Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from Argentinian pig and dairy farms reveals animal-specific patterns of co-resistance and resistance mechanisms.

Control measures are being introduced globally to reduce the prevalence of antibiotic resistance (ABR) in bacteria on farms. However, little is known about the current prevalence and molecular ecology of ABR in bacterial species with the potential to be key opportunistic human pathogens, such as Escherichia coli, on South American farms. Working with 30 dairy cattle farms and 40 pig farms across two provinces in central-eastern Argentina, we report a comprehensive genomic analysis of third-generation cephalosporin-resistant (3GC-R) E. coli, which were recovered from 34.8% (cattle) and 47.8% (pigs) of samples from fecally contaminated sites. Phylogenetic analysis revealed substantial diversity suggestive of long-term horizontal and vertical transmission of 3GC-R mechanisms. CTX-M-15 and CTX-M-2 were more often produced by isolates from dairy farms, while CTX-M-8 and CMY-2 and co-carriage of amoxicillin/clavulanate resistance and florfenicol resistance were more common in isolates from pig farms. This suggests different selective pressures for antibiotic use in these two animal types. We identified the ß-lactamase gene blaROB, which has previously only been reported in the family Pasteurellaceae, in 3GC-R E. coli. blaROB was found alongside a novel florfenicol resistance gene, ydhC, also mobilized from a pig pathogen as part of a new composite transposon. As the first comprehensive genomic survey of 3GC-R E. coli in Argentina, these data set a baseline from which to measure the effects of interventions aimed at reducing on-farm ABR and provide an opportunity to investigate the zoonotic transmission of resistant bacteria in this region. IMPORTANCE: Little is known about the ecology of critically important antibiotic resistance among bacteria with the potential to be opportunistic human pathogens (e.g., Escherichia coli) on South American farms. By studying 70 pig and dairy cattle farms in central-eastern Argentina, we identified that third-generation cephalosporin resistance (3GC-R) in E. coli was mediated by mechanisms seen more often in certain species and that 3GC-R pig E. coli were more likely to be co-resistant to florfenicol and amoxicillin/clavulanate. This suggests that on-farm antibiotic usage is key to selecting the types of E. coli present on these farms. 3GC-R E. coli and 3GC-R plasmids were diverse, suggestive of long-term circulation in this region. We identified the de novo mobilization of the resistance gene blaROB from pig pathogens into E. coli on a novel mobile genetic element, which shows the importance of surveying poorly studied regions for antibiotic resistance that might impact human health.

Validation, visibility, vagueness and variation: A qualitative assessment of existing veterinary guidelines for antimicrobial use in cattle and sheep in the UK.

Antimicrobials are essential in veterinary medicine to treat and control bacterial disease in animals. Their prudent use in food-producing animals has been encouraged to reduce the development and spread of antimicrobial resistance. National and international guidelines for responsible antimicrobial use have been developed as tools to guide and rationalise antimicrobial prescribing decisions by veterinarians and usage decisions by farmers. Yet, there is little understanding of whether these existing guidelines are fit for purpose. Accordingly, this study rigorously assessed 128 veterinary guidelines for antimicrobial use in ruminants in the UK, following established qualitative methodologies. Findings revealed four pertinent themes: validation of the veterinarian as the prescriber, visibility of responsible use realities, vagueness in interpretation and variation in directing behaviour. These themes encompassed the roles and responsibilities of the veterinarian and the realities of prescribing scenarios, alongside concerns relating to the specificity within and variation between guidelines. Resultant recommendations to inform and support the future development of guidelines include establishing species-specific and disease-specific guidelines, expanding guidelines to include disease prevention measures, including definitions to resolve vagueness and promoting congruence in interpretation, encouraging the development of practice-level guidelines to endorse collaboration and ownership, and fostering active working between stakeholders to align priorities and messaging.

New Insight into the Prevalence and Risk Factors for Three Distinct Hoof Conformation Traits in UK Commercial Sheep Flocks.

