Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 200,000 reported COVID-19 cases in Spain resulting in more than 20,800 deaths as of April 21, 2020. Faecal shedding ...of SARS-CoV-2 RNA from COVID-19 patients has extensively been reported. Therefore, we investigated the occurrence of SARS-CoV-2 RNA in six wastewater treatments plants (WWTPs) serving the major municipalities within the Region of Murcia (Spain), the area with the lowest COVID-19 prevalence within Iberian Peninsula. Firstly, an aluminum hydroxide adsorption-precipitation concentration method was validated using a porcine coronavirus (Porcine Epidemic Diarrhea Virus, PEDV) and mengovirus (MgV). The procedure resulted in average recoveries of 10 ± 3.5% and 10 ± 2.1% in influent water (n = 2) and 3.3 ± 1.6% and 6.2 ± 1.0% in effluent water (n = 2) samples for PEDV and MgV, respectively. Then, the method was used to monitor the occurrence of SARS-CoV-2 from March 12 to April 14, 2020 in influent, secondary and tertiary effluent water samples. By using the real-time RT-PCR (RT-qPCR) Diagnostic Panel validated by US CDC that targets three regions of the virus nucleocapsid (N) gene, we estimated quantification of SARS-CoV-2 RNA titers in untreated wastewater samples of 5.4 ± 0.2 log10 genomic copies/L on average. Two secondary water samples resulted positive (2 out of 18) and all tertiary water samples tested as negative (0 out 12). This environmental surveillance data were compared to declared COVID-19 cases at municipality level, revealing that members of the community were shedding SARS-CoV-2 RNA in their stool even before the first cases were reported by local or national authorities in many of the cities where wastewaters have been sampled. The detection of SARS-CoV-2 in wastewater in early stages of the spread of COVID-19 highlights the relevance of this strategy as an early indicator of the infection within a specific population. At this point, this environmental surveillance could be implemented by municipalities right away as a tool, designed to help authorities to coordinate the exit strategy to gradually lift its coronavirus lockdown.
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•An adsorption-precipitation concentration method was validated using a porcine coronavirus.•First detection of SARS-CoV-2 RNA in untreated wastewater in Spain.•11% secondary treated water samples tested positive for at least one SARS-CoV-2 RT-qPCR target.•None of the tertiary effluent samples (n = 12) tested positive for SARS-CoV-2.•SARS-CoV-2 RNA was detected in wastewater before the first COVID-19 cases were declared by local authorities.
Wastewater based epidemiology (WBE) has emerged as a reliable strategy to assess the coronavirus disease 2019 (COVID-19) pandemic. Recent publications suggest that SARS-CoV-2 detection in wastewater ...is technically feasible; however, many different protocols are available and most of the methods applied have not been properly validated. To this end, different procedures to concentrate and extract inactivated SARS-CoV-2 and surrogates were initially evaluated. Urban wastewater seeded with gamma-irradiated SARS-CoV-2, porcine epidemic diarrhea virus (PEDV), and mengovirus (MgV) was used to test the concentration efficiency of an aluminum-based adsorption-precipitation method and a polyethylene glycol (PEG) precipitation protocol. Moreover, two different RNA extraction methods were compared in this study: a commercial manual spin column centrifugation kit and an automated protocol based on magnetic silica beads. Overall, the evaluated concentration methods did not impact the recovery of gamma-irradiated SARS-CoV-2 nor MgV, while extraction methods showed significant differences for PEDV. Mean recovery rates of 42.9 ± 9.5%, 27.5 ± 14.3% and 9.0 ± 2.2% were obtained for gamma-irradiated SARS-CoV-2, PEDV and MgV, respectively. Limits of detection (LoD95%) for five genomic SARS-CoV-2 targets (N1, N2, gene E, IP2 and IP4) ranged from 1.56 log genome equivalents (ge)/mL (N1) to 2.22 log ge/mL (IP4) when automated system was used; while values ranging between 2.08 (N1) and 2.34 (E) log ge/mL were observed when using column-based extraction method. Different targets were also evaluated in naturally contaminated wastewater samples with 91.2%, 85.3%, 70.6%, 79.4% and 73.5% positivity, for N1, N2, E, IP2 and IP4, respectively. Our benchmarked comparison study suggests that the aluminum precipitation method coupled with the automated nucleic extraction represents a method of acceptable sensitivity to provide readily results of interest for SARS-CoV-2 WBE surveillance.
