Whole-genome sequencing of Klebsiella pneumoniae isolates to track strain progression in a single patient with recurrent urinary tract infection

Klebsiella pneumoniae is an important uropathogen that increasingly harbors broad-spectrum antibiotic resistance determinants. Evidence suggests that some same-strain recurrences in women with frequent urinary tract infections (UTIs) may emanate from a persistent intravesicular reservoir. Our objective was to analyze K. pneumoniae isolates collected over weeks from multiple body sites of a single patient with recurrent UTI in order to track ordered strain progression across body sites, as has been employed across patients in outbreak settings. Whole-genome sequencing of 26 K. pneumoniae isolates was performed utilizing the Illumina platform. PacBio sequencing was used to create a refined reference genome of the original urinary isolate (TOP52). Sequence variation was evaluated by comparing the 26 isolate sequences to the reference genome sequence. Whole-genome sequencing of the K. pneumoniae isolates from six different body sites of this patient with recurrent UTI demonstrated 100% chromosomal sequence identity of the isolates, with only a small P2 plasmid deletion in a minority of isolates. No single nucleotide variants were detected. The complete absence of single-nucleotide variants from 26 K. pneumoniae isolates from multiple body sites collected over weeks from a patient with recurrent UTI suggests that, unlike in an outbreak situation with strains collected from numerous patients, other methods are necessary to discern strain progression within a single host over a relatively short time frame.</p

Planetary health as a laboratory for enhanced evidence synthesis

Abstract : Please refer to full text to view abstract

Outsourcing CO2 within China

Recent studies have shown that the high standard of living enjoyed by people in the richest countries often comes at the expense of CO2 emissions produced with technologies of low efficiency in less affluent, developing countries. Less apparent is that this relationship between developed and developing can exist within a single country’s borders, with rich regions consuming and exporting high-value goods and services that depend upon production of low-cost and emission-intensive goods and services from poorer regions in the same country. As the world’s largest emitter of CO2, China is a prominent and important example, struggling to balance rapid economic growth and environmental sustainability across provinces that are in very different stages of development. In this study, we track CO2 emissions embodied in products traded among Chinese provinces and internationally. We find that 57% of China’s emissions are related to goods that are consumed outside of the province where they are produced. For instance, up to 80% of the emissions related to goods consumed in the highly developed coastal provinces are imported from less developed provinces in central and western China where many low–value-added but high–carbon-intensive goods are produced. Without policy attention to this sort of interprovincial carbon leakage, the less developed provinces will struggle to meet their emissions intensity targets, whereas the more developed provinces might achieve their own targets by further outsourcing. Consumption-based accounting of emissions can thus inform effective and equitable climate policy within China

Climate action for health and wellbeing in cities: a protocol for the systematic development of a database of peer-reviewed studies using machine learning methods [version 1; peer review: awaiting peer review]

