Salmonella contamination of pork carcasses : UK baseline culture-based data determined by sponge sampling during 2006

During 2006-7, microbiological baseline data on the frequency and distribution of Salmonella contamination of pig carcasses in UK slaughterhouses were collected. Data were generated from four separate abattoirs which were determined as having practices representative of the UK slaughter industry. Studies were designed to provide estimates of the prevalence and levels of Salmonella contamination of the UK pork industry

A rapid, sensitive enrichment PCR to detect Salmonella and ETEC infections in pigs

Salmonella and Escherichia coli infections, particularly enterotoxigenic E. coli (ETEC), are a problem in piglet production. In addition, Salmonella is a major concem in the pork industry as a carrier state can be induced post infection allowing the pathogen to spread across the pig herd, onto many carcasses at slaughter and into the human food chain. Detection methods for these pathogens are currently highly laborious, with Salmonella detection taking over 5 days to give a verified positive result. Identification of ETEC isolates involves detecting the presence of toxin or fimbriae (or their genes by PCR), particularly F4, the most common fimbriae in piglet ETEC infection. Altemative methods such as real time PCR are unable to detect low levels of infection directly from the sample. Enrichment PCR assays have been successfully implemented for the detection of pathogens in foodstuffs, however, faecal material often is inhibitory to PCR based methods

Assessment of processes and operating conditions in UK pork abattoirs

In order to determine typical and atypical operations in the slaughtering and dressing of pigs for pork and bacon practices and operations were recorded at eight pig abattoirs. Data included physical parameters such as temperatures and durations. The results indicate that plants are reasonably similar if processing pigs mainly for pork, but those processing mainly for bacon had more aggressive singeing and polishing (black scraper) arrangements. The plants visited used either hot water (tank) or vertical (sprayed hot water) scalding systems prior to dehairing

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

Background: Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle in the UK producing 7–8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as fertiliser, and widely spread over crop fields, yet little is known about their microbial composition. We analysed the virome of agricultural slurry over a 5-month period using short and long-read sequencing. Results: Hybrid sequencing uncovered more high-quality viral genomes than long or short-reads alone; yielding 7682 vOTUs, 174 of which were complete viral genomes. The slurry virome was highly diverse and dominated by lytic bacteriophage, the majority of which represent novel genera (~ 98%). Despite constant influx and efflux of slurry, the composition and diversity of the slurry virome was extremely stable over time, with 55% of vOTUs detected in all samples over a 5-month period. Functional annotation revealed a diverse and abundant range of auxiliary metabolic genes and novel features present in the community, including the agriculturally relevant virulence factor VapE, which was widely distributed across different phage genera that were predicted to infect several hosts. Furthermore, we identified an abundance of phage-encoded diversity-generating retroelements, which were previously thought to be rare on lytic viral genomes. Additionally, we identified a group of crAssphages, including lineages that were previously thought only to be found in the human gut. Conclusions: The cattle slurry virome is complex, diverse and dominated by novel genera, many of which are not recovered using long or short-reads alone. Phages were found to encode a wide range of AMGs that are not constrained to particular groups or predicted hosts, including virulence determinants and putative ARGs. The application of agricultural slurry to land may therefore be a driver of bacterial virulence and antimicrobial resistance in the environment. [MediaObject not available: see fulltext.

How can cunent slaughter and dressing procedures in UK pig slaughterhouses be improved to reduce contamination of pig meat with pathogenic bacteria?

In pork slaughterhouses a number of dressing stages have the potential to improve the hygienic condition of the carcass surface. The operations performed at each of these dressing stages can be undertaken using a diverse range of mechanized systems that each have different reductive effects on the levels of microbial contamination. Our results show that pre-washing optimizes the effectiveness of condensation scalding in improving carcass hygiene, and that the same areas of carcasses are consistently not effectively heated by singeing/flaming, independent of the different systems used in pork and bacon slaughterhouses

Multidrug-Resistant ESBL-Producing E. coli in Clinical Samples from the UK

Globally, cephalosporin therapy failure is a serious problem for infection control. One causative agent of cephalosporin-resistant infections is multidrug-resistant (MDR) E. coli producing extended-spectrum β-lactamases (ESBLs) and/or plasmid-encoded AmpC (pAmpC) β-lactamases. We evaluated the occurrence of ESBL/pAmpC genetic determinants in phenotypically MDR E. coli isolated from clinical samples of blood, faeces, ear effusion, urine and sputum from a UK hospital. Phenotypic resistance profiling for 18 antibiotics (from seven classes) showed that 32/35 isolates were MDR, with resistance to 4–16 of the tested antibiotics. Of the isolates, 97.1% showed resistance to ampicillin, 71.4% showed resistance to co-amoxiclav, cefotaxime, ceftazidime and ceftiofur, and 68.5% showed resistance to cefquinome. blaCTX-M, blaTEM and blaOXA-1 genes were detected in 23, 13 and 12 strains, respectively, and Intl1 was detected in 17 isolates. The most common subtypes among the definite sequence types were CTX-M-15 (40%) and TEM-1 (75%). No E. coli isolates carried pAmpC genes. Significant correlations were seen between CTX-M carriage and cefotaxime, ceftiofur, aztreonam, ceftazidime and cefquinome resistance; between blaCTX-M, blaTEM and blaOXA-1 carriage and ciprofloxacin resistance; and between Intl1 carriage and trimethoprim/sulfamethoxazole resistance. Thus, MDR phenotypes may be conferred by a relatively small number of genes. The level and pattern of antibiotic resistance highlight the need for better antibiotic therapy guidelines, including reduced use and improved surveillance

Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate

Antimicrobial resistance is of global concern. Most antimicrobial use is in agriculture; manures and slurry are especially important because they contain a mix of bacteria, including potential pathogens, antimicrobial resistance genes and antimicrobials. In many countries, manures and slurry are stored, especially over winter, before spreading onto fields as organic fertilizer. Thus these are a potential location for gene exchange and selection for resistance. We develop and analyze a mathematical model to quantify the spread of antimicrobial resistance in stored agricultural waste. We use parameters from a slurry tank on a UK dairy farm as an exemplar. We show that the spread of resistance depends in a subtle way on the rates of gene transfer and antibiotic inflow. If the gene transfer rate is high, then its reduction controls resistance, while cutting antibiotic inflow has little impact. If the gene transfer rate is low, then reducing antibiotic inflow controls resistance. Reducing length of storage can also control spread of resistance. Bacterial growth rate, fitness costs of carrying antimicrobial resistance and proportion of resistant bacteria in animal faeces have little impact on spread of resistance. Therefore effective treatment strategies depend critically on knowledge of gene transfer rates

ALS/FTD Mutation-Induced Phase Transition of FUS Liquid Droplets and Reversible Hydrogels into Irreversible Hydrogels Impairs RNP Granule Function.

The mechanisms by which mutations in FUS and other RNA binding proteins cause ALS and FTD remain controversial. We propose a model in which low-complexity (LC) domains of FUS drive its physiologically reversible assembly into membrane-free, liquid droplet and hydrogel-like structures. ALS/FTD mutations in LC or non-LC domains induce further phase transition into poorly soluble fibrillar hydrogels distinct from conventional amyloids. These assemblies are necessary and sufficient for neurotoxicity in a C. elegans model of FUS-dependent neurodegeneration. They trap other ribonucleoprotein (RNP) granule components and disrupt RNP granule function. One consequence is impairment of new protein synthesis by cytoplasmic RNP granules in axon terminals, where RNP granules regulate local RNA metabolism and translation. Nuclear FUS granules may be similarly affected. Inhibiting formation of these fibrillar hydrogel assemblies mitigates neurotoxicity and suggests a potential therapeutic strategy that may also be applicable to ALS/FTD associated with mutations in other RNA binding proteins.Supported by Canadian Institutes of Health Research (PEF, PStGH), Alzheimer Society of Ontario (PEF, PStGH), Wellcome Trust (PStGH, MEV, CFK, GSK, DR, CEH), Medical Research Council (PStGH, MEV, CFK, GSK), National Institutes of Health Research, Alzheimer Research UK (CFK, GSK), Gates Cambridge Scholarship (JQL), Engineering and Physical Sciences Research Council (CFK, GSK), European Research Council Starting Grant RIBOMYLOME_309545 (GGT), European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement no. 322817 (CEH), and National Institute of Neurological Disorders and Stroke R01 NS07377 (NAS). The authors thank Tom Cech and Roy Parker for helpful discussions.This is the final version of the article. It was first available from Elsevier via http://dx.doi.org/10.1016/j.neuron.2015.10.03

Modelling the impact of wastewater flows and management practices on antimicrobial resistance in dairy farms

Dairy slurry is a major source of environmental contamination with antimicrobial resistant genes and bacteria. We developed mathematical models and conducted on-farm research to explore the impact of wastewater flows and management practices on antimicrobial resistance (AMR) in slurry. Temporal fluctuations in cephalosporin-resistant Escherichia coli were observed and attributed to farm activities, specifically the disposal of spent copper and zinc footbath into the slurry system. Our model revealed that resistance should be more frequently observed with relevant determinants encoded chromosomally rather than on plasmids, which was supported by reanalysis of sequenced genomes from the farm. Additionally, lower resistance levels were predicted in conditions with lower growth and higher death rates. The use of muck heap effluent for washing dirty channels did not explain the fluctuations in cephalosporin resistance. These results highlight farm-specific opportunities to reduce AMR pollution, beyond antibiotic use reduction, including careful disposal or recycling of waste antimicrobial metals. Antimicrobial resistance (AMR) is one of the most important global public health problems. It is estimated that 1.27 million deaths were attributed to AMR bacteria globally in 2019 1 , and, unless suitable countermeasures are taken, that number is predicted to rise to 10 million by 2050 2. AMR is driven by antibiotic use; the majority (73%) of antibiotic (Ab) sales are for use for food-producing livestock 3. The use of Abs in agriculture can result in drug-resistant strains infecting human populations through the food chain 4,5 , or may lead to the transfer of antibiotic resistance genes (ARGs) from livestock-associated bacteria to human-acquired infections 6-8. The importance of mitigating the risks of AMR in the agricultural sector has been recognised by many countries, including the UK, the European Union and the UN 2,9 , with reductions and restrictions being imposed on Ab use in agriculture, particularly on human critical antibiotics. However, despite a 55% reduction in Ab use in the UK agriculture sector since 2014 10 , use remains high, representing 36% of the total UK Ab use 11 , with consequent risk of spread of ARGs and AMR. In addition to antibiotics, other antimicrobials such as metals (copper and zinc) and other chemicals (e.g., formalin, disinfectants) are widely used across farms globally, particularly in footbaths to prevent lameness in livestock-a prevalent concern in dairy and sheep farming 12. Metals and other antimicrobial agents (such as formalin and glutaraldehyde) are known to have a co-selective effect on antibiotic resistance, allowing for th