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•Gamma-irradiated SARS-CoV-2 was used to assess method performance.•Different methods were compared for SARS-CoV-2 WBE surveillance.•Tested methods showed no significant differences for SARS-CoV-2 recovery from wastewater.•Automated nucleic acid extraction showed lower LoD95% than column based method.•Different sensitivity of RT-qPCR assays was observed.
It is well known that fresh-cut processors usually rely on wash water sanitizers to reduce microbial counts in order to maintain quality and extend shelf-life of the end product. Water is a useful ...tool for reducing potential contamination but it can also transfer pathogenic microorganisms. Washing with sanitizers is important in fresh-cut produce hygiene, particularly removing soil and debris, but especially in water disinfection to avoid cross-contamination between clean and contaminated product. Most of the sanitizing solutions induce higher microbial reduction after washing when compared to water washing, but after storage, epiphytic microorganisms grow rapidly, reaching similar levels. In fact, despite the general idea that sanitizers are used to reduce the microbial population on the produce, their main effect is maintaining the microbial quality of the water. The use of potable water instead of water containing chemical disinfection agents for washing fresh-cut vegetables is being advocated in some European countries. However, the problems of using an inadequate sanitizer or even none are considered in this manuscript. The need for a standardized approach to evaluate and compare the efficiency of sanitizing agents is also presented. Most new alternative techniques accentuate the problems with chlorine suggesting that the industry should move away from this traditional disinfection agent. However, the use of chlorine based sanitizers are presented as belonging to the most effective and efficient sanitizers when adequate doses are used. In this review improvements in water disinfection and sanitation strategies, including a shower pre-washing step and a final rinse of the produce, are suggested.
Fresh-cut cilantro is particularly susceptible to microbial growth and, therefore, use of an effective sanitizer on this product is of great importance. The objective of this study was to evaluate ...the efficacy of different sanitizing treatments on reducing
Escherichia coli O157:H7 populations, aerobic mesophilic bacterial, yeast and mould counts on fresh-cut cilantro. Cut cilantro was treated with sodium hypochlorite (SH) at 0.2
g
L
−1 free chlorine and acidified sodium chlorite (ASC) at 0.1, 0.25, 0.5 and 1
g
L
−1, along with the components of ASC, i.e., citric acid (CA) at 6
g
L
−1 and sodium chlorite (SC) at 1
g
L
−1. In the present study, it was found that SH inactivated, at maximum, 1–1.3
log
cfu
g
−1 of background or pathogenic microflora present on cut cilantro. However, reductions of more than 3
