The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

2 1 The innovative transport systems and the CityMobil project 10 1.1 The research questions 10 2 The state of art in the field of automatic transport systems 12 2.1 Case studies and demand studies for innovative transport systems 12 3 The design and implementation of surveys 14 3.1 Definition of experimental design 14 3.2 Questionnaire design and delivery 16 3.3 First analyses on the collected sample 18 4 Calibration of Logit Multionomial demand models 21 4.1 Methodology 21 4.2 Calibration of the “full” model. 22 4.3 Calibration of the “final” model 24 4.4 The demand analysis through the final Multinomial Logit model 25 5 The analysis of interaction between the demand and socioeconomic attributes 31 5.1 Methodology 31 5.2 Application of Mixed Logit models to the demand 31 5.3 Analysis of the interactions between demand and socioeconomic attributes through Mixed Logit models 32 5.4 Mixed Logit model and interaction between age and the demand for the CTS 38 5.5 Demand analysis with Mixed Logit model 39 6 Final analyses and conclusions 45 6.1 Comparison between the results of the analyses 45 6.2 Conclusions 48 6.3 Answers to the research questions and future developments 52

The European commission

Summary Background Since December, 2019, Wuhan, China, has experienced an outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Epidemiological and clinical characteristics of patients with COVID-19 have been reported but risk factors for mortality and a detailed clinical course of illness, including viral shedding, have not been well described. Methods In this retrospective, multicentre cohort study, we included all adult inpatients (≥18 years old) with laboratory-confirmed COVID-19 from Jinyintan Hospital and Wuhan Pulmonary Hospital (Wuhan, China) who had been discharged or had died by Jan 31, 2020. Demographic, clinical, treatment, and laboratory data, including serial samples for viral RNA detection, were extracted from electronic medical records and compared between survivors and non-survivors. We used univariable and multivariable logistic regression methods to explore the risk factors associated with in-hospital death. Findings 191 patients (135 from Jinyintan Hospital and 56 from Wuhan Pulmonary Hospital) were included in this study, of whom 137 were discharged and 54 died in hospital. 91 (48%) patients had a comorbidity, with hypertension being the most common (58 [30%] patients), followed by diabetes (36 [19%] patients) and coronary heart disease (15 [8%] patients). Multivariable regression showed increasing odds of in-hospital death associated with older age (odds ratio 1·10, 95% CI 1·03–1·17, per year increase; p=0·0043), higher Sequential Organ Failure Assessment (SOFA) score (5·65, 2·61–12·23; p Interpretation The potential risk factors of older age, high SOFA score, and d-dimer greater than 1 μg/mL could help clinicians to identify patients with poor prognosis at an early stage. Prolonged viral shedding provides the rationale for a strategy of isolation of infected patients and optimal antiviral interventions in the future. Funding Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences; National Science Grant for Distinguished Young Scholars; National Key Research and Development Program of China; The Beijing Science and Technology Project; and Major Projects of National Science and Technology on New Drug Creation and Development.

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

Food production requires application of fertilizers containing phosphorus, nitrogen and potassium on agricultural fields in order to sustain crop yields. However modern agriculture is dependent on phosphorus derived from phosphate rock, which is a non-renewable resource and current global reserves may be depleted in 50–100 years. While phosphorus demand is projected to increase, the expected global peak in phosphorus production is predicted to occur around 2030. The exact timing of peak phosphorus production might be disputed, however it is widely acknowledged within the fertilizer industry that the quality of remaining phosphate rock is decreasing and production costs are increasing. Yet future access to phosphorus receives little or no international attention. This paper puts forward the case for including long-term phosphorus scarcity on the priority agenda for global food security. Opportunities for recovering phosphorus and reducing demand are also addressed together with institutional challenges.

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The story of phosphorus: Global food security and food for thought

The causes of antibiotic resistance are complex and include human behaviour at many levels of society; the consequences affect everybody in the world. Similarities with climate change are evident. Many efforts have been made to describe the many different facets of antibiotic resistance and the interventions needed to meet the challenge. However, coordinated action is largely absent, especially at the political level, both nationally and internationally. Antibiotics paved the way for unprecedented medical and societal developments, and are today indispensible in all health systems. Achievements in modern medicine, such as major surgery, organ transplantation, treatment of preterm babies, and cancer chemotherapy, which we today take for granted, would not be possible without access to effective treatment for bacterial infections. Within just a few years, we might be faced with dire setbacks, medically, socially, and economically, unless real and unprecedented global coordinated actions are immediately taken. Here, we describe the global situation of antibiotic resistance, its major causes and consequences, and identify key areas in which action is urgently needed.

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Antibiotic resistance—the need for global solutions

https://web.iitd.ac.in/~arunku/files/CEL795_2011/Microbial%20contamination%20of%20drinking%20water%20and%20disease%20outcomes%20in%20developing%20regions_Ashbolt.pdf

Microbial contamination of drinking water and disease outcomes in developing regions.

