Biology subjects

Barrett, D. C.

Publications and source records attributed to Barrett, D. C..

7 recordsLinked to original sources

bioRxiv2021

Fluoroquinolone-Resistant Escherichia coli Originating on Dairy Farms are an Infrequent Cause of Bacteriuria in Humans Living in the Same Geographical Region

SynopsisO_ST_ABSBackgroundC_ST_ABSOur primary aim was to test whether cattle-associated fluoroquinolone-resistant (FQ-R) Escherichia coli found on dairy farms were a significant cause of bacteriuria in humans living in the same 50 x 50 km geographical region located in South West England. Another aim was to identify risk factors for the presence of FQ-R E. coli on dairy farms. MethodsFQ-R E. coli were isolated during 2017-18 from 42 dairy farms and from community urine samples. Forty-two cattle and 489 human urinary isolates were subjected to WGS, allowing phylogenetic comparisons. Risk factors were identified using a Bayesian regularisation approach. ResultsOf 489 FQ-R human isolates, 255 were also 3rd generation cephalosporin-resistant (3GC-R), with strong genetic linkage between aac(6)Ib-cr and blaCTX-M-15. We identified possible farm-to-human sharing for pairs of ST744 and ST162 isolates, but core genome SNP distances (71 and 63, respectively) were smaller in pairs of ST744 and ST162 isolates from different farms (7 and 3 SNPs, respectively). Total farm fluoroquinolone use showed a positive association with the odds of isolating FQ-R E. coli while total dry cow therapy use showed a negative association. ConclusionsThis work suggests that FQ-R E. coli found on dairy farms have a limited impact on community bacteriuria within the local human population, however, this appears greater than observed for 3GC-R E. coli when studied in parallel. Reducing fluoroquinolone use may reduce the on-farm prevalence of FQ-R E. coli, and this reduction may be greater when dry cow therapy is targeted to the ecology of resistant E. coli on the farm.

microbiology↗

bioRxiv2020

Measuring antimicrobial use on dairy farms: a longitudinal method comparison study

Antimicrobial use on UK dairy farms is measured for surveillance purposes and utilizes veterinary sales data as a proxy for use. Two other methods of recording use have been used commonly on-farm: medicine waste bins and farm medicine records. However, none of these methods have been validated to measure antimicrobial use. The objectives of this research are to assess agreement between the 3 most common methods for measuring on-farm antimicrobial use with a pre-determined "gold standard" measure. Antimicrobial use was measured prospectively on 26 UK dairy farms using medicine waste bins into which participants placed all discarded medicine packaging for a 12-month period. At the end of 12 months, farm medicine records and veterinary sales data were obtained retrospectively for participating farms. The systematic difference between the mean on-farm antimicrobial use measured by each of the 3 methods with a gold standard measure was investigated using one-way repeated measures ANOVAs. Reliability and clinical relevance of the agreement between each pair of methods was quantified using the concordance correlation coefficient and the Bland-Altman method, respectively. Veterinary sales data shows excellent reliability for all forms of antimicrobial when compared with the gold standard. Medicine waste bins show moderate to excellent reliability for injectables, poor to good reliability for intramammaries and no agreement for other forms of antimicrobial. Farm medicine records do not show agreement for any form of antimicrobial when compared with the gold standard. The use of veterinary sales data as a proxy for on-farm antimicrobial use in the UK represents excellent statistical reliability and offers a clinically acceptable agreement with a gold standard method when used to measure both injectable antimicrobials and intramammary antimicrobials. These results have policy implications both nationally and internationally and are essential in quantifying the actual impact of agricultural antimicrobial use on both animal and human health.

pharmacology and toxicology↗

bioRxiv2019

Characterisation of AmpC Hyper-Producing Escherichia coli from Humans and Dairy Farms Collected in Parallel in the Same Geographical Region

ObjectivesTo characterise putative AmpC hyper-producing 3rd generation cephalosporin-resistant E. coli from dairy farms and their phylogenetic relationships as well as to identify risk factors for their presence; to assess evidence for their zoonotic transmission into the local human population\n\nMethodsProteomics was used to explain differences in antimicrobial susceptibility. Whole genome sequencing allowed phylogenetic analysis. Multilevel, multivariable logistic regression modelling was used to identify risk factors.\n\nResultsIncreased use of amoxicillin-clavulanate was associated with an increased risk of finding AmpC hyper-producers on farms. Expansion of cephalosporin resistance in AmpC hyper-producers was seen in farm isolates with marR mutations (conferring cefoperazone resistance) or when AmpC was mutated (conferring 4th generation cephalosporin and cefoperazone resistance). Phylogenetic analysis confirmed the dominance of ST88 amongst farm AmpC hyper-producers but there was no evidence for acquisition of farm isolates by members of the local human population.\n\nConclusionsIn this two-year surveillance study of 53 dairy farms, AmpC hyper-production was the cause of cefotaxime resistance in 46.2% of E. coli. There was evidence of recent farm-to-farm transmission and of adaptive mutations to expand resistance. Whilst there was no evidence of isolates entering the local human population, efforts to reduce 3rd generation cephalosporin resistance on dairy farms must address the high prevalence of AmpC hyper-producers. The finding that amoxicillin-clavulanate use was associated with increased risk of finding AmpC hyper-producers is important because this is not currently categorised as a highest-priority critically important antimicrobial and so is not currently targeted for specific usage restrictions in the UK.

microbiology↗

bioRxiv2019

Evidence for reduced CTX-M carriage in cattle-associated Escherichia coli at low temperatures and on publicly accessible farmland: implications for surveillance and potential for farm-to-human transmission

