Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae.

Oxford Nanopore Technologies (ONT) sequencing has rich potential for genomic epidemiology and public health investigations of bacterial pathogens, particularly in low-resource settings and at the point of care, due to its portability and affordability. However, low base-call accuracy has limited the reliability of ONT data for critical tasks such as antimicrobial resistance (AMR) and virulence gene detection and typing, serotype prediction, and cluster identification. Thus, Illumina sequencing remains the standard for genomic surveillance despite higher capital and running costs. We tested the accuracy of ONT-only assemblies for common applied bacterial genomics tasks (genotyping and cluster detection, implemented via Kleborate, Kaptive and Pathogenwatch), using data from 54 unique Klebsiella pneumoniae isolates. ONT reads generated via MinION with R9.4.1 flowcells were basecalled using three alternative models [Fast, High-accuracy (HAC) and Super-accuracy (SUP), available within ONT's Guppy software], assembled with Flye and polished using Medaka. Accuracy of typing using ONT-only assemblies was compared with that of Illumina-only and hybrid ONT+Illumina assemblies, constructed from the same isolates as reference standards. The most resource-intensive ONT-assembly approach (SUP basecalling, with or without Medaka polishing) performed best, yielding reliable capsule (K) type calls for all strains (100 % exact or best matching locus), reliable multi-locus sequence type (MLST) assignment (98.3 % exact match or single-locus variants), and good detection of acquired AMR genes and mutations (88-100 % correct identification across the various drug classes). Distance-based trees generated from SUP+Medaka assemblies accurately reflected overall genetic relationships between isolates. The definition of outbreak clusters from ONT-only assemblies was problematic due to inflation of SNP counts by high base-call errors. However, ONT data could be reliably used to 'rule out' isolates of distinct lineages from suspected transmission clusters. HAC basecalling + Medaka polishing performed similarly to SUP basecalling without polishing. Therefore, we recommend investing compute resources into basecalling (SUP model), wherever compute resources and time allow, and note that polishing is also worthwhile for improved performance. Overall, our results show that MLST, K type and AMR determinants can be reliably identified with ONT-only R9.4.1 flowcell data. However, cluster detection remains challenging with this technology.

Planet Patrolling: A citizen science brand audit of anthropogenic litter in the context of national legislation and international policy.

Anthropogenic Litter (AL) is ubiquitous in distribution and diverse in type and impact. Citizen science AL clean-ups engage citizens with the environment and have the potential to generate data that can inform policy. Here we present a detailed citizen science survey of AL across freshwater, terrestrial, and coastal environments of the United Kingdom (UK), coordinated by the not-for-profit Planet Patrol throughout 2020. Key materials, industries, brands, and parent companies associated with AL are identified. Plastic dominated AL (63%), followed by metal (14%), and composite materials (12%). The majority of AL (56%) had been used as beverage containers and non-beverage packaging, and 38.8% of AL was branded. Of the branded AL, 26% was associated with The Coca-Cola Company, Anheuser-Busch InBev, and PepsiCo. These three companies were associated with significantly more branded litter than any other. We place these data in the context of upcoming UK legislation and the Environmental Social Governance (ESG) statements of the companies associated with the majority of the recorded litter. Knowledge gaps and recommendations for AL surveying are made, and the focus of corporate and government actions are discussed.

Synthesis of dominant plastic microfibre prevalence and pollution control feasibility in Chinese freshwater environments.

Microplastic pollution of freshwaters is known to be a great concern in China and these pollutants can be discharged into the coastal environment through fluvial processes, posing threats to the global marine ecosystem. This paper reviewed the literature measuring microplastic pollution in the Chinese freshwater environment and found that microfibres dominate other plastic morphologies in more than 65% of samples collected in surface water, sediments and effluents of wastewater treatment plants and domestic sewers. Current potential sources of microfibre pollution are identified including fishery activities, laundry sewage, and waste textiles according to previous research. Recommendations are offered using the circular economy management framework, such as textile waste reuse and recycling systems in China, for improving current control measures for microplastics in freshwaters.

Freshwater microplastic concentrations vary through both space and time.

Plastic pollution represents one of the most salient indicators of society's impact on the environment. The microplastic component of this is ubiquitous, however, microplastic studies are seldom representative of the locations they sample. Over 12 months we explored spatiotemporal variation in microplastic prevalence across a freshwater system and in atmospheric deposition within its catchment, in one of the most temporally comprehensive studies of microplastic pollution. Microplastics were quantified in low concentrations (max 0.4 particles L-1) at all freshwater sites, including upstream of urban areas, and on rivers that do not receive wastewater treatment plant effluent. Extrapolated microplastic abundances at each site varied by up to 8 orders of magnitude over the course of the sampling campaign, suggesting that microplastic surveys that do not account for temporal variability misrepresent microplastic prevalence. Whilst we do not wish to underplay the potential impacts of microplastic particles in the environment, we argue that microplastic pollution needs to be placed in a more critical context, including assessment of temporal variability, to appropriately inform legislators and consumers.

Freshwater and airborne textile fibre populations are dominated by 'natural', not microplastic, fibres.

The potential role of natural textile fibres as environmental pollutants has been speculated upon by some environmental scientists, however, there is a general consensus that their biodegradability reduces their environmental threat. Whilst the risks that they pose remain poorly understood, their environmental prevalence has been noted in several recent microplastic pollution manuscripts. Here we highlight the extent to which natural textile fibres dominate fibre populations of upstream reaches of the River Trent, UK, as well as the atmospheric deposition within its catchment, over a twelve month microplastic sampling campaign. Across 223 samples, natural textile fibres represented 93.8% of the textile fibre population quantified. Moreover, though microplastic particles including synthetic fibres are known to be pervasive environmental pollutants, extruded textile fibres were absent from 82.8% of samples. Natural textile fibres were absent from just 9.7% of samples.

Knowing the risk of SUDEP: two family's perspectives and The Danny Did Foundation.

There is much debate in the epilepsy community about whether neurologists should discuss the risk of sudden unexpected death in epilepsy (SUDEP) with their patients and family members. Those in favor purport that patients have a right to know about SUDEP. Opponents say the risk is so low that discussions only worry patients and families, especially if there is nothing that can be done to prevent SUDEP. North American surveys show that the epilepsy community knows little about SUDEP and neurologists are unlikely to talk about it. However, surveys of those bereaved by SUDEP show that an overwhelming majority of the parents, spouses, and family members want to be told about SUDEP immediately after the diagnosis of epilepsy. This article is written by two families bereaved by SUDEP and their strong belief that neurologists should have the discussion about the risk of SUDEP soon after the diagnosis of epilepsy.