Rosina Gironés

Rosina Gironés
University of Barcelona | UB · Department of Genetics Microbiology and Statistics

PhD.

About

370
Publications
63,536
Reads
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11,582
Citations
Additional affiliations
January 2010 - present
University of Barcelona
Position
  • Professor (Full)

Publications

Publications (370)
Article
Full-text available
SARS-CoV-2 variants are emerging worldwide and monitoring them is key in providing early warnings. Here, we summarize the different analytical approaches currently used to study the dissemination of SARS-CoV-2 variants in wastewater and discuss their advantages and disadvantages. We also provide preliminary results of two sensitive and cost-effecti...
Article
Full-text available
Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food saf...
Article
Full-text available
In the wake of the COVID-19 pandemic, the use of next generation sequencing (NGS) has proved to be an important tool for the genetic characterization of SARS-CoV-2 from clinical samples. The use of different available NGS tools applied to wastewater samples could be the key for an in-depth study of the excreted virome, not only focusing on SARS-CoV...
Book
Full-text available
Recreational use of water can have major benefits for health and well-being. From children playing in a river to families relaxing on a beach, from people taking part in water sports to observing waterside nature, all shapes and sizes of bodies – be they oceans, lakes or rivers – of water can uplift the spirit and enhance physical and mental well-b...
Article
Quantitative measurements of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in raw wastewater have been implemented worldwide since the beginning of the pandemic. Recent efforts are being made to evaluate different viral concentration methodologies to overcome supplier shortages during lockdowns. A set of 22-wastewater samples see...
Article
Full-text available
Wastewater based epidemiology was employed to track the spread of SARS-CoV-2 within the sewershed areas of 10 wastewater treatment plants (WWTPs) in Catalonia, Spain. A total of 185 WWTPs inflow samples were collected over the period consisting of both the first wave (mid-March to June) and the second wave (July to November). Concentrations of SARS...
Article
Full-text available
Acute infectious gastroenteritis is an important illness worldwide, especially on children, with viruses accounting for approximately 70% of the acute cases. A high number of these cases have an unknown etiological agent and the rise of next generation sequencing technologies has opened new opportunities for viral pathogen detection and discovery....
Article
Since the novel SARS-CoV-2 was detected in faeces, environmental researchers have been using centrifugal ultrafiltration, polyethylene glycol precipitation and aluminium hydroxide flocculation to describe its presence in wastewater samples. High recoveries (up to 65%) are described with electronegative filtration when using surrogate viruses, but f...
Article
Full-text available
The COVID-19 pandemic placed hygiene at the centre of disease prevention. Yet, access to the levels of water supply that support good hand hygiene and institutional cleaning, our understanding of hygiene behaviours, and access to soap are deficient in low-, middle-and high-income countries. This paper reviews the role of water, sanitation and hygie...
Article
Full-text available
The COVID-19 pandemic placed hygiene at the centre of disease prevention. Yet, access to the levels of water supply that support good hand hygiene and institutional cleaning, our understanding of hygiene behaviours, and access to soap are deficient in low-, middle- and high-income countries. This paper reviews the role of water, sanitation and hygi...
Article
Full-text available
The COVID-19 pandemic placed hygiene at the centre of disease prevention. Yet, access to the levels of water supply that support good hand hygiene and institutional cleaning, our understanding of hygiene behaviours, and access to soap are deficient in low-, middle- and high-income countries. This paper reviews the role of water, sanitation and hygi...
Article
Worldwide, clinical data remain the gold standard for disease surveillance and tracking. However, such data are limited due to factors such as reporting bias and inability to track asymptomatic disease carriers. Disease agents are excreted in the urine and feces of infected individuals regardless of disease symptom severity. Wastewater surveillance...
Article
Full-text available
Bivins, Aaron et al. "Wastewater-Based Epidemiology: Global Collaborative to Maximize Contributions in the Fight Against COVID-19." Environmental Science & Technology (June 2020) © 2020 American Chemical Society
Article
Full-text available
Rotavirus A (RVA) is the most common virus associated with infantile gastroenteritisworldwide, being a public health threat, as it is excreted in large amounts in stool and can persist inthe environment for extended periods. In this study, we performed the detection of RVA and humanadenovirus (HAdV) by TaqMan qPCR and assessed the circulation of RV...
Article
NGS techniques are excellent tools to monitor and identify viral pathogens circulating among the population with some limitations that need to be overcome, especially in complex matrices. Sewage contains a high amount of other microorganisms that could interfere when trying to sequence viruses for which random PCR amplifications are needed before N...
Article
Viruses (e.g., noroviruses and hepatitis A and E virus), bacteria (e.g., Salmonella spp. and pathogenic Escherichia coli) and protozoa (e.g., Cryptosporidium parvum and Giardia intestinalis) are well-known contributors to food-borne illnesses linked to contaminated fresh produce. As agricultural irrigation increases the total amount of water used a...
Article