In 2006 the World Health Organization published its new Guidelines for the safe use of wastewater, excreta and greywater. Together the Guidelines offer a safety framework, and minimum requirements for the safe use of wastewater, excreta and greywater in agriculture and aquaculture. Anyone interested in safe wastewater management will benefit from getting acquainted with the guidelines. The first volume Policy and regulatory aspects deals with policies and regulations regarding safe water management. It is primarily meant for persons in policy-making positions, as well as for controlling officials. Aside from offering guidelines for example on how to formulate, harmonize and mainstream policies in effect, it also gives an introduction to Volumes 2, 3, and 4 of the Guidelines, by means of executive summaries. In the end of Volume 1 index and a glossary of terms for all the volumes (1-4) can be found. Volume 2 of the Guidelines Wastewater use in agriculture focuses on the health impacts that wastewater use in agriculture has, for instance, on consumers and those who work in this field. The main focus of this volume is thus on safety maximization (such as food safety) when it comes to wastewater use in agriculture. The second volume of the Guidelines is primarily meant for use when developing national and international methods for safe water management. Volume 3 of the GuidelinesWastewater and excreta use in aquaculture also centers on the safety matters, the risks and the benefits this time especially related to wastewater and excreta use. The focus of this volume is specifically on aquaculture. Similarly to Volumes 2 and 3, Volume 4 Excreta and greywater use in agriculture also focuses on the safety matters; however, the center of attention is on agriculture, with a specific view on excreta and greywater use.

Guidelines for the safe use of wastewater, excreta and greywater

The survival of culturable fecal coliforms, fecal streptococci, and Clostridium perfringens spores in freshwater and marine sediments from sites near sewage outfalls was studied. In laboratory studies, the inhibition of protozoan predators with cycloheximide allowed the fecal coliforms to grow in the sediment whereas the presence of predators resulted in a net die-off. C. perfringens spores did not appear either to be affected by predators or to die off throughout the duration of the experiments (28 days). Studies using in situ membrane diffusion chambers showed that, with the exception of C. perfringens, die-off of the test organisms to 10% of their initial numbers occurred in both marine and freshwater sediments within 85 days. The usual exponential decay model could not be applied to the sediment survival data, with the exception of the data for fecal streptococci. It was concluded that application of the usual decay model to the fecal coliform data was confounded by the complex relationship between growth and predation. The survival of seeded Escherichia coli in marine sediment was studied by using an enumeration method which detected viable but nonculturable bacteria. Throughout the duration of the experiment (68 days), the same proportion of E. coli organisms remained culturable, suggesting that sediment provides a favorable, nonstarvation environment for the bacteria.

Survival of fecal microorganisms in marine and freshwater sediments.

Background: Only recently has the environment been clearly implicated in the risk of antibiotic resistance to clinical outcome, but to date there have been few documented approaches to formally assess these risks.

Objective: We examined possible approaches and sought to identify research needs to enable human health risk assessments (HHRA) that focus on the role of the environment in the failure of antibiotic treatment caused by antibiotic-resistant pathogens.

Methods: The authors participated in a workshop held 4–8 March 2012 in Quebec, Canada, to define the scope and objectives of an environmental assessment of antibiotic-resistance risks to human health. We focused on key elements of environmental-resistance-development “hot spots,” exposure assessment (unrelated to food), and dose response to characterize risks that may improve antibiotic-resistance management options.

Discussion: Various novel aspects to traditional risk assessments were identified to enable an assessment of environmental antibiotic resistance. These include a) accounting for an added selective pressure on the environmental resistome that, over time, allows for development of antibiotic-resistant bacteria (ARB); b) identifying and describing rates of horizontal gene transfer (HGT) in the relevant environmental “hot spot” compartments; and c) modifying traditional dose–response approaches to address doses of ARB for various health outcomes and pathways.

Conclusions: We propose that environmental aspects of antibiotic-resistance development be included in the processes of any HHRA addressing ARB. Because of limited available data, a multicriteria decision analysis approach would be a useful way to undertake an HHRA of environmental antibiotic resistance that informs risk managers.

Citation: Ashbolt NJ, Amezquita A, Backhaus T, Borriello P, Brandt KK, Collignon P, Coors A, Finley R, Gaze WH, Heberer T, Lawrence JR, Larsson DG, McEwen SA, Ryan JJ, Schonfeld J, Silley P, Snape JR, Van den Eede C, Topp E. 2013. Human health risk assessment (HHRA) for environmental development and transfer of antibiotic resistance. Environ Health Perspect 121:993–1001; http://dx.doi.org/10.1289/ehp.1206316

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Human Health Risk Assessment (HHRA) for environmental development and transfer of antibiotic resistance.

Current guidelines in the three water-related areas (drinking water, wastewater and recreational water) assess quality, in microbiological terms, by measuring indicator organisms. This chapter looks at the history and examines some of the methods used to assess the microbiological quality of water, highlighting the current limitations and also possible future developments. Traditionally, indicator microorganisms have been used to suggest the presence of pathogens (Berg 1978). Today, however, we understand a myriad of possible reasons for indicator presence and pathogen absence, or vice versa. In short, there is no direct correlation between numbers of any indicator and enteric pathogens (Grabow 1996). To eliminate the ambiguity in the term 'microbial indicator', the following three groups (outlined in Table 13.1) are now recognised:

https://www.who.int/water_sanitation_health/dwq/iwachap13.pdf

Nicholas J. Ashbolt

Papers

Microbial contamination of drinking water and disease outcomes in developing regions.

Guidelines for the safe use of wastewater, excreta and greywater

Survival of fecal microorganisms in marine and freshwater sediments.

Human Health Risk Assessment (HHRA) for environmental development and transfer of antibiotic resistance.

Indicators of microbial water quality