A mixed method approach to analysing patterns and drivers of antibiotic use and resistance in beef farms in Argentina.

Introduction: Antimicrobial resistance is a challenge to be faced by all livestock sectors; within beef farming, antibiotic use patterns vary by country and management practices. Argentina is a country with high beef production & consumption but limited information surrounding antibiotic use. The aims of this project was to understand how antibiotics are being used across the beef industry in Argentina and exploring drivers of usage.

Comparison of multiple international metrics for benchmarking antibiotic usage (ABU) using UK beef and sheep data.

Background: Accurate surveillance of livestock antibiotic usage (ABU) at the farm level is an increasingly important part of national antibiotic stewardship initiatives. Numerous ABU indicators or metrics have been developed in Europe and North America but the comparability of these metrics is poorly understood. For policymakers, understanding the relationship between metrics is important when considering the risks posed by ABU and how to regulate them, at the national level, and regulate international trade access in livestock products between countries who use different ABU metrics.

Longitudinal study of antimicrobial use patterns, vaccination and disease prevalence in British sheep flocks.

Background: The aim of the study was to describe the longitudinal dynamics of antimicrobial use (AMU) on sheep farms and explore associations between AMU and management factors, vaccination strategies, reproductive performance and prevalence of lameness.

Methods: Antimicrobial supply data were collected for 272 British sheep farms for 3-6 consecutive years between 2015 and 2021. These data were obtained from the farms' veterinary practices.

Associations between small ruminant lentivirus infection and total milk yield and somatic cell count in a dairy sheep flock.

Background: Small ruminant lentiviruses (SRLVs) are lentiviruses of sheep and goats, formerly known as maedi-visna (MV) in sheep and caprine encephalitis and arthritis in goats. In sheep, SRLVs commonly cause progressive pneumonia, wasting and indurative mastitis. SRLVs have a long latent period, and chronic production losses are often not recognised until very late.

To scan or not to scan? The economics of transthoracic ultrasonography for 'whole-flock' ovine pulmonary adenocarcinoma screening in UK sheep flocks.

Background: Transthoracic ultrasonography (TTUS) is currently the only widely used method to diagnose suspected preclinical or subclinical cases of ovine pulmonary adenocarcinoma/Jaagsiekte (OPA) in live sheep. However, the economic impact of using TTUS as a screening test has not been described previously.

Methods: Test characteristics for TTUS in a low-prevalence situation were obtained from a previous study of 1074 breeding ewes that underwent TTUS with an experienced operator.

The impact of glutaraldehyde based footbaths on Dichelobacter nodosus prevalence and the antimicrobial resistant community of the ovine interdigital skin.

Ovine footrot, is a highly contagious polymicrobial bacterial infection, primarily caused by Dichelobacter nodosus. Preventative bactericidal footbaths are commonly used in the sheep industry to reduce the spread of bacteria. However, their effect on the bacterial community is poorly understood.

Failure to detect Schmallenberg virus RNA in ram semen in the UK (2016-2018).

Background: Schmallenberg virus (SBV) is a midge-borne arbovirus that first emerged in the European ruminant population in 2011 and has since settled to an endemic pattern of disease outbreaks on an approximately 4-year cycle when herd immunity from the previous circulation drops to a point allowing renewed widescale virus circulation. The impacts of trade restrictions on genetic products (semen, embryos) from affected areas were severe, particularly after the discovery that the virus is intermittently shed in the semen of a small number of bulls. The trade in small ruminant (ram and goat) semen is less than that of bulls; nonetheless, there has been no study into the shedding rate of SBV in ram semen.

To scan or not to scan? Efficacy of transthoracic ultrasonography for ovine pulmonary adenocarcinoma screening in a large commercial UK sheep flock.

Background: Transthoracic ultrasonography (TTUS) is currently the only widely used method to diagnose preclinical or subclinical ovine pulmonary adenocarcinoma (OPA) in the live sheep. However, little is known about the test characteristics of TTUS.

Methods: One thousand and seventy-four breeding ewes in a flock with evidence of low OPA prevalence underwent TTUS by an experienced operator.

Clearance of Maedi-visna infection in a longitudinal study of naturally infected rams is associated with homozygosity for the resistance allele.

Maedi-visna (MV) is a lentiviral disease of sheep responsible for severe production losses in affected flocks. There are no vaccination or treatment options with control reliant on test and cull strategies. The most common diagnostic methods used at present are combination ELISAs for Gag and Env proteins with virus variability making PCR diagnostics still largely an experimental tool.

Variable selection for inferential models with relatively high-dimensional data: Between method heterogeneity and covariate stability as adjuncts to robust selection.