Little is known about the drivers of critically important antibacterial resistance in species with zoonotic potential present on farms (e.g. CTX-M {square}-lactamase-positive Escherichia coli). Here, we collected samples, monthly over a two-year period, on 53 dairy farms in the South West of England, and data for 610 variables concerning antimicrobial usage, management practices and meteorological factors. We detected E. coli resistant to amoxicillin, ciprofloxacin streptomycin and tetracycline, respectively, in 2754/4145 (66%), 263/4145 (6%), 1475/4145 (36%) and 2874/4145 (69%) of all samples from faecally contaminated sites. E. coli positive for blaCTX-M were detected in 224/4145 (5.4%) of samples. Multilevel, multivariable logistic regression showed antibiotic dry cow therapeutic choice (including use of cefquinome or framycetin) to be associated with increased odds of blaCTX-M positivity. Low temperature was associated with reduced odds of blaCTX-M E. coli positivity in samples and to reduced odds of finding E. coli resistant to each of the four test antibacterials. This was additional to the effect of temperature on total E. coli density. Furthermore, samples collected close to calves had increased odds of having E. coli resistance to each antibacterial or positive for blaCTX-M. Samples collected on pastureland had reduced odds of having E. coli resistant to amoxicillin or tetracycline, and being positive for blaCTX-M. ImportanceAntibacterial resistance poses a significant threat to human and animal health and global food security. Surveillance for resistance on farms is important for many reasons, including to track the impacts of interventions aimed at reducing the prevalence of resistance. In this epidemiological survey of dairy farm antibacterial resistance, we show that local temperature, as it changes over the course of a year, is associated with the prevalence of antibacterial resistant E. coli. Also, that prevalence of resistant E. coli is higher in indoor environments and in environments inhabited by young animals. These findings have profound implications for routine surveillance and for surveys carried out for research. They provide important evidence that sampling at a single time-point and/or single location on a farm is unlikely to be adequate to accurately determine the status of the farm with regard to the presence or number of resistant E. coli.

microbiology↗

bioRxiv2018

Storage of prescription veterinary medicines on UK dairy farms: a cross-sectional study

Prescription veterinary medicine (PVM) use in the United Kingdom is an area of increasing focus for the veterinary profession. While many studies measure antimicrobial use on dairy farms, none report the quantity of antimicrobials stored on farms, nor the ways in which they are stored. The majority of PVM treatments occur in the absence of the prescribing veterinarian, yet there is an identifiable knowledge gap surrounding PVM use and farmer decision making. To provide an evidence base for future work on PVM use, data were collected from 27 dairy farms in England and Wales in Autumn 2016. The number of different PVM stored on farms ranged from 9-35, with antimicrobials being the most common therapeutic group stored. Injectable antimicrobials comprised the greatest weight of active ingredient found while intramammary antimicrobials were the most frequent unit of medicine stored. Antimicrobials classed by the European Medicines Agency as critically-important to human health were present on most farms, and the presence of expired medicines and medicines not licensed for use in dairy cattle was also common. The medicine resources available to farmers are likely to influence their treatment decisions, therefore evidence of the PVM stored on farms can help inform understanding of medicine use.

epidemiology↗

bioRxiv2017

Evaluation of Metrics for Benchmarking Antimicrobial Use in the United Kingdom Dairy Industry

The issue of antimicrobial resistance is of global concern across human and animal health. In 2016 the UK government committed to new targets for reducing antimicrobial use (AMU) in livestock. However, though a number of metrics for quantifying AMU are defined in the literature, all give slightly different interpretations.\n\nThis paper reviews a selection of metrics for AMU in the dairy industry: total mg, total mg/kg, daily dose and daily course metrics. Although the focus is on their application to the dairy industry, the metrics and issues discussed are relevant across livestock sectors.\n\nIn order to be used widely, a metric should be understandable and relevant to the veterinarians and farmers who are prescribing and using antimicrobials. This means that clear methods, assumptions (and possible biases), standardised values and exceptions should be published for all metrics. Particularly relevant are assumptions around the number and weight of cattle at risk of treatment and definitions of dose rates and course lengths; incorrect assumptions can mean metrics over- or under-represent AMU.\n\nThe authors recommend that the UK dairy industry work towards UK-specific metrics using UK-specific medicine dose and course regimens as well as cattle weights in order to monitor trends nationally.

epidemiology↗

bioRxiv2017

Ceasing the use of the highest priority critically important antimicrobials does not adversely affect production, health or welfare parameters in dairy cows

Due to scientific, public and political concern regarding antimicrobial resistance (AMR), several EU countries have already taken steps to reduce antimicrobial (AM) usage in production animal medicine, particularly that of the highest priority critically important AMs (HP-CIAs). While veterinarians are aware of issues surrounding AMR, barriers to change such as concerns of reduced animal health, welfare or production may inhibit AM prescribing changes.\n\nFarmers from seven dairy farms in South West England engaged in changing AM use through an active process of education and herd health planning meetings. Prescribing data was collected from veterinary sales records; production and health data were accessed via milk recording and farm-recorded data.\n\nThis study demonstrates that cattle health and welfare - as measured by production parameters, fertility, udder health, mobility data and culling rates - can be maintained and even improved alongside a complete cessation in the use of HP-CIAs as well as an overall reduction of AM use on dairy farms.\n\nThis study also identified a need to consider different metrics when analysing AM use data, including dose-based metrics as well as those of total quantities to allow better representation of the direction and magnitude of changes in AM use.

epidemiology↗