Small-scale sheep and cattle enterprises in Scotland: Demographics, animal health, and biosecurity.

Livestock keepers who operate on a small scale in the United Kingdom are often described as either smallholders or hobby farmers; however, this is not always the case. There is another distinct population in Scotland. The crofting system promotes the preservation of a way of life that is significant to the cultural heritage of Scotland, whilst at the same time utilising and maintaining marginal land that could otherwise be deemed of very low productive value. We developed two cross-sectional questionnaire surveys to gather descriptive data about individuals from two populations (crofters and smallholders) who kept sheep and/or cattle. Our aim was to explore demographics, animal health, husbandry, and biosecurity practices of these two communities, including how they may interact with other livestock sectors. Most respondents in each population kept sheep, with far fewer keeping cattle. There was a distinct geographical difference in the approximate location of respondents' holdings. Movement of sheep was often local, temporary, and exempt from reporting to national databases. Visits from the vet were infrequent, but the vet remained an important source of animal health advice, alongside peer networks. The information from these surveys is valuable because policy decisions taken with predominantly larger, commercial-scale enterprises in mind also frequently apply to small-scale enterprises, even though these smaller enterprises may not have the same opportunity to influence those decisions or implement the requirements. Aspects of agricultural activity and food production at the scale explored in these surveys - including plurality of employment and diversification away from purely agricultural activities - are relevant to the United Nations Sustainable Development Goals of sustainable cities and communities, zero hunger and life on land. In this context, competent authorities should support this type of context-sensitive agriculture, alongside seeking to maintain animal health and welfare standards at the highest possible level on a national scale. Our surveys contribute to improved understanding of how these enterprises function and therefore will support policy makers when considering the breadth of keepers and circumstances affected by rules and regulations governing agriculture.

Bacteriological Survey of Fresh Minced Beef on Sale at Retail Outlets in Scotland in 2019: Three Foodborne Pathogens, Hygiene Process Indicators, and Phenotypic Antimicrobial Resistance.

ABSTRACT: The health and economic burden of foodborne illness is high, with approximately 2.4 million cases occurring annually in the United Kingdom. A survey to understand the baseline microbial quality and prevalence of food-related hazards of fresh beef mince on retail sale could inform risk assessment, management, and communication to ensure the safety of this commodity. In such a survey, a two-stage sampling design was used to reflect variations in population density and the market share of five categories of retail outlets in Scotland. From January to December 2019, 1,009 fresh minced beef samples were collected from 15 geographic areas. The microbial quality of each sample was assessed using aerobic colony count and Escherichia coli count. Samples were cultured for Campylobacter and Salmonella, and PCR was used to detect target genes (stx1 all variants, stx2 a to g, and rfbO157) for Shiga toxin-producing E. coli (STEC). The presence of viable E. coli O157 and STEC in samples with a positive PCR signal was confirmed via culture and isolation. Phenotypic antimicrobial sensitivity patterns of cultured pathogens and 100 E. coli isolates were determined, mostly via disk diffusion. The median aerobic colony count and E. coli counts were 6.4 × 105 (interquartile range, 6.9 × 104 to 9.6 × 106) and <10 CFU/g (interquartile range, <10 to 10) of minced beef, respectively. The prevalence was 0.1% (95% confidence interval [CI], 0 to 0.7%) for Campylobacter, 0.3% (95% CI, 0 to 1%) for Salmonella, 22% (95% CI, 20 to 25%) for PCR-positive STEC, and 4% (95% CI, 2 to 5%) for culture-positive STEC. The evidence for phenotypic antimicrobial resistance detected did not give cause for concern, mainly occurring in a few E. coli isolates as single nonsusceptibilities to first-line active substances. The low prevalence of pathogens and phenotypic antimicrobial resistance is encouraging, but ongoing consumer food safety education is necessary to mitigate the residual public health risk.

Detection of extended-spectrum ß-lactam, AmpC and carbapenem resistance in Enterobacteriaceae in beef cattle in Great Britain in 2015.

AIMS: This study investigated the occurrence and genetic diversity of Enterobacteriaceae with extended-spectrum ß-lactamase (ESBL)-, AmpC- and carbapenemase-mediated resistance in British beef cattle, and related risk factors. METHODS AND RESULTS: Faecal samples (n = 776) were obtained from farms in England and Wales (n = 20) and Scotland (n = 20) in 2015. Isolates from selective agars were identified by MALDI ToF mass spectrometry. Selected isolates were characterized by multiplex PCR (blaCTX -M, blaOXA , blaSHV and blaTEM genes), whole-genome sequencing (WGS), minimum inhibitory concentrations and pulsed-field gel electrophoresis. None of the faecal samples yielded carbapenem-resistant Escherichia coli. Ten (25%) of the farms tested positive for ESBL-producing CTX-M Enterobacteriaceae, 15 (37·5%) of the farms were positive for AmpC phenotype E. coli and none were positive for carbapenem-resistant E. coli. WGS showed a total of 30 different resistance genes associated with E. coli, Citrobacter and Serratia from ESBL agars, and colocation of resistance genes with blaCTX -M1 . Buying bulls and bringing in fattening cattle from another farm were identified as significant risk factors for positive samples harbouring CTX-M Enterobacteriaceae or AmpC phenotype E. coli respectively. CONCLUSIONS: Beef cattle on a proportion of farms in GB carry ESBL-producing Enterobacteriaceae. Factors, such as operating as a closed herd, may have an important role in reducing introduction and transmission of resistant Enterobacteriaceae. The results indicate management factors may play an important role in impacting ESBL prevalence. In particular, further study would be valuable to understand the impact of maintaining a closed herd on reducing the introduction of resistant Enterobacteriaceae. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study showing the presence of ESBL-producing Enterobacteriaceae in British beef cattle.

