Isabel Henriques

University of Coimbra | UC · Department of Life Sciences and Centre for Environmental and Marine Studies (CESAM)

Aquaculture is a crucial industry in the agri-food sector, but it is linked to serious environmental problems. There is a need for efficient treatment systems that allow water recirculation to mitigate pollution and water scarcity. This work aimed to evaluate the self-granulation process of a microalgae-based consortium and its capacity to bioremed...

Background: New Delhi metallo-beta-lactamase (NDM) has been spreading across the globe, but the causes of its success are poorly understood. We characterized a blaNDM-5-positive Escherichia coli strain from a Portuguese hospital and conducted comparative genomic analyses to understand the role of clonal background and horizontal gene transfer in b...

Enterobacteriaceae resistant to third-generation cephalosporins are a great concern for public health, as these are first-line drugs to treat infections. The production of carbapenemases and extended spectrum beta-lactamases (ESBLs) and/or the overexpression of AmpC β-lactamases are the main mechanisms of resistance to these antibiotics. Among the...

The Klebsiella pneumoniae complex is comprised of ubiquitous bacteria that can be found in soils, plants or water, and as humans’ opportunistic pathogens. This study aimed at inferring common and distinctive features in clinical and environmental K. pneumoniae. Whole genome sequences of members of the K. pneumoniae complex (including K. variicola,...

We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community’s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrat...

Carbapenems are antibiotics of pivotal importance in human medicine, the efficacy of which is threatened by the increasing prevalence of carbapenem-resistant Enterobacterales (CRE). Urban ponds may be reservoirs of CRE, although this hypothesis has been poorly explored. We assessed the proportion of CRE in urban ponds over a one-year period and ret...

Essential oil (EO), hydrolate, and nondistilled aqueous phase (decoction) obtained from the hydrodistillation of lemongrass byproducts were studied in terms of their potential as food ingredients under a circular economy. The EO (0.21%, dry weight basis) was composed mainly of monoterpenoids (61%), the majority being citral (1.09 g/kg). The minimal...

Deep coral-dominated communities play paramount roles in benthic environments by increasing their complexity and biodiversity. Coral-associated microbes are crucial to maintain fitness and homeostasis at the holobiont level. However, deep-sea coral biology and their associated microbiomes remain largely understudied, and less from remote and abyssa...

We determined the distribution and temporal variation of Carbapenem Resistant Enterobacterales (CRE), carbapenemase-encoding genes and other antibiotic resistance genes (ARGs) in a highly polluted river (Lis River; Portugal), also assessing the potential influence of water quality to this distribution. Water samples were collected in two sampling c...

Background Klebsiella pneumoniae are ubiquitous bacteria and recognized multidrug-resistant opportunistic pathogens that can be released into the environment, mainly through sewage, where they can survive even after wastewater treatment. A major question is if once released into wastewater, the selection of lineages missing clinically-relevant trai...

Members of Shewanella are ubiquitous in aquatic environments, some of which have been implicated in human infections. The progenitors of antibiotic resistance genes with clinical relevance, such as qnrA genes, have been identified in Shewanella. qnrA code for a pentapeptide repeat protein that protects type II topoisomerases, decreasing susceptibil...

This work aimed to characterize the gut and faeces bacterial communities (BC) of Porcellionides pruinosus using high-throughput sequencing. Isopods were collected from the field and kept in laboratory conditions similar to those normally applied in ecotoxicology tests. Faeces and purged guts of isopods (n = 3 × 30) were analysed by pyrosequencing t...

The rhizobiome is being increasingly acknowledged as a key player in plant health and breeding strategies. The pine pitch canker (PPC), caused by the fungus Fusarium circinatum, affects pine species with varying susceptibility degrees. Our aims were to explore the bacterial rhizobiome of a susceptible (Pinus radiata) and a resistant (Pinus pinea) s...

The toxicity of silver nanoparticles (AgNPs) in soil bacterial communities (SBC) has been widely reported. However, the bacterial related endpoints have not been effectively considered in the environmental risk assessment (ERA) for nanomaterials. Thus, we aimed to study the long-term effects of AgNPs, or AgNO 3 (counterpart), [5 μg (Ag) kg − 1 ] on...

