Temporal, Spatial, and Genomic Analyses of Enterobacteriaceae Clinical Antimicrobial Resistance in Companion Animals Reveals Phenotypes and Genotypes of One Health Concern

BackgroundAntimicrobial resistance (AMR) is a globally important one health threat. The impact of resistant infections on companion animals, and the potential public health implications of such infections, has not been widely explored, largely due to an absence of structured population-level data.ObjectivesWe aimed to efficiently capture and repurpose antimicrobial susceptibility test (AST) results data from several veterinary diagnostic laboratories (VDLs) across the United Kingdom to facilitate national companion animal clinical AMR surveillance. We also sought to harness and genotypically characterize isolates of potential AMR importance from these laboratories.MethodsWe summarized AST results for 29,330 canine and 8,279 feline Enterobacteriaceae isolates originating from companion animal clinical practice, performed between April 2016 and July 2018 from four VDLs, with submissions from 2,237 United Kingdom veterinary practice sites.ResultsEscherichia coli (E. coli) was the most commonly isolated Enterobacteriaceae in dogs (69.4% of AST results, 95% confidence interval, CI, 68.7–70.0) and cats (90.5%, CI 89.8–91.3). Multi-drug resistance was reported in 14.1% (CI 13.5–14.8) of canine and 12.0% (CI 11.1–12.9) of feline E. coli isolates. Referral practices were associated with increased E. coli 3rd generation ≤ cephalosporin resistance odds (dogs: odds ratio 2.0, CI 1.2–3.4). We selected 95 E. coli isolates for whole genome analyses, of which seven belonged to sequence type 131, also carrying the plasmid-associated extended spectrum β-lactamase gene blaCTX–M–15. The plasmid-mediated colistin resistance gene mcr-9 was also identified for the first time in companion animals.ConclusionsLinking clinical AMR data with genotypic characterization represents an efficient means of identifying important resistance trends in companion animals on a national scale.</sec

The first tropical ‘metal farm’: some perspectives from field and pot experiments

Agromining is the chain of processes of phytoextraction of economically valuable elements by selected hyperaccumulator plants, and subsequent processing of biomass to produce targeted metals or commercial compounds of high value. Although substantial unrealized opportunities exist for developing economic nickel (Ni) agromining in the tropics, this technology has remained relatively unexplored. This study investigated the soil chemistry of a newly established tropical ‘metal farm’ and elucidated the performance of a prospective ‘metal crop’ species (Phyllanthus rufuschaneyi) to be used in a large-scale tropical Ni agromining program on ultramafic soils in Sabah (Malaysia). We found that a major portion of the site (>90%) had high total Ni concentrations (>2000 μg g) in the soil (shallow Eutric Cambisol Magnesic). This study also recorded high phytoavailable soil Ni concentrations in the field site, which is a desired property of soils intended for Ni agromining. Moreover, the average soil pH of the field (pH 6.4) is ideal for maximum Ni uptake in the local candidate species. We recorded low concentrations of Ca, K and P, suggesting the need for a fertilizer regime in the farm. The extraordinary shoot Ni concentrations (>2 wt%), coupled with the high purity of the ‘bio-ore’ derived from Phyllanthus rufuschaneyi, confirm its high potential for economic Ni agromining. The success of our first field trial is critical to provide ‘real-life’ evidence of the value of large-scale tropical ‘metal farming’. Research priorities include the need to intensify the search for candidate species, determine their agronomy, develop mass propagation methods, and to test technologies to process the biomass to recover valuable products

Greenhouse gas emissions from agricultural food production to supply Indian diets: Implications for climate change mitigation

Agriculture is a major source of greenhouse gas (GHG) emissions globally. The growing global population is putting pressure on agricultural production systems that aim to secure food production while minimising GHG emissions. In this study, the GHG emissions associated with the production of major food commodities in India are calculated using the Cool Farm Tool. GHG emissions, based on farm management for major crops (including cereals like wheat and rice, pulses, potatoes, fruits and vegetables) and livestock-based products (milk, eggs, chicken and mutton meat), are quantified and compared. Livestock and rice production were found to be the main sources of GHG emissions in Indian agriculture with a country average of 5.65 kg CO2eq kg-1 rice, 45.54 kg CO2eq kg-1 mutton meat and 2.4 kg CO2eq kg-1 milk. Production of cereals (except rice), fruits and vegetables in India emits comparatively less GHGs with <1 kg CO2eq kg-1 product. These findings suggest that a shift towards dietary patterns with greater consumption of animal source foods could greatly increase GHG emissions from Indian agriculture. A range of mitigation options are available that could reduce emissions from current levels and may be compatible with increased future food production and consumption demands in India

A comparative genomics study of 23 Aspergillus species from section Flavi

Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi. However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi.Peer reviewe

Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (, , ) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors. Overall, this large-scale analysis reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining sarcoma therapy and relationships to other cancer types

Competition for nitrogen by three sympatric species of

• Nitrogen (N) exists in the soil in a variety of different forms and thus plants may avoid competition by taking up N as different chemical forms. • This study examined the uptake of nitrate, ammonium and glycine by three co-occurring species of Eucalyptus (E. obliqua, E. radiata and E. rubida) from dry sclerophyll forest in south-eastern Australia. Species preference for N forms was determined by measuring uptake of glycine, nitrate and ammonium from 15N-labelled solutions containing equimolar 100 μmol L−1 concentrations of all three N forms. KCl extracts were used to assess the relative abundance of the different forms of N in the soil’s exchangeable pool. • KCl extracts of soil indicated that amino acids comprised 30–40% of the soluble non-protein N, while ammonium varied from 10–70% and nitrate from 5–70%. In all species, ammonium was the preferred source of nitrogen and was taken up 2.5–4.5 times faster than glycine, and 30–50 times faster than nitrate. Species did not differ in preference for N-forms (species*N-form interaction, not significant). • This study indicates that nitrate, ammonium and amino acids are all present in soil, and thus there is the potential for niche differentiation based on chemical forms of N. However, there is no evidence that co-occurring Eucalyptus avoid competition for N by taking up different chemical forms

Facultative hyperaccumulation of heavy metals and metalloids

Approximately 500 species of plants are known to hyperaccumulate heavy metals and metalloids. The majority are obligate metallophytes, species that are restricted to metalliferous soils. However, a smaller but increasing list of plants are "facultative hyperaccumulators" that hyperaccumulate heavy metals when occurring on metalliferous soils, yet also occur commonly on normal, non-metalliferous soils. This paper reviews the biology of facultative hyperaccumulators and the opportunities they provide for ecological and evolutionary research. The existence of facultative hyperaccumulator populations across a wide edaphic range allows intraspecific comparisons of tolerance and uptake physiology. This approach has been used to study zinc and cadmium hyperaccumulation by Noccaea (Thlaspi) caerulescens and Arabidopsis halleri, and it will be instructive to make similar comparisons on species that are distributed even more abundantly on normal soil. Over 90% of known hyperaccumulators occur on serpentine (ultramafic) soil and accumulate nickel, yet there have paradoxically been few experimental studies of facultative nickel hyperaccumulation. Several hypotheses suggested to explain the evolution of hyperaccumulation seem unlikely when most populations of a species occur on normal soil, where plants cannot hyperaccumulate due to low metal availability. In such species, it may be that hyperaccumulation is an ancestral phylogenetic trait or an anomalous manifestation of physiological mechanisms evolved on normal soils, and may or may not have direct adaptive benefits