological Perspective}, volume={7}, ISSN={["2297-1769"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85089210118&partnerID=MN8TOARS}, DOI={10.3389/fvets.2020.00419}, abstractNote={Nairobi Sheep Disease virus (NSDv) is a zoonotic and tick-borne disease that can cause over 90% mortality in small ruminants. NSDv has historically circulated in East Africa and has recently emerged in the Asian continent. Despite efforts to control the disease, some regions, mostly in warmer climates, persistently report disease outbreaks. Consequently, it is necessary to understand how environmental tolerances and factors that influence transmission may shed light on its possible emergence in other regions. In this study, we quantified the available literature of NSDv from which occurrence data was extracted. In total, 308 locations from Uganda, Kenya, Tanzania, Somalia, India, Sri Lanka and China were coupled with landscape conditions to reconstruct the ecological conditions for NSDv circulation and identify areas of potential disease transmission risk. Our results identified areas suitable for NSDv in Ethiopia, Malawi, Zimbabwe, Southeastern China, Taiwan, and Vietnam. Unsuitable areas included Democratic Republic of Congo, Zambia, and Southern Somalia. In summary, soil moisture, livestock density, and precipitation predispose certain areas to NSDv circulation. It is critical to investigate the epidemiology of NSDv in order to promote better allocation of resources to control its spread in regions that are more at risk. This will help reduce disease impact worldwide as climate change will favor emergence of such vector-borne diseases in areas with dense small ruminant populations.}, journal={FRONTIERS IN VETERINARY SCIENCE}, publisher={Frontiers Media SA}, author={Krasteva, Stephanie and Jara, Manuel and Frias-De-Diego, Alba and Machado, Gustavo}, year={2020}, month={Jul} }
 @article{jara_frias-de-diego_machado_2020, title={Phylogeography of Equine Infectious Anemia Virus}, volume={8}, ISSN={["2296-701X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85085374042&partnerID=MN8TOARS}, DOI={10.3389/fevo.2020.00127}, abstractNote={Equine Infectious Anemia virus (EIAV) is the causative agent of one of the most impacting infectious diseases affecting equids. EIAV is genetically diverse with several lineages circulating globally. To elucidate EIAV global spread patterns, we studied its spatiotemporal dynamics applying Bayesian phylodynamic analyses, using a worldwide compiled dataset composed of unique sequences of the gag gene. In addition, we performed a scoping review of 1.470 publications on EIAV to characterize the spatiotemporal trends in EAIV research. Phylogeographic reconstruction suggested Hungary as the most likely country of origin for current EIAV circulation (root state posterior probability = 0.21), and one of the most important centers of diversification for the disease. Historical EIAV spread was predominantly characterized by long-distance spread across continents. As a result, we found that the American and Asian circulating EIAV (i.e., Mongolia) are more related to European lineages than to other Asian countries, being Europe the continent with the highest EIAV phylogenetic diversity. Our bibliometric analysis showed a continuous increment in the number of publications per year, where the United States and China appeared as the countries with highest EIAV-related scientific production. This study provides a historical geographic mapping of the EIAV linages’ spread patterns. In addition, we identified important asymmetry between the current research effort and the availability of genetic data which restricted our abilities to quantify for example the time frame of virus dispersal.}, journal={FRONTIERS IN ECOLOGY AND EVOLUTION}, publisher={Frontiers Media SA}, author={Jara, Manuel and Frias-De-Diego, Alba and Machado, Gustavo}, year={2020}, month={May} }
 @article{jara_garcia-roa_escobar_torres-carvajal_pincheira-donoso_2019, title={Alternative reproductive adaptations predict asymmetric responses to climate change in lizards}, volume={9}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-019-41670-8}, abstractNote={Abstract}, journal={SCIENTIFIC REPORTS}, author={Jara, Manuel and Garcia-Roa, Roberto and Escobar, Luis E. and Torres-Carvajal, Omar and Pincheira-Donoso, Daniel}, year={2019}, month={Mar} }
 @article{hickcox_jara_deacon_harvey_pincheira-donoso_2019, title={Global terrestrial distribution of penguins (Spheniscidae) and their conservation by protected areas}, volume={28}, ISSN={["1572-9710"]}, DOI={10.1007/s10531-019-01801-z}, abstractNote={Establishing protected areas (PAs) ranks among the top priority actions to mitigate the global scale of modern biodiversity declines. However, the distribution of biodiversity is spatially asymmetric among regions and lineages, and the extent to which PAs offer effective protection for species and ecosystems remains uncertain. Penguins, regarded as prime bioindicator birds of the ecological health of their terrestrial and marine habitats, represent priority targets for such quantitative assessments. Of the world’s 18 penguin species, eleven are undergoing population declines, for which ten are classified as ‘Vulnerable’ or ‘Endangered’. Here, we employ a global-scale dataset to quantify the extent to which their terrestrial breeding areas are currently protected by PAs. Using quantitative methods for spatial ecology, we compare the global distribution of penguin colonies, including range and population size analyses, with the distribution of terrestrial PAs classified by the International Union for Conservation of Nature, and generate hotspot and endemism maps worldwide. Our assessment quantitatively reveals < 40% of the terrestrial range of eleven penguin species is currently protected, and that range size is the significant factor in determining PA protection. We also show that there are seven global hotspots of penguin biodiversity where four or five penguin species breed. We suggest that future penguin conservation initiatives should be implemented based on more comprehensive, quantitative assessments of the multi-dimensional interactions between areas and species to further the effectiveness of PA networks.}, number={11}, journal={BIODIVERSITY AND CONSERVATION}, author={Hickcox, Rachel P. and Jara, Manuel and Deacon, Laura A. K. and Harvey, Lilly P. and Pincheira-Donoso, Daniel}, year={2019}, month={Sep}, pages={2861–2876} }
 @article{frias-de-diego_jara_escobar_2019, title={Papillomavirus in Wildlife}, volume={7}, ISSN={["2296-701X"]}, url={http://dx.doi.org/10.3389/fevo.2019.00406}, DOI={10.3389/fevo.2019.00406}, abstractNote={Papillomaviruses (PV) are associated with epithelial malignancies in animals, including cancer in humans. Limited knowledge exists regarding the evolutionary history of non-human PV. We assessed the phylogeography of PV with emphasis in wildlife hosts. We explored the phylogenetic, geographic, and environmental relationships of PV and hosts applying Bayesian inference and spatial analyses of virus and hosts. We found that the available wildlife PV data support previous reports on the higher incidence of fibropapillomatosis over carcinoma in humans and wildlife, being mammals the most common host. We also found geographic bias on the available wildlife papillomavirus (WPV) information towards the Northern Hemisphere, which may have influenced our results to show Europe as the most likely origin of the available WPV lineages. Therefore, we highlight the need for detailed studies on the presence of WPV in regions and species not included in this study (e.g., reptiles from the tropics) to better inform sites of WPV origin, susceptible species, and spillover potential. Future studies of the clinical and subclinical occurrence, distribution, and phylogenetic signatures of WPV may help understand the spread, virulence, and epidemiology of PV in general. From an evolutionary perspective, our overview suggests that WPV are a promising host-pathogen system to untangle questions regarding co-evolution due to its large geographic distribution and occurrence in a wide variety of aquatic and terrestrial wildlife species.}, journal={FRONTIERS IN ECOLOGY AND EVOLUTION}, publisher={Frontiers Media SA}, author={Frias-De-Diego, Alba and Jara, Manuel and Escobar, Luis E.}, year={2019}, month={Oct} }