The use of biosolids as fertilizers in agriculture can lead to the exposure of soil biota to sulfidised silver nanoparticles (Ag2S NPs), generated during the wastewater treatment procedures. Considering the crucial role of microorganisms on soil functions, we aimed to study the effects of 10 mg kg⁻¹ soil of Ag2S NPs or AgNO3 on the soil microbiome,...

Amphibian’s skin bacterial community may help them to cope with several types of environmental perturbations, including osmotic stress caused by increased salinity. This work assessed whether an amphibian skin bacterium could increase its tolerance to NaCl after a long-term exposure to this salt. A strain of Erwinia toletana, isolated from the skin...

Although urban wastewater treatment plants (UWWTPs) are important sites for antibiotic resistance elimination, their limitation in producing resistance-free effluents is recognized. Despite the critical importance of carbapenems to human health, the fate and diversity of carbapenem-resistant bacteria (CRB) in UWWTPs is still poorly understood. We a...

The emergence of antibiotic-resistant pathogens due to worldwide antibiotic use is raising concern in several settings, including aquaculture. In this work, the selection of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) was evaluated after exposure of zebrafish to oxytetracycline (OTC) for two months, followed by a reco...

Vegetables may become contaminated with antibiotic-resistant bacteria from farm-to-fork. Here we report draft genome sequences of two multidrug-resistant Escherichia coli isolated from lettuce. Whole genomes of strains Y15 V.22 and Y15 V.54 were sequenced. Available tools were used to inspect for virulence factors (VF), metals tolerance, resistome...

The global spread of antibiotic-resistant bacteria and their resistance genes is a critical issue that is no longer restricted to hospital settings, but also represents a growing problem involving environmental and food safety. In this study, we have performed a microbiological and genomic investigation of critical priority pathogens resistant to b...

Amphibian’s skin bacterial community may help them to cope with several types of environmental perturbations, including osmotic stress caused by increased salinity. This work aimed at assessing if an amphibian skin bacterium could increase its tolerance to NaCl after a long-term exposure to this salt. A strain of Erwinia toletana , isolated from th...

Copper-based (nano)pesticides in agroecosystems may result in unintended consequences on non-target soil microbial communities, due to their antimicrobial broad spectrum. We studied the impact of a commercial Cu(OH) 2-nanopesticide, over 90 days, at single and season agricultural application doses, in the presence and absence of an edaphic organism...

Antibiotic resistance is a health challenge across human, animal and environmental settings. In the environment, metals may contribute to antibiotic resistance selection. This study aimed to investigate the role of copper and zinc in the selection of antibioticresistant bacteria (ARB) and antibiotic resistance genes (ARGs) in a riverine bacterial c...

Soils might be a final sink for Ag2S nanoparticles (NPs). Still, there are limited data on their effects on soil bacterial communities (SBC). To bridge this gap, we investigated the effects of Ag2S NPs (10 mg kg−1 soil) on the structure and function of SBC in a terrestrial indoor mesocosm, using a multi-species design. During 28 days of exposure, t...

Oxytetracycline (OTC) is a broad-spectrum antibiotic widely used in aquaculture, resulting in contamination of aquatic environments. In a previous study, we observed significant effects of OTC sublethal concentrations in zebrafish, its microbiome and the water bacterial community. Here we assessed the extent to which these effects are reversible af...

IntroductionFreshwater ecosystems provide propitious conditions for the acquisition and spread of antibiotic resistance genes (ARGs), and integrons play an important role in this process.Material and methodsIn the present study, the diversity of putative environmental integron-cassettes, as well as their potential bacterial hosts in the Velhas Rive...

The World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the environment. In this tra...

Concentration of bacterial species indicative of fecal contamination in the gut of mangrove oysters (Crassostrea gasar) is a major concern for public health and food surveillance. Our work aimed to determine the occurrence, antibiotic-resistance, phylogenetic profile and virulence of Escherichia coli strains isolated from C. gasar farmed in four es...