An empirical comparison of isolate-based and sample-based definitions of antimicrobial resistance and their effect on estimates of prevalence.

Antimicrobial resistance is primarily a problem in human medicine but there are unquantified links of transmission in both directions between animal and human populations. Quantitative assessment of the costs and benefits of reduced antimicrobial usage in livestock requires robust quantification of transmission of resistance between animals, the environment and the human population. This in turn requires appropriate measurement of resistance. To tackle this we selected two different methods for determining whether a sample is resistant - one based on screening a sample, the other on testing individual isolates. Our overall objective was to explore the differences arising from choice of measurement. A literature search demonstrated the widespread use of testing of individual isolates. The first aim of this study was to compare, quantitatively, sample level and isolate level screening. Cattle or sheep faecal samples (n=41) submitted for routine parasitology were tested for antimicrobial resistance in two ways: (1) "streak" direct culture onto plates containing the antimicrobial of interest; (2) determination of minimum inhibitory concentration (MIC) of 8-10 isolates per sample compared to published MIC thresholds. Two antibiotics (ampicillin and nalidixic acid) were tested. With ampicillin, direct culture resulted in more than double the number of resistant samples than the MIC method based on eight individual isolates. The second aim of this study was to demonstrate the utility of the observed relationship between these two measures of antimicrobial resistance to re-estimate the prevalence of antimicrobial resistance from a previous study, in which we had used "streak" cultures. Boot-strap methods were used to estimate the proportion of samples that would have tested resistant in the historic study, had we used the isolate-based MIC method instead. Our boot-strap results indicate that our estimates of prevalence of antimicrobial resistance would have been considerably lower in the historic study had the MIC method been used. Finally we conclude that there is no single way of defining a sample as resistant to an antimicrobial agent. The method used greatly affects the estimated prevalence of antimicrobial resistance in a sampled population of animals, thus potentially resulting in misleading results. Comparing methods on the same samples allows us to re-estimate the prevalence from other studies, had other methods for determining resistance been used. The results of this study highlight the importance of establishing what the most appropriate measure of antimicrobial resistance is, for the proposed purpose of the results.

British Escherichia coli O157 in Cattle Study (BECS): to determine the prevalence of E. coli O157 in herds with cattle destined for the food chain.

Escherichia coli O157 are zoonotic bacteria for which cattle are an important reservoir. Prevalence estimates for E. coli O157 in British cattle for human consumption are over 10 years old. A new baseline is needed to inform current human health risk. The British E. coli O157 in Cattle Study (BECS) ran between September 2014 and November 2015 on 270 farms across Scotland and England & Wales. This is the first study to be conducted contemporaneously across Great Britain, thus enabling comparison between Scotland and England & Wales. Herd-level prevalence estimates for E. coli O157 did not differ significantly for Scotland (0·236, 95% CI 0·166-0·325) and England & Wales (0·213, 95% CI 0·156-0·283) (P = 0·65). The majority of isolates were verocytotoxin positive. A higher proportion of samples from Scotland were in the super-shedder category, though there was no difference between the surveys in the likelihood of a positive farm having at least one super-shedder sample. E. coli O157 continues to be common in British beef cattle, reaffirming public health policy that contact with cattle and their environments is a potential infection source.

The importance of the PrP genotype in active surveillance for ovine scrapie.

Surveillance activities for ovine scrapie have expanded in the 21st century, following concerns about the potential for a hidden epidemic of bovine spongiform encephalopathy in European sheep populations. Large-scale surveys have been used to estimate the prevalence of scrapie infection. In this study we analyse data from the surveys in Great Britain between 2002 and 2004. When we estimate genotype-specific prevalences for each of the two screening tests used a difference is observed. One test underestimates the number of positive cases in genotypes classically considered to be at a low relative risk of developing clinical disease (ARR- and AHQ-containing genotypes). By comparison, the other test underestimates the number of positive cases in genotypes classically considered to be at an increased relative risk of developing clinical disease (VRQ-containing genotypes). These findings have implications for surveillance, disease control, and diagnostic test evaluation.

Descriptive spatial analysis of scrapie-affected flocks in Great Britain between January 1993 and December 2002.

