Browsing by Author "Torres, Rita Tinoco"
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- Emergence of colistin resistance genes (mcr-1) in Escherichia coli among widely distributed wild ungulatesPublication . Torres, Rita Tinoco; Cunha, Mónica V.; Araujo, Débora; Ferreira, Helena; Fonseca, Carlos; Palmeira, Josman DantasThe environment is considered a major reservoir of antimicrobial resistant microorganisms (AMR) and antimicrobial resistance genes (ARG). Colistin, a “last resort” antibiotic, is used for the treatment of severe infections caused by multidrug-resistant Gram-negative bacteria. The global dissemination of mobile colistin resistance genes (mcr) in natural and non-natural environments is a major setback in the fight against antimicrobial resistance. Hitherto, there is a limited number of studies screening this resistance determinant in bacteria from wildlife. In this study, we describe for the first time the detection of plasmid-mediated colistin resistance in Escherichia coli from wild ungulates in Portugal, which are also widely distributed across Europe. This information is critical to identify the importance of ungulates in the dissemination of resistant bacteria, and their corresponding genes, across the environment. Here, 151 resistant-Enterobacteriaceae isolated from 181 samples collected from different wild ungulate species throughout Portugal were screened for mcr genes. Four mcr-1-positive Escherichia coli were detected from four fallow deer individuals that were sampled in the same hunting ground. These four isolates harboured mcr-1-related IncP plasmids belonging to sequencing types ST155, ST533 and ST345 (n = 2), suggesting bacterial and/or plasmid circulation. All mcr-1-positive E. coli also showed other resistance phenotypes, including MDR, including the B1 commensal phylogenetic profile. All mcr-1-positive E. coli show additional resistance phenotypes, including MDR, including the B1 commensal phylogenetic profile. Our findings are upsetting, highlighting the global dissemination of colistin resistance genes in the whole ecosystem, which, under the One Health framework, emphasizes the urgent need for effective implementation of AMR surveillance and control in the human-animal-environment interfaces.
- Eucalyptus plantations alter spatiotemporal relationships of wild ungulatesPublication . Ares-Pereira, Guilherme; Rosalino, L. M.; Teixeira, Daniela; Castro, Guilherme; Magalhães, Ana; Lima, Cátia; Fonseca, Carlos; Torres, Rita TinocoEucalyptus plantations, the second most economically important exotic tree in Europe, cover circa 1,5 million hectares on this continent. However, little is known about their effect on the ecological patterns of widely distributed and increasing populations of wild ungulates. This lack of knowledge jeopardizes our ability to correctly manage these populations in increasingly ubiquitous exotic forests. We aimed to understand how exotic forestry plantations influence ungulates spatial and temporal dimensions of their niche and determine how the species interactions may be changed by these artificial systems. We used roe deer and red deer as wildlife models, the Portuguese Eucalyptus plantation as standards for forestry plantations, and camera-trapping, occupancy modeling, and kernel density estimators as tools to fulfill our goals. Eucalyptus plantations had a strong effect on roe deer and red deer spatial behavior when compared to areas dominated by native vegetation. Both species seem to avoid disturbed areas such as agricultural land and Eucalyptus plantations. Even when using plantations, they shift their activity to reduce human encounters. Furthermore, plantations are not a homogeneous landcover, and thus distinct production phases of Eucalyptus plantations affect species interactions and activity patterns differently. Our results show that the pre-harvesting phases seem to be the more critical period for deer. Thus, production forest managers must guarantee that plantation structure encompasses areas with different tree ages to minimize this effect and fulfill deer’s food and cover requirements. Forestry activities should avoid dawn and dusk, to minimize disturbance and to reduce the negative interaction between sympatric guild members, by allowing species to be sparsely distributed (and not clustered in the few undisturbed patches). Plantations should include dispersed native patches to which animals may move in search of food and refuge, therefore creating discontinuities within plantations.
- A high-risk carbapenem-resistant Pseudomonas aeruginosa clone detected in red deer (Cervus elaphus) from PortugalPublication . Torres, Rita Tinoco; Cunha, Mónica V.; Ferreira, Helena; Fonseca, Carlos; Palmeira, Josman DantasPseudomonas aeruginosa is a ubiquitous bacterium, successfully exploiting a variety of environmental niches due to its remarkable metabolic versatility. The World Health Organization classifies P. aeruginosa as a “priority pathogen” due to its a great ability to overcome the action of antimicrobials, including carbapenems. Hitherto, most studies have focused on clinical settings from humans, but much less on animal and environmental settings, particularly on wildlife. In this work, we report the isolation of a carbapenem-resistant Pseudomonas aeruginosa strain recovered from the faeces of a red deer adult female sampled in a humanized area. This isolate was obtained during a nationwide survey on antimicrobial resistance in wildlife aimed to determine the occurrence of carbapenem-resistant bacteria among 181 widely distributed wild ungulates. This P. aeruginosa isolate was found to be a high-risk clone, belonging to the sequence type (ST) 274. The genomic analysis of P. aeruginosa isolate UP4, classified this isolate as belonging to serogroup O3, which was also found to harbour the genes blaPAO, blaPDC-24, blaOXA-486 (encoding resistance to beta-lactams), aph(3′)-IIb (aminoglycosides resistance), fosA (fosfomycin resistance) and catB7 (chloramphenicol resistance). Antimicrobial susceptibility screening, according to EUCAST, showed resistance to imipenem and intermediate resistance to meropenem and doripenem. To our knowledge, this is the first description of carbapenem-resistant P. aeruginosa in deer in Europe. Our results highlight the importance of wild ungulates either as victims of human activity or amplifiers of AMR, either way with potential impacts on animal, human and ecosystem health, since excretion of AMR bacteria might directly or indirectly contaminate other animals and the surrounding environment, perpetuating the spill-over and chain dissemination of AMR determinants.