log
cfu
g
−1 were observed after washing with 1
g
L
−1 of ASC. Moreover, when lower concentrations of ASC were used (0.25 and 0.5
g
L
−1), microbial populations were reduced by about 2
log
cfu
g
−1. SC was as effective as ASC at 1
g
L
−1 in reducing aerobic mesophilic bacteria and
E. coli O157:H7 populations, although it was not as effective as ASC in reducing yeast and mould populations.
The contamination of pathogenic bacteria through irrigation water is a recognized risk factor for fresh produce. Irrigation water disinfection is an intervention strategy that could be applied to ...reduce the probability of microbiological contamination of crops. Disinfection treatments should be applied ensuring minimum effective doses, which are efficient in inhibiting the microbial contamination while avoiding formation and accumulation of chemical residues. Among disinfection technologies available for growers, chlorine dioxide (ClO2) represents, after sodium hypochlorite, an alternative disinfection treatment, which is commercially applied by growers in the USA and Spain. However, in most of the cases, the suitability of this treatment has been tested against pathogenic bacteria and low attention have been given to the impact of chemical residues on the bacterial community of the vegetable tissue. The aim of this study was to (i) to evaluate the continual application of chlorine dioxide (ClO2) as a water disinfection treatment of irrigation water during baby spinach growth in commercial production open fields, and (ii) to determine the subsequent impact of these treatments on the bacterial communities in water, soil, and baby spinach. To gain insight into the changes in the bacterial community elicited by ClO2, samples of treated and untreated irrigation water as well as the irrigated soil and baby spinach were analyzed using Miseq® Illumina sequencing platform. Next generation sequencing and multivariate statistical analysis revealed that ClO2 treatment of irrigation water did not affect the diversity of the bacterial community of water, soil and crop, but significant differences were observed in the relative abundance of specific bacterial genera. This demonstrates the different susceptibility of the bacteria genera to the ClO2 treatment. Based on the obtained results it can be concluded that the phyllosphere bacterial community of baby spinach was more influenced by the soil bacteria community rather than that of irrigation water. In the case of baby spinach, the use of low residual ClO2 concentrations (approx. 0.25 mg/L) to treat irrigation water decreased the relative abundance of Pseudomonaceae (2.28-fold) and Enterobacteriaceae (2.5-fold) when comparing treated versus untreated baby spinach. Members of these two bacterial families are responsible for food spoilage and foodborne illnesses. Therefore, a reduction of these bacterial families might be beneficial for the crop and for food safety. In general it can be concluded that the constant application of ClO2 as a disinfection treatment for irrigation water only caused changes in two bacterial families of the baby spinach and soil microbiota, without affecting the major phyla and classes. The significance of these changes in the bacterial community should be further evaluated.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Wastewater-based epidemiology (WBE) has proven to be an effective tool for epidemiological surveillance of SARS-CoV-2 during the current COVID-19 pandemic. Furthermore, combining WBE together with ...high-throughput sequencing techniques can be useful for the analysis of SARS-CoV-2 viral diversity present in a given sample. The present study focuses on the genomic analysis of SARS-CoV-2 in 76 sewage samples collected during the three epidemiological waves that occurred in Spain from 14 wastewater treatment plants distributed throughout the country. The results obtained demonstrate that the metagenomic analysis of SARS-CoV-2 in wastewater allows the detection of mutations that define the B.1.1.7 lineage and the ability of the technique to anticipate the detection of certain mutations before they are detected in clinical samples. The study proves the usefulness of sewage sequencing to track Variants of Concern that can complement clinical testing to help in decision-making and in the analysis of the evolution of the pandemic.
•Spatial and temporal analysis of SARS-CoV-2 sequences from Spanish wastewaters.•Presence of amino acid substitutions in the spike protein not previously described in Spain.•Detection of amino acid substitutions in the spike protein even months before their detection in clinical samples.•SARS-CoV-2 genomics in wastewater as a complementary tool for WBE.
Summary
Among the many vascular complications of sickle cell disease (SCD), retinopathy is the most prevalent and represents a leading cause of blindness. Hydroxycarbamide therapy ameliorates many ...symptoms of SCD, and high fetal haemoglobin (HbF) levels have been shown to protect against the development of retinopathy in children with HbSS. Its effect on adults with SCD, who are at a much higher risk of developing retinopathy, has not been studied. We aimed to investigate the effect of hydroxycarbamide use and HbF level on sickle cell retinopathy development in adults. We performed a retrospective cross‐sectional study and collected demographics, comorbidities, and ocular and haematological data from 300 adult sickle cell subjects examined at the Henkind Eye Institute at Montefiore Medical Center during a 5‐year period, from October 2012 to November 2017. The cohort was comprised mainly of Black and Hispanic subjects with all SCD genotypes, aged 18–71 years. Results show that in HbSS patients treated with hydroxycarbamide, those with retinopathy had significantly lower HbF levels compared to patients without retinopathy (P = 0·018). Our study identified the optimal HbF cut‐off point for retinopathy protection to be 14·87%. Thus, a HbF level of 15% appears to be the threshold above which the odds for developing retinopathy in SS patients are reduced by 50%.