Home Browse Climate action for health and wellbeing in cities: a protocol for... ALL METRICS 99 VIEWS 11 DOWNLOADS Get PDF Get XML Cite Export Track Email Share ▬ STUDY PROTOCOL Climate action for health and wellbeing in cities: a protocol for the systematic development of a database of peer-reviewed studies using machine learning methods [version 1; peer review: awaiting peer review] Kristine Belesova https://orcid.org/0000-0002-6160-50411, Max Callaghan https://orcid.org/0000-0001-8292-87582, Jan C Minx https://orcid.org/0000-0002-2862-01782, Felix Creutzig2, Catalina Turcu https://orcid.org/0000-0003-2663-25863, Emma Hutchinson1, James Milner1, Melanie Crane https://orcid.org/0000-0002-3058-22114, Andy Haines https://orcid.org/0000-0002-8053-46051, Michael Davies5, Paul Wilkinson1 Author details 1 Department of Public Health, Environments and Society and Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK 2 Mercator Research Institute on Global Commons and Climate Change, Berlin, 10829, Germany 3 Bartlett School of Planning, University College London, London, WC1H 0QB, UK 4 Charles Perkins Centre, Sydney School of Public Health, University of Sydney, Sydney, Australia 5 Bartlett School Environment, Energy & Resources, University College London, London, WC1H 0QB, UK Kristine Belesova Roles: Conceptualization, Data Curation, Investigation, Methodology, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing Max Callaghan Roles: Data Curation, Investigation, Methodology, Software, Writing – Review & Editing Jan C Minx Roles: Conceptualization, Investigation, Methodology, Software, Writing – Review & Editing Felix Creutzig Roles: Conceptualization, Investigation, Methodology, Software, Writing – Review & Editing Catalina Turcu Roles: Investigation, Methodology, Writing – Review & Editing Emma Hutchinson Roles: Investigation, Methodology, Writing – Review & Editing James Milner Roles: Methodology, Writing – Review & Editing Melanie Crane Roles: Methodology, Writing – Review & Editing Andy Haines Roles: Conceptualization, Funding Acquisition, Methodology, Supervision, Writing – Review & Editing Michael Davies Roles: Conceptualization, Funding Acquisition, Methodology, Writing – Review & Editing Paul Wilkinson Roles: Conceptualization, Funding Acquisition, Methodology, Supervision, Writing – Review & Editing Abstract Cities produce more than 70% of global greenhouse gas emissions. Action by cities is therefore crucial for climate change mitigation as well as for safeguarding the health and wellbeing of their populations under climate change. Many city governments have made ambitious commitments to climate change mitigation and adaptation and implemented a range of actions to address them. However, a systematic record and synthesis of the findings of evaluations of the effect of such actions on human health and wellbeing is currently lacking. This, in turn, impedes the development of robust knowledge on what constitutes high-impact climate actions of benefit to human health and wellbeing, which can inform future action plans, their implementation and scale-up. The development of a systematic record of studies reporting climate and health actions in cities is made challenging by the broad landscape of relevant literature scattered across many disciplines and sectors, which is challenging to effectively consolidate using traditional literature review methods. This protocol reports an innovative approach for the systematic development of a database of studies of climate change mitigation and adaptation actions implemented in cities, and their benefits (or disbenefits) for human health and wellbeing, derived from peer-reviewed academic literature. Our approach draws on extensive tailored search strategies and machine learning methods for article classification and tagging to generate a database for subsequent systematic reviews addressing questions of importance to urban decision-makers on climate actions in cities for human health and wellbeing

The technological and economic prospects for CO2 utilization and removal

The capture and use of carbon dioxide to create valuable products might lower the net costs of reducing emissions or removing carbon dioxide from the atmosphere. Here we review ten pathways for the utilization of carbon dioxide. Pathways that involve chemicals, fuels and microalgae might reduce emissions of carbon dioxide but have limited potential for its removal, whereas pathways that involve construction materials can both utilize and remove carbon dioxide. Land-based pathways can increase agricultural output and remove carbon dioxide. Our assessment suggests that each pathway could scale to over 0.5 gigatonnes of carbon dioxide utilization annually. However, barriers to implementation remain substantial and resource constraints prevent the simultaneous deployment of all pathways

Secure robust carbon dioxide removal policy through credible certification

Carbon Dioxide Removal (CDR) is a key element of any mitigation strategy aiming to achieve the long-term temperature goal of the Paris Agreement, as well as national net-zero and net-negative greenhouse gas emissions targets. For robust CDR policy, the credibility of certification schemes is essential

The Landscape of Extreme Genomic Variation in the Highly Adaptable Atlantic Killifish

Understanding and predicting the fate of populations in changing environments require knowledge about the mechanisms that support phenotypic plasticity and the adaptive value and evolutionary fate of genetic variation within populations. Atlantic killifish (Fundulus heteroclitus) exhibit extensive phenotypic plasticity that supports large population sizes in highly fluctuating estuarine environments. Populations have also evolved diverse local adaptations. To yield insights into the genomic variation that supports their adaptability, we sequenced a reference genome and 48 additional whole genomes from a wild population. Evolution of genes associated with cell cycle regulation and apoptosis is accelerated along the killifish lineage, which is likely tied to adaptations for life in highly variable estuarine environments. Genome-wide standing genetic variation, including nucleotide diversity and copy number variation, is extremely high. The highest diversity genes are those associated with immune function and olfaction, whereas genes under greatest evolutionary constraint are those associated with neurological, developmental, and cytoskeletal functions. Reduced genetic variation is detected for tight junction proteins, which in killifish regulate paracellular permeability that supports their extreme physiological flexibility. Low-diversity genes engage in more regulatory interactions than high-diversity genes, consistent with the influence of pleiotropic constraint on molecular evolution. High genetic variation is crucial for continued persistence of species given the pace of contemporary environmental change. Killifish populations harbor among the highest levels of nucleotide diversity yet reported for a vertebrate species, and thus may serve as a useful model system for studying evolutionary potential in variable and changing environments