Genomic characterisation of Escherichia coli isolated from poultry at retail through Sink Surveillance in Dhaka, Bangladesh reveals high levels of multi-drug resistance.

The surveillance of antimicrobial resistance (AMR) in commensal Escherichia coli from livestock at slaughter is widely employed to assess the potential for risk to humans. There is currently a limited understanding of AMR in Bangladesh poultry at retail in live bird markets, with studies focussing solely on phenotypic characterisation of resistance. To address this evidence gap we performed antimicrobial susceptibility testing and whole genome sequencing on E. coli obtained from chickens from live bird markets in Dhaka in 2018 (n = 38) and 2020 (n = 45). E. coli were isolated from caeca samples following ISO guidelines and sequenced using short and long read methods. Multidrug resistance was extremely common (n = 77) and there was excellent concordance between AMR phenotype and the presence of corresponding AMR genes or mutations. There was considerable genomic diversity, with 43 different sequence types detected. Public health considerations included the high occurrence of resistance to ciprofloxacin (n = 75) associated with plasmid-residing qnrS or mutations in the gyrA and parC chromosomal genes; and the detection of a tigecycline resistant isolate harbouring tet(X4) on an IncHI1A/B-IncFIA mosaic plasmid. Thirty-nine isolates were resistant to azithromycin and harboured mphA, with a significant increase in the incidence of resistance between 2018 and 2020. Although azithromycin is banned for veterinary use in Bangladesh it remains an important treatment option for humans. Interestingly, mphA confers high-level resistance to azithromycin and erythromycin, and the latter is commonly used on poultry farms in Bangladesh. Seven isolates were colistin resistant and carried mcr1. For two isolates hybrid assemblies revealed that mcr1 resided on a highly conserved IncHI2 plasmid that had 93% nucleotide identity to a plasmid from the published genome of an E. coli isolate of Bangladeshi human origin. Six isolates had resistance to third generation cephalosporins, associated with plasmid-residing bla CTX-M-55, bla CTX-M-65, or bla DHA-1. By employing phenotypic and genomic approaches for AMR surveillance we have provided new insights into the potential for One Health AMR linkages in Bangladesh. Employing similar approaches in human and environmental sectors will help inform the One Health approach to addressing AMR, and generate evidence to support mitigation measures such as improved antimicrobial stewardship.

Genomics to detect transmission of livestock-associated methicillin-resistant Staphylococcus aureus from UK pigs in abattoirs during slaughter.

BACKGROUND: Livestock-associated MRSA (LA-MRSA) transmission/cross-contamination can occur at abattoir through colonized pigs, increasing occupational hazards and health concerns for workers. To assess this risk we used genomics to identify LA-MRSA lineages present in batches of pigs sent to slaughter and distribution of clones. METHODS: WGS was performed on 85 LA-MRSA previously isolated from six abattoirs from 105 batches of pigs sent from 100 UK farms. spa typing and MLST were performed on all isolates. A mashtree tree was constructed to compare genomes of the LA-MRSA with 1281 global isolates from livestock and humans. A phylogenetic tree and pairwise SNP distance matrices were built from whole genomes of 109 isolates closest to those from abattoirs to compare evolutionary relationships and identify clones. RESULTS: All abattoir isolates belonged to CC398 and were mainly of spa type t011, although other spa types were present. Phylogenetic analysis confirmed the abattoir isolates were most closely related to each other and to pig LA-MRSA from across Europe, indicating a common evolutionary origin with related lineages colonizing UK pigs.Comparison of genomes using SNPs suggested between one and four clones were transferring between pigs from different batches. Transmission likely occurred on farm premises, during transportation, and/or within abattoirs through contact with contaminated surfaces in lairage or post-stunning. CONCLUSIONS: Genomics forensically identified related isolates/clones circulating in pigs at slaughter, showing contamination occurs often. Results suggest that further genomic tracking will identify hotspots, and improvements in measures such as biosecurity and disinfection will help reduce risk for workers.

Antimicrobial resistance of Escherichia coli in the UK: comparison of single vs. pooled samples from healthy pigs.

