Microbial Risk Analysis最新文献

{"title":"Eris - another brick in the wall: Empirical formulas, molar masses, biosynthesis reactions, enthalpy, entropy and Gibbs energy of Omicron EG.5 Eris and EG.5.1 variants of SARS-CoV-2","authors":"Marko E. Popović ,&nbsp;Marijana Pantović Pavlović ,&nbsp;Marta Popović","doi":"10.1016/j.mran.2023.100280","DOIUrl":"https://doi.org/10.1016/j.mran.2023.100280","url":null,"abstract":"<div><p>Since 2019, when it appeared in Wuhan, in the wild type form later labeled Hu-1, SARS-CoV-2 mutated dozens of times and evolved towards increase in infectivity and decrease or maintenance of constant pathogenicity through dozens of variants. The last of them are Omicron EG.5 and EG.5.1. Until 2019, an empirical formula was known only for the poliovirus. Until now empirical formulas and thermodynamic properties were reported for all variants of SARS-CoV-2 and some other viruses. Also, models were developed that describe the biothermodynamic background of SARS-CoV-2 interaction with its human host. With every new mutation in SARS-CoV-2, the question is raised about the further evolution of the virus. This paper reports for the first time empirical formulas and molar masses of Omicron EG.5 and EG.5.1 variants, as well as thermodynamic properties (enthalpy, entropy and Gibbs energy) of formation and biosynthesis. Moreover, the driving force of virus multiplication was analyzed, as well as multiplication rate and pathogenicity of Omicron EG.5 and EG.5.1.</p></div>","PeriodicalId":48593,"journal":{"name":"Microbial Risk Analysis","volume":"25 ","pages":"Article 100280"},"PeriodicalIF":2.8,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49762866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Death from the Nile: Empirical formula, molar mass, biosynthesis reaction and Gibbs energy of biosynthesis of the West Nile virus","authors":"Marko Popovic ,&nbsp;Marta Popovic ,&nbsp;Gavrilo Šekularac","doi":"10.1016/j.mran.2023.100281","DOIUrl":"https://doi.org/10.1016/j.mran.2023.100281","url":null,"abstract":"<div><p>From July to October, West Nile virus is the leading cause of mosquito born disease in Europe and North America. This paper reports for the first time a chemical and thermodynamic analysis of the West Nile virus particles, genome and proteins, as well as interactions with its host organism. The empirical formula of mature West Nile virus particles was found through the atom counting method. Based on the empirical formula, biosynthesis reactions were formulated, which describe the formation of new virus live matter. Based on the biosynthesis reactions, Gibbs energy of biosynthesis was determined, which represents the physical driving force for the production of viral and host cell components. Gibbs energy of biosynthesis of the West Nile virus was found to be several times more negative than that of its host tissues. Due to the more negative Gibbs energy of biosynthesis, the West Nile virus components are produced much faster than those of its host cells. This allows the virus to hijack the host cell metabolism. Therefore, the virus-host interactions of the West Nile virus were explained through chemical and thermodynamic analysis.</p></div>","PeriodicalId":48593,"journal":{"name":"Microbial Risk Analysis","volume":"25 ","pages":"Article 100281"},"PeriodicalIF":2.8,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49739064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modelling the kinetics of Staphylococcus aureus in goat's raw milk under different sub-pasteurisation temperatures","authors":"Beatriz Nunes Silva ,&nbsp;Sara Coelho-Fernandes ,&nbsp;José António Teixeira ,&nbsp;Vasco Cadavez ,&nbsp;Ursula Gonzales-Barron","doi":"10.1016/j.mran.2023.100279","DOIUrl":"https://doi.org/10.1016/j.mran.2023.100279","url":null,"abstract":"<div><p>In this study, the heat resistance of <em>S. aureus</em> in goats’ raw milk subjected to thermisation temperatures was characterised through tests at various temperatures and modelling the survival curves using the Weibull model, through a two-step and an omnibus approach, which can model a full dataset covering all experimental conditions in one step. The fitting capacity of the secondary models obtained from the two-step approach was reasonable (adj. R² &gt; 0.639) and both demonstrated the negative linear effects of temperature on <span><math><msqrt><mi>χ</mi></msqrt></math></span> (<em>p</em> = 0.0004) and <span><math><msqrt><mi>β</mi></msqrt></math></span> (<em>p</em> = 0.017). The fitting capacity of the omnibus model was more satisfactory (adj. R² = 0.996) and also hinted at the negative linear effect of temperature on <span><math><msqrt><mi>χ</mi></msqrt></math></span> (<em>p</em> &lt; 0.0001), with the added advantage that, in this model, random effects can be used to account for the variability in the parameters. Our study estimated the significant inactivation parameters and established a model capable of predicting <em>S. aureus</em> behaviour at various temperatures. This information is useful to create time-temperature tables to reach target log reductions of <em>S. aureus</em> in goats’ raw milk to be used by artisanal cheesemakers; hence providing an opportunity to increase the microbiological safety of cheeses made from unpasteurised milk.