- Mapping the scientific knowledge of antimicrobial resistance in food-producing animalsPublication . Torres, Rita Tinoco; Carvalho, João; Fernandes, Joana; Palmeira, Josman D.; Cunha, Mónica V.; Fonseca, CarlosAntimicrobial resistance (AMR) can be highlighted as one of the most significant health concerns among the last decades, for which antimicrobial drug use in food-producing animals has contributed as one of the major drivers. Food-producing animals are one of the most important and rapidly expanding commercial agricultural sectors worldwide but there is currently limited knowledge on the temporal and geographical distribution of scientific research on antimicrobial resistance in food-producing animals. We provide a global overview of the spatial and temporal trends of scientific knowledge on AMR in food-producing animals. Peer-reviewed papers of AMR on food-producing animals were retrieved from the Web of Science, systemized and dissected. The final validated dataset contained 1341 occurrences observations covering the 1957–2018 period. There has been a shift of research efforts, both geographically and temporally, emphasizing regional differences in food animal production and changing practices in the food production industry. It becomes evident that many regions have been poorly surveyed, wherein intensified sampling and testing efforts should be most valuable. This systematization of knowledge will be crucial in helping to determine how to optimally allocate limited resources available for AMR monitor and control, aiding in the prediction where the threat of new resistant infections will be greatest. AMR research in food-producing animals in developing countries is markedly growing, reflecting changes in food animals production systems but also posing a particularly significant threat, not only due to intensive animal production, but also exacerbated by poor sanitation. We highlight that the use of antibiotics in food producing animals is pervasive, calling for urgent action. These findings raise the possibility to finetuning key priorities on AMR global issues.
- Temporal and geographical research trends of antimicrobial resistance in wildlife - A bibliometric analysisPublication . Torres, Rita Tinoco; Carvalho, João; Cunha, Mónica V.; Serrano, Emmanuel; Palmeira, Josman Dantas; Fonseca, CarlosAntimicrobial resistance (AMR) is a complex and global problem. Despite the growing literature on AMR in the medical and veterinary settings, there is still a lack of knowledge on the wildlife compartment. The main aim of this study was to report the global trends in AMR research in wildlife, through a bibliometric study of articles found in the Web of Science database. Search terms were "ANTIMICROBIAL" OR "ANTIBIOTIC" AND "RESISTANT" OR "RESISTANCE" and "WILDLIFE" "MAMMAL" "BIRD" "REPTILE" "FERAL" "FREE RANGE". A total of 219 articles were obtained, published between 1979 and 2019. A rising interest in the last decades towards this topic becomes evident. During this period, the scientific literature was distributed among several scientific areas, however it became more multidisciplinary in the last years, focusing on the "One Health" paradigm. There was a geographical bias in the research outputs: most published documents were from the United States, followed by Spain, Portugal and the United Kingdom. The most productive institutions in terms of publication number were located in Portugal and Spain. An important level of international collaboration was identified. An analysis of the main keywords showed an overall dominance of "AMR", "E. coli", "genes", "prevalence", "bacteria", "Salmonella spp." and "wild birds". This is the first study providing a global overview of the spatial and temporal trends of research related to AMR in wildlife. Given the growth tendency over the last years, it is envisaged that scientific production will expand in the future. In addition to offering a broad view of the existing research trends, this study identifies research gaps both in terms of geographical incidence and in relation to unexplored subtopics. Unearthing scientific areas that should be explored in the future is key to designing new strategic research agendas in AMR research in wildlife and to inform funding programs.