This study compared the antimicrobial resistance (AMR) of Escherichia coli detected from single samples vs. pooled samples at herd level. The national monitoring dataset included isolates from one sample per pig holding, whereas the research study included isolates from pooled samples of 10 pigs per holding. In both datasets, caecal samples were collected from healthy pigs randomly selected at slaughterhouses and plated on non-selective and antibiotic selective media. Resistance against a panel of nine antibiotics was compared between datasets by generalized linear mixed effects models (GLMMs) and by bootstrapped generalized linear model (GLM) to account for pooling. The highest proportion of resistant E. coli was observed against tetracycline and ampicillin in both datasets. In non-selective media, single and pooled samples showed similar results, but the bootstrapped GLM detected significantly lower resistance to ciprofloxacin and nalidixic acid in the national dataset. In selective media, a significantly greater proportion of resistant isolates was observed in the research dataset for ceftazidime (OR: 0.05, 95%CI = 0.01-0.42) and nalidixic acid (OR: 0.15, 95%CI = 0.05-0.51). The results suggest that one sample per holding provides similar information on AMR at herd level as pooled samples for most of the tested antibiotics, although less resistance to ciprofloxacin, ceftazidime, and nalidixic acid was detected.

Assessing pig farm biosecurity measures for the control of Salmonella on European farms.

Salmonella spp. is a common zoonotic pathogen, causing gastrointestinal infections in people. Pigs and pig meat are a major source of infection. Although farm biosecurity is believed to be important for controlling Salmonella transmission, robust evidence is lacking on which measures are most effective. This study enrolled 250 pig farms across nine European countries. From each farm, 20 pooled faecal samples (or similar information) were collected and analysed for Salmonella presence. Based on the proportion of positive results, farms were categorised as at higher or lower Salmonella risk, and associations with variables from a comprehensive questionnaire investigated. Multivariable analysis indicated that farms were less likely to be in the higher-risk category if they had '<400 sows'; used rodent baits close to pig enclosures; isolated stay-behind (sick) pigs; did not answer that the hygiene lock/ anteroom was easy to clean; did not have a full perimeter fence; did apply downtime of at least 3 days between farrowing batches; and had fully slatted flooring in all fattener buildings. A principal components analysis assessed the sources of variation between farms, and correlation between variables. The study results suggest simple control measures that could be prioritised on European pig farms to control Salmonella.

Development of soil health benchmarks for managed and semi-natural landscapes.

Efforts to improve soil health require that target values of key soil properties are established. No agreed targets exist but providing population data as benchmarks is a useful step to standardise soil health comparison between landscapes. We exploited nationally representative topsoil (0-15 cm) measurements to derive soil health benchmarks for managed and semi-natural environments across Great Britain. In total, 4587 soil organic matter (SOM), 3860 pH, 2908 bulk density (BD), and 465 earthworm abundance (EA) datapoints were used. As soil properties are sensitive to site-specific characteristics, data were stratified by habitat, soil type, and mean annual precipitation, with benchmarks defined as the middle 80 % of values in each distribution - yielding 135 benchmarks. BD and pH decreased with land management intensity (agriculture > semi-natural grasslands > woodlands > heathlands > wetlands), and vice versa for SOM and EA. Normalising benchmark ranges by medians revealed soil health indicator benchmark widths increased in the order: pH < BD < SOM < EA, while width increased with decreasing land management intensity. Arable and horticulture and improved grassland exhibited narrow benchmarks for SOM, pH and BD, yet the widest EA benchmark, suggesting additional drivers impact EA patterns. Upland wetlands had the widest BD benchmarks, important when determining carbon stocks. East Anglia currently possesses the largest proportions of atypical soils, including below typical SOM (19.2 %), above typical BD (17.4 %) and pH (39.1 %), and the smallest proportions of above typical SOM (2.4 %), and below typical BD (5.8 %) and pH (2.3 %). This is found even after land use, soil type and rainfall have been considered, underscoring how urgently soil health should be addressed here. Our benchmarking framework allows landowners to compare where their measured soil health indicators fall within expected ranges and is applicable to other biomes, national and multinational contexts.

A longitudinal study reveals persistence of antimicrobial resistance on livestock farms is not due to antimicrobial usage alone.