Lameness in sheep continues to be a global health, welfare and economic concern. Damaged, misshapen or overgrown feet have the potential to cause lameness either directly, or indirectly. There is a lack of understanding of the predisposing factors for different hoof conformation traits in sheep. Our exploratory study aimed to investigate the prevalence of, and risk factors for, three distinct hoof conformation traits relating to the sole and heel, hoof wall, and hoof wall overgrowth. Feet of 400 ewes from four UK commercial sheep farms were inspected at four time points across 12 months. For each conformation trait, a four-point ordinal system was used to score each individual claw, and foot-level scores were calculated. We present 92.4% of foot-level observations to be affected by ≥1 conformation traits. Whilst hoof conformation traits were correlated to some degree, a unique set of sheep-, foot- and farm-level factors were associated with each distinct conformation trait. We provide, for the first time, key insight into the multifaceted and multifactorial aetiology of hoof conformation in sheep, building upon previous landmark studies. Our results inform hypotheses for future prospective studies investigating the risk factors for adverse hoof conformation in sheep.

Prevalence and Temporal Dynamics of White Line Disease in Sheep: An Exploratory Investigation into Disease Distribution and Associated Risk Factors.

Lameness in sheep is a global health, welfare and economic concern. White line disease (WLD), also known as shelly hoof, is a prevalent, non-infectious cause of lameness, characterised by the breakdown of the white line. Little is known about the predisposing factors, nor the individual disease dynamics over time. Our exploratory study aimed to investigate the prevalence and temporal dynamics of WLD, and the associated risk factors. Feet of 400 ewes from four UK commercial sheep farms were inspected for WLD at four time points across 12 months. The change in WLD state at foot-level (develop or recover) was calculated for three transition periods. We present WLD to be widespread, affecting 46.8% of foot-level and 76.6% of sheep-level observations. States in WLD changed over time, with feet readily developing and recovering from WLD within the study period. The presence of WLD at foot-level, the number of feet affected at sheep-level and dynamics in development and recovery were driven by a variety of foot-, sheep- and farm-level factors. We provide key insight into the multifaceted aetiology of WLD and corroborate previous studies demonstrating its multifactorial nature. Our study highlights an opportunity to reduce WLD prevalence and informs hypotheses for future prospective studies.

Characterisation of Dichelobacter nodosus on Misshapen and Damaged Ovine Feet: A Longitudinal Study of Four UK Sheep Flocks.

Dichelobacter nodosus is the causal agent of ovine footrot, a contagious disease of welfare and economic concern worldwide. Damaged feet may be subclinical carriers of D. nodosus and covertly spread infection. Accordingly, we evaluated the risk of misshapen and damaged feet on D. nodosus presence and load in four commercial UK sheep flocks. Foot-level observations and swabs (n = 972) were collected from ewes (n = 85) over 12 months. On average, ewes were sampled three times. Feet were inspected for disease and scored (good/poor) for three hoof conformation traits (sole and heel, wall, and wall overgrowth). Swabs were analysed for presence and load of D. nodosus, and mixed models were constructed. Poor hoof conformation traits were present in 92.5% of foot-level observations. Feet with poor sole and heel conformation were more likely to have higher D. nodosus loads (ß = 0.19, 95% CI: 0.04-0.35) than those with good conformation. Furthermore, on feet positive for D. nodosus, wall overgrowth was associated with higher D. nodosus loads (ß = 0.27, 95% CI: 0.01-0.52). Feet with aspects of poor conformation covertly harbour D. nodosus and are a source of infection. Flock management should be guided by hoof conformation to reduce disease challenge.

Sheep farmers' attitudes towards lameness control: Qualitative exploration of factors affecting adoption of the lameness Five-Point Plan.

