Biology subjects

Sanchez-Vizcaino, F.

Publications and source records attributed to Sanchez-Vizcaino, F..

3 recordsLinked to original sources

bioRxiv2026

Local Temperature and Humidity are Associated with Proportion of Antimicrobial-Resistant Escherichia coli isolates in Farm Environments: Considerations for On-Farm Surveillance

Evidence suggests that increased local temperatures are associated with higher prevalence of antimicrobial resistance (AMR) in environmental bacteria. This study investigates the association between local climate and the proportion of antimicrobial-resistant Escherichia coli isolated from 2,766 farm environment samples from 53 English dairy farms. To do this, a non-linear Bayesian model that specifically accounts for decreased test sensitivity at low E. coli abundance was developed and used to estimate the proportion of isolates resistant to four antimicrobials (amoxicillin, cephalexin, streptomycin and tetracycline) from colony count data. Mean 7-day temperature and relative humidity at the farm location was modelled using a generalised additive model formulation. A higher proportion of E. coli isolates were resistant to cephalexin and streptomycin in samples collected from adult cow collecting yards, than heifer housing sheds. In contrast, a greater proportion of E. coli isolates from heifer housing sheds were resistant to amoxicillin and tetracycline. Evidence that local temperature is associated with an increase in the proportion of E. coli isolates resistant to streptomycin (20{degrees}C increase associated with a 5.0-fold increase; 95% CI: 1.03-33.0) and tetracycline (2.6-fold increase; 90% CI: 1.1-5.2) was observed. Additionally, relative humidity was associated with an increase in the proportion of isolates resistant to amoxicillin streptomycin and tetracycline. The influence of weather on the proportion of antimicrobial-resistant E. coli varied between samples collected from adult animals in collecting yards and heifers in housing sheds. These findings highlight the importance of considering weather conditions, sample characterises and seasonality when designing on-farm AMR surveillance systems. ImportanceUnderstanding how environmental conditions are associated with variability in AMR prevalence is critical for developing robust livestock AMR surveillance and anticipating the potential effects of climate change. The non-linear Bayesian modelling approach developed here adjusts for E. coli abundance associated variability in test sensitivity, enabling the influence of risk factors associated with the proportion of antimicrobial-resistant E. coli within samples to be more accurately estimated. Applying this approach to 2,766 faecal samples from 53 dairy farms in Southwest England indicated that the proportion of antimicrobial-resistant E. coli generally increased under warmer and wetter conditions. These findings suggest that environmental conditions can influence the prevalence of AMR E. coli in dairy farm environments and demonstrate the importance of accounting for weather related variability in livestock AMR surveillance. Adjusting for these associations in livestock AMR surveillance could improve the accuracy of modelling AMR trends and strengthen the assessment of climate-associated AMR risks.

microbiology↗

bioRxiv2022

Emerging variants of canine enteric coronavirus associated with seasonal outbreaks of severe canine gastroenteric disease

Canine enteric coronavirus (CECoV) variants have an emerging role in severe outbreaks of canine gastroenteritis. Here we used syndromic health data from a sentinel network of UK veterinary practices to identify an outbreak of severe canine gastroenteritis. Affected dogs frequently presented with vomiting, diarrhoea and inappetence. Data from sentinel diagnostic laboratories showed similar seasonal increases in CECoV diagnosis. Membrane glycoprotein (M) gene sequence analysis implied wide geographical circulation of a new CECoV variant. Whole genome sequencing suggested the main circulating 2022 variant was most closely related to one previously identified in 2020 with additional spike gene recombination; all variants were unrelated to CECoV-like viruses recently associated with human respiratory disease. Identifying factors that drive population-level evolution, and its implications for host protection and virulence, will be important to understand the emerging role of CECoV variants in canine and human health, and may act as a model for coronavirus population adaptation more widely.

genomics↗

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↗