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With the global concerns on antibiotic resistance (AR) as a public health issue, it is pivotal to have data exchange platforms for studies on antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the environment. For this purpose, the NORMAN Association is hosting the NORMAN ARB&ARG database, which was developed within the European project ANSWER. The present article provides an overview on the database functionalities, the extraction and the contribution of data to the database. In this study, AR data from three studies from China and Nepal were extracted and imported into the NORMAN ARB&ARG in addition to the existing AR data from 11 studies (mainly European studies) on the database. This feasibility study demonstrates how the scientific community can share their data on AR to generate an international evidence base to inform AR mitigation strategies. The open and FAIR data are of high potential relevance for regulatory applications, including the development of emission limit values / environmental quality standards in relation to AR. The growth in sharing of data and analytical methods will foster collaboration on risk management of AR worldwide, and facilitate the harmonization in the effort for identification and surveillance of critical hotspots of AR. The NORMAN ARB&ARG database is publicly available at: https://www.norman-network.com/nds/bacteria/.

The occurrence of antibiotics (ABs) in four types of commercially grown vegetables (lettuce leaves, tomato fruits, cauliflower inflorescences, and broad bean seeds) was analyzed to assess the human exposure and health risks associated with different agronomical practices. Out of 16 targeted AB residues, seven ABs belonging to three groups (i.e., benzyl pyrimidines, fluoroquinolones, and sulfonamides) were above the method detection limit in vegetable samples ranging from 0.09 ng g−1 to 3.61 ng g−1 fresh weight. Data analysis (quantile regression models, principal component and hierarchical cluster analysis) showed manure application, irrigation with river water (indirect wastewater reuse), and vegetable type to be the most significant factors for AB occurrence in the targeted crops. Metabolites were detected in 70 of the 80 vegetable samples analyzed, and their occurrence was both plant- and compound-specific. In 73 % of the total samples, the concentration of AB metabolites was higher than the concentration of their parent compound. Finally, the potential human health risk estimated using the hazard quotient approach, based on the acceptable daily intake and the estimated daily intake, showed a negligible risk for human health from vegetable consumption. However, canonical-correspondence analysis showed that detected ABs explained 54 % of the total variation in AB resistance genes abundance in the vegetable samples. Thus, further studies are needed to assess the risks of antibiotic resistance promotion in vegetables and the significance of the occurrence of their metabolites.

Antibiotic (AB) Resistance is an increasing global problem for public health, with multi-resistant bacteria persisting and spreading not only in clinical settings but also in the environment. One of the possible vectors of this spread is the use and re-use of waste water (WW) and of manure and sludge from WW treatment plants (WWTPs) in different agriculture practices (irrigation, soil amendment). These practices are becoming widespread in regions with scarcity of water. WWTPs are known as AB resistance hotspots, whereas soil amendment by organic fertilization is known to increase AB resistance in the soil microbiomes. Hence, there is a growing concern about the possible transmission of AB resistance from agricultural soils to crops and, ultimately, to the microbiomes of consumers' guts. In this Thesis, this issue was assessed in commercial fields producing vegetable crops. This strategy allowed us to analyze AB resistance elements in foodstuffs actually reaching the consumers, and to understand the risk their consumption poses. Moreover, this Thesis tackles the alterations in soil, plant and crops bacterial communities due to these agricultural practices. To achieve this, five agricultural fields located in the area of Barcelona (NE Spain) were selected, under different irrigation regimes and soil amendment. The selected crops were lettuce, tomatoes, and broad beans as they represent vegetables with different edible parts, commonly eaten either raw or beans, as cooked. The Thesis is divided into five chapters. Chapter I describes the state of the art of the studies of ABR in food and agricultural fields and presents the objectives of the PhD project. Chapter II and III assess the distribution of ARGs and microbiomes along the soil-plant continuum in Lycopersicum esculentum and, grown in peri-urban and rural agricultural fields under different irrigation regimes and soil amendment. Our data show that field practices influenced the distribution of ARGs and intI1 along, La resistencia a los antibióticos (AB) es un problema mundial cada vez mayor para la salud pública, con bacterias multirresistentes que persisten y se propagan no solo en entornos clínicos sino también en el medio ambiente. Uno de los posibles vectores de esta propagación es el uso y la reutilización de aguas residuales (WW) y de estiércol y lodos de plantas de tratamiento de WW (WWTP) en diferentes prácticas agrícolas (riego, enmienda del suelo). Estas prácticas se están generalizando en regiones con escasez de agua. Las WWTP se conocen como puntos calientes de resistencia AB, mientras que la enmienda del suelo por fertilización orgánica aumenta la resistencia AB en los microbiomas del suelo. Existe una creciente preocupación por la posible transmisión de la resistencia AB de los suelos agrícolas a los cultivos y, en última instancia, a los microbiomas de los intestinos de los consumidores. En esta Tesis, este tema se evaluó en campos comerciales que producen cultivos de hortalizas. Esta estrategia nos permitió analizar los elementos de resistencia AB en los alimentos que realmente llegan a los consumidores, y comprender el riesgo que representa su consumo. Además, esta Tesis aborda las alteraciones en las comunidades bacterianas del suelo, plantas y cultivos debido a estas prácticas agrícolas. Para lograr esto, se seleccionaron cinco campos agrícolas ubicados en el área de Barcelona (NE España), bajo diferentes regímenes de riego y enmienda del suelo. Los cultivos seleccionados fueron lechuga, tomate y habas, ya que representan vegetales con diferentes partes comestibles, que comúnmente se comen crudos o frijoles, como cocidos. La tesis se divide en cinco capítulos. El Capítulo I describe el estado del arte de los estudios de ABR en campos agrícolas y alimentarios y presenta los objetivos del proyecto de doctorado. Los capítulos II y III evalúan la distribución de ARG y microbiomas a lo largo del continuo suelo-planta en Lycopersicum esculentum y, cultivados en ca, Postprint (published version)