</p></div>","PeriodicalId":48593,"journal":{"name":"Microbial Risk Analysis","volume":"25 ","pages":"Article 100279"},"PeriodicalIF":2.8,"publicationDate":"2023-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2352352223000348/pdfft?md5=000a570b29c8f2b4b01b9065ebbda8a5&pid=1-s2.0-S2352352223000348-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92046169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comparative study between the top 10 origin countries involved in the EU RASFF notifications on aflatoxins from 1997 to 2022","authors":"Fawzy Eissa ,&nbsp;Ahmed Salem Sebaei","doi":"10.1016/j.mran.2023.100277","DOIUrl":"https://doi.org/10.1016/j.mran.2023.100277","url":null,"abstract":"<div><p>Aflatoxin B1 (AFB1), is among the most carcinogenic and genotoxic food and feed contaminants and there is no acceptable level of their intake. An analysis of the top 10 countries of origin notifications on aflatoxins (AFs) involved in the EU RASFF database over the last 26 years was undertaken. A risk assessment was estimated for simulating the worst-case scenario for the serious notifications of the mostly notified products as well. Out of 12,400 notifications on AFs over the period between 1997 and 2022, of which 10,340 (83.39 %) concerned Iran which was the most frequently notified country (21.56 %), followed by Turkey (20.48), China (9.99 %), India (7.88 %), the USA (7.74 %), Argentina (5.82 %), Egypt (3.94 %), Brazil (3.05 %), Pakistan (1.52 %), and Nigeria (1.41 %). Germany was the most notifying country, followed by the Netherlands. Among all notifications, 53.3 % have been border rejected. Nuts, nuts products, and seeds were the highest notified product category followed by fruits and vegetables. The highest serious risk decision in terms of notification number was taken for contaminated dried fig from Turkey, followed by pistachio from Iran. The estimated margin of exposure (MOE) values for the mostly notified products i.e., pistachio, dried fig, and peanut were &lt;10,000 which is not safe and represents a health concern.</p></div>","PeriodicalId":48593,"journal":{"name":"Microbial Risk Analysis","volume":"25 ","pages":"Article 100277"},"PeriodicalIF":2.8,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49739526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico binding affinity of the spike protein with ACE2 and the relative evolutionary distance of S gene may be potential factors rapidly obtained for the initial risk of SARS-CoV-2","authors":"Aki Sugano ,&nbsp;Junon Murakami ,&nbsp;Haruyuki Kataguchi ,&nbsp;Mika Ohta ,&nbsp;Yoshiaki Someya ,&nbsp;Shigemi Kimura ,&nbsp;Akira Kanno ,&nbsp;Yoshimasa Maniwa ,&nbsp;Toshihide Tabata ,&nbsp;Kazuyuki Tobe ,&nbsp;Yutaka Takaoka","doi":"10.1016/j.mran.2023.100278","DOIUrl":"https://doi.org/10.1016/j.mran.2023.100278","url":null,"abstract":"<div><h3>Objectives</h3><p>In this research, we aimed to find potential factors which are rapidly obtained for the risk of the coming new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), when their genetic substitutions were detected in late 2022.</p></div><div><h3>Methods</h3><p>We first performed molecular docking simulation<span> analyses of the spike proteins with human angiotensin-converting enzyme 2 (ACE2) by using ZDOCK program to determine the binding affinities to human cells of three new variants of SARS-CoV-2: Omicron BQ.1, XBB, and XBB.1.5. We then investigated the three variants to determine the relative evolutionary distance of the spike protein gene (S gene) from the Wuhan, Omicron BA.1, and Omicron BA.4/5 variants.</span></p></div><div><h3>Results</h3><p>The results indicated that Omicron BQ.1. had a highest binding affinity but had the shortest evolutionary distance from BA.4/5. The XBB variant had a lower binding affinity and long evolutionary distances from all the three variants. However, the XBB.1.5 variant had the highest binding affinity of the spike protein with ACE2 and the longest evolutionary distance of the S gene.</p></div><div><h3>Conclusion</h3><p>This result suggested that <em>in silico</em> binding affinity of the spike protein with ACE2 and the relative evolutionary distance of S gene may be potential factors for the risk of SARS-CoV-2 variants based on the comparison of infectivity of BQ.1, XBB, and XBB.1.5.