Variable selection in inferential modelling is problematic when the number of variables is large relative to the number of data points, especially when multicollinearity is present. A variety of techniques have been described to identify 'important' subsets of variables from within a large parameter space but these may produce different results which creates difficulties with inference and reproducibility. Our aim was evaluate the extent to which variable selection would change depending on statistical approach and whether triangulation across methods could enhance data interpretation.

Schmallenberg virus neutralising antibody responses in sheep.

Background: Schmallenberg virus (SBV) is a midge borne virus of cattle and sheep. Infection is typically asymptomatic in adult sheep but fetal infection during pregnancy can result in abortion, stillbirth, neurological disorders and malformations of variable severity in newborn animals. It was first identified in Germany and the Netherlands in 2011 and then circulated throughout Europe in 2012 and 2013.

Use of bootstrapped, regularised regression to identify factors associated with lamb-derived revenue on commercial sheep farms.

The profitability of UK sheep farms is variable with many farms making a net loss. For economic sustainability, farms have to be profitable, therefore it is important to maximise income whilst controlling costs. The most important source of income in sheep flocks is from lamb production but there is little information on factors that explain variability between farms in revenue from lamb sales.

Sustainable lamb production: Evaluation of factors affecting lamb growth using hierarchical, cross classified and multiple memberships models.

In light of current concerns about the sustainability of red meat production in a world with increasing global demand for food from animal origin there is a need for a better understanding of factors that influence the growth rate and feed conversion efficiency of animals on commercial farms. The primary objective of this observational study was to use longitudinal data to quantify the simultaneous effects of multiple ewe and lamb factors on lamb growth rate. A secondary aim was to evaluate model structures that specifically account for lamb grouping effects during the growth period and compare these to classical hierarchical growth rate models.

DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples.

High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test the statistical significance of differences in bacterial population or gene composition, applicable to metagenomic or quantitative polymerase chain reaction data. Our method goes beyond previous published work in being universally most powerful, thus better able to detect statistically significant differences, and through being more reliable for smaller sample sizes.

Discrimination of contagious and environmental strains of Streptococcus uberis in dairy herds by means of mass spectrometry and machine-learning.

Streptococcus uberis is one of the most common pathogens of clinical mastitis in the dairy industry. Knowledge of pathogen transmission route is essential for the selection of the most suitable intervention. Here we show that spectral profiles acquired from clinical isolates using matrix-assisted laser desorption ionization/time of flight (MALDI-TOF) can be used to implement diagnostic classifiers based on machine learning for the successful discrimination of environmental and contagious S.

The Applied Development of a Tiered Multilocus Sequence Typing (MLST) Scheme for .

() is the causative pathogen of ovine footrot, a disease that has a significant welfare and financial impact on the global sheep industry. Previous studies into the phylogenetics of have focused on Australia and Scandinavia, meaning the current diversity in the United Kingdom (U.K.

Drivers for precision livestock technology adoption: A study of factors associated with adoption of electronic identification technology by commercial sheep farmers in England and Wales.

The UK is the largest lamb meat producer in Europe. However, the low profitability of sheep farming sector suggests production efficiency could be improved. Although the use of technologies such as Electronic Identification (EID) tools could allow a better use of flock resources, anecdotal evidence suggests they are not widely used.

Quantitative analysis of antimicrobial use on British dairy farms.

Antimicrobial resistance has been reported to represent a growing threat to both human and animal health, and concerns have been raised around levels of antimicrobial usage (AMU) within the livestock industry. To provide a benchmark for dairy cattle AMU and identify factors associated with high AMU, data from a convenience sample of 358 dairy farms were analysed using both mass-based and dose-based metrics following standard methodologies proposed by the European Surveillance of Veterinary Antimicrobial Consumption project. Metrics calculated were mass (mg) of antimicrobial active ingredient per population correction unit (mg/PCU), defined daily doses (DDDvet) and defined course doses (DCDvet).

Quantitative analysis of antibiotic usage in British sheep flocks.

The aim of this study was to examine the variation in antibiotic usage between 207 commercial sheep flocks using their veterinary practice prescribing records. Mean and median prescribed mass per population corrected unit (mg/PCU) was 11.38 and 5.

Prediction of Streptococcus uberis clinical mastitis risk using Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) in dairy herds.

The purpose of this study was to evaluate whether the risk of Streptococcus uberis clinical mastitis at cow level could be predicted from the historical presence of specific strains of S. uberis on dairy farms. Matrix-assisted laser desorption ionization time of flight mass spectrometry was used to identify S.