Despite the social concern about the generalization of antibiotic resistance hotspots worldwide, very little is known about the contribution of different potential sources to the global risk. Here we present a quantitative analysis of the distribution of Antibiotic Resistance Genes (ARGs) in soil, rhizospheric soil, roots, leaves and beans in tomato, lettuce and broad beans crops (165 samples in total), grown in nine commercial plots distributed in four geographical zones in the vicinity of Barcelona (North East Spain). We also analyzed five soil samples from a nearby forest, with no record of agricultural activities. DNA samples were analyzed for their content in the ARGs sul1, tetM, qnrS1, blaCTX-M-32, blaOXA-58, mecA, and blaTEM, plus the integron intI1, using qPCR methods. In addition, soil microbiomes from the different plots were analyzed by amplicon-targeted 16S rRNA gene sequencing. Our data show a decreasing gradient of ARG loads from soil to fruits and beans, the latter showing only from 0.1 to 0.01% of the abundance values in soil. The type of crop was the main determinant for both ARG distribution and microbiome composition among the different plots, with minor contributions of geographic location and irrigation water source. We propose that soil amendment and/or fertilization, more than irrigation water, are the main drivers of ARG loads on the edible parts of the crop, and that they should therefore be specifically controlled. © 2019 Elsevier Inc.

While the presence of antibiotic resistance genes (ARGs) in agricultural soils and products has been firmly established, their distribution among the different plant parts and the contribution of agricultural practices, including irrigation with reclaimed water, have not been adequately addressed yet. To this end, we analyzed the levels of seven ARGs (sul1, blaTEM, blaCTX-M-32, mecA, qnrS1, tetM, blaOXA-58), plus the integrase gene intl1, in soils, roots, leaves, and fruits from two commercial tomato fields irrigated with either unpolluted groundwater or from a channel impacted by treated wastewater, using culture-independent, quantitative real-time PCR methods. ARGs and intl1 sequences were found in leaves and fruits at levels representing from 1 to 10% of those found in roots or soil. The relative abundance of intl1 sequences correlated with tetM, blaTEM, and sul1 levels, suggesting a high horizontal mobility potential for these ARGs. High-throughput 16S rDNA sequencing revealed microbiome differences both between sample types (soil plus roots versus leaves plus fruits) and sampling zones, and a correlation between the prevalence of Pseudomonadaceae and the levels of different ARGs, particularly in fruits and leaves. We concluded that both microbiome composition and ARGs levels in plants parts, including fruits, were likely influenced by agricultural practices. © 2018