</p></div>","PeriodicalId":48593,"journal":{"name":"Microbial Risk Analysis","volume":"25 ","pages":"Article 100278"},"PeriodicalIF":2.8,"publicationDate":"2023-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49739485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Risk of African swine fever incursion into the Netherlands by wild boar carcasses and meat carried by Dutch hunters from hunting trips abroad","authors":"Manon Swanenburg,&nbsp;Tosca Ploegaert,&nbsp;Michiel Kroese,&nbsp;Clazien J. de Vos","doi":"10.1016/j.mran.2023.100276","DOIUrl":"10.1016/j.mran.2023.100276","url":null,"abstract":"<div><p>After the first introduction of African swine fever (ASF) in the European Union in 2014, the ASF virus (ASFV) has steadily spread in the European Union. The virus has occasionally been transmitted over unexpectedly large distances that are believed to be related to human-mediated spread. Hunting tourism has been mentioned as a potential contributor to these long-distance jumps, although evidence is lacking. In this study, the possible role of hunters carrying ASFV-contaminated wild boar products (WBP) from hunting trips in affected countries was evaluated. A quantitative risk model was developed to estimate the expected annual number of ASF exposures of wild boar and domestic pigs in the Netherlands via this introduction route. Main input data into the model were the ASF prevalence in hunted wild boar, the number and destination of hunting trips of Dutch hunters, and the probabilities that hunters take WBP home and dispose leftovers such that wild boar or domestic pigs have access. The model indicated that the total expected annual number of exposures (wild boar and domestic pigs together) in the Netherlands is 0.048 (95% uncertainty interval 7.5 × 10⁻³ – 0.15). Model results were most sensitive to uncertainty on leftovers fed to domestic pigs (swill feeding), which is an illegal practice. Uncertainties on the ASF prevalence of hunted wild boar and the probabilities that hunters take WBP home also impacted model results. Default model results were based on the 2019 situation. Alternative scenarios were run with the model to account for the change of ASF status of Belgium (recovery of ASF-free status) and Germany (ASF-infected) in 2020. Results indicated that especially the presence of ASF in Germany increased the incursion risk. However, this increase might be counteracted by a change in travel behavior of hunters.</p></div>","PeriodicalId":48593,"journal":{"name":"Microbial Risk Analysis","volume":"25 ","pages":"Article 100276"},"PeriodicalIF":2.8,"publicationDate":"2023-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43988596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Risk factors for contaminated blood cultures in the emergency department: A prospective cohort study","authors":"Koshi Ota ,&nbsp;Yuriko Takeda ,&nbsp;Daisuke Nishioka ,&nbsp;Masahiro Oka ,&nbsp;Emi Hamada ,&nbsp;Kanna Ota ,&nbsp;Yuriko Shibata ,&nbsp;Kazuma Yamakawa ,&nbsp;Akira Takasu","doi":"10.1016/j.mran.2023.100264","DOIUrl":"10.1016/j.mran.2023.100264","url":null,"abstract":"<div><h3>Background</h3><p>We aimed to determine risk factors associated with rates of contaminated blood cultures in the emergency department (ED).</p></div><div><h3>Methods</h3><p>This single-center, cohort study of 1098 consecutive patients ≥ 20 years of age was performed in the ED of university hospital over a 26-month period.</p></div><div><h3>Results</h3><p>We analyzed 2096 pairs of blood cultures. Potential contamination was identified in 172 (8.2%) of the 2096 pairs of blood cultures. Multivariate analysis revealed more frequent contamination when puncture sites were disinfected with povidone-iodine (PVI) than with alcohol/chlorhexidine gluconate (adjusted odds ratio, 7.13; 95% confidence interval [CI], 4.8–10.7; <em>P</em> &lt; 0.001). Femoral and central venous catheters showed more frequent contamination than peripheral venous sites. Blood collection by first- or second-year residents did not show an increase in contaminated blood cultures.</p></div><div><h3>Conclusions</h3><p>Rates of contaminated blood cultures were significantly associated with PVI and specific sites, but were not significantly associated with blood collection by residents.</p></div>","PeriodicalId":48593,"journal":{"name":"Microbial Risk Analysis","volume":"24 ","pages":"Article 100264"},"PeriodicalIF":2.8,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45302867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ghosts of the past: Elemental composition, biosynthesis reactions and thermodynamic properties of Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2","authors":"Marko Popovic ,&nbsp;Marijana Pantović Pavlović ,&nbsp;Miroslav Pavlović","doi":"10.1016/j.mran.2023.100263","DOIUrl":"10.1016/j.mran.2023.100263","url":null,"abstract":"<div><p>From the perspectives of molecular biology, genetics and biothermodynamics, SARS-CoV-2 is the among the best characterized viruses. Research on SARS-CoV-2 has shed a new light onto driving forces and molecular mechanisms of viral evolution. This paper reports results on empirical formulas, biosynthesis reactions and thermodynamic properties of biosynthesis (multiplication) for the Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2. Thermodynamic analysis has shown that the physical driving forces for evolution of SARS-CoV-2 are Gibbs energy of biosynthesis and Gibbs energy of binding. The driving forces have led SARS-CoV-2 through the evolution process from the original Hu-1 to the newest variants in accordance with the expectations of the evolution theory.