The significance of viable but non-culturable (VBNC) cells in the food industry is not well known, mainly because of the lack of suitable detection methodologies to distinguish them from dead cells. ...The study aimed at the selection of the method to differentiate dead and VBNC cells of
in process wash water (PWW) from the fruit and vegetable industry. Different methodologies were examined including (i) flow cytometry, (ii) viability quantitative polymerase chain reaction (v-qPCR) using an improved version of the propidium monoazide (PMAxx) dye as DNA amplificatory inhibitor, and (iii) v-qPCR combining ethidium monoazide (EMA) and PMAxx. The results showed that the flow cytometry, although previously recommended, was not a suitable methodology to differentiate between dead and VBNC cells in PWW, probably because of the complex composition of the water, causing interferences and leading to an overestimation of the dead cells. Based on results obtained, the v-qPCR combined with EMA and PMAxx was the most suitable technique for the detection and quantification of VBNC cells in PWW. Concentrations of 10 μM EMA and 75 μM PMAxx incubated at 40°C for 40 min followed by a 15-min light exposure inhibited most of the qPCR amplification from dead cells. For the first time, this methodology was validated in an industrial processing line for shredded lettuce washed with chlorine (10 mg/L). The analysis of PWW samples allowed the differentiation of dead and VBNC cells. Therefore, this method can be considered as a rapid and reliable one recommended for the detection of VBNC cells in complex water matrixes such as those of the food industry. However, the complete discrimination of dead and VBNC cells was not achieved, which led to a slight overestimation of the percentage of VBNC cells in PWW, mostly, due to the complex composition of this type of water. More studies are needed to determine the significance of VBNC cells in case of potential cross-contamination of fresh produce during washing.
The qualified presumption of safety (QPS) was developed to provide a safety pre‐assessment within EFSA for microorganisms. Strains belonging to QPS taxonomic units (TUs) still require an assessment ...based on a specific data package, but QPS status facilitates fast track evaluation. QPS TUs are unambiguously defined biological agents assessed for the body of knowledge, their safety and their end use. Safety concerns are, where possible, to be confirmed at strain or product level, and reflected as ‘qualifications’. Qualifications need to be evaluated at strain level by the respective EFSA units. The lowest QPS TU is the species level for bacteria, yeasts and protists/algae, and the family for viruses. The QPS concept is also applicable to genetically modified microorganisms used for production purposes if the recipient strain qualifies for the QPS status, and if the genetic modification does not indicate a concern. Based on the actual body of knowledge and/or an ambiguous taxonomic position, the following TUs were excluded from the QPS assessment: filamentous fungi, oomycetes, streptomycetes, Enterococcus faecium, Escherichia coli and bacteriophages. The list of QPS‐recommended biological agents was reviewed and updated in the current opinion and therefore now becomes the valid list. For this update, reports on the safety of previously assessed microorganisms, including bacteria, yeasts and viruses (the latter only when used for plant protection purposes) were reviewed, following an Extensive Literature Search strategy. All TUs previously recommended for 2016 QPS list had their status reconfirmed as well as their qualifications. The TUs related to the new notifications received since the 2016 QPS opinion was periodically evaluated for QPS status in the Statements of the BIOHAZ Panel, and the QPS list was also periodically updated. In total, 14 new TUs received a QPS status between 2017 and 2019: three yeasts, eight bacteria and three algae/protists.
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 in the EU/EEA indicated an increasing trend of the monthly notified incidence rate of confirmed human invasive listeriosis of the over 75 age groups and female age group between 25 and 44 years old (probably related to pregnancies). A conceptual model was used to identify factors in the food chain as potential drivers for L. monocytogenes contamination of RTE foods and listeriosis. Factors were related to the host (i. population size of the elderly and/or susceptible people; ii. underlying condition rate), the food (iii. L. monocytogenes prevalence in RTE food at retail; iv. L. monocytogenes concentration in RTE food at retail; v. storage conditions after retail; vi. consumption), the national surveillance systems (vii. improved surveillance), and/or the bacterium (viii. virulence). Factors considered likely to be responsible for the increasing trend in cases are the increased population size of the elderly and susceptible population except for the 25–44 female age group. For the increased incidence rates and cases, the likely factor is the increased proportion of susceptible persons in the age groups over 45 years old for both genders. Quantitative modelling suggests that more than 90% of invasive listeriosis is caused by ingestion of RTE food containing > 2,000 colony forming units (CFU)/g, and that one‐third of cases are due to growth in the consumer phase. Awareness should be increased among stakeholders, especially in relation to susceptible risk groups. Innovative methodologies including whole genome sequencing (WGS) for strain identification and monitoring of trends are recommended.
This publication is linked to the following EFSA Supporting Publications article: http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2018.EN-1352/full
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