The spatial distribution of sheep flocks in Great Britain with confirmed clinical scrapie between January 1993 and December 2002 inclusive was investigated by using kernel density estimation and a cluster scan test statistic. Six statistically significant clusters were identified: three were lower risk, and were centred on the north-western coast of Scotland, the north-western coast of Wales and the South Yorkshire/Pennine region; three were of higher risk, and were centred in the central south, North Yorkshire and north Cumbria. General knowledge and the results of previous epidemiological studies were used to generate biologically plausible hypotheses that might explain these findings. They included aspects of flock management and disease transmission, and factors associated with the identification of cases, including their detection, recognition and, in particular, reporting levels, as well as diagnosis and animal movements.

Estimation of the relative risk of developing clinical scrapie: the role of prion protein (PrP) genotype and selection bias.

Prion protein (PrP) genotype data from statutory confirmed cases and from three non-case datasets have been used to calculate the odds ratio (or) for the development of clinical scrapie for an individual sheep of a given PrP genotype, compared with one possessing the "wild-type" ARQ/ARQ genotype. Logistic regression has been used to estimate the ors, and a multiple-test procedure has been used to evaluate the statistical significance of each comparison. The results are similar to those observed in other studies: the VRQ/VRQ genotype has or point estimates greater than 20; the ARQ/VRQ and ARH/VRQ genotypes have or point estimates between 5 and 20; AHQ/VRQ between 0.03 and 0.1; ARR/VRQ 0.4 and 0.5; all the other PrP genotypes, excluding ARR/ARR, ARR/ARH and AHQ/ARH for which no clinical cases have been recorded have or point estimates of less than 0.3. The estimates derived from each dataset are comparable, but not identical. This can be explained by plausible biases inherent in the sampling of the non-case populations.

Risk of scrapie in British sheep of different prion protein genotype.

There is a well-established association between sheep prion protein (PrP) genotype and the risk of death from scrapie. Certain genotypes are clearly associated with susceptibility to the disease and others to resistance. However, there have been no attempts to quantify the disease risk for all 15 PrP genotypes. Here, datasets of the PrP genotypes of nearly 14 000 British sheep and of more than 1500 confirmed scrapie cases were combined to yield an estimate of scrapie risk (reported cases per annum per million sheep of the genotype, or RCAM) for British sheep. The greatest scrapie risk by far, ranging from 225 to 545 RCAM, was for the VRQ-encoding genotypes ARQ/VRQ, ARH/VRQ and VRQ/VRQ. The next greatest risk (37 RCAM) was for the ARQ/ARQ genotype. The ARR/ARR genotype was the only numerically significant genotype for which no scrapie cases have been reported. The AHQ allele conferred resistance and the risk of scrapie in AHQ/VRQ sheep was very low (0.7 RCAM), although there was a higher and moderate risk for the AHQ homozygote (5 RCAM). The ARH allele appeared to confer susceptibility when encoded with VRQ, but possible resistance when encoded with other alleles. Scrapie risk varied with age: for VRQ/VRQ and ARH/VRQ the risk peaked at 2 years of age; that for ARQ/VRQ peaked at 3 years. There was some evidence that, following the lower risk at 4 and 5 years, a second rise occurred from about 6 years. Comparison with other published data indicated that the scrapie risk of certain PrP genotypes may differ between Great Britain and other countries.

Demonstration of lateral transmission of scrapie between sheep kept under natural conditions using lymphoid tissue biopsy.

Scrapie free adult sheep were introduced to a sheep flock specifically maintained to maximise scrapie infection. Native born sheep of the highly susceptible VRQ/VRQ genotype in this flock show highly efficient transmission, evidenced by 100% infection, with an age at death of less than 2 years. Infection in introduced sheep was identified by biopsy of tonsilar and nictitating membrane lymphoid tissue. Progeny of these sheep were monitored and clinical disease confirmed by examination of the brain using routine diagnostic methods. Naïve sheep of New Zealand origin introduced to the flock in adulthood became infected, demonstrating that lateral transmission had occurred. Lambs born to introduced ewes became infected and died at the same age as lambs born to native ewes, consistent with lateral transmission of scrapie to lambs. Although maternal transmission cannot be totally excluded for the lambs in this study, the data are consistent with lateral transmission being the most important means of spread leading to the high incidence of scrapie observed in this flock.

Frequencies of prion protein (PrP) genotypes and distribution of ages in 15 scrapie-affected flocks in Great Britain.

The frequencies of prion protein (PrP) genotypes were investigated in 15 scrapie-affected flocks in Great Britain. The flocks were heterogeneous in the frequencies of different genotypes and alleles, and in their age distributions. The median flock frequency of animals with VRQ-containing genotypes was 21 per cent (range 2 to 82 per cent, mean 25 per cent). The VRQ-containing and other non-ARR genotypes made up 11 to 82 per cent of a flock (median 46 per cent, mean 48 per cent). In comparison with data from the general population the scrapie-affected population had a lower frequency of the ARR/ARR genotype, and so of the ARR allele, and had a higher frequency of VRQ/non-ARR heterozygote genotypes, and thus of the VRQ allele.