Metagenomic profiling of hospital wastewater: A comprehensive national scale analysis of antimicrobial resistance genes and opportunistic pathogens.

Background: Healthcare settings are recognised as potential hotspots for the emergence and spread of antimicrobial resistance (AMR).

Method: Metagenomic sequencing was conducted on a national scale using wastewater from hospitals across Wales to screen for antimicrobial resistance genes (ARGs) and opportunistic pathogens.

Results: The total abundance and diversity of ARGs varied significantly across the hospitals.

Complete genome sequence of sp. PP3, a dehalogenase-producing bacterium, confirms the unusual mobile genetic element .

sp. PP3, originally isolated from contaminated soil enriched in a chemostat culture on 2,2-dichloropropionic acid, has a 6.42 Mb genome, most closely related to .

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Wastewater-based analysis of antimicrobial resistance at UK airports: Evaluating the potential opportunities and challenges.

With 40 million annual passenger flights, airports are key hubs for microbial communities from diverse geographic origins to converge, mix, and distribute. Wastewater derived from airports and aircraft represent both a potential route for the global dispersion of antimicrobial resistant (AMR) organisms and an under-utilised resource for strengthening global AMR surveillance. This study investigates the abundance and diversity of antimicrobial resistance genes (ARGs) in wastewater samples collected from airport terminals (n = 132), aircraft (n = 25), and a connected wastewater treatment plant (n = 11) at three international airports in the UK (London Heathrow, Edinburgh and Bristol).

Metagenomics unveils the role of hospitals and wastewater treatment plants on the environmental burden of antibiotic resistance genes and opportunistic pathogens.

Antimicrobial resistance (AMR) is a global health challenge, with hospitals and wastewater treatment plants (WWTPs) serving as significant pathways for the dissemination of antibiotic resistance genes (ARGs). This study investigates the potential of wastewater-based epidemiology (WBE) as an early warning system for assessing the burden of AMR at the population level. In this comprehensive year-long study, effluent was collected weekly from three large hospitals, and treated and untreated wastewater were collected monthly from three associated community WWTPs.

Complete genome sequence of the biopesticidal strain BCC0191.

Here, we report the genome sequence of BCC0191, a biopesticide originally isolated from the barley rhizosphere. The genome was assembled using an Illumina-Nanopore hybrid approach and consisted of 7.62 Mbp distributed across three replicons.

Wastewater sample storage for physicochemical and microbiological analysis.

Wastewater-based epidemiology (WBE) is a crucial tool for health and environmental monitoring, providing real-time data on public health indicators by analysis of sewage samples. Ensuring the integrity of these samples from collection to analysis is paramount. This study investigates the effects of different cold-storage conditions on the integrity of wastewater samples, focusing on both microbiological markers (such as extractable nucleic acids, SARS-CoV-2, and crAssphage) and physicochemical parameters (including ammonium, orthophosphate, pH, conductivity, and turbidity).

PyPop: a mature open-source software pipeline for population genomics.

Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well.

Microbial community and antimicrobial resistance niche differentiation in a multistage, surface flow constructed wetland.

Free-living (FL) and particulate-associated (PA) communities are distinct bacterioplankton lifestyles with different mobility and dissemination routes. Understanding spatio-temporal dynamics of PA and FL fractions will allow improvement to wastewater treatment processes including pathogen and AMR bacteria removal. In this study, PA, FL and sediment community composition and antimicrobial resistance gene (ARG; tetW, ermB, sul1, intI1) dynamics were investigated in a full-scale municipal wastewater free-water surface polishing constructed wetland.

VarLOCK: sequencing-independent, rapid detection of SARS-CoV-2 variants of concern for point-of-care testing, qPCR pipelines and national wastewater surveillance.

The COVID-19 pandemic demonstrated the need for rapid molecular diagnostics. Vaccination programs can provide protection and facilitate the opening of society, but newly emergent and existing viral variants capable of evading the immune system endanger their efficacy. Effective surveillance for Variants of Concern (VOC) is therefore important.

Polyyne-producing suppress damping-off disease of (pea).

Extensive crop losses are caused by oomycete and fungal damping-off diseases. Agriculture relies heavily on chemical pesticides to control disease, but due to safety concerns multiple agents have been withdrawn. were successfully used as commercial biopesticides because of their fungicidal activity and plant protective traits.

Species Isolated from Sand Filter Biofilm at an Australian Drinking Water Treatment Works.

Three strains isolated by geosmin enrichment from a sand filter in an Australian drinking water treatment works were genome sequenced to identify their taxonomic placement, and a bench-scale batch experiment confirmed their geosmin-degrading capability. Using the average nucleotide identity based on the MUMmer algorithm (ANIm), pairwise digital DNA-DNA hybridization (dDDH), and phylogenomic analyses, the strains were identified as species.

Methanogen activity and microbial diversity in Gulf of Cádiz mud volcano sediments.

The Gulf of Cádiz is a tectonically active continental margin with over sixty mud volcanoes (MV) documented, some associated with active methane (CH) seepage. However, the role of prokaryotes in influencing this CH release is largely unknown. In two expeditions (MSM1-3 and JC10) seven Gulf of Cádiz MVs (Porto, Bonjardim, Carlos Ribeiro, Captain Arutyunov, Darwin, Meknes, and Mercator) were analyzed for microbial diversity, geochemistry, and methanogenic activity, plus substrate amended slurries also measured potential methanogenesis and anaerobic oxidation of methane (AOM).