In 2014, best-practice recommendations to treat and control lameness in sheep in the UK were consolidated into a national program, the Five-Point Plan (5PP). As recent evidence suggests that only the minority of sheep farmers are implementing all management practices listed in the 5PP, qualitative investigation is vital to ensure future promotion is aligned with psychological and contextual factors affecting farmers' decision-making. This qualitative study sought to explore farmers' attitudes and the factors affecting uptake of best-practice measures listed in the 5PP. Semi-structured interviews were conducted in 2019 with 12 sheep farmers from England and Wales. In accordance with Thematic Analysis and the principles of Grounded Theory, data collection and analysis were performed iteratively. Two overarching themes, delineated by subthemes, emerged during analysis; (1) Barriers to adoption of 5PP measures and (2) Motivation to adopt 5PP measures. Various farmer-centric factors and physical resources were identified as key barriers or obstacles that limited farmers' ability to implement 5PP measures outright, or restricted their ability to make changes to facilitate future adoption. Conversely, internal and external influences were identified to increase farmers' willingness and motivation to implement practices listed on the 5PP. Heterogeneity in farmer perceptions, attitudes, experiences and circumstances identified in this study highlights the difficulty in promoting a one-size-fits-all lameness control plan, where a unique combination of intrinsic factors, social influences, and physical restrictions affect implementation. Future initiatives should focus on removing barriers by changing farmers' perceptions and mindset towards lameness control, and building farmers' confidence in their ability to implement practices. Furthermore, farmers' social licence to farm and their desire to improve their reputation within society, presents an important opportunity to further engage farmers in implementing control practices. Increasing peer-to-peer knowledge transfer opportunities and effective farmer-veterinarian communication and rapport could help establish 5PP measures as normative behaviours.

Uptake of the lameness Five-Point Plan and its association with farmer-reported lameness prevalence: A cross-sectional study of 532 UK sheep farmers.

The aims of this research were to determine the uptake of a national strategy to reduce lameness in the UK flock, known as the Five-Point Plan (5 P P); explore the association between footrot vaccination (Footvax®) use and 5 P P adoption; investigate the management practices associated with farmer-reported percentage lameness through risk factor analysis; and identify the population attributable fractions of these management practices. In 2014, the 5 P P was launched to provide a practical, farm-level framework to help farmers reduce lameness to reach Farm Animal Welfare Committee (FAWC) targets. No published studies have explicitly explored its uptake in UK flocks nor its association with lameness prevalence. Understanding what parts of the 5 P P farmers adopt and which elements contribute towards the greatest reduction in lameness are integral in informing future strategies. Between November 2018 and February 2019, 532 UK sheep farmers completed a cross-sectional online and paper-based survey. The geometric mean of farmer-reported percentage lameness in ewes was 3.2 % (95 % CI: 2.8-3.6). Farmers adopted a median of 3 points of the plan, but was only fully-adopted by 5.8 % of farmers. The number of points adopted increased with flock size, with larger commercial flocks more likely to cull and vaccinate against footrot, but smaller, pedigree flocks were more likely to treat individual lame sheep. Vaccination was poorly associated with the uptake of other points of the 5 P P. Eight flock management factors were associated with significantly higher percentage lameness in ewes; not carrying out measures to avoid lameness transmission, not quarantining bought in stock, not treating individual lame sheep within three days, maintaining an open flock and foot trimming were all associated with a higher risk of lameness in flocks studied. In addition, using Footvax® for ≤5 years was associated with a higher risk of lameness, although vaccination could be a consequence of high flock lameness or these farmers were not implementing other effective managements, such as treating promptly. The highest PAFs were calculated for trimming lame sheep (16.9 %), maintaining an open flock (13.5 %) and not carrying out measures to avoid lameness transmission (11.8 %). We provide new evidence documenting the benefits of adopting parts of the 5 P P on reducing lameness prevalence in UK flocks, although uptake of these measures could be improved in flocks. Encouraging uptake of these measures could make an important contribution towards reducing the prevalence of lameness and reaching 2021 FAWC ≤ 2% lameness prevalence targets.