- Three Decades of Research on Iberian Wild Ungulates: Key Insights and Promising Research AvenuesPublication . Carvalho, João; Carpio, António; Figueiredo, Ana M.; Fonseca, Carlos; Ferreira, Eduardo; Serrano, Emmanuel; Barja, Isabel; Sánchez‐Zapata, José; Carranza, Juan; Palacios, Laura Barbero; Ortiz‐Jiménez, Lorena; Rosalino, L. M.; Rossa, Mariana; Velamazán, Mario; Santos, Nuno; Fandos, Paulino; Acevedo, Pelayo; Perea, Ramón; Castillo‐Contreras, Raquel; Pascual‐Rico, Roberto; Jiménez‐Ruiz, Saúl; Torres, Rita TinocoThe Iberian Peninsula is witnessing ever-faster environmental changes, and new challenges for wild ungulates are continuously emerging as they become more abundant and widespread. We conducted a systematic review to analyse the knowledge on wild ungulates inhabiting the Iberian Peninsula. We used Web of Science and Scopus search engines, complemented by searches in nonindexed journals, to examine peer-reviewed articles published between January 1990 and July 2023. The annual average growth rate in the number of publications was 17%. Most studies focussed on diseases and pathogens (36%), physiology, endocrinology and reproduction (19%), and behaviour, population and community ecology (17%). Red deer and wild boar are the most targeted species in scientific literature, followed by the Iberian wild goat, roe deer, fallow deer, Southern chamois, mouflon and aoudad. We identify key knowledge gaps that deserve further attention such as the ecological and social impacts of (re)introductions, the effects of increasing ungulate densities on ecosystem integrity and the impact of different hunting and management techniques (some unique to the Iberian Peninsula) on population dynamics. We also highlight the need to stimulate Iberian collaboration and extend the discussion to a wider range of stakeholders to integrate different perspectives on the research agenda for Iberian wild ungulates.
- A walk on the wild side: Wild ungulates as potential reservoirs of multi-drug resistant bacteria and genes, including Escherichia coli harbouring CTX-M beta-lactamasesPublication . Torres, Rita Tinoco; Cunha, Mónica V.; Araujo, Débora; Ferreira, Helena; Fonseca, Carlos; Palmeira, Josman DantasExtended-spectrum β-lactamases (ESBL)-producing Enterobacterales have been classified as critical priority pathogens by the World Health Organization (WHO). ESBL are universally distributed and, in 2006, were firstly reported on a wild animal. Understanding the relative contributions of wild animals to ESBL circulation in the environment is urgently needed. In this work, we have conducted a nationwide study in Portugal to investigate the occurrence of bacteria carrying clinically significant antimicrobial resistance genes (ARG), using widely distributed wild ungulates as model species. A total of 151 antimicrobial resistant-Enterobacterales isolates were detected from 181 wild ungulates: 50% (44/88) of isolates from wild boar (Sus scrofa), 40.3% (25/62) from red deer (Cervus elaphus), 41.4% (12/29) from fallow deer (Dama dama) and 100% (2/2) from mouflon (Ovis aries subsp. musimon). Selected isolates showed a diversified resistance profile, with particularly high values corresponding to ampicillin (71.5%) and tetracycline (63.6%). Enterobacterales strains carried blaTEM, tetA, tetB, sul2, sul1 or dfrA1 ARG genes. They also carried blaCTX-M-type genes, which are prevalent in human infections, namely CTX-M-14, CTX-M-15 and CTX-M-98. Strikingly, this is the first report of CTX-M-98 in wildlife. Almost 40% (n = 59) of Enterobacterales were multi-drug resistant. The diversity of plasmids carried by ESBL isolates was remarkable, including IncF, K and P. This study highlights the potential role of wild ungulates as environmental reservoirs of CTX-M ESBL-producing E. coli and in the spill-over of AMR bacteria and their determinants. Our findings suggest that wild ungulates are useful as strategic sentinel species of AMR in terrestrial environments, especially in response to potential sources of anthropogenic pollution, providing early warning of potential risks to human, animal and environmental health.
- Wild boar as a reservoir of antimicrobial resistancePublication . Torres, Rita Tinoco; Fernandes, Joana; Carvalho, João; Cunha, Mónica V.; Caetano, Tânia; Mendo, Sónia; Serrano, Emmanuel; Fonseca, CarlosAntimicrobial resistance (AMR) has been recognized as an emerging and growing problem worldwide. Knowledge concerning AMR bacteria circulating in wildlife is currently limited, although it could provide important insights into AMR emergence and persistence. Across Europe, wild boar (Sus scrofa) populations have dramatically increased their distribution and number over the last decades. In the context of AMR dynamics, wild boar is a perfect model species to unveil the emergence, spread and persistence of AMR at the human-livestock-wildlife interface. Here, we summarize the current knowledge on the importance of wild boar as a reservoir of antimicrobial resistant bacteria, and its possible use as sentinel species for surveillance. Analyses of available data showed a rising interest on this topic in the last years, highlighting the growing concern on wild boar potential role as AMR facilitator and it is foreseen that the importance of antimicrobial resistance research in wild boar will continue to increase in years to come. Available studieshave been focused on specific bacterial species, particularlyE. coli, Salmonellaspp. andEnterococcusspp., bioindicators of AMR, and have been mainly conducted in three countries: Spain, Portugal and Germany.Strikingly, AMR surveillance in wild boar is uneven and still poorly allocated as many wild boar high-density countries do not yet have publications on the topic.Overall, accumulated data showed thatwild boar are carriers of antimicrobial resistant bacteria, withvariation in the prevalence of bacterial species and thepercentage of resistance to different antibiotics. Thelack of harmonized sampling and testing protocols makes it difficult to compare AMR in wild boar.The need for the establishment of standardised protocols keen to provide quantitative comparable data is highlighted. We finally suggest the long-term monitoring of wild boar as a sentinel species for AMR surveillance in order to inform public policies on this topic.