Thewide diversity of irrigationwater sources (i.e., drinking water, groundwater, reservoirwater, riverwater) includes reclaimedwater as a requested measure for increasing water availability, but it is also a challenge as pathogen exposure may increase. This study evaluates the level of microbial contamination in different irrigation waters to impro...
Article
The aim of this study is to investigate the occurrence of faecal indicator and microbial pathogens (bacteria and virus) in the shallow urban aquifer of the Besòs River Delta (NE Spain). To this end, human adenovirus (HAdV) and Norovirus of genogroups I and II (NoV GI and NoV GII) as well as the faecal indicator bacteria (FIB) Escherichia coli (EC)...
Article
Wastewater is an important resource in water-scarce regions of the world, and its use in agriculture requires the guarantee of acceptable public health risks. The use of fecal indicator bacteria to evaluate safety does not represent viruses, the main potential health hazards. Viral pathogens could complement the use of fecal indicator bacteria in t...
Article
In Quito, the microbiological contamination of surface water represents a public health problem, mainly due to the lack of sewage treatment from urban wastewater. Contaminated water contributes to the transmission of many enteric pathogens through direct consumption, agricultural and recreational use. Among the different pathogens present in urban...
Article
Full-text available
The qualified presumption of safety (QPS) was developed to provide a harmonised generic pre-evaluation procedure to support safety risk assessments of biological agents performed by EFSA's Scientific Panels. The identity, body of knowledge, safety concerns and antimicrobial resistance of valid taxonomic units were assessed. Safety concerns identifi...
Article
Full-text available
EFSA was requested: to assess the impact of a proposed quantitative real-time polymerase chain reaction (qPCR) 'technical zero' on the limit of detection of official controls for constituents of ruminant origin in feed, to review and update the 2011 QRA, and to estimate the cattle bovine spongiform encephalopathy (BSE) risk posed by the contaminati...
Article
Full-text available
EFSA received an application from the Dutch Competent Authority, under Article 20 of Regulation (EC) No 1069/2009 and Regulation (EU) No 142/2011, for the evaluation of an alternative method for treatment of Category 3 animal by-products (ABP). It consists of the hydrolysis of the material to short-carbon chains, resulting in medium-chain fatty aci...
Article
Full-text available
Abstract The qualified presumption of safety (QPS) concept was developed to provide a harmonised generic pre‐evaluation to support safety risk assessments of biological agents performed by EFSA's scientific Panels. The identity, body of knowledge, safety concerns and antimicrobial resistance of valid taxonomic units were assessed. Safety concerns i...
Article
Full-text available
Abstract Food safety criteria for Listeria monocytogenes in ready‐to‐eat (RTE) foods have been applied from 2006 onwards (Commission Regulation (EC) 2073/2005). Still, human invasive listeriosis was reported to increase over the period 2009–2013 in the European Union and European Economic Area (EU/EEA). Time series analysis for the 2008–2015 period...
Article
Full-text available
Abstract The European Commission asked EFSA for a scientific opinion on chronic wasting disease in two parts. Part one, on surveillance, animal health risk‐based measures and public health risks, was published in January 2017. This opinion (part two) addresses the remaining Terms of Reference, namely, ‘are the conclusions and recommendations in the...
Article
Full-text available
The European Food Safety Authority asked the Panel on Biological Hazards (BIOHAZ) to deliver a scientific opinion providing: (i) a review of the approaches used by the BIOHAZ Panel to address requests from risk managers to suggest the establishment of microbiological criteria; (ii) guidance on the required scientific evidence, data and methods/tool...
Article
Full-text available
A new alternative method for the production of biodiesel from rendered fat of all categories of animal by-products was assessed. The process was compared to the approved biodiesel production process described in Chapter IV Section 2 D of Annex IV of Commission Regulation (EU) 142/2011. Tallow derived from Category 1 material is treated according to...
Article
Full-text available
Hepatitis is a general term meaning inflammation of the liver, which can be caused by a variety of viruses. However, a substantial number of cases remain with unknown aetiology. We analysed the serum of patients with clinical signs of hepatitis using a metagenomics approach to characterize their viral species composition. Four pools of patients wit...
Data
Individual phylogenetic trees computed from contigs over reference genome locations in HEV. (DOCX)
Data
Individual phylogenetic trees computed from contigs over reference genome locations in Anelloviridae family. (DOCX)
Article
Full-text available
ECDC, EFSA and EMA have jointly established a list of harmonised outcome indicators to assist EU Member States in assessing their progress in reducing the use of antimicrobials and antimicrobial resistance (AMR) in both humans and food-producing animals. The proposed indicators have been selected on the basis of data collected by Member States at t...
Article
The application of next-generation sequencing (NGS) techniques for the identification of viruses present in urban sewage has not been fully explored. This is partially due to a lack of reliable and sensitive protocols for studying viral diversity and to the highly complex analysis required for NGS data processing. One important step towards this go...
Article
Full-text available