Introduction: There are concerns that antimicrobial usage (AMU) is driving an increase in multi-drug resistant (MDR) bacteria so treatment of microbial infections is becoming harder in humans and animals. The aim of this study was to evaluate factors, including usage, that affect antimicrobial resistance (AMR) on farm over time. Methods: A population of 14 cattle, sheep and pig farms within a defined area of England were sampled three times over a year to collect data on AMR in faecal Enterobacterales flora; AMU; and husbandry or management practices. Ten pooled samples were collected at each visit, with each comprising of 10 pinches of fresh faeces. Up to 14 isolates per visit were whole genome sequenced to determine presence of AMR genes. Results: Sheep farms had very low AMU in comparison to the other species and very few sheep isolates were genotypically resistant at any time point. AMR genes were detected persistently across pig farms at all visits, even on farms with low AMU, whereas AMR bacteria was consistently lower on cattle farms than pigs, even for those with comparably high AMU. MDR bacteria was also more commonly detected on pig farms than any other livestock species. Discussion: The results may be explained by a complex combination of factors on pig farms including historic AMU; co-selection of AMR bacteria; variation in amounts of antimicrobials used between visits; potential persistence in environmental reservoirs of AMR bacteria; or importation of pigs with AMR microbiota from supplying farms. Pig farms may also be at increased risk of AMR due to the greater use of oral routes of group antimicrobial treatment, which were less targeted than cattle treatments; the latter mostly administered to individual animals. Also, farms which exhibited either increasing or decreasing trends of AMR across the study did not have corresponding trends in their AMU. Therefore, our results suggest that factors other than AMU on individual farms are important for persistence of AMR bacteria on farms, which may be operating at the farm and livestock species level.

What is a biosecurity measure? A definition proposal for animal production and linked processing operations.

While biosecurity, a central component of the One Health concept, is clearly defined, a harmonized definition of the term ´biosecurity measure´ (BSM) is missing. In turn, particularly at the farm and policy level, this leads to misunderstandings, low acceptance, poor implementation, and thus suboptimal biosecurity along the food animal production chain. Moreover, different views on BSMs affects making comparisons both at the policy level as well as in the scientific community. Therefore, as part of the One Health EJP BIOPIGEE project, a work group i) collected and discussed relevant inclusion and exclusion criteria for measures to be considered in the context of biosecurity and ii) conducted a systematic literature review for potentially existing definitions for the term BSM. This exercise confirmed the lack of a definition of BSM, underlining the importance of the topic. In the pool of articles considered relevant to defining the term BSM, specific research themes were identified. Based on these outcomes, we propose a definition of the term BSM: "A biosecurity measure (BSM) - is the implementation of a segregation, hygiene, or management procedure (excluding medically effective feed additives and preventive/curative treatment of animals) that specifically aims at reducing the probability of the introduction, establishment, survival, or spread of any potential pathogen to, within, or from a farm, operation or geographical area." The definition provides a basis for policymakers to identify factual BSMs, highlights the point of implementation and supports to achieve the necessary quality standards of biosecurity in food animal production. It also enables clear, harmonized, cross-sectoral communication of best biosecurity practices to and from relevant stakeholders and thus contribute to improving biosecurity and thereby strengthen the One Health approach.

The effectiveness of short-duration in-feed organic acid use in finisher pigs for Salmonella control at slaughter.

Reducing the risk of Salmonella contaminated pork products entering the food chain is important for improving food safety. This study aimed to evaluate the effectiveness of the short-duration use of three acidified feed interventions in finisher pigs for reducing the faecal shedding, caecal carriage and carcase contamination of Salmonella at slaughter. We also investigated the presence of Salmonella in transportation vehicles and abattoir lairages used prior to slaughter. In a series of seven farm trials, two groups of pigs received either their normal ration (control), or a ration containing one of three organic acid products (intervention) for a four-week period before slaughter. Product A was trialled on five farms, and Products B and C were trialled on one farm each, included in the ration of intervention pigs at the manufacturers recommended rate. Faecal samples were collected and examined before and after the four-week intervention; caecal content samples and carcase swab samples were collected at slaughter. The lorry used to transport pigs to slaughter and abattoir lairage pens used to hold pigs were also sampled. During one trial (farm ID: AT03), no Salmonella was detected during either farm visit, and therefore this farm was excluded from further analysis of the effectiveness of organic acid interventions. Overall regression analysis indicated there was no significant difference in faecal shedding between the control groups at the baseline visit and the follow-up visit in pigs which received Product A (P = 0.262) or Product B (P = 0.094) in comparison to the control groups. On the other hand, there was evidence to suggest that the use of Product C was associated with an increase in faecal shedding compared to the control groups (P < 0.001). Similarly, Product A was not significantly associated (P > 0.05) with the caecal carriage of Salmonella. However, Product B (P = 0.029) and Product C (P = 0.050) were associated with an increase in caecal carriage in comparison to the control groups. These latter products were only trialled on one farm each, and these results may be attributable to natural random variation.

Efficacy of Five Disinfectant Products Commonly Used in Pig Herds against a Panel of Bacteria Sensitive and Resistant to Selected Antimicrobials.