</p></div>","PeriodicalId":48593,"journal":{"name":"Microbial Risk Analysis","volume":"24 ","pages":"Article 100263"},"PeriodicalIF":2.8,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10199755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9990864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SARS-CoV-2 strain wars continues: Chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants","authors":"Marko Popovic","doi":"10.1016/j.mran.2023.100260","DOIUrl":"10.1016/j.mran.2023.100260","url":null,"abstract":"<div><p>SARS-CoV-2 has during the last 3 years mutated several dozen times. Most mutations in the newly formed variants have been chemically and thermodynamically characterized. New variants have been declared as variants under monitoring. The European Centre for Disease Prevention and Control has suggested the hypothesis that the new BN.1, CH.1.1 and XBC variants could have properties similar to those of VOC. Thermodynamic properties of new variants have been reported in this manuscript for the first time. Gibbs energy of biosynthesis, as the driving force for viral multiplication, is less negative for the new variants than for the earlier variants. This indicates that the virus has evolved towards decrease in pathogenicity, which leads to less severe forms of COVID-19.</p></div>","PeriodicalId":48593,"journal":{"name":"Microbial Risk Analysis","volume":"24 ","pages":"Article 100260"},"PeriodicalIF":2.8,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10032061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9972096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel approach to biological risk surveillance in occupational hygiene: A case study on the use of quantitative microbial risk assessment to determine occupational risks for wastewater treatment plants workers in Costa Rica","authors":"Eric Morales ,&nbsp;Andrei Badilla ,&nbsp;Pablo Rivera ,&nbsp;Ernesto Alfaro ,&nbsp;Erin M. Symonds ,&nbsp;Kenia Barrantes ,&nbsp;Clemens Ruepert ,&nbsp;Jennifer Crowe ,&nbsp;Luz Chacón","doi":"10.1016/j.mran.2023.100262","DOIUrl":"10.1016/j.mran.2023.100262","url":null,"abstract":"<div><p>Wastewater treatment is essential for preventing infectious diseases and water pollution. To perform this process, workers operate and maintain wastewater treatment plants (WWTPs); thus, they are exposed to the many pathogens in domestic wastewater. Consequently, it is necessary assess occupational exposure to pathogens in WWTPs. Quantitative microbial risk assessment (QMRA) is an approach for estimating the risk posed by a specific pathogen which can be useful for occupational hygiene assessments of biological risk. In this study, we applied QMRA, informed by occupational field surveillance, to estimate the potential risk for WWTP workers. Furthermore, we used simulations to test additional control strategies such as personal protective equipment (PPE). The QMRA was conducted for three WWTPs in Costa Rica with data collected between May 2020 and May 2021. Observation in each workplace showed a need for more consistent application of risk reduction strategies in the work environment, especially in behavior, infrastructure, and use of appropriate PPE. <span><em>Cryptosporidium</em></span> sp., <span><em>Giardia</em></span><span> sp., norovirus, and enterovirus genus were measured and detected in the WWTPs, and the treatment performance was unsatisfactory. As a result, the total health disease burden was higher than the benchmark for drinking water recommended by WHO (1.00 × 10</span>⁻⁶ DALY per person per year) by between one and three magnitudes orders in all WWTPs for the three exposure scenarios (operation, maintenance, and visitors). The simulation demonstrated that using PPE could reduce the estimated disease burden by nearly two orders of magnitude. Still, this control measure did not reach a level below the benchmark risk (less than 1.00 × 10⁻⁶ DALY per person per year) for the WWTP workers. This study highlights the importance of using PPE with other control measures, such as automation or barriers, to isolate exposure sources. However, this study employed an uncommon approach in occupational health and hygiene, which combined field inspections, survival analysis, and QMRA, using field surveillance to understand the occupational environment and potential exposure routes, which is crucial for hazard identification and risk assessment. In addition, exposure modeling and QMRA were used to simulate different control scenarios, providing a robust estimate of potential risks associated with occupational exposure.</p></div>","PeriodicalId":48593,"journal":{"name":"Microbial Risk Analysis","volume":"24 ","pages":"Article 100262"},"PeriodicalIF":2.8,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47220472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}