The increasing number of Chromobacterium haemolyticum human infection reports, especially in tropical regions and connected with environmental sources, resulted in an urge to better describe this species. This study aimed to characterize the C. haemolyticum resistome, virulence determinants and genetic platforms related with genome plasticity. A co...

A comprehensive monitoring of a broad set of antibiotics in the final effluent of wastewater treatment plants (WWTPs) of 7 European countries (Portugal, Spain, Ireland, Cyprus, Germany, Finland, and Norway) was carried out in two consecutive years (2015 and 2016). This is the first study of this kind performed at an international level. Within the...

Wastewater treatment plants (WWTPs) are relevant sources of antibiotic resistance into aquatic environments. Disinfection of WWTPs' effluents (e.g. by UV-C irradiation) may attenuate this problem, though some clinically relevant bacteria have been shown to survive disinfection. In this study we characterized 25 CTX-M-producing Escherichia coli stra...

Silver nanoparticles (AgNPs) are broadly used due to their antimicrobial properties. Consequently, AgNPs can be released into the terrestrial environment, leading to effects on soil bacterial community (SBC), essential to regulate nutrient cycles. This work aimed to study the impact of AgNPs and the ionic control (AgNO3) on SBC, (1) at community st...

Due to food demand, aquaculture industry has been growing fast. Thus, to supply all the necessities, fish are usually grown in stressfully conditions, allowing the easy dissemination of diseases. Due to its broad-spectrum, oxytetracycline (OTC) is one of the most used antibiotics in the aquaculture industry to prevent economic loss. It is known tha...

Resistance to antibiotics is one of the most relevant public health concerns in the world. Aquatic environments play an important role because they are reservoirs for antibiotic resistance genes and antibiotic-resistant strains, contributing to the spread of resistance. The present study investigated the resistome in Lake Bolonha (three sampling si...

In this study, we characterized the diversity of Pseudomonas associated with Bursaphelenchus xylophilus, its insect vector (Monochamus galloprovincialis) and its host (Pinus pinaster), by a culture‐independent approach using rpoD clone libraries. Clone libraries of Pseudomonas rpoD were obtained from B. xylophilus, M. galloprovincialis and infected...

The application of Cu(OH)2 nanopesticides in modern agriculture has been increasing to improve the crop protection. However, the repeated applications of these nanopesticides might result into the accumulation of nanomaterials (NM) in agroecosystems. Due to their broad antimicrobial activity and NM accumulation on soils, the dynamic of non-target s...

In order to supply human demand for food, the aquaculture industry has been growing fast in the last years, being fish usually cultivated in overcrowded conditions. Hence, to prevent the rapidly disease spreading, antibiotics may be applied to both sick and healthy animals. Due to its broad spectrum, oxytetracycline (OTC) is one of the most used an...

Metal contamination, as well as pesticides, organic matter and nutrient input are main factors leading to freshwater ecosystems degradation. The Water Framework Directive (WFD) was implemented within the European Union with the ultimate goal of promoting a good ecological status in all European waterbodies. However, the broad implementation of the...

Carbapenems are last-resort drugs used to treat severe infections. Despite the increasing number of reports of carbapenem-resistant Enterobacteriaceae (CRE), there is still limited information on their distribution in the environment. Here we report the characterization of CRE isolates from a polluted river.

Satureja montana is a worldwide consumed aromatic plant whose essential oils (EOs) are used as spice and preservative by food industry. Only the leaves are marketed, generating a large amount of stems as byproducts. It is possible that the EOs present in these byproducts represent a source of compounds with antimicrobial activity, as observed for t...

Wastewater represents one of the major entry points of antibiotic resistance into the environment. In this study we characterized cefotaxime-resistant strains isolated from a wastewater effluent, to understand the potential risk for human health. From 25 E. coli isolates, using rep-PCR and PFGE, 6 strains were selected for Illumina whole-genome seq...

Oxytetracycline (OTC) is a broad-spectrum antibiotic widely used in livestock production. Like many other pharmaceuticals, OTC is not completely metabolized by the organism and thus, increasing amounts of the compound are being detected in the aquatic environment. The assessment of the environmental risk of pharmaceuticals is hindered by their very...

Upon consumption, dietary nitrate is reduced to nitrite in the oral cavity and to nitric oxide ( • NO) in the stomach. Here, • NO increases mucosal blood flow, mucus thickness and prevents microbial infections. However, the impact of nitrate on gut microbiota, a pleiotropic organism essential to maintain gastrointestinal and systemic welfare, remai...

Integrated antibiotic resistance (AR) surveillance is one of the objectives of the World Health Organization global action plan on antimicrobial resistance. Urban wastewater treatment plants (UWTPs) are among the most important receptors and sources of environmental AR. On the basis of the consistent observation of an increasing north-to-south clin...

Aquatic systems have been described as antibiotic resistance reservoirs, where water may act as a vehicle for the spread of resistant bacteria and resistance genes. We evaluated the occurrence and diversity of third generation cephalosporin-resistant gram-negative bacteria in a lake in the Amazonia region. This water is used for human activities, i...

Seven endophytic strains were isolated from the halophyte Halimione portulacoides, collected from Ria de Aveiro, Portugal. To determine their exact taxonomic position, comparative analyses were performed with these strains and closely related type strains of Salinicola species. Genome sequencing and comparison indicated that five of the seven isola...

Disinfection by UV radiation is one of the most promising solutions to reduce the bacterial load and antibiotic resistance in the final effluents of urban wastewater treatment plants (UWTP). Our aim was to evaluate the fate of cefotaxime-resistant Enterobacteriaceae and Extended Spectrum Beta-Lactamase (ESBL) producers in a full-scale system that i...

Exiguobacterium antarcticum strain B7 is a psychrophilic Gram-positive bacterium that possesses enzymes that can be used for several biotechnological applications. However, many proteins from its genome are considered hypothetical proteins (HPs). These functionally unknown proteins may indicate important functions regarding the biological role of t...

Dataset of annotation function of 100 proteins functionally known from E. antarcticum B7 using the same pipeline used for the HP prediction. (XLSX)

Annotation dataset results for the 304 hypothetical proteins from E. antarcticum B7, submitted to the pipeline with Go feat, Pfam, CATH, SUPERFAMILY, SVMProt, CDART, SMART and InterPro. (XLSX)

Result of essential gene prediction using DEG. (XLSX)

List of protein with no GO term prediction. (XLSX)

Protein-protein interaction of all 11 proteins tested. This image shows how each of the proteins tested interacts with each other and with other proteins form the E. antarcticum B7. (TIFF)

Three-dimensional models and Ramachandran values for the proteins Eab7_0655, Eab7_1015, Eab7_2599 and Eab7_1666 from E. antarcticum. (TIF)

Accuracy, sensitivity, specificity and ROC area results of tools of the pipeline used for the annotation of 100 proteins functionally known from E. antarcticum B7 by ROC analysis. (XLSX)

List of predicted physicochemical parameters, sub-cellular localization and topology of transmembrane helices for the HPs from E. antarcticum B7. (XLSX)

Results of the Blastp search for similar sequences against non-reduntant (nr) database. (XLSX)

List of GO terms represented by only one protein for molecular function and biological process. (XLSX)

List of bioinformatics tools and databases. (XLSX)

Urban wastewater treatment plants (UWTPs) are reservoirs of antibiotic resistance. Wastewater treatment changes the bacterial community and inevitably impacts the fate of antibiotic resistant bacteria and antibiotic resistance genes (ARGs). Some bacterial groups are major carriers of ARGs and hence, their elimination during wastewater treatment may...

Pine Wilt Disease (PWD) has a significant impact on Eurasia pine forests. The microbiome of the nematode (the primary cause of the disease), its insect vector, and the host tree may be relevant for the disease mechanism. The aim of this study was to characterize these microbiomes, from three PWD-affected areas in Portugal, using Denaturing Gradient...