The growing threat of antimicrobial resistance worldwide has led to an increasing concern in the human, veterinary, and environmental fields, highlighting the need for strategies to effectively control bacterial contamination. Correct biosecurity practices, including the appropriate use of disinfectants, play a crucial role in controlling bacterial contamination. This study aimed to verify whether the recommended concentrations defined according to the Defra General Orders concentration (GO, published by the UK Department for Environment, Food and Rural Affairs' disinfectant-approval scheme) of five commercial disinfectant preparations (peroxygen-based, phenol-based, two halogen-releasing agents, and glutaraldehyde/quaternary ammonium compound-based; disinfectants A to E, respectively) were sufficient to inhibit growth and inactivate selected bacterial strains, including some that carry known phenotypic patterns of multidrug resistance. The effectiveness of each disinfectant was expressed as the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values, determined by the broth-microdilution method. The results indicate that the type of disinfectant and its concentration influence the inhibitory and bactericidal efficacy. The glutaraldehyde/quaternary ammonium compound-based (disinfectant D) and chlorocresol-based products (disinfectant B) were the most effective, and the GO concentration was bactericidal in all the strains tested. The efficacy of the other compounds varied, depending on the bacterial species tested. The GO concentrations were at least able to inhibit the bacterial growth in all the products and bacterial strains tested. A greater tolerance to the compounds was observed in the strains of E. coli with multidrug-resistance profiles compared to the strains that were sensitive to the same antimicrobials.

A systematized review and qualitative synthesis of potential risk factors associated with the occurrence of non-O157 Shiga toxin-producing Escherichia coli (STEC) in the primary production of cattle.

Human infection with Shiga toxin-producing Escherichia coli (STEC) causes an estimated 2.8 million cases of acute illness worldwide each year. Serogroup O157 is the most commonly diagnosed STEC in humans, but cases linked to non-O157 STEC serogroups have increased recently due to increased surveillance and improvements to detection methods. Cattle are an important reservoir for STEC O157 and the same may be true for non-O157 STEC; therefore, reducing the occurrence of these pathogens in cattle could mitigate human infection risk. A systematized literature review of articles published within the Scopus database since 2010 (employing a partially systematic approach) was therefore conducted followed by qualitative synthesis of evidence to provide a structured overview of potential risk factors for non-O157 STEC in primary cattle production. Overall, few relevant studies were identified (n = 22), highlighting that more studies are needed. Consistently significant associations were only identified with respect to cattle age (broadly higher rate of isolation from young animals compared to adults) and season of sampling (generally increased isolation of non-O157 STEC in summer). However, wide variation in study designs, including notable differences in laboratory detection methods, means drawing more general conclusions is currently not possible based on the results of this review. However, it is likely that the development of more sensitive methods for non-O157 STEC detection in potential livestock reservoirs and increased standardization across statistically sound epidemiological investigations are required to identify pertinent risk factors.

Study of Animal Mixing and the Dynamics of Hepatitis E Virus Infection on a Farrow-to-Finish Pig Farm.

In Europe, swine are a livestock reservoir for Hepatitis E virus genotype 3 (HEV-3). Consumption of food containing HEV-3 can cause zoonotic human infection, though risk is reduced by heat treatment. Implementing controls that limit infection in slaughter pigs may further reduce foodborne transmission risk but knowledge of infection dynamics on commercial farms is limited. This study addressed this knowledge gap and in particular investigated the influence of group mixing. Faeces were collected from grower (n = 212) and fattener (n = 262) pigs on a farrow-to-finish farm on four occasions. HEV RNA was detected on all occasions, and prevalence was higher in growers (85.8%) than fatteners (26.0%; p < 0.001). HEV-positive samples were also collected from the wider farm environment (n = 67; 64.7% prevalence), indicating potential sources for HEV re-circulation within the herd. Timing of infection in a cohort was also investigated. HEV was absent from all piglet faeces (n = 98) and first detected at weaner stage (25.7% prevalence), but only in groups weaned earlier or comprising pigs from many different litters. Farrowing sow faeces (n = 75) were HEV-negative but antibodies were detected in blood from two sows. Results suggest that multiple factors influence HEV infection dynamics on pig farms, and potential foci for further study into practical control solutions are highlighted.

RuO2 Nanorods as an Electrocatalyst for Proton Exchange Membrane Water Electrolysis.