Microplastic biofilm, associated pathogen and antimicrobial resistance dynamics through a wastewater treatment process incorporating a constructed wetland.

Microplastics in wastewater are colonized by biofilms containing pathogens and antimicrobial resistance (AMR) genes that can be exported into receiving water bodies. This study investigated establishment and changes in microplastic-associated biofilm and AMR during a conventional full-scale 2100 population equivalent wastewater treatment process combined with a free water surface polishing constructed wetland. Sequential microplastic colonization experiments were conducted at different stages of the wastewater treatment process, including in raw sewage, treated effluent and the constructed wetland.

Biostimulation of jarosite and iron oxide-bearing mine waste enhances subsequent metal recovery.

Novel resource recovery technologies are required for metals-bearing hazardous wastes in order to achieve circular economy outcomes and industrial symbiosis. Iron oxide and co-occurring hydroxysulphate-bearing wastes are globally abundant and often contain other elements of value. This work addresses the biostimulation of indigenous microbial communities within an iron oxide/ hydroxysulphate-bearing waste and its effect on the subsequent recoverability of metals by hydrochloric, sulphuric, citric acids, and EDTA.

Cloning and expression of Burkholderia polyyne biosynthetic gene clusters in Paraburkholderia hosts provides a strategy for biopesticide development.

Burkholderia have potential as biocontrol agents because they encode diverse biosynthetic gene clusters (BGCs) for a range of antimicrobial metabolites. Given the opportunistic pathogenicity associated with Burkholderia species, heterologous BGC expression within non-pathogenic hosts is a strategy to construct safe biocontrol strains. We constructed a yeast-adapted Burkholderia-Escherichia shuttle vector (pMLBAD_yeast) with a yeast replication origin 2 μ and URA3 selection marker and optimised it for cloning BGCs using the in vivo recombination ability of Saccharomyces cerevisiae.

Towards passive bioremediation of dye-bearing effluents using hydrous ferric oxide wastes: Mechanisms, products and microbiology.

A novel, circular economy-inspired approach for the "passive" (non-powered and reagent-free) treatment of dye-bearing effluent is presented. The treatment utilises the biogeochemical interaction of dye-bearing wastewater with hydrous ferric oxide (HFO) bearing sludges. The work presented demonstrates for the first time the reuse of HFO-rich waste sludges from potable water and mine water treatment.

Discovery of the Pseudomonas Polyyne Protegencin by a Phylogeny-Guided Study of Polyyne Biosynthetic Gene Cluster Diversity.

Natural products that possess alkyne or polyyne moieties have been isolated from a variety of biological sources and possess a broad a range of bioactivities. In bacteria, the basic biosynthesis of polyynes is known, but their biosynthetic gene cluster (BGC) distribution and evolutionary relationship to alkyne biosynthesis have not been addressed. Through comprehensive genomic and phylogenetic analyses, the distribution of alkyne biosynthesis gene cassettes throughout bacteria was explored, revealing evidence of multiple horizontal gene transfer events.

Genomics reveals the novel species placement of industrial contaminant isolates incorrectly identified as .

The complex (Bcc) is a closely related group of bacteria, composed of at least 20 different species, the accurate identification of which is essential in the context of infectious diseases. In industry, they can contaminate non-food products, including home and personal care products and cosmetics. The Bcc are problematic contaminants due to their ubiquitous presence and intrinsic antimicrobial resistance, which enables them to occasionally overcome preservation systems in non-sterile products.

Kill and cure: genomic phylogeny and bioactivity of bacteria capable of pathogenic and beneficial lifestyles.

is a bacterium with a broad ecology spanning disease in humans, animals and plants, but also encompassing multiple beneficial interactions. It is a plant pathogen, a toxin-producing food-poisoning agent, and causes lung infections in people with cystic fibrosis (CF). Contrasting beneficial traits include antifungal production exploited by insects to protect their eggs, plant protective abilities and antibiotic biosynthesis.

Reclassification of the biocontrol agents BY-2 and Tu-100 as and insights into the genomic and specialized metabolite diversity of the species.

The genomes of two historical species strains isolated from the roots of oilseed rape and used routinely in PR China as biocontrol agents to suppress disease were sequenced. Average nucleotide identity (ANI) and digital DNA-DNA hybridization analyses demonstrated that they were originally misclassified as and now belong to the bacterial species . A broader ANI analysis of available genomes identified 292 genomes that were then subjected to core gene analysis and phylogenomics.

Genomic Assemblies of Members of and Related Genera as a Resource for Natural Product Discovery.

The genomes of 450 members of , isolated from clinical and environmental sources, were sequenced and assembled as a resource for genome mining. Genomic analysis of the collection has enabled the identification of multiple metabolites and their biosynthetic gene clusters, including the antibiotics gladiolin, icosalide A, enacyloxin, and cepacin A.

A rapid screening method for the detection of specialised metabolites from bacteria: Induction and suppression of metabolites from Burkholderia species.

Screening microbial cultures for specialised metabolites is essential for the discovery of new biologically active compounds. A novel, cost-effective and rapid screening method is described for extracting specialised metabolites from bacteria grown on agar plates, coupled with HPLC for basic identification of known and potentially novel metabolites. The method allows the screening of culture collections to identify optimal production strains and metabolite induction conditions.