Breeding programmes to promote resistance to classical scrapie, similar to those for sheep in existing transmissible spongiform encephalopathies (TSE) regulations, have not been established in goats. The European Commission requested a scientific opinion from EFSA on the current knowledge of genetic resistance to TSE in goats. An evaluation tool, w...
Article
Full-text available
Hepatitis E virus (HEV) is an important infection in humans in EU/EEA countries, and over the last 10 years more than 21,000 acute clinical cases with 28 fatalities have been notified with an overall 10-fold increase in reported HEV cases; the majority (80%) of cases were reported from France, Germany and the UK. However, as infection in humans is...
Article
Full-text available
Sixty bovine spongiform encephalopathy (BSE) cases of Classical or unknown type (BARB-60 cases) were born after the date of entry into force of the EU total feed ban on 1 January 2001. The European Commission has requested EFSA to provide a scientific opinion on the most likely origin(s) of these BARB-60 cases; whether feeding with material contami...
Article
Full-text available
The qualified presumption of safety (QPS) concept was developed to provide a harmonised generic pre-evaluation to support safety risk assessments of biological agents performed by EFSA's scientific Panels. The identity, body of knowledge, safety concerns and antimicrobial resistance of valid taxonomic units were assessed. Safety concerns identified...
Article
Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contam...
Article
Full-text available
EFSA is requested to assess the safety of a broad range of biological agents in the context of notification for market authorisation as sources of food and feed additives, food enzymes and plant protection products. The qualified presumption of safety (QPS) assessment was developed to provide a harmonised generic pre-assessment to support safety ri...
Article
Full-text available
Under current European hygiene legislation, food businesses are obliged to develop and implement food safety management systems (FSMS) including prerequisite programme (PRP) activities and hazard analysis and critical control point principles. This requirement is especially challenging for small food retail establishments, where a lack of expertise...
Article
Full-text available
EFSA was requested to assess the safety of a broad range of biological agents in the context of notifications for market authorisation as sources of food and feed additives, enzymes and plant protection products. The qualified presumption of safety (QPS) assessment was developed to provide a harmonised generic pre-assessment to support safety risk...
Article
Full-text available
EFSA was requested to: 1) assess the risk for the development of antimicrobial resistance (AMR) due to feeding on farm of calves with colostrum potentially containing residues of antibiotics; 2) assess the risk for the development of AMR due to feeding on farm of calves with milk of cows treated during lactation with an antibiotic and milked during...
Article
Full-text available
Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentrati...
Article
Full-text available
In April and May of 2016, Norway confirmed two cases of chronic wasting disease (CWD) in a wild reindeer and a wild moose, respectively. In the light of this emerging issue, the European Commission requested EFSA to recommend surveillance activities and, if necessary, additional animal health risk-based measures to prevent the introduction of the d...
Data
Distribution of reads on kingdom level of the 16 method combinations and their associated negative controls. Samples were processed in triplicate, and the data shown is the average. _S = sample, _C = Negative extraction control. Databases used are listed in S1 Table. (PDF)
Data
HAdV concentration measured by qPCR. (A) HAdV concentration in extracts obtained by using four different concentration methods and (B) extraction methods. The bar, box, whiskers and circles represents median, inter-quartile range, inter-quartile range times 1.5, and outliers, respectively. Asterisks represent significance level of a pairwise t-test...
Data
Overview of reference sequence databases and associated download information. Reference sequence information can be obtained from the URL’s shown in ‘Download information’. (PDF)
Data
Sequence information. Number of raw reads, reads after quality assessment, and reads not mapping to PhiX, and thus usable for subsequent analysis. _S = sample, _C = Negative control. (PDF)
Data
qPCR inhibition of MNV and HAdV. Inhibition of the 16 combinations of concentration and extraction methods. Inhibition was measured using qPCR of undiluted (1:1) and tenfold diluted (1:10) DNA/RNA extracts. The values in the tables represents Δct between the undiluted and 10 fold diluted samples. A Δct = -3.3 represent a perfect 10 fold dilution. S...
Data
MNV concentrations measured by qPCR. (A) MNV concentration in extracts obtained by using four different concentration methods and (B) extraction methods. The bar, box and whiskers represents the median, the inter-quartile range, and the inter-quartile range times 1.5, respectively. Asterisks represent significance level of a pairwise t-test with “H...
Data
Abundance of all detected viral families. Heatmap showing the abundance of all detected viral families, measured in reads per million, in each biological replica for the different method combinations as well as the controls. _S = sample, _C = Negative control. (PDF)
Data
Specifications of the four concentration methods applied in this study. (PDF)
Data
Properties of the four nucleic acid extraction kits applied in this study. (PDF)
Article
Full-text available
In this study, the use of skimmed milk flocculation (SMF) to simultaneously concentrate viruses, bacteria and protozoa was evaluated. We selected strains of faecal indicator bacteria and pathogens, such as Escherichia coli and Helicobacter pylori. The viruses selected were adenovirus (HAdV 35), rotavirus (RoV SA-11), the bacteriophage MS2 and bovin...