A custom-built PEM electrolyzer cell was assembled using 6" stainless-steel ConFlat flanges which were fitted with a RuO2 nanorod-decorated, mixed metal oxide (MMO) ribbon mesh anode catalyst. The current density-voltage characteristics were measured for the RuO2 nanorod electrocatalyst while under constant water feed operation. The electrocatalytic behavior was investigated by making a series of physical modifications to the anode catalyst material. These experiments showed an improved activity due to the RuO2 nanorod electrocatalyst, resulting in a corresponding decrease in the electrochemical overpotential. These overpotentials were identified by collecting experimental data from various electrolyzer cell configurations, resulting in an improved understanding of the enhanced catalytic behavior. The micro-to-nano surface structure of the anode electrocatalyst layer is a critical factor determining the overall operation of the PEM electrolyzer. The improvement was determined to be due to the lowering of the potential barrier to electron escape in an electric field generated in the vicinity of a nanorod.

Risk factor analysis for Salmonella contamination of broiler chicken (Gallus gallus) hatcheries in Great Britain.

Salmonellosis is the second most commonly reported zoonosis in the European Union and contaminated meat from broiler chickens (Gallus gallus) is an important source of human infection. In Great Britain (GB), prevalence of Salmonella enterica in broiler flocks is low, having declined considerably since the introduction of the Salmonella National Control Programme in 2010. However, this decreasing trend has stabilised in recent years and serovars with known ability to persistently colonise hatcheries have been isolated from broiler flocks with increasing frequency, indicating that further controls on hatchery contamination are required. The broiler industry in GB has changed dramatically over the last 15 years, with greater intensification and dominance by a small number of very large companies which rely on relatively few hatcheries. An investigation of risk factors for Salmonella contamination in GB broiler hatcheries was therefore carried out so that relevant up-to-date advice on Salmonella control can be provided. Twenty-two hatcheries, representing most commercial scale GB broiler hatcheries, were visited between 2015 and 2018. Salmonella contamination was comprehensively investigated at each hatchery by collecting between 108 and 421 environmental swab samples per hatchery (6990 samples in total from all hatcheries). An in-depth questionnaire on hatchery operations was completed for each hatchery, and results were incorporated into a risk factor analysis (univariable followed by multivariable mixed effects logistic regression) to identify factors associated with Salmonella occurrence. Overall, 6.0 % (416/6990) of environmental samples were Salmonella-positive and Salmonella was isolated from 17/22 hatcheries. Ten different serovars were isolated, the most common being S. Senftenberg and S. Mbandaka which are known hatchery colonisers. Sixty-four risk factor variables were investigated. Twenty-two of these were initially retained based on univariable analyses (p ≤ 0.25) and six were ultimately left in the final multivariable model (p ≤ 0.05). Salmonella detection was positively associated with having ≥30 hatchers in regular use compared to fewer (Odds ratio [OR] 23.7, 95 % confidence interval [CI] 6.7-84.2), storing trays in process rooms (OR 28.8, CI 7.8-106.3), drying set-up trolleys in corridors (OR 15.6, CI 5.9-41.4) and having skips located in enclosed areas (OR 8.99, CI 5.89-41.35). Using a closed waste disposal system was negatively associated with Salmonella detection (OR 0.08, CI 0.04-0.18) and the odds of detecting Salmonella in hatcheries with 31-60 total workers was lower compared to hatcheries with ≤30 staff (OR 0.16, CI 0.06-0.40). Despite the complexities of hatchery enterprises, changes to a relatively small number of features may significantly reduce the occurrence of hatchery contamination.

Corrigendum: Characterizing Antimicrobial Resistant Escherichia coli and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain.

[This corrects the article DOI: 10.3389/fmicb.2020.00861.].

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae.

Escherichia coli and other Enterobacteriaceae are diverse species with "open" pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553 Escherichia and 274 non-Escherichia spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.

Review of investigations of premises housing animals that were linked to human outbreaks of cryptosporidiosis in England and Wales between 2009 and 2019.

BACKGROUND: Cryptosporidium can be an important human health risk, predominantly causing gastroenteritis. With increased public attendance at commercial and open farms, there is a need to improve the understanding of Cryptosporidium risk on premises that are visited by the public. METHODS: This study was designed to explore the animal premises-related and animal sampling-related data routinely collected, during 2009-2019, from human outbreak sampling investigations where animal contact was suggested as a source of Cryptosporidium. RESULTS: The results from the 23 eligible investigations indicated a diverse population of animals on the premises and that sheep and cattle, including bottle feeding, were frequently identified as contacts made by the human cases on these premises. Faecal samples from cattle and sheep were found to have a relatively high proportion of positive results and frequently matched the Cryptosporidium species and strain identified in the outbreak cases. Generally, investigations where no positive samples were detected had fewer samples collected. CONCLUSION: The findings support the advice to prioritise sampling of groups of animals which have been identified as being contacted by the human cases, and to use statistically valid sample size calculations for the number of samples to collect at each investigation.

Genomic network analysis of environmental and livestock F-type plasmid populations.

F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum ß-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.

Risk factor analysis for "diagnosis not reached" results from bovine samples submitted to British veterinary laboratories in 2013-2017.

Routine diagnostic data from laboratories are an important source of information for passive animal health surveillance. In Great Britain, the Veterinary Investigation Diagnosis Analysis (VIDA) database includes records of diagnostic submissions made to a nationwide network of 28 veterinary post-mortem facilities (VPFs). Data on "diagnosis not reached" (DNR), i.e. where submissions do not lead to a confirmed diagnosis, are analysed quarterly to look for unexpectedly high incidences of DNRs which could indicate the presence of a new or emerging disease in British livestock populations. The objective of the present study was to provide a better understanding about the reasons of DNR occurrence and to inform improvements of the coverage and reporting of this kind of surveillance data. A subset of the VIDA database comprising diagnostic submissions from cattle received from 2013 to 2017 (122,444 records) was analysed. A mixed-effects multivariable logistic regression model, accounting for clustering by farm and county, was used to investigate associations between potential predictors and DNR. The variables included in the model were: VPF identity, animal sex, age, production purpose, main presenting sign of the animal from which the sample was obtained, and sample submission type. The variable that showed the strongest association with DNR was the main presenting sign of the animal, followed by submission type, VPF identity, animal age, sex, and production purpose, in that order. Submissions from animals with abortion as the main clinical sign had the highest odds ratio (OR 21.6, 95 % confidence interval [CI] 19.6-23.9, with mastitis taken as the baseline). Submissions where neither carcasses (i.e. a whole dead animal provided for post-mortem examination) nor foetuses (i.e. an unborn dead animal) were provided had approximately 12 times the odds of being DNR, compared to submissions of a carcass (OR 11.6, 95 % CI 10.7-12.5). In addition, submission type and main presenting sign can be considered as important confounders in the association between the other predictors and DNR. This study has helped characterise DNR occurrence and suggests some possible improvements that could be made to the passive surveillance system investigated, such as encouraging greater carcase submission, accounting for identified issues when interpreting increased occurrence of DNR and further investigating reduced submissions or greater DNR occurrence in some geographical regions.

Characterizing Antimicrobial Resistant Escherichia coli and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain.

Combatting antimicrobial resistant (AMR) using a One-Health approach is essential as various bacteria, including Escherichia coli, a common bacteria, are becoming increasingly resistant and livestock may be a reservoir. The AMR gene content of 492 E. coli, isolated from 56 pig farms across Great Britain in 2014-2015, and purified on antibiotic selective and non-selective plates, was determined using whole genome sequencing (WGS). The E. coli were phylogenetically diverse harboring a variety of AMR profiles with widespread resistance to "old" antibiotics; isolates harbored up to seven plasmid Inc-types. None showed concurrent resistance to third-generation cephalosporins, fluoroquinolones and clinically relevant aminoglycosides, although ∼3% harbored AMR genes to both the former two. Transferable resistance to carbapenem and colistin were absent, and six of 117 E. coli STs belonged to major types associated with human disease. Prevalence of genotypically MDR E. coli, gathered from non-selective media was 46.9% and that of extended-spectrum-beta-lactamase E. coli was low (∼4% from non-selective). Approximately 72.6% of E. coli from ciprofloxacin plates and only 8.5% from the other plates harbored fluoroquinolone resistance due to topoisomerase mutations; the majority were MDR. In fact, multivariable analysis confirmed E. coli purified from CIP enrichment plates were more likely to be MDR, and suggested MDR isolates were also more probable from farms with high antibiotic usage, specialist finisher farms, and farms emptying their manure pits only after each batch. Additionally, farms from the South East were more likely to have MDR E. coli, whereas farms in Yorkshire and the Humber were less likely. Future investigations will determine whether suggested improvements such as better biosecurity or lower antimicrobial use decreases MDR E. coli on pig farms. Although this study focuses on pig farms, we believe the methodology and findings can be applied more widely to help livestock farmers in the United Kingdom